diff options
Diffstat (limited to 'wqflask')
55 files changed, 3427 insertions, 1324 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index b324ac74..41de8492 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -46,6 +46,8 @@ from utility import chunks from utility import gen_geno_ob from utility.tools import locate, locate_ignore_error, flat_files +from wqflask.api import gen_menu + from maintenance import get_group_samplelists from MySQLdb import escape_string as escape @@ -92,7 +94,7 @@ Publish or ProbeSet. E.g. """ self.datasets = {} if USE_GN_SERVER: - data = menu_main() + data = gen_menu.gen_dropdown_json() else: file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: @@ -289,7 +291,6 @@ class DatasetGroup(object): self.parlist = None self.get_f1_parent_strains() - self.accession_id = self.get_accession_id() self.mapping_id, self.mapping_names = self.get_mapping_methods() self.species = webqtlDatabaseFunction.retrieve_species(self.name) @@ -299,20 +300,6 @@ class DatasetGroup(object): self._datasets = None self.genofile = None - def get_accession_id(self): - results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where - InbredSet.Name = %s and - PublishFreeze.InbredSetId = InbredSet.Id and - InfoFiles.InfoPageName = PublishFreeze.Name and - PublishFreeze.public > 0 and - PublishFreeze.confidentiality < 1 order by - PublishFreeze.CreateTime desc""", (self.name)).fetchone() - - if results != None: - return str(results[0]) - else: - return "None" - def get_mapping_methods(self): mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0] @@ -384,7 +371,7 @@ class DatasetGroup(object): [result.extend(l) for l in lists if l] return result - def read_genotype_file(self): + def read_genotype_file(self, use_reaper=False): '''Read genotype from .geno file instead of database''' #genotype_1 is Dataset Object without parents and f1 #genotype_2 is Dataset Object with parents and f1 (not for intercross) @@ -396,9 +383,12 @@ class DatasetGroup(object): full_filename = str(locate(self.genofile, 'genotype')) else: full_filename = str(locate(self.name + '.geno', 'genotype')) - #genotype_1.read(full_filename) - genotype_1 = gen_geno_ob.genotype(full_filename) + if use_reaper: + genotype_1 = reaper.Dataset() + genotype_1.read(full_filename) + else: + genotype_1 = gen_geno_ob.genotype(full_filename) if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) @@ -445,7 +435,7 @@ def datasets(group_name, this_group = None): and InbredSet.Name like %s and ProbeSetFreeze.public > %s and ProbeSetFreeze.confidentiality < 1 - ORDER BY Tissue.Name) + ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC) ''' % (group_name, webqtlConfig.PUBLICTHRESH, group_name, webqtlConfig.PUBLICTHRESH, "'" + group_name + "'", webqtlConfig.PUBLICTHRESH)) @@ -507,6 +497,7 @@ class DataSet(object): self.check_confidentiality() self.retrieve_other_names() self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype + self.accession_id = self.get_accession_id() if get_samplelist == True: self.group.get_samplelist() self.species = species.TheSpecies(self) @@ -521,6 +512,31 @@ class DataSet(object): def riset(): Weve_Renamed_This_As_Group + def get_accession_id(self): + if self.type == "Publish": + results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where + InbredSet.Name = %s and + PublishFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = PublishFreeze.Name and + PublishFreeze.public > 0 and + PublishFreeze.confidentiality < 1 order by + PublishFreeze.CreateTime desc""", (self.group.name)).fetchone() + elif self.type == "Geno": + results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where + InbredSet.Name = %s and + GenoFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = GenoFreeze.ShortName and + GenoFreeze.public > 0 and + GenoFreeze.confidentiality < 1 order by + GenoFreeze.CreateTime desc""", (self.group.name)).fetchone() + else: + results = None + + if results != None: + return str(results[0]) + else: + return "None" + def retrieve_other_names(self): """This method fetches the the dataset names in search_result. diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 6fecf725..58169b5c 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -3,6 +3,7 @@ from __future__ import absolute_import, division, print_function import string import resource import codecs +import requests import redis Redis = redis.StrictRedis() @@ -120,11 +121,34 @@ class GeneralTrait(object): @property def alias_fmt(self): '''Return a text formatted alias''' + + alias = 'Not available' if self.alias: alias = string.replace(self.alias, ";", " ") alias = string.join(string.split(alias), ", ") - else: - alias = 'Not available' + + return alias + + @property + def wikidata_alias_fmt(self): + '''Return a text formatted alias''' + + alias = 'Not available' + if self.symbol: + human_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.upper()) + mouse_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.capitalize()) + other_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.lower()) + alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content) + + filtered_aliases = [] + seen = set() + for item in alias_list: + if item in seen: + continue + else: + filtered_aliases.append(item) + seen.add(item) + alias = "; ".join(filtered_aliases) return alias @@ -396,8 +420,10 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): #XZ: assign SQL query result to trait attributes. for i, field in enumerate(dataset.display_fields): holder = trait_info[i] - if isinstance(trait_info[i], basestring): - holder = unicode(trait_info[i], "utf-8", "ignore") + # if isinstance(trait_info[i], basestring): + # logger.debug("HOLDER:", holder) + # logger.debug("HOLDER2:", holder.decode(encoding='latin1')) + # holder = unicode(trait_info[i], "utf-8", "ignore") setattr(trait, field, holder) if dataset.type == 'Publish': diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index b14cc4b0..0b884815 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -43,6 +43,7 @@ HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/homologene/?term=%s" GENOTATION_URL = "http://www.genotation.org/Getd2g.pl?gene_list=%s" GTEX_URL = "https://www.gtexportal.org/home/gene/%s" GENEBRIDGE_URL = "https://www.systems-genetics.org/modules_by_gene/%s?organism=%s" +GENEMANIA_URL = "https://genemania.org/search/%s/%s" UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgTracks?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s" BIOGPS_URL = "http://biogps.org/?org=%s#goto=genereport&id=%s" STRING_URL = "http://string-db.org/newstring_cgi/show_network_section.pl?identifier=%s" @@ -52,7 +53,9 @@ ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=% EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s" WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s" ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s" -DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s' +DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s' +PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s" +OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s" # Temporary storage (note that this TMPDIR can be set as an # environment variable - use utility.tools.TEMPDIR when you @@ -87,4 +90,3 @@ if not valid_path(JSON_GENODIR): PORTADDR = "http://50.16.251.170" INFOPAGEHREF = '/dbdoc/%s.html' CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' -SCRIPTFILE = 'main.py' diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 5824b0b3..5172369f 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,135 +1,137 @@ -from __future__ import absolute_import, division, print_function
-
-class genotype(object):
- """
- Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
- """
-
- def __init__(self, filename):
- self.group = None
- self.type = "riset"
- self.prgy = []
- self.nprgy = 0
- self.mat = -1
- self.pat = 1
- self.het = 0
- self.unk = "U"
- self.filler = False
- self.mb_exists = False
-
- #ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary
- self.cm_column = 2
- self.mb_column = 3
-
- self.chromosomes = []
-
- self.read_file(filename)
-
- def __iter__(self):
- return iter(self.chromosomes)
-
- def __getitem__(self, index):
- return self.chromosomes[index]
-
- def __len__(self):
- return len(self.chromosomes)
-
- def read_file(self, filename):
-
- with open(filename, 'r') as geno_file:
- lines = geno_file.readlines()
-
- this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers
- chr_ob = None
- for line in lines:
- if line[0] == "#":
- continue
- elif line[0] == "@":
- label = line.split(":")[0][1:]
- if label == "name":
- self.group = line.split(":")[1]
- elif label == "filler":
- if line.split(":")[1] == "yes":
- self.filler = True
- elif label == "type":
- self.type = line.split(":")[1]
- elif label == "mat":
- self.mat = line.split(":")[1]
- elif label == "pat":
- self.pat = line.split(":")[1]
- elif label == "het":
- self.het = line.split(":")[1]
- elif label == "unk":
- self.unk = line.split(":")[1]
- else:
- continue
- elif line[:3] == "Chr":
- header_row = line.split("\t")
- if header_row[2] == "Mb":
- self.mb_exists = True
- self.mb_column = 2
- self.cm_column = 3
- elif header_row[3] == "Mb":
- self.mb_exists = True
- self.mb_column = 3
- elif header_row[2] == "cM":
- self.cm_column = 2
-
- if self.mb_exists:
- self.prgy = header_row[4:]
- else:
- self.prgy = header_row[3:]
- self.nprgy = len(self.prgy)
- else:
- if line.split("\t")[0] != this_chr:
- if this_chr != "":
- self.chromosomes.append(chr_ob)
- this_chr = line.split("\t")[0]
- chr_ob = Chr(line.split("\t")[0], self)
- chr_ob.add_marker(line.split("\t"))
-
-class Chr(object):
- def __init__(self, name, geno_ob):
- self.name = name
- self.loci = []
- self.mb_exists = geno_ob.mb_exists
- self.cm_column = geno_ob.cm_column
- self.mb_column = geno_ob.mb_column
- self.geno_ob = geno_ob
-
- def __iter__(self):
- return iter(self.loci)
-
- def __getitem__(self, index):
- return self.loci[index]
-
- def __len__(self):
- return len(self.loci)
-
- def add_marker(self, marker_row):
- self.loci.append(Locus(marker_row, self.geno_ob))
-
-class Locus(object):
- def __init__(self, marker_row, geno_ob):
- self.chr = marker_row[0]
- self.name = marker_row[1]
- self.cM = float(marker_row[geno_ob.cm_column])
- self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None
-
- geno_table = {
- geno_ob.mat: -1,
- geno_ob.pat: 1,
- geno_ob.het: 0,
- geno_ob.unk: "U"
- }
-
- self.genotype = []
- if geno_ob.mb_exists:
- start_pos = 4
- else:
- start_pos = 3
- for allele in marker_row[start_pos:]:
- if allele in geno_table.keys():
- self.genotype.append(geno_table[allele])
- else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown
+from __future__ import absolute_import, division, print_function + +class genotype(object): + """ + Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure + """ + + def __init__(self, filename): + self.group = None + self.type = "riset" + self.prgy = [] + self.nprgy = 0 + self.mat = -1 + self.pat = 1 + self.het = 0 + self.unk = "U" + self.filler = False + self.mb_exists = False + + #ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary + self.cm_column = 2 + self.mb_column = 3 + + self.chromosomes = [] + + self.read_file(filename) + + def __iter__(self): + return iter(self.chromosomes) + + def __getitem__(self, index): + return self.chromosomes[index] + + def __len__(self): + return len(self.chromosomes) + + def read_file(self, filename): + + with open(filename, 'r') as geno_file: + lines = geno_file.readlines() + + this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers + chr_ob = None + for line in lines: + if line[0] == "#": + continue + elif line[0] == "@": + label = line.split(":")[0][1:] + if label == "name": + self.group = line.split(":")[1] + elif label == "filler": + if line.split(":")[1] == "yes": + self.filler = True + elif label == "type": + self.type = line.split(":")[1] + elif label == "mat": + self.mat = line.split(":")[1] + elif label == "pat": + self.pat = line.split(":")[1] + elif label == "het": + self.het = line.split(":")[1] + elif label == "unk": + self.unk = line.split(":")[1] + else: + continue + elif line[:3] == "Chr": + header_row = line.split("\t") + if header_row[2] == "Mb": + self.mb_exists = True + self.mb_column = 2 + self.cm_column = 3 + elif header_row[3] == "Mb": + self.mb_exists = True + self.mb_column = 3 + elif header_row[2] == "cM": + self.cm_column = 2 + + if self.mb_exists: + self.prgy = header_row[4:] + else: + self.prgy = header_row[3:] + self.nprgy = len(self.prgy) + else: + if line.split("\t")[0] != this_chr: + if this_chr != "": + self.chromosomes.append(chr_ob) + this_chr = line.split("\t")[0] + chr_ob = Chr(line.split("\t")[0], self) + chr_ob.add_marker(line.split("\t")) + + self.chromosomes.append(chr_ob) + +class Chr(object): + def __init__(self, name, geno_ob): + self.name = name + self.loci = [] + self.mb_exists = geno_ob.mb_exists + self.cm_column = geno_ob.cm_column + self.mb_column = geno_ob.mb_column + self.geno_ob = geno_ob + + def __iter__(self): + return iter(self.loci) + + def __getitem__(self, index): + return self.loci[index] + + def __len__(self): + return len(self.loci) + + def add_marker(self, marker_row): + self.loci.append(Locus(marker_row, self.geno_ob)) + +class Locus(object): + def __init__(self, marker_row, geno_ob): + self.chr = marker_row[0] + self.name = marker_row[1] + self.cM = float(marker_row[geno_ob.cm_column]) + self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None + + geno_table = { + geno_ob.mat: -1, + geno_ob.pat: 1, + geno_ob.het: 0, + geno_ob.unk: "U" + } + + self.genotype = [] + if geno_ob.mb_exists: + start_pos = 4 + else: + start_pos = 3 + for allele in marker_row[start_pos:]: + if allele in geno_table.keys(): + self.genotype.append(geno_table[allele]) + else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown self.genotype.append("U")
\ No newline at end of file diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 8b2260f5..ec9f01bd 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -107,6 +107,9 @@ def js_path(module=None): return try_guix raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)" +def reaper_command(guess=None): + return get_setting("REAPER_COMMAND",guess) + def gemma_command(guess=None): return assert_bin(get_setting("GEMMA_COMMAND",guess)) @@ -274,6 +277,7 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT') SMTP_USERNAME = get_setting('SMTP_USERNAME') SMTP_PASSWORD = get_setting('SMTP_PASSWORD') +REAPER_COMMAND = app_set("REAPER_COMMAND",reaper_command()) GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command()) assert(GEMMA_COMMAND is not None) PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command()) @@ -285,11 +289,14 @@ assert_dir(TEMPDIR) JS_GUIX_PATH = get_setting("JS_GUIX_PATH") assert_dir(JS_GUIX_PATH) assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom') + CSS_PATH = "UNKNOWN" # assert_dir(JS_PATH) -JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher")) + +JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher")) assert_dir(JS_TWITTER_POST_FETCHER_PATH) assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") + JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape")) assert_dir(JS_CYTOSCAPE_PATH) assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js') diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py index 220e5f62..f15b17e2 100644 --- a/wqflask/utility/type_checking.py +++ b/wqflask/utility/type_checking.py @@ -27,7 +27,7 @@ def get_float(vars,name,default=None): if name in vars: if is_float(vars[name]): return float(vars[name]) - return None + return default def get_int(vars,name,default=None): if name in vars: diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py new file mode 100644 index 00000000..5182ea13 --- /dev/null +++ b/wqflask/wqflask/api/gen_menu.py @@ -0,0 +1,239 @@ +from __future__ import print_function, division + +import sys + +from flask import g + +from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI +from utility.benchmark import Bench + +import MySQLdb + +import urlparse + +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +def gen_dropdown_json(): + """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" + + species = get_species() + groups = get_groups(species) + types = get_types(groups) + datasets = get_datasets(types) + + species.append(('All Species', 'All Species')) + groups['All Species'] = [('All Groups', 'All Groups')] + types['All Species'] = {} + types['All Species']['All Groups'] = [('Phenotypes', 'Phenotypes')] + datasets['All Species'] = {} + datasets['All Species']['All Groups'] = {} + datasets['All Species']['All Groups']['Phenotypes'] = [('All Phenotypes','All Phenotypes')] + + data = dict(species=species, + groups=groups, + types=types, + datasets=datasets) + + return data + +def get_species(): + """Build species list""" + results = g.db.execute("""SELECT Name, MenuName + FROM Species + WHERE Species.Name != 'macaque monkey' + ORDER BY OrderId""").fetchall() + + species = [] + for result in results: + species.append([str(result[0]), str(result[1])]) + + return species + +def get_groups(species): + """Build groups list""" + groups = {} + for species_name, _species_full_name in species: + groups[species_name] = [] + # results = g.db.execute("""SELECT InbredSet.Name, InbredSet.FullName + # FROM InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze + # WHERE Species.Name = '{}' AND + # InbredSet.SpeciesId = Species.Id AND + # (PublishFreeze.InbredSetId = InbredSet.Id OR + # GenoFreeze.InbredSetId = InbredSet.Id OR + # ProbeFreeze.InbredSetId = InbredSet.Id) + # GROUP by InbredSet.Name + # ORDER BY InbredSet.FullName""".format(species_name)).fetchall() + + results = g.db.execute("""SELECT InbredSet.Name, InbredSet.FullName + FROM InbredSet, Species + WHERE Species.Name = '{}' AND + InbredSet.SpeciesId = Species.Id + GROUP by InbredSet.Name + ORDER BY InbredSet.FullName""".format(species_name)).fetchall() + + for result in results: + groups[species_name].append([str(result[0]), str(result[1])]) + + return groups + +def get_types(groups): + """Build types list""" + types = {} + + for species, group_dict in groups.iteritems(): + types[species] = {} + for group_name, _group_full_name in group_dict: + if phenotypes_exist(group_name): + types[species][group_name] = [("Phenotypes", "Phenotypes")] + if genotypes_exist(group_name): + if group_name in types[species]: + types[species][group_name] += [("Genotypes", "Genotypes")] + else: + types[species][group_name] = [("Genotypes", "Genotypes")] + if group_name in types[species]: + types_list = build_types(species, group_name) + if len(types_list) > 0: + types[species][group_name] += types_list + else: + if not phenotypes_exist(group_name) and not genotypes_exist(group_name): + types[species].pop(group_name, None) + groups[species] = list(group for group in groups[species] if group[0] != group_name) + else: #ZS: This whole else statement might be unnecessary, need to check + types_list = build_types(species, group_name) + if len(types_list) > 0: + types[species][group_name] = types_list + else: + types[species].pop(group_name, None) + groups[species] = list(group for group in groups[species] if group[0] != group_name) + return types + +def phenotypes_exist(group_name): + results = g.db.execute("""SELECT Name + FROM PublishFreeze + WHERE PublishFreeze.Name = '{}'""".format(group_name+"Publish")).fetchone() + + if results != None: + return True + else: + return False + +def genotypes_exist(group_name): + results = g.db.execute("""SELECT Name + FROM GenoFreeze + WHERE GenoFreeze.Name = '{}'""".format(group_name+"Geno")).fetchone() + + if results != None: + return True + else: + return False + +def build_types(species, group): + """Fetches tissues + + Gets the tissues with data for this species/group + (all types except phenotype/genotype are tissues) + + """ + + query = """SELECT DISTINCT Tissue.Name + FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species + WHERE Species.Name = '{0}' AND + Species.Id = InbredSet.SpeciesId AND + InbredSet.Name = '{1}' AND + ProbeFreeze.TissueId = Tissue.Id AND + ProbeFreeze.InbredSetId = InbredSet.Id AND + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND + ProbeSetFreeze.public > 0 AND + ProbeSetFreeze.confidentiality < 1 + ORDER BY Tissue.Name""".format(species, group) + + results = [] + for result in g.db.execute(query).fetchall(): + if len(result): + these_datasets = build_datasets(species, group, result[0]) + if len(these_datasets) > 0: + results.append([str(result[0]), str(result[0])]) + + return results + +def get_datasets(types): + """Build datasets list""" + datasets = {} + for species, group_dict in types.iteritems(): + datasets[species] = {} + for group, type_list in group_dict.iteritems(): + datasets[species][group] = {} + for type_name in type_list: + these_datasets = build_datasets(species, group, type_name[0]) + if len(these_datasets) > 0: + datasets[species][group][type_name[0]] = these_datasets + + return datasets + + +def build_datasets(species, group, type_name): + """Gets dataset names from database""" + dataset_text = dataset_value = None + datasets = [] + if type_name == "Phenotypes": + results = g.db.execute("""SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, PublishFreeze.FullName + FROM InfoFiles, PublishFreeze, InbredSet + WHERE InbredSet.Name = '{}' AND + PublishFreeze.InbredSetId = InbredSet.Id AND + InfoFiles.InfoPageName = PublishFreeze.Name + ORDER BY PublishFreeze.CreateTime ASC""".format(group)).fetchall() + + if len(results) > 0: + for result in results: + dataset_id = str(result[0]) + dataset_value = str(result[1]) + if group == 'MDP': + dataset_text = "Mouse Phenome Database" + else: + #dataset_text = "%s Phenotypes" % group + dataset_text = str(result[2]) + datasets.append([dataset_id, dataset_value, dataset_text]) + else: + dataset_id = "None" + dataset_value = "%sPublish" % group + dataset_text = "%s Phenotypes" % group + datasets.append([dataset_id, dataset_value, dataset_text]) + + elif type_name == "Genotypes": + results = g.db.execute("""SELECT InfoFiles.GN_AccesionId + FROM InfoFiles, GenoFreeze, InbredSet + WHERE InbredSet.Name = '{}' AND + GenoFreeze.InbredSetId = InbredSet.Id AND + InfoFiles.InfoPageName = GenoFreeze.ShortName AND + GenoFreeze.public > 0 AND + GenoFreeze.confidentiality < 1 + ORDER BY GenoFreeze.CreateTime DESC""".format(group)).fetchone() + + if results != None: + dataset_id = str(results[0]) + else: + dataset_id = "None" + dataset_value = "%sGeno" % group + dataset_text = "%s Genotypes" % group + datasets.append([dataset_id, dataset_value, dataset_text]) + + else: # for mRNA expression/ProbeSet + results = g.db.execute("""SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName + FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species + WHERE Species.Name = '{0}' AND + Species.Id = InbredSet.SpeciesId AND + InbredSet.Name = '{1}' AND + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '{2}' AND + ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id AND + ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0 + ORDER BY ProbeSetFreeze.CreateTime DESC""".format(species, group, type_name)).fetchall() + + datasets = [] + for dataset_info in results: + this_dataset_info = [] + for info in dataset_info: + this_dataset_info.append(str(info)) + datasets.append(this_dataset_info) + + return datasets
\ No newline at end of file diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index 83c61796..d830cefc 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -1,122 +1,141 @@ -from __future__ import absolute_import, division, print_function
-
-import string
-
-from base import data_set
-from base import webqtlConfig
-from base.trait import GeneralTrait, retrieve_sample_data
-
-from utility import helper_functions
-from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
-
-import utility.logger
-logger = utility.logger.getLogger(__name__ )
-
-def do_mapping_for_api(start_vars):
- assert('db' in start_vars)
- assert('trait_id' in start_vars)
-
- dataset = data_set.create_dataset(dataset_name = start_vars['db'])
- dataset.group.get_markers()
- this_trait = GeneralTrait(dataset = dataset, name = start_vars['trait_id'])
- this_trait = retrieve_sample_data(this_trait, dataset)
-
- samples = []
- vals = []
-
- for sample in dataset.group.samplelist:
- in_trait_data = False
- for item in this_trait.data:
- if this_trait.data[item].name == sample:
- value = str(this_trait.data[item].value)
- samples.append(item)
- vals.append(value)
- in_trait_data = True
- break
- if not in_trait_data:
- vals.append("x")
-
- mapping_params = initialize_parameters(start_vars, dataset, this_trait)
-
- covariates = "" #ZS: It seems to take an empty string as default. This should probably be changed.
-
- if mapping_params['mapping_method'] == "gemma":
- header_row = ["name", "chr", "Mb", "lod_score", "p_value"]
- if mapping_params['use_loco'] == "True": #ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api
- result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0]
- else:
- result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])
- elif mapping_params['mapping_method'] == "rqtl":
- header_row = ["name", "chr", "Mb", "lod_score"]
- if mapping_params['num_perm'] > 0:
- _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'],
- mapping_params['perm_check'], mapping_params['num_perm'],
- mapping_params['do_control'], mapping_params['control_marker'],
- mapping_params['manhattan_plot'], mapping_params['pair_scan'])
- else:
- result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'],
- mapping_params['perm_check'], mapping_params['num_perm'],
- mapping_params['do_control'], mapping_params['control_marker'],
- mapping_params['manhattan_plot'], mapping_params['pair_scan'])
-
- output_rows = []
- output_rows.append(header_row)
- for marker in result_markers:
- this_row = [marker[header] for header in header_row]
- output_rows.append(this_row)
-
- return output_rows
-
-
-def initialize_parameters(start_vars, dataset, this_trait):
- mapping_params = {}
- mapping_params['mapping_method'] = "gemma"
- if 'method' in start_vars:
- mapping_params['mapping_method'] = start_vars['method']
-
- if mapping_params['mapping_method'] == "rqtl":
- mapping_params['rqtl_method'] = "hk"
- mapping_params['rqtl_model'] = "normal"
- mapping_params['do_control'] = False
- mapping_params['control_marker'] = ""
- mapping_params['manhattan_plot'] = True
- mapping_params['pair_scan'] = False
- if 'rqtl_method' in start_vars:
- mapping_params['rqtl_method'] = start_vars['rqtl_method']
- if 'rqtl_model' in start_vars:
- mapping_params['rqtl_model'] = start_vars['rqtl_model']
- if 'control_marker' in start_vars:
- mapping_params['control_marker'] = start_vars['control_marker']
- mapping_params['do_control'] = True
- if 'pair_scan' in start_vars:
- if start_vars['pair_scan'].lower() == "true":
- mapping_params['pair_scan'] = True
-
- if 'interval_mapping' in start_vars:
- if start_vars['interval_mapping'].lower() == "true":
- mapping_params['manhattan_plot'] = False
- elif 'manhattan_plot' in start_vars:
- if start_vars['manhattan_plot'].lower() != "true":
- mapping_params['manhattan_plot'] = False
-
- mapping_params['maf'] = 0.01
- if 'maf' in start_vars:
- mapping_params['maf'] = start_vars['maf'] # Minor allele frequency
-
- mapping_params['use_loco'] = False
- if 'use_loco' in start_vars:
- if start_vars['use_loco'].lower() != "false":
- mapping_params['use_loco'] = start_vars['use_loco']
-
- mapping_params['num_perm'] = 0
- mapping_params['perm_check'] = False
- if 'num_perm' in start_vars:
- try:
- mapping_params['num_perm'] = int(start_vars['num_perm'])
- mapping_params['perm_check'] = "ON"
- except:
- mapping_params['perm_check'] = False
-
- return mapping_params
-
-
+from __future__ import absolute_import, division, print_function + +import string + +from base import data_set +from base import webqtlConfig +from base.trait import GeneralTrait, retrieve_sample_data + +from utility import helper_functions +from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping + +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +def do_mapping_for_api(start_vars): + assert('db' in start_vars) + assert('trait_id' in start_vars) + + dataset = data_set.create_dataset(dataset_name = start_vars['db']) + dataset.group.get_markers() + this_trait = GeneralTrait(dataset = dataset, name = start_vars['trait_id']) + this_trait = retrieve_sample_data(this_trait, dataset) + + samples = [] + vals = [] + + for sample in dataset.group.samplelist: + in_trait_data = False + for item in this_trait.data: + if this_trait.data[item].name == sample: + value = str(this_trait.data[item].value) + samples.append(item) + vals.append(value) + in_trait_data = True + break + if not in_trait_data: + vals.append("x") + + mapping_params = initialize_parameters(start_vars, dataset, this_trait) + + covariates = "" #ZS: It seems to take an empty string as default. This should probably be changed. + + if mapping_params['mapping_method'] == "gemma": + header_row = ["name", "chr", "Mb", "lod_score", "p_value"] + if mapping_params['use_loco'] == "True": #ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api + result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0] + else: + result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf']) + elif mapping_params['mapping_method'] == "rqtl": + header_row = ["name", "chr", "cM", "lod_score"] + if mapping_params['num_perm'] > 0: + _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], + mapping_params['perm_check'], mapping_params['num_perm'], + mapping_params['do_control'], mapping_params['control_marker'], + mapping_params['manhattan_plot'], mapping_params['pair_scan']) + else: + result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], + mapping_params['perm_check'], mapping_params['num_perm'], + mapping_params['do_control'], mapping_params['control_marker'], + mapping_params['manhattan_plot'], mapping_params['pair_scan']) + + if mapping_params['limit_to']: + result_markers = result_markers[:mapping_params['limit_to']] + + if mapping_params['format'] == "csv": + output_rows = [] + output_rows.append(header_row) + for marker in result_markers: + this_row = [marker[header] for header in header_row] + output_rows.append(this_row) + + return output_rows, mapping_params['format'] + elif mapping_params['format'] == "json": + return result_markers, mapping_params['format'] + else: + return result_markers, None + + + +def initialize_parameters(start_vars, dataset, this_trait): + mapping_params = {} + + mapping_params['format'] = "json" + if 'format' in start_vars: + mapping_params['format'] = start_vars['format'] + + mapping_params['limit_to'] = False + if 'limit_to' in start_vars: + if start_vars['limit_to'].isdigit(): + mapping_params['limit_to'] = int(start_vars['limit_to']) + + mapping_params['mapping_method'] = "gemma" + if 'method' in start_vars: + mapping_params['mapping_method'] = start_vars['method'] + + if mapping_params['mapping_method'] == "rqtl": + mapping_params['rqtl_method'] = "hk" + mapping_params['rqtl_model'] = "normal" + mapping_params['do_control'] = False + mapping_params['control_marker'] = "" + mapping_params['manhattan_plot'] = True + mapping_params['pair_scan'] = False + if 'rqtl_method' in start_vars: + mapping_params['rqtl_method'] = start_vars['rqtl_method'] + if 'rqtl_model' in start_vars: + mapping_params['rqtl_model'] = start_vars['rqtl_model'] + if 'control_marker' in start_vars: + mapping_params['control_marker'] = start_vars['control_marker'] + mapping_params['do_control'] = True + if 'pair_scan' in start_vars: + if start_vars['pair_scan'].lower() == "true": + mapping_params['pair_scan'] = True + + if 'interval_mapping' in start_vars: + if start_vars['interval_mapping'].lower() == "true": + mapping_params['manhattan_plot'] = False + elif 'manhattan_plot' in start_vars: + if start_vars['manhattan_plot'].lower() != "true": + mapping_params['manhattan_plot'] = False + + mapping_params['maf'] = 0.01 + if 'maf' in start_vars: + mapping_params['maf'] = start_vars['maf'] # Minor allele frequency + + mapping_params['use_loco'] = True + if 'use_loco' in start_vars: + if (start_vars['use_loco'].lower() == "false") or (start_vars['use_loco'].lower() == "no"): + mapping_params['use_loco'] = False + + mapping_params['num_perm'] = 0 + mapping_params['perm_check'] = False + if 'num_perm' in start_vars: + try: + mapping_params['num_perm'] = int(start_vars['num_perm']) + mapping_params['perm_check'] = "ON" + except: + mapping_params['perm_check'] = False + + return mapping_params + + diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 845873a0..8ec93e48 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -11,7 +11,7 @@ from flask import g, Response, request, make_response, render_template, send_fro import sqlalchemy from wqflask import app -from wqflask.api import correlation, mapping +from wqflask.api import correlation, mapping, gen_menu from utility.tools import flat_files @@ -22,7 +22,7 @@ version = "pre1" @app.route("/api/v_{}/".format(version)) def hello_world(): - return flask.jsonify({'hello':'world'}) + return flask.jsonify({"hello":"world"}) @app.route("/api/v_{}/species".format(version)) def get_species_list(): @@ -31,10 +31,10 @@ def get_species_list(): species_list = [] for species in the_species: species_dict = { - 'Id' : species[0], - 'Name' : species[1], - 'FullName' : species[2], - 'TaxonomyId' : species[3] + "Id" : species[0], + "Name" : species[1], + "FullName" : species[2], + "TaxonomyId" : species[3] } species_list.append(species_dict) @@ -45,34 +45,34 @@ def get_species_list(): def get_species_info(species_name, file_format = "json"): results = g.db.execute("""SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species - WHERE (Name='{0}' OR FullName='{0}' OR SpeciesName='{0}');""".format(species_name)) + WHERE (Name="{0}" OR FullName="{0}" OR SpeciesName="{0}");""".format(species_name)) the_species = results.fetchone() species_dict = { - 'Id' : the_species[0], - 'Name' : the_species[1], - 'FullName' : the_species[2], - 'TaxonomyId' : the_species[3] + "Id" : the_species[0], + "Name" : the_species[1], + "FullName" : the_species[2], + "TaxonomyId" : the_species[3] } return flask.jsonify(species_dict) @app.route("/api/v_{}/groups".format(version)) -@app.route("/api/v_{}/<path:species_name>/groups".format(version)) +@app.route("/api/v_{}/groups/<path:species_name>".format(version)) def get_groups_list(species_name=None): if species_name: - results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, - InbredSet.Name, InbredSet.FullName, InbredSet.public, - InbredSet.MappingMethodId, InbredSet.GeneticType + results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, + InbredSet.Name, InbredSet.FullName, InbredSet.public, + IFNULL(InbredSet.MappingMethodId, "None"), IFNULL(InbredSet.GeneticType, "None") FROM InbredSet, Species WHERE InbredSet.SpeciesId = Species.Id AND - (Species.Name = '{0}' OR - Species.FullName='{0}' OR - Species.SpeciesName='{0}');""".format(species_name)) + (Species.Name = "{0}" OR + Species.FullName="{0}" OR + Species.SpeciesName="{0}");""".format(species_name)) else: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - InbredSet.MappingMethodId, InbredSet.GeneticType + IFNULL(InbredSet.MappingMethodId, "None"), IFNULL(InbredSet.GeneticType, "None") FROM InbredSet;""") the_groups = results.fetchall() @@ -80,14 +80,14 @@ def get_groups_list(species_name=None): groups_list = [] for group in the_groups: group_dict = { - 'Id' : group[0], - 'SpeciesId' : group[1], - 'DisplayName' : group[2], - 'Name' : group[3], - 'FullName' : group[4], - 'public' : group[5], - 'MappingMethodId' : group[6], - 'GeneticType' : group[7] + "Id" : group[0], + "SpeciesId" : group[1], + "DisplayName" : group[2], + "Name" : group[3], + "FullName" : group[4], + "public" : group[5], + "MappingMethodId" : group[6], + "GeneticType" : group[7] } groups_list.append(group_dict) @@ -103,35 +103,35 @@ def get_group_info(group_name, species_name = None, file_format = "json"): if species_name: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - InbredSet.MappingMethodId, InbredSet.GeneticType + IFNULL(InbredSet.MappingMethodId, "None"), IFNULL(InbredSet.GeneticType, "None") FROM InbredSet, Species WHERE InbredSet.SpeciesId = Species.Id AND - (InbredSet.InbredSetName = '{0}' OR - InbredSet.Name = '{0}' OR - InbredSet.FullName = '{0}') AND - (Species.Name = '{1}' OR - Species.FullName='{1}' OR - Species.SpeciesName='{1}');""".format(group_name, species_name)) + (InbredSet.InbredSetName = "{0}" OR + InbredSet.Name = "{0}" OR + InbredSet.FullName = "{0}") AND + (Species.Name = "{1}" OR + Species.FullName="{1}" OR + Species.SpeciesName="{1}");""".format(group_name, species_name)) else: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - InbredSet.MappingMethodId, InbredSet.GeneticType + IFNULL(InbredSet.MappingMethodId, "None"), IFNULL(InbredSet.GeneticType, "None") FROM InbredSet - WHERE (InbredSet.InbredSetName = '{0}' OR - InbredSet.Name = '{0}' OR - InbredSet.FullName = '{0}');""".format(group_name)) + WHERE (InbredSet.InbredSetName = "{0}" OR + InbredSet.Name = "{0}" OR + InbredSet.FullName = "{0}");""".format(group_name)) group = results.fetchone() if group: group_dict = { - 'Id' : group[0], - 'SpeciesId' : group[1], - 'DisplayName' : group[2], - 'Name' : group[3], - 'FullName' : group[4], - 'public' : group[5], - 'MappingMethodId' : group[6], - 'GeneticType' : group[7] + "Id" : group[0], + "SpeciesId" : group[1], + "DisplayName" : group[2], + "Name" : group[3], + "FullName" : group[4], + "public" : group[5], + "MappingMethodId" : group[6], + "GeneticType" : group[7] } return flask.jsonify(group_dict) @@ -150,9 +150,9 @@ def get_datasets_for_group(group_name, species_name=None): FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Species WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND - (InbredSet.Name = '{0}' OR InbredSet.InbredSetName = '{0}' OR InbredSet.FullName = '{0}') AND + (InbredSet.Name = "{0}" OR InbredSet.InbredSetName = "{0}" OR InbredSet.FullName = "{0}") AND InbredSet.SpeciesId = Species.Id AND - (Species.SpeciesName = '{1}' OR Species.MenuName = '{1}' OR Species.FullName = '{1}'); + (Species.SpeciesName = "{1}" OR Species.MenuName = "{1}" OR Species.FullName = "{1}"); """.format(group_name, species_name)) else: results = g.db.execute(""" @@ -163,7 +163,7 @@ def get_datasets_for_group(group_name, species_name=None): FROM ProbeSetFreeze, ProbeFreeze, InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND - (InbredSet.Name = '{0}' OR InbredSet.InbredSetName = '{0}' OR InbredSet.FullName = '{0}'); + (InbredSet.Name = "{0}" OR InbredSet.InbredSetName = "{0}" OR InbredSet.FullName = "{0}"); """.format(group_name)) the_datasets = results.fetchall() @@ -172,17 +172,17 @@ def get_datasets_for_group(group_name, species_name=None): datasets_list = [] for dataset in the_datasets: dataset_dict = { - 'Id' : dataset[0], - 'ProbeFreezeId' : dataset[1], - 'AvgID' : dataset[2], - 'Short_Abbreviation' : dataset[3], - 'Long_Abbreviation' : dataset[4], - 'FullName' : dataset[5], - 'ShortName' : dataset[6], - 'CreateTime' : dataset[7], - 'public' : dataset[8], - 'confidentiality' : dataset[9], - 'DataScale' : dataset[10] + "Id" : dataset[0], + "ProbeFreezeId" : dataset[1], + "AvgID" : dataset[2], + "Short_Abbreviation" : dataset[3], + "Long_Abbreviation" : dataset[4], + "FullName" : dataset[5], + "ShortName" : dataset[6], + "CreateTime" : dataset[7], + "public" : dataset[8], + "confidentiality" : dataset[9], + "DataScale" : dataset[10] } datasets_list.append(dataset_dict) @@ -197,7 +197,7 @@ def get_datasets_for_group(group_name, species_name=None): def get_dataset_info(dataset_name, group_name = None, file_format="json"): #ZS: First get ProbeSet (mRNA expression) datasets and then get Phenotype datasets - datasets_list = [] #ZS: I figure I might as well return a list if there are multiple matches, though I don't know if this will actually happen in practice + datasets_list = [] #ZS: I figure I might as well return a list if there are multiple matches, though I don"t know if this will actually happen in practice probeset_query = """ SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, @@ -212,12 +212,12 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): """ if dataset_name.isdigit(): where_statement += """ - ProbeSetFreeze.Id = '{}' + ProbeSetFreeze.Id = "{}" """.format(dataset_name) else: where_statement += """ - (ProbeSetFreeze.Name = '{0}' OR ProbeSetFreeze.Name2 = '{0}' OR - ProbeSetFreeze.FullName = '{0}' OR ProbeSetFreeze.ShortName = '{0}') + (ProbeSetFreeze.Name = "{0}" OR ProbeSetFreeze.Name2 = "{0}" OR + ProbeSetFreeze.FullName = "{0}" OR ProbeSetFreeze.ShortName = "{0}") """.format(dataset_name) probeset_query += where_statement @@ -226,16 +226,16 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): if dataset: dataset_dict = { - 'dataset_type' : "mRNA expression", - 'id' : dataset[0], - 'name' : dataset[1], - 'full_name' : dataset[2], - 'short_name' : dataset[3], - 'data_scale' : dataset[4], - 'tissue_id' : dataset[5], - 'tissue' : dataset[6], - 'public' : dataset[7], - 'confidential' : dataset[8] + "dataset_type" : "mRNA expression", + "id" : dataset[0], + "name" : dataset[1], + "full_name" : dataset[2], + "short_name" : dataset[3], + "data_scale" : dataset[4], + "tissue_id" : dataset[5], + "tissue" : dataset[6], + "public" : dataset[7], + "confidential" : dataset[8] } datasets_list.append(dataset_dict) @@ -249,7 +249,7 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): WHERE PublishXRef.InbredSetId = InbredSet.Id AND PublishXRef.PhenotypeId = Phenotype.Id AND PublishXRef.PublicationId = Publication.Id AND - InbredSet.Name = '{0}' AND PublishXRef.Id = '{1}' + InbredSet.Name = "{0}" AND PublishXRef.Id = "{1}" """.format(group_name, dataset_name) logger.debug("QUERY:", pheno_query) @@ -260,25 +260,25 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): if dataset: if dataset[5]: dataset_dict = { - 'dataset_type' : "phenotype", - 'id' : dataset[0], - 'name' : dataset[1], - 'description' : dataset[2], - 'pubmed_id' : dataset[5], - 'title' : dataset[6], - 'year' : dataset[7] + "dataset_type" : "phenotype", + "id" : dataset[0], + "name" : dataset[1], + "description" : dataset[2], + "pubmed_id" : dataset[5], + "title" : dataset[6], + "year" : dataset[7] } elif dataset[4]: dataset_dict = { - 'dataset_type' : "phenotype", - 'id' : dataset[0], - 'name' : dataset[3], - 'description' : dataset[4] + "dataset_type" : "phenotype", + "id" : dataset[0], + "name" : dataset[3], + "description" : dataset[4] } else: dataset_dict = { - 'dataset_type' : "phenotype", - 'id' : dataset[0] + "dataset_type" : "phenotype", + "id" : dataset[0] } datasets_list.append(dataset_dict) @@ -290,11 +290,129 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") +@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=("GET",)) +@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=("GET",)) +def fetch_traits(dataset_name, file_format = "json"): + trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args) + if ("ids_only" in request.args) and (len(trait_ids) > 0): + if file_format == "json": + filename = dataset_name + "_trait_ids.json" + return flask.jsonify(trait_ids) + else: + filename = dataset_name + "_trait_ids.csv" + + si = StringIO.StringIO() + csv_writer = csv.writer(si) + csv_writer.writerows([[trait_id] for trait_id in trait_ids]) + output = make_response(si.getvalue()) + output.headers["Content-Disposition"] = "attachment; filename=" + filename + output.headers["Content-type"] = "text/csv" + return output + elif ("names_only" in request.args) and (len(trait_ids) > 0): + if file_format == "json": + filename = dataset_name + "_trait_names.json" + return flask.jsonify(trait_names) + else: + filename = dataset_name + "_trait_names.csv" + + si = StringIO.StringIO() + csv_writer = csv.writer(si) + csv_writer.writerows([[trait_name] for trait_name in trait_names]) + output = make_response(si.getvalue()) + output.headers["Content-Disposition"] = "attachment; filename=" + filename + output.headers["Content-type"] = "text/csv" + return output + else: + if len(trait_ids) > 0: + if data_type == "ProbeSet": + query = """ + SELECT + ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias, + ProbeSetXRef.mean, ProbeSetXRef.se, ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.h2 + FROM + ProbeSet, ProbeSetXRef + WHERE + ProbeSetXRef.ProbeSetFreezeId = "{0}" AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id + ORDER BY + ProbeSet.Id + """ + + field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"] + elif data_type == "Geno": + query = """ + SELECT + Geno.Id, Geno.Name, Geno.Marker_Name, Geno.Chr, Geno.Mb, Geno.Sequence, Geno.Source + FROM + Geno, GenoXRef + WHERE + GenoXRef.GenoFreezeId = "{0}" AND + GenoXRef.GenoId = Geno.Id + ORDER BY + Geno.Id + """ + + field_list = ["Id", "Name", "Marker_Name", "Chr", "Mb", "Sequence", "Source"] + else: + query = """ + SELECT + PublishXRef.Id, PublishXRef.PhenotypeId, PublishXRef.PublicationId, PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive, PublishXRef.Sequence + FROM + PublishXRef + WHERE + PublishXRef.InbredSetId = {0} + ORDER BY + PublishXRef.Id + """ + + field_list = ["Id", "PhenotypeId", "PublicationId", "Locus", "LRS", "Additive", "Sequence"] + + if 'limit_to' in request.args: + limit_number = request.args['limit_to'] + query += "LIMIT " + str(limit_number) + + if file_format == "json": + filename = dataset_name + "_traits.json" + + final_query = query.format(dataset_id) + + result_list = [] + for result in g.db.execute(final_query).fetchall(): + trait_dict = {} + for i, field in enumerate(field_list): + if result[i]: + trait_dict[field] = result[i] + result_list.append(trait_dict) + + return flask.jsonify(result_list) + elif file_format == "csv": + filename = dataset_name + "_traits.csv" + + results_list = [] + header_list = [] + header_list += field_list + results_list.append(header_list) + + final_query = query.format(dataset_id) + for result in g.db.execute(final_query).fetchall(): + results_list.append(result) + + si = StringIO.StringIO() + csv_writer = csv.writer(si) + csv_writer.writerows(results_list) + output = make_response(si.getvalue()) + output.headers["Content-Disposition"] = "attachment; filename=" + filename + output.headers["Content-type"] = "text/csv" + return output + else: + return return_error(code=400, source=request.url_rule.rule, title="Invalid Output Format", details="Current formats available are JSON and CSV, with CSV as default") + else: + return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @app.route("/api/v_{}/sample_data/<path:dataset_name>".format(version)) @app.route("/api/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version)) def all_sample_data(dataset_name, file_format = "csv"): - trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name) + trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args) if len(trait_ids) > 0: sample_list = get_samplelist(dataset_name) @@ -308,8 +426,8 @@ def all_sample_data(dataset_name, file_format = "csv"): LEFT JOIN ProbeSetSE ON (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) WHERE - ProbeSetXRef.ProbeSetFreezeId = '{0}' AND - ProbeSetXRef.ProbeSetId = '{1}' AND + ProbeSetXRef.ProbeSetFreezeId = "{0}" AND + ProbeSetXRef.ProbeSetId = "{1}" AND ProbeSetXRef.DataId = ProbeSetData.Id AND ProbeSetData.StrainId = Strain.Id ORDER BY @@ -324,8 +442,8 @@ def all_sample_data(dataset_name, file_format = "csv"): LEFT JOIN GenoSE ON (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) WHERE - GenoXRef.GenoFreezeId = '{0}' AND - GenoXRef.GenoId = '{1}' AND + GenoXRef.GenoFreezeId = "{0}" AND + GenoXRef.GenoId = "{1}" AND GenoXRef.DataId = GenoData.Id AND GenoData.StrainId = Strain.Id ORDER BY @@ -343,8 +461,8 @@ def all_sample_data(dataset_name, file_format = "csv"): (NStrain.DataId = PublishData.Id AND NStrain.StrainId = PublishData.StrainId) WHERE - PublishXRef.InbredSetId = '{0}' AND - PublishXRef.PhenotypeId = '{1}' AND + PublishXRef.InbredSetId = "{0}" AND + PublishXRef.PhenotypeId = "{1}" AND PublishData.Id = PublishXRef.DataId AND PublishData.StrainId = Strain.Id ORDER BY @@ -382,7 +500,7 @@ def all_sample_data(dataset_name, file_format = "csv"): output.headers["Content-type"] = "text/csv" return output else: - return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + return return_error(code=415, source=request.url_rule.rule, title="Unsupported file format", details="") else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @@ -397,9 +515,9 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): LEFT JOIN ProbeSetSE ON (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) WHERE - ProbeSet.Name = '{0}' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSet.Name = "{0}" AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetFreeze.Name = '{1}' AND + ProbeSetFreeze.Name = "{1}" AND ProbeSetXRef.DataId = ProbeSetData.Id AND ProbeSetData.StrainId = Strain.Id ORDER BY @@ -413,13 +531,13 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): sample_list = [] for sample in sample_data: sample_dict = { - 'sample_name' : sample[0], - 'sample_name_2' : sample[1], - 'value' : sample[2], - 'data_id' : sample[3], + "sample_name" : sample[0], + "sample_name_2" : sample[1], + "value" : sample[2], + "data_id" : sample[3], } if sample[4]: - sample_dict['se'] = sample[4] + sample_dict["se"] = sample[4] sample_list.append(sample_dict) return flask.jsonify(sample_list) @@ -434,7 +552,7 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): dataset_or_group = dataset_name pheno_query = """ - SELECT + SELECT DISTINCT Strain.Name, Strain.Name2, PublishData.value, PublishData.Id, PublishSE.error, NStrain.count FROM (PublishData, Strain, PublishXRef, PublishFreeze) @@ -445,9 +563,9 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): NStrain.StrainId = PublishData.StrainId) WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = '{1}' AND - (PublishFreeze.Id = '{0}' OR PublishFreeze.Name = '{0}' OR - PublishFreeze.ShortName = '{0}' OR PublishXRef.InbredSetId = '{0}') AND + PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = "{1}" AND + (PublishFreeze.Id = "{0}" OR PublishFreeze.Name = "{0}" OR + PublishFreeze.ShortName = "{0}" OR PublishXRef.InbredSetId = "{0}") AND PublishData.StrainId = Strain.Id ORDER BY Strain.Name @@ -460,15 +578,15 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): sample_list = [] for sample in sample_data: sample_dict = { - 'sample_name' : sample[0], - 'sample_name_2' : sample[1], - 'value' : sample[2], - 'data_id' : sample[3] + "sample_name" : sample[0], + "sample_name_2" : sample[1], + "value" : sample[2], + "data_id" : sample[3] } if sample[4]: - sample_dict['se'] = sample[4] + sample_dict["se"] = sample[4] if sample[5]: - sample_dict['n_cases'] = sample[5] + sample_dict["n_cases"] = sample[5] sample_list.append(sample_dict) return flask.jsonify(sample_list) @@ -482,15 +600,15 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): def get_trait_info(dataset_name, trait_name, file_format = "json"): probeset_query = """ SELECT - ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias, + ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias, ProbeSetXRef.mean, ProbeSetXRef.se, ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze WHERE - ProbeSet.Name = '{0}' AND + ProbeSet.Name = "{0}" AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetFreeze.Name = '{1}' + ProbeSetFreeze.Name = "{1}" """.format(trait_name, dataset_name) probeset_results = g.db.execute(probeset_query) @@ -498,19 +616,19 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"): trait_info = probeset_results.fetchone() if trait_info: trait_dict = { - 'id' : trait_info[0], - 'name' : trait_info[1], - 'symbol' : trait_info[2], - 'description' : trait_info[3], - 'chr' : trait_info[4], - 'mb' : trait_info[5], - 'alias' :trait_info[6], - 'mean' : trait_info[7], - 'se' : trait_info[8], - 'locus' : trait_info[9], - 'lrs' : trait_info[10], - 'p_value' : trait_info[11], - 'additive' : trait_info[12] + "id" : trait_info[0], + "name" : trait_info[1], + "symbol" : trait_info[2], + "description" : trait_info[3], + "chr" : trait_info[4], + "mb" : trait_info[5], + "alias" :trait_info[6], + "mean" : trait_info[7], + "se" : trait_info[8], + "locus" : trait_info[9], + "lrs" : trait_info[10], + "p_value" : trait_info[11], + "additive" : trait_info[12] } return flask.jsonify(trait_dict) @@ -525,28 +643,26 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"): FROM PublishXRef WHERE - PublishXRef.Id = '{0}' AND - PublishXRef.InbredSetId = '{1}' + PublishXRef.Id = "{0}" AND + PublishXRef.InbredSetId = "{1}" """.format(trait_name, group_id) - - logger.debug("QUERY:", pheno_query) pheno_results = g.db.execute(pheno_query) trait_info = pheno_results.fetchone() if trait_info: trait_dict = { - 'id' : trait_info[0], - 'locus' : trait_info[1], - 'lrs' : trait_info[2], - 'additive' : trait_info[3] + "id" : trait_info[0], + "locus" : trait_info[1], + "lrs" : trait_info[2], + "additive" : trait_info[3] } return flask.jsonify(trait_dict) else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/correlation".format(version), methods=('GET',)) +@app.route("/api/v_{}/correlation".format(version), methods=("GET",)) def get_corr_results(): results = correlation.do_correlation(request.args) @@ -555,53 +671,71 @@ def get_corr_results(): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/mapping".format(version), methods=('GET',)) +@app.route("/api/v_{}/mapping".format(version), methods=("GET",)) def get_mapping_results(): - results = mapping.do_mapping_for_api(request.args) + results, format = mapping.do_mapping_for_api(request.args) if len(results) > 0: - filename = "mapping_" + datetime.datetime.utcnow().strftime('%b_%d_%Y_%I:%M%p') + ".csv" + if format == "csv": + filename = "mapping_" + datetime.datetime.utcnow().strftime("%b_%d_%Y_%I:%M%p") + ".csv" - si = StringIO.StringIO() - csv_writer = csv.writer(si) - csv_writer.writerows(results) - output = make_response(si.getvalue()) - output.headers["Content-Disposition"] = "attachment; filename=" + filename - output.headers["Content-type"] = "text/csv" + si = StringIO.StringIO() + csv_writer = csv.writer(si) + csv_writer.writerows(results) + output = make_response(si.getvalue()) + output.headers["Content-Disposition"] = "attachment; filename=" + filename + output.headers["Content-type"] = "text/csv" - return output + return output + elif format == "json": + return flask.jsonify(results) + else: + return return_error(code=415, source=request.url_rule.rule, title="Unsupported Format", details="") else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @app.route("/api/v_{}/genotypes/<path:group_name>".format(version)) @app.route("/api/v_{}/genotypes/<path:group_name>.<path:file_format>".format(version)) def get_genotypes(group_name, file_format="csv"): + limit_num = None + if 'limit_to' in request.args: + if request.args['limit_to'].isdigit(): + limit_num = int(request.args['limit_to']) + si = StringIO.StringIO() if file_format == "csv" or file_format == "geno": filename = group_name + ".geno" - if os.path.isfile('{0}/{1}.geno'.format(flat_files('genotype'), group_name)): + if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)): output_lines = [] - with open('{0}/{1}.geno'.format(flat_files('genotype'), group_name)) as genofile: + with open("{0}/{1}.geno".format(flat_files("genotype"), group_name)) as genofile: + i = 0 for line in genofile: if line[0] == "#" or line[0] == "@": output_lines.append([line.strip()]) else: + if limit_num and i >= limit_num: + break output_lines.append(line.split()) + i += 1 - csv_writer = csv.writer(si, delimiter = '\t', escapechar = "\\", quoting = csv.QUOTE_NONE) + csv_writer = csv.writer(si, delimiter = "\t", escapechar = "\\", quoting = csv.QUOTE_NONE) else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") else: filename = group_name + ".bimbam" - if os.path.isfile('{0}/{1}.geno'.format(flat_files('genotype'), group_name)): + if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)): output_lines = [] - with open('{0}/{1}_geno.txt'.format(flat_files('genotype/bimbam'), group_name)) as genofile: + with open("{0}/{1}_geno.txt".format(flat_files("genotype/bimbam"), group_name)) as genofile: + i = 0 for line in genofile: + if limit_num and i >= limit_num: + break output_lines.append([line.strip() for line in line.split(",")]) + i += 1 - csv_writer = csv.writer(si, delimiter = ',') + csv_writer = csv.writer(si, delimiter = ",") else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @@ -612,12 +746,14 @@ def get_genotypes(group_name, file_format="csv"): return output -@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=('GET',)) -@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=('GET',)) -def get_traits(dataset_name, file_format = "json"): - #ZS: Need to check about the "start" and "stop" stuff since it seems to just limit the number of results to stop - start + 1 in Pjotr's elixir code +@app.route("/api/v_{}/gen_dropdown".format(version), methods=("GET",)) +def gen_dropdown_menu(): + results = gen_menu.gen_dropdown_json() - NotImplemented + if len(results) > 0: + return flask.jsonify(results) + else: + return return_error(code=500, source=request.url_rule.rule, title="Some error occurred", details="") def return_error(code, source, title, details): json_ob = {"errors": [ @@ -631,7 +767,13 @@ def return_error(code, source, title, details): return flask.jsonify(json_ob) -def get_dataset_trait_ids(dataset_name): +def get_dataset_trait_ids(dataset_name, start_vars): + + if 'limit_to' in start_vars: + limit_string = "LIMIT " + str(start_vars['limit_to']) + else: + limit_string = "" + if "Geno" in dataset_name: data_type = "Geno" #ZS: Need to pass back the dataset type query = """ @@ -642,8 +784,9 @@ def get_dataset_trait_ids(dataset_name): WHERE Geno.Id = GenoXRef.GenoId AND GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoFreeze.Name = '{0}' - """.format(dataset_name) + GenoFreeze.Name = "{0}" + {1} + """.format(dataset_name, limit_string) results = g.db.execute(query).fetchall() @@ -652,7 +795,7 @@ def get_dataset_trait_ids(dataset_name): dataset_id = results[0][2] return trait_ids, trait_names, data_type, dataset_id - elif "Publish" in dataset_name: + elif "Publish" in dataset_name or get_group_id(dataset_name): data_type = "Publish" dataset_name = dataset_name.replace("Publish", "") dataset_id = get_group_id(dataset_name) @@ -663,8 +806,9 @@ def get_dataset_trait_ids(dataset_name): FROM PublishXRef WHERE - PublishXRef.InbredSetId = '{0}' - """.format(dataset_id) + PublishXRef.InbredSetId = "{0}" + {1} + """.format(dataset_id, limit_string) results = g.db.execute(query).fetchall() @@ -682,8 +826,9 @@ def get_dataset_trait_ids(dataset_name): WHERE ProbeSet.Id = ProbeSetXRef.ProbeSetId AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetFreeze.Name = '{0}' - """.format(dataset_name) + ProbeSetFreeze.Name = "{0}" + {1} + """.format(dataset_name, limit_string) results = g.db.execute(query).fetchall() @@ -743,13 +888,16 @@ def get_group_id_from_dataset(dataset_name): result = g.db.execute(query).fetchone() - return result[0] + if len(result) > 0: + return result[0] + else: + return None def get_group_id(group_name): query = """ SELECT InbredSet.Id FROM InbredSet - WHERE InbredSet.Name = '{}' + WHERE InbredSet.Name = "{}" """.format(group_name) group_id = g.db.execute(query).fetchone() diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 74013239..7e3337a0 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -214,6 +214,8 @@ def collections_new(): if "create_new" in params: logger.debug("in create_new") collection_name = params['new_collection'] + if collection_name.strip() == "": + collection_name = datetime.datetime.utcnow().strftime('Collection_%b_%d_%H:%M') return create_new(collection_name) elif "add_to_existing" in params: logger.debug("in add to existing") diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 925e8783..07aa947e 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -1,5 +1,7 @@ from __future__ import absolute_import, print_function, division +import math + from flask import g from base.trait import GeneralTrait @@ -35,17 +37,30 @@ class CorrScatterPlot(object): vals_2.append(samples_2[sample].value) self.data.append(vals_2) - x = np.array(vals_1) - y = np.array(vals_2) - slope, intercept, r_value, p_value, std_err = stats.linregress(x, y) + slope, intercept, r_value, p_value, std_err = stats.linregress(vals_1, vals_2) - rx = stats.rankdata(x) - ry = stats.rankdata(y) + x_buffer = (max(vals_1) - min(vals_1))*0.1 + y_buffer = (max(vals_2) - min(vals_2))*0.1 + + x_range = [min(vals_1) - x_buffer, max(vals_1) + x_buffer] + y_range = [min(vals_2) - y_buffer, max(vals_2) + y_buffer] + + intercept_coords = get_intercept_coords(slope, intercept, x_range, y_range) + + rx = stats.rankdata(vals_1) + ry = stats.rankdata(vals_2) self.rdata = [] self.rdata.append(rx.tolist()) self.rdata.append(ry.tolist()) srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(rx, ry) + x_buffer = (max(rx) - min(rx))*0.1 + y_buffer = (max(ry) - min(ry))*0.1 + + sr_range = [min(rx) - x_buffer, max(rx) + x_buffer] + + sr_intercept_coords = get_intercept_coords(srslope, srintercept, sr_range, sr_range) + #vals_3 = [] #for sample in self.trait_3.data: # vals_3.append(self.trait_3.data[sample].value) @@ -68,6 +83,11 @@ class CorrScatterPlot(object): num_overlap = num_overlap, vals_1 = vals_1, vals_2 = vals_2, + x_range = x_range, + y_range = y_range, + sr_range = sr_range, + intercept_coords = intercept_coords, + sr_intercept_coords = sr_intercept_coords, slope = slope, intercept = intercept, @@ -83,3 +103,17 @@ class CorrScatterPlot(object): #vals_3 = vals_3 ) self.jsdata = self.js_data + + +def get_intercept_coords(slope, intercept, x_range, y_range): + intercept_coords = [] + + y1 = slope*x_range[0] + intercept + y2 = slope*x_range[1] + intercept + x1 = (y1-intercept)/slope + x2 = (y2-intercept)/slope + + intercept_coords.append([x1, y1]) + intercept_coords.append([x2, y2]) + + return intercept_coords
\ No newline at end of file diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 1aa7945d..0db8fa38 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -83,7 +83,7 @@ class CorrelationResults(object): assert('corr_sample_method' in start_vars) assert('corr_samples_group' in start_vars) assert('corr_dataset' in start_vars) - assert('min_expr' in start_vars) + #assert('min_expr' in start_vars) assert('corr_return_results' in start_vars) if 'loc_chr' in start_vars: assert('min_loc_mb' in start_vars) @@ -117,6 +117,8 @@ class CorrelationResults(object): self.location_chr = get_string(start_vars,'loc_chr') self.min_location_mb = get_int(start_vars,'min_loc_mb') self.max_location_mb = get_int(start_vars,'max_loc_mb') + else: + self.location_chr = self.min_location_mb = self.max_location_mb = None self.get_formatted_corr_type() self.return_number = int(start_vars['corr_return_results']) @@ -146,6 +148,15 @@ class CorrelationResults(object): self.target_dataset = data_set.create_dataset(start_vars['corr_dataset']) self.target_dataset.get_trait_data(self.sample_data.keys()) + self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method) + + if self.target_dataset.type == "ProbeSet": + self.filter_cols = [7, 6] + elif self.target_dataset.type == "Publish": + self.filter_cols = [6, 0] + else: + self.filter_cols = [4, 0] + self.correlation_results = [] self.correlation_data = {} @@ -179,8 +190,9 @@ class CorrelationResults(object): #ZS: Convert min/max chromosome to an int for the location range option range_chr_as_int = None for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): - if chr_info.name == self.location_chr: - range_chr_as_int = order_id + if 'loc_chr' in start_vars: + if chr_info.name == self.location_chr: + range_chr_as_int = order_id for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) @@ -534,3 +546,80 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap results_list.append(results_dict) return json.dumps(results_list) + +def get_header_fields(data_type, corr_method): + if data_type == "ProbeSet": + if corr_method == "pearson": + header_fields = ['Index', + 'Record', + 'Symbol', + 'Description', + 'Location', + 'Mean', + 'Sample r', + 'N', + 'Sample p(r)', + 'Lit r', + 'Tissue r', + 'Tissue p(r)', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] + else: + header_fields = ['Index', + 'Record', + 'Symbol', + 'Description', + 'Location', + 'Mean', + 'Sample rho', + 'N', + 'Sample p(rho)', + 'Lit rho', + 'Tissue rho', + 'Tissue p(rho)', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] + elif data_type == "Publish": + if corr_method == "pearson": + header_fields = ['Index', + 'Record', + 'Description', + 'Authors', + 'Year', + 'Sample r', + 'N', + 'Sample p(r)', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] + else: + header_fields = ['Index', + 'Record', + 'Description', + 'Authors', + 'Year', + 'Sample rho', + 'N', + 'Sample p(rho)', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] + else: + if corr_method == "pearson": + header_fields = ['Index', + 'ID', + 'Location' + 'Sample r', + 'N', + 'Sample p(r)'] + else: + header_fields = ['Index', + 'ID', + 'Location' + 'Sample rho', + 'N', + 'Sample p(rho)'] + + return header_fields
\ No newline at end of file diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py index 96c2c301..adeed6ad 100644 --- a/wqflask/wqflask/database.py +++ b/wqflask/wqflask/database.py @@ -9,7 +9,7 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) -engine = create_engine(SQL_URI, convert_unicode=True) +engine = create_engine(SQL_URI, encoding="latin1") db_session = scoped_session(sessionmaker(autocommit=False, autoflush=False, diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index c7dbc972..8476649f 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -22,12 +22,13 @@ class DoSearch(object): # Used to translate search phrases into classes search_types = dict() - def __init__(self, search_term, search_operator=None, dataset=None): + def __init__(self, search_term, search_operator=None, dataset=None, search_type=None): self.search_term = search_term # Make sure search_operator is something we expect assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator" self.search_operator = search_operator self.dataset = dataset + self.search_type = search_type if self.dataset: logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) @@ -69,7 +70,7 @@ class DoSearch(object): logger.debug("search_types are:", pf(cls.search_types)) search_type_string = search_type['dataset_type'] - if 'key' in search_type: + if 'key' in search_type and search_type['key'] != None: search_type_string += '_' + search_type['key'] logger.debug("search_type_string is:", search_type_string) @@ -444,12 +445,13 @@ class LrsSearch(DoSearch): """ - DoSearch.search_types['LRS'] = 'LrsSearch' + for search_key in ('LRS', 'LOD'): + DoSearch.search_types[search_key] = "LrsSearch" def get_from_clause(self): #If the user typed, for example "Chr4", the "Chr" substring needs to be removed so that all search elements can be converted to floats - if len(self.search_term) > 2 and "Chr" in self.search_term[2]: - chr_num = self.search_term[2].replace("Chr", "") + if len(self.search_term) > 2 and "chr" in self.search_term[2].lower(): + chr_num = self.search_term[2].lower().replace("chr", "") self.search_term[2] = chr_num self.search_term = [float(value) for value in self.search_term] @@ -465,6 +467,9 @@ class LrsSearch(DoSearch): if self.search_operator == "=": assert isinstance(self.search_term, (list, tuple)) lrs_min, lrs_max = self.search_term[:2] + if self.search_type == "LOD": + lrs_min = lrs_min*4.61 + lrs_max = lrs_max*4.61 where_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s """ % self.mescape(self.dataset.type, @@ -489,6 +494,10 @@ class LrsSearch(DoSearch): else: # Deal with >, <, >=, and <= logger.debug("self.search_term is:", self.search_term) + lrs_val = self.search_term[0] + if self.search_type == "LOD": + lrs_val = lrs_val*4.61 + where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, self.search_operator, self.search_term[0]) @@ -505,9 +514,11 @@ class LrsSearch(DoSearch): return self.execute(self.query) + class MrnaLrsSearch(LrsSearch, MrnaAssaySearch): - DoSearch.search_types['ProbeSet_LRS'] = 'MrnaLrsSearch' + for search_key in ('LRS', 'LOD'): + DoSearch.search_types['ProbeSet_' + search_key] = "MrnaLrsSearch" def run(self): @@ -520,7 +531,8 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch): class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch): - DoSearch.search_types['Publish_LRS'] = 'PhenotypeLrsSearch' + for search_key in ('LRS', 'LOD'): + DoSearch.search_types['Publish_' + search_key] = "PhenotypeLrsSearch" def run(self): @@ -532,7 +544,6 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch): return self.execute(self.query) - class CisTransLrsSearch(DoSearch): def get_from_clause(self): @@ -557,6 +568,10 @@ class CisTransLrsSearch(DoSearch): else: SomeError + if self.search_type == "CISLOD" or self.search_type == "TRANSLOD": + lrs_min = lrs_min * 4.61 + lrs_max = lrs_max * 4.61 + sub_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s and """ % ( escape(self.dataset.type), @@ -619,7 +634,8 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch): """ - DoSearch.search_types['ProbeSet_CISLRS'] = 'CisLrsSearch' + for search_key in ('LRS', 'LOD'): + DoSearch.search_types['ProbeSet_CIS'+search_key] = "CisLrsSearch" def get_where_clause(self): return CisTransLrsSearch.get_where_clause(self, "cis") @@ -648,7 +664,8 @@ class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch): """ - DoSearch.search_types['ProbeSet_TRANSLRS'] = 'TransLrsSearch' + for search_key in ('LRS', 'LOD'): + DoSearch.search_types['ProbeSet_TRANS'+search_key] = "TransLrsSearch" def get_where_clause(self): return CisTransLrsSearch.get_where_clause(self, "trans") diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 62398154..dbb77826 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -61,6 +61,7 @@ class GSearch(object): with Bench("Running query"): logger.sql(sql) re = g.db.execute(sql).fetchall() + trait_list = [] with Bench("Creating trait objects"): for i, line in enumerate(re): @@ -74,11 +75,14 @@ class GSearch(object): this_trait['group'] = line[1] this_trait['tissue'] = line[2] this_trait['symbol'] = line[6] - this_trait['description'] = line[7] + this_trait['description'] = line[7].decode('utf-8', 'replace') this_trait['location_repr'] = 'N/A' if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): this_trait['location_repr'] = 'Chr%s: %.6f' % (line[8], float(line[9])) - this_trait['mean'] = '%.3f' % line[10] + try: + this_trait['mean'] = '%.3f' % line[10] + except: + this_trait['mean'] = "N/A" this_trait['LRS_score_repr'] = "N/A" if line[11] != "" and line[11] != None: this_trait['LRS_score_repr'] = '%3.1f' % line[11] @@ -97,6 +101,7 @@ class GSearch(object): trait_list.append(this_trait) + self.trait_count = len(trait_list) self.trait_list = json.dumps(trait_list) elif self.type == "phenotype": @@ -147,9 +152,9 @@ class GSearch(object): this_trait['species'] = line[0] this_trait['group'] = line[1] if line[9] != None and line[6] != None: - this_trait['description'] = unicode(line[6], "utf-8", "ignore") + this_trait['description'] = line[6].decode('utf-8', 'replace') elif line[5] != None: - this_trait['description'] = unicode(line[5], "utf-8", "ignore") + this_trait['description'] = line[5].decode('utf-8', 'replace') else: this_trait['description'] = "N/A" this_trait['authors'] = line[7] @@ -183,4 +188,5 @@ class GSearch(object): trait_list.append(this_trait) + self.trait_count = len(trait_list) self.trait_list = json.dumps(trait_list) diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 9d33961c..37454dfb 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -120,14 +120,14 @@ class Heatmap(object): self.dataset.group.get_markers() this_trait = trait_db[0] #this_db = trait_db[1] - genotype = self.dataset.group.read_genotype_file() + genotype = self.dataset.group.read_genotype_file(use_reaper=True) samples, values, variances, sample_aliases = this_trait.export_informative() trimmed_samples = [] trimmed_values = [] for i in range(0, len(samples)): if samples[i] in self.dataset.group.samplelist: - trimmed_samples.append(samples[i]) + trimmed_samples.append(str(samples[i])) trimmed_values.append(values[i]) reaper_results = genotype.regression(strains = trimmed_samples, diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 6a3eeccc..00f9acb3 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -31,6 +31,7 @@ import piddle as pid import sys,os import cPickle import httplib +import json from flask import Flask, g @@ -182,7 +183,7 @@ class DisplayMappingResults(object): self.dataset = start_vars['dataset'] self.this_trait = start_vars['this_trait'] - self.n_samples = len(start_vars['vals']) + self.n_samples = start_vars['num_vals'] self.species = start_vars['species'] self.genofile_string = "" if 'genofile_string' in start_vars: @@ -204,8 +205,8 @@ class DisplayMappingResults(object): self.mapmodel_rqtl_geno = start_vars['model'] self.pair_scan = start_vars['pair_scan'] - if self.mapping_method != "gemma" and self.mapping_method != "plink": - self.js_data = start_vars['js_data'] + #if self.mapping_method != "gemma" and self.mapping_method != "plink": + self.js_data = start_vars['js_data'] self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table if self.dataset.group.species == "rat": @@ -264,17 +265,24 @@ class DisplayMappingResults(object): self.covariates = start_vars['covariates'] if 'maf' in start_vars.keys(): self.maf = start_vars['maf'] + if 'output_files' in start_vars.keys(): + self.output_files = start_vars['output_files'] if 'use_loco' in start_vars.keys() and self.mapping_method == "gemma": self.use_loco = start_vars['use_loco'] - if self.use_loco == "True": - self.gwa_filename = start_vars['gwa_filename'] + + if 'reaper_version' in start_vars.keys() and self.mapping_method == "reaper": + self.reaper_version = start_vars['reaper_version'] + if 'output_files' in start_vars: + self.output_files = ",".join(start_vars['output_files']) self.selectedChr = int(start_vars['selected_chr']) self.strainlist = start_vars['samples'] - self.genotype = self.dataset.group.read_genotype_file() + if self.mapping_method == "reaper" and self.manhattan_plot != True: - self.genotype = self.genotype.addinterval() + self.genotype = self.dataset.group.read_genotype_file(use_reaper=True) + else: + self.genotype = self.dataset.group.read_genotype_file() #Darwing Options try: @@ -790,7 +798,7 @@ class DisplayMappingResults(object): locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale break if locPixel >= 0 and self.plotScale == 'physic': - traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12)) + traitPixel = ((locPixel, yZero), (locPixel-7, yZero+14), (locPixel+7, yZero+14)) canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) if self.legendChecked: @@ -801,7 +809,7 @@ class DisplayMappingResults(object): leftOffset = xLeftOffset else: leftOffset = xLeftOffset+(nCol-1)*200*fontZoom - canvas.drawPolygon(((leftOffset+6, startPosY-6), (leftOffset, startPosY+6), (leftOffset+12, startPosY+6)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) + canvas.drawPolygon(((leftOffset+7, startPosY-7), (leftOffset, startPosY+7), (leftOffset+14, startPosY+7)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) canvas.drawString("Sequence Site", (leftOffset+15), (startPosY+5), smallLabelFont, self.TOP_RIGHT_INFO_COLOR) def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): @@ -1451,9 +1459,9 @@ class DisplayMappingResults(object): if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - PHENOGEN_HREF = "https://phenogen.ucdenver.edu/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) + PHENOGEN_HREF = "https://phenogen.org/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) else: - PHENOGEN_HREF = "https://phenogen.ucdenver.edu/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) + PHENOGEN_HREF = "https://phenogen.org/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen" gifmap.areas.append(make_map_area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE)) canvas.drawRect(xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_PHENOGEN_REGION_COLOR, fillColor=self.CLICKABLE_PHENOGEN_REGION_COLOR) @@ -1730,6 +1738,14 @@ class DisplayMappingResults(object): else: LRS_LOD_Max = self.lrsMax + #ZS: Needed to pass to genome browser + js_data = json.loads(self.js_data) + if self.LRS_LOD == "LRS": + js_data['max_score'] = LRS_LOD_Max/4.61 + else: + js_data['max_score'] = LRS_LOD_Max + self.js_data = json.dumps(js_data) + if LRS_LOD_Max > 100: LRSScale = 20.0 elif LRS_LOD_Max > 20: @@ -1827,11 +1843,10 @@ class DisplayMappingResults(object): m = 0 thisLRSColor = self.colorCollection[0] if qtlresult['chr'] != previous_chr and self.selectedChr == -1: - if self.manhattan_plot != True: canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - if not self.multipleInterval and not self.manhattan_plot and self.additiveChecked: + if not self.multipleInterval and self.additiveChecked: plusColor = self.ADDITIVE_COLOR_POSITIVE minusColor = self.ADDITIVE_COLOR_NEGATIVE for k, aPoint in enumerate(AdditiveCoordXY): @@ -1902,10 +1917,18 @@ class DisplayMappingResults(object): if self.manhattan_plot == True: if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1): - point_color = pid.grey + point_color = pid.red + else: + point_color = pid.blue + + final_x_pos = Xc-canvas.stringWidth("5",font=symbolFont)/2+1 + if final_x_pos > (xLeftOffset + plotWidth): + continue + #break ZS: This is temporary until issue with sorting for GEMMA is fixed + elif final_x_pos < xLeftOffset: + continue else: - point_color = pid.black - canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=point_color, font=symbolFont) + canvas.drawString("5", final_x_pos,Yc+2,color=point_color, font=symbolFont) else: LRSCoordXY.append((Xc, Yc)) @@ -2082,11 +2105,11 @@ class DisplayMappingResults(object): ######################################### # Permutation Graph ######################################### - myCanvas = pid.PILCanvas(size=(400,300)) + myCanvas = pid.PILCanvas(size=(500,300)) if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS": - perm_output = [value*4.16 for value in self.perm_output] + perm_output = [value*4.61 for value in self.perm_output] elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD": - perm_output = [value/4.16 for value in self.perm_output] + perm_output = [value/4.61 for value in self.perm_output] else: perm_output = self.perm_output @@ -2245,7 +2268,7 @@ class DisplayMappingResults(object): this_row = [] #container for the cells of each row selectCheck = make_input(type_="checkbox", name="searchResult", class_="checkbox", onClick="highlight(this)").__str__() #checkbox for each row - webqtlSearch = make_link(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], content=(">>",), target="_blank").__str__() + #webqtlSearch = make_link(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], content=(">>",), target="_blank").__str__() if theGO["GeneID"] != "": geneSymbolNCBI = make_link("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % theGO["GeneID"], content=(theGO["GeneSymbol"],), class_="normalsize", target="_blank").__str__() @@ -2269,14 +2292,14 @@ class DisplayMappingResults(object): #Mouse Gene if theGO['mouseGene']: mouseChr = theGO['mouseGene']["Chromosome"] - mouseTxStart = theGO['mouseGene']["TxStart"] + mouseTxStart = "%0.6f" % theGO['mouseGene']["TxStart"] else: mouseChr = mouseTxStart = "" #the chromosomes for human 1 are 1qXX.XX if theGO['humanGene']: humanChr = theGO['humanGene']["Chromosome"] - humanTxStart = theGO['humanGene']["TxStart"] + humanTxStart = "%0.6f" % theGO['humanGene']["TxStart"] else: humanChr = humanTxStart = "" @@ -2286,9 +2309,9 @@ class DisplayMappingResults(object): this_row = [selectCheck.__str__(), str(gIndex+1), - webqtlSearch.__str__() + geneSymbolNCBI, - theGO["TxStart"], - make_link(geneLengthURL, content=("%0.3f" % (geneLength*1000.0),)).__str__(), + geneSymbolNCBI, + "%0.6f" % theGO["TxStart"], + HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)).__str__(), avgExprVal, mouseChr, mouseTxStart, diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 0f37e711..5b34e837 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -12,7 +12,7 @@ GEMMAOPTS = "-debug" if WEBSERVER_MODE == 'PROD': GEMMAOPTS = "-no-check" -def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf=0.01, first_run=True, gwa_output_filename=None): +def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf=0.01, first_run=True, output_files=None): """Generates p-values for each marker using GEMMA""" if this_dataset.group.genofile != None: @@ -73,61 +73,43 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf gwa_output_filename) else: - generate_k_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk -outdir %s/gn2/ -o %s' % (flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - trait_filename, - flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - k_output_filename) - #generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), - # genofile_name, - # flat_files('genotype/bimbam'), - # trait_filename, - # flat_files('genotype/bimbam'), - # genofile_name, - # TEMPDIR, - # k_output_filename) + generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + trait_filename, + flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + k_output_filename) logger.debug("k_command:" + generate_k_command) os.system(generate_k_command) - gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -k %s/gn2/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - trait_filename, - flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - k_output_filename, - maf) - - #gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (flat_files('genotype/bimbam'), - # genofile_name, - # flat_files('genotype/bimbam'), - # genofile_name) + gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), + genofile_name, + flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + trait_filename) if covariates != "": - gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'), - this_dataset.group.name, - webqtlConfig.GENERATED_IMAGE_DIR, - genofile_name) + gemma_command += ' -c %s/%s_covariates.txt > %s/gn2/%s.json' % (flat_files('mapping'), this_dataset.group.name, TEMPDIR, gwa_output_filename) else: - gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR, - genofile_name) + gemma_command += ' > %s/gn2/%s.json' % (TEMPDIR, gwa_output_filename) logger.debug("gemma_command:" + gemma_command) os.system(gemma_command) + else: + gwa_output_filename = output_files if use_loco == "True": marker_obs = parse_loco_output(this_dataset, gwa_output_filename) return marker_obs, gwa_output_filename else: - marker_obs = parse_gemma_output(genofile_name) - return marker_obs + marker_obs = parse_loco_output(this_dataset, gwa_output_filename) + return marker_obs, gwa_output_filename def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename): """Generates phenotype file for GEMMA""" @@ -220,7 +202,11 @@ def parse_loco_output(this_dataset, gwa_output_filename): marker_obs = [] previous_chr = 0 + no_results = False for this_file in output_filelist: + if not os.path.isfile(this_file): + no_results = True + break with open(this_file) as output_file: for line in output_file: if line.startswith("chr\t"): diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 35bed8d8..bbc8b513 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -1,8 +1,126 @@ +import os, math, string, random, json + +from base import webqtlConfig +from base.trait import GeneralTrait +from base.data_set import create_dataset +from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR + import utility.logger logger = utility.logger.getLogger(__name__ ) -def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): - genotype = dataset.group.read_genotype_file() +def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boot_check, num_bootstrap, do_control, control_marker, manhattan_plot, first_run=True, output_files=None): + """Generates p-values for each marker using qtlreaper""" + + if first_run: + if this_dataset.group.genofile != None: + genofile_name = this_dataset.group.genofile[:-5] + else: + genofile_name = this_dataset.group.name + + trait_filename = str(this_trait.name) + "_" + str(this_dataset.name) + "_pheno" + gen_pheno_txt_file(this_dataset, genofile_name, samples, vals, trait_filename) + + output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + bootstrap_filename = None + permu_filename = None + + opt_list = [] + if boot_check and num_bootstrap > 0: + bootstrap_filename = this_dataset.group.name + "_BOOTSTRAP_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + + opt_list.append("-b") + opt_list.append("--n_bootstrap " + str(num_bootstrap)) + opt_list.append("--bootstrap_output " + webqtlConfig.GENERATED_IMAGE_DIR + bootstrap_filename + ".txt") + if num_perm > 0: + permu_filename = this_dataset.group.name + "_PERM_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + opt_list.append("-n " + str(num_perm)) + opt_list.append("--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt") + if control_marker != "" and do_control == "true": + opt_list.append("-c " + control_marker) + + reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'), + genofile_name, + TEMPDIR, + trait_filename, + " ".join(opt_list), + webqtlConfig.GENERATED_IMAGE_DIR, + output_filename) + + logger.debug("reaper_command:" + reaper_command) + os.system(reaper_command) + else: + output_filename, permu_filename, bootstrap_filename = output_files + + marker_obs, permu_vals, bootstrap_vals = parse_reaper_output(output_filename, permu_filename, bootstrap_filename) + + suggestive = 0 + significant = 0 + if len(permu_vals) > 0: + suggestive = permu_vals[int(num_perm*0.37-1)] + significant = permu_vals[int(num_perm*0.95-1)] + + return marker_obs, permu_vals, suggestive, significant, bootstrap_vals, [output_filename, permu_filename, bootstrap_filename] + +def gen_pheno_txt_file(this_dataset, genofile_name, samples, vals, trait_filename): + """Generates phenotype file for GEMMA""" + + with open("{}/gn2/{}.txt".format(TEMPDIR, trait_filename), "w") as outfile: + outfile.write("Trait\t") + + filtered_sample_list = [] + filtered_vals_list = [] + for i, sample in enumerate(samples): + if vals[i] != "x": + filtered_sample_list.append(sample) + filtered_vals_list.append(vals[i]) + + samples_string = "\t".join(filtered_sample_list) + outfile.write(samples_string + "\n") + outfile.write("T1\t") + values_string = "\t".join(filtered_vals_list) + outfile.write(values_string) + +def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): + included_markers = [] + p_values = [] + marker_obs = [] + + with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, gwa_filename)) as output_file: + for line in output_file: + if line.startswith("ID\t"): + continue + else: + marker = {} + marker['name'] = line.split("\t")[1] + try: + marker['chr'] = int(line.split("\t")[2]) + except: + marker['chr'] = line.split("\t")[2] + marker['cM'] = float(line.split("\t")[3]) + marker['Mb'] = float(line.split("\t")[4]) + if float(line.split("\t")[7]) != 1: + marker['p_value'] = float(line.split("\t")[7]) + marker['lrs_value'] = float(line.split("\t")[5]) + marker['lod_score'] = marker['lrs_value'] / 4.61 + marker['additive'] = float(line.split("\t")[6]) + marker_obs.append(marker) + + permu_vals = [] + if permu_filename: + with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, permu_filename)) as permu_file: + for line in permu_file: + permu_vals.append(float(line)) + + bootstrap_vals = [] + if bootstrap_filename: + with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, bootstrap_filename)) as bootstrap_file: + for line in bootstrap_file: + bootstrap_vals.append(int(line)) + + return marker_obs, permu_vals, bootstrap_vals + +def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): + genotype = dataset.group.read_genotype_file(use_reaper=True) if manhattan_plot != True: genotype = genotype.addinterval() diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 2bde2b53..56d901fc 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -7,6 +7,7 @@ from pprint import pformat as pf import string import math +from decimal import Decimal import random import sys import datetime @@ -85,14 +86,11 @@ class RunMapping(object): self.samples.append(sample) self.vals.append(value) + self.num_vals = start_vars['num_vals'] + #ZS: Check if genotypes exist in the DB in order to create links for markers - if "geno_db_exists" in start_vars: - self.geno_db_exists = start_vars['geno_db_exists'] - else: - try: - self.geno_db_exists = "True" - except: - self.geno_db_exists = "False" + + self.geno_db_exists = geno_db_exists(self.dataset) self.mapping_method = start_vars['method'] if "results_path" in start_vars: @@ -183,18 +181,18 @@ class RunMapping(object): self.dataset.group.get_markers() if self.mapping_method == "gemma": self.first_run = True - self.gwa_filename = None + self.output_files = None + if 'output_files' in start_vars: + self.output_files = start_vars['output_files'] if 'first_run' in start_vars: #ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) self.first_run = False - if 'gwa_filename' in start_vars: - self.gwa_filename = start_vars['gwa_filename'] self.score_type = "-log(p)" self.manhattan_plot = True with Bench("Running GEMMA"): if self.use_loco == "True": - marker_obs, self.gwa_filename = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.gwa_filename) + marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) else: - marker_obs = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run) + marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) results = marker_obs elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() @@ -239,20 +237,45 @@ class RunMapping(object): self.bootCheck = False self.num_bootstrap = 0 + self.reaper_version = start_vars['reaper_version'] + self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] logger.info("Running qtlreaper") - results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait, - self.dataset, - self.samples, - self.vals, - self.json_data, - self.num_perm, - self.bootCheck, - self.num_bootstrap, - self.do_control, - self.control_marker, - self.manhattan_plot) + + if self.reaper_version == "new": + self.first_run = True + self.output_files = None + if 'first_run' in start_vars: #ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + self.first_run = False + if 'output_files' in start_vars: + self.output_files = start_vars['output_files'].split(",") + + results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait, + self.dataset, + self.samples, + self.vals, + self.json_data, + self.num_perm, + self.bootCheck, + self.num_bootstrap, + self.do_control, + self.control_marker, + self.manhattan_plot, + self.first_run, + self.output_files) + else: + results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.run_original_reaper(self.this_trait, + self.dataset, + self.samples, + self.vals, + self.json_data, + self.num_perm, + self.bootCheck, + self.num_bootstrap, + self.do_control, + self.control_marker, + self.manhattan_plot) elif self.mapping_method == "plink": self.score_type = "-log(p)" self.manhattan_plot = True @@ -295,14 +318,52 @@ class RunMapping(object): else: self.qtl_results = [] + self.qtl_results_for_browser = [] + self.annotations_for_browser = [] highest_chr = 1 #This is needed in order to convert the highest chr to X/Y for marker in results: + browser_marker = dict( + chr = str(marker['chr']), + rs = marker['name'], + ps = marker['Mb']*1000000, + url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" + ) + + if self.geno_db_exists == "True": + annot_marker = dict( + name = str(marker['name']), + chr = str(marker['chr']), + rs = marker['name'], + pos = marker['Mb']*1000000, + url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" + ) + else: + annot_marker = dict( + name = str(marker['name']), + chr = str(marker['chr']), + rs = marker['name'], + pos = marker['Mb']*1000000 + ) + #if 'p_value' in marker: + # logger.debug("P EXISTS:", marker['p_value']) + #else: + if 'lrs_value' in marker and marker['lrs_value'] > 0: + browser_marker['p_wald'] = 10**-(marker['lrs_value']/4.61) + elif 'lod_score' in marker and marker['lod_score'] > 0: + browser_marker['p_wald'] = 10**-(marker['lod_score']) + else: + browser_marker['p_wald'] = 0 + + self.qtl_results_for_browser.append(browser_marker) + self.annotations_for_browser.append(annot_marker) if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y": if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y": highest_chr = marker['chr'] if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): self.qtl_results.append(marker) + browser_files = write_input_for_browser(self.dataset, self.qtl_results_for_browser, self.annotations_for_browser) + with Bench("Exporting Results"): export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type) @@ -313,51 +374,55 @@ class RunMapping(object): with Bench("Trimming Markers for Table"): self.trimmed_markers = trim_markers_for_table(results) + chr_lengths = get_chr_lengths(self.mapping_scale, self.dataset, self.qtl_results_for_browser) + + #ZS: For zooming into genome browser, need to pass chromosome name instead of number + if self.dataset.group.species == "mouse": + if self.selected_chr == 20: + this_chr = "X" + else: + this_chr = str(self.selected_chr) + elif self.dataset.group.species == "rat": + if self.selected_chr == 21: + this_chr = "X" + else: + this_chr = str(self.selected_chr) + else: + if self.selected_chr == 22: + this_chr = "X" + elif self.selected_chr == 23: + this_chr = "Y" + else: + this_chr = str(self.selected_chr) + if self.mapping_method != "gemma": - self.json_data['chr'] = [] - self.json_data['pos'] = [] - self.json_data['lod.hk'] = [] - self.json_data['markernames'] = [] - - self.json_data['suggestive'] = self.suggestive - self.json_data['significant'] = self.significant - - #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary - for index, qtl in enumerate(self.qtl_results): - #if index<40: - # logger.debug("lod score is:", qtl['lod_score']) - if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y": - #logger.debug("changing to X") - self.json_data['chr'].append("X") - else: - self.json_data['chr'].append(str(qtl['chr'])) - self.json_data['pos'].append(qtl['Mb']) - if 'lrs_value' in qtl.keys(): - self.json_data['lod.hk'].append(str(qtl['lrs_value'])) - else: - self.json_data['lod.hk'].append(str(qtl['lod_score'])) - self.json_data['markernames'].append(qtl['name']) - - #Get chromosome lengths for drawing the interval map plot - chromosome_mb_lengths = {} - self.json_data['chrnames'] = [] - for key in self.species.chromosomes.chromosomes.keys(): - self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) - chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length + if self.score_type == "LRS": + significant_for_browser = self.significant / 4.61 + else: + significant_for_browser = self.significant self.js_data = dict( - result_score_type = self.score_type, - json_data = self.json_data, - this_trait = self.this_trait.name, - data_set = self.dataset.name, - maf = self.maf, - manhattan_plot = self.manhattan_plot, - mapping_scale = self.mapping_scale, - chromosomes = chromosome_mb_lengths, - qtl_results = self.qtl_results, + #result_score_type = self.score_type, + #this_trait = self.this_trait.name, + #data_set = self.dataset.name, + #maf = self.maf, + #manhattan_plot = self.manhattan_plot, + #mapping_scale = self.mapping_scale, + #chromosomes = chromosome_mb_lengths, + #qtl_results = self.qtl_results, + chr_lengths = chr_lengths, num_perm = self.num_perm, perm_results = self.perm_output, + browser_files = browser_files, + significant = significant_for_browser, + selected_chr = this_chr ) + else: + self.js_data = dict( + chr_lengths = chr_lengths, + browser_files = browser_files, + selected_chr = this_chr + ) def run_rqtl_plink(self): # os.chdir("") never do this inside a webserver!! @@ -397,6 +462,7 @@ class RunMapping(object): def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type): with open(results_path, "w+") as output_file: + output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") output_file.write("Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") output_file.write("Data Set: " + dataset.fullname + "\n") if dataset.type == "ProbeSet": @@ -404,6 +470,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("Location: " + str(trait.chr) + " @ " + str(trait.mb) + " Mb\n") output_file.write("\n") output_file.write("Name,Chr,") + if score_type.lower() == "-log(p)": + score_type = "'-log(p)" if mapping_scale == "physic": output_file.write("Mb," + score_type) else: @@ -453,15 +521,15 @@ def trim_markers_for_figure(markers): else: filtered_markers.append(marker) else: - if marker[score_type] < 4.16: + if marker[score_type] < 4.61: if low_counter % 20 == 0: filtered_markers.append(marker) low_counter += 1 - elif 4.16 <= marker[score_type] < (2*4.16): + elif 4.61 <= marker[score_type] < (2*4.61): if med_counter % 10 == 0: filtered_markers.append(marker) med_counter += 1 - elif (2*4.16) <= marker[score_type] <= (3*4.16): + elif (2*4.61) <= marker[score_type] <= (3*4.61): if high_counter % 2 == 0: filtered_markers.append(marker) high_counter += 1 @@ -481,3 +549,47 @@ def trim_markers_for_table(markers): return trimmed_sorted_markers else: return sorted_markers + +def write_input_for_browser(this_dataset, gwas_results, annotations): + file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + gwas_filename = file_base + "_GWAS" + annot_filename = file_base + "_ANNOT" + gwas_path = "{}/gn2/".format(TEMPDIR) + gwas_filename + annot_path = "{}/gn2/".format(TEMPDIR) + annot_filename + + with open(gwas_path + ".json", "w") as gwas_file, open(annot_path + ".json", "w") as annot_file: + gwas_file.write(json.dumps(gwas_results)) + annot_file.write(json.dumps(annotations)) + + return [gwas_filename, annot_filename] + +def geno_db_exists(this_dataset): + geno_db_name = this_dataset.group.name + "Geno" + try: + geno_db = data_set.create_dataset(dataset_name=geno_db_name, get_samplelist=False) + return "True" + except: + return "False" + +def get_chr_lengths(mapping_scale, dataset, qtl_results): + chr_lengths = [] + if mapping_scale == "physic": + for i, the_chr in enumerate(dataset.species.chromosomes.chromosomes): + this_chr = { + "chr": dataset.species.chromosomes.chromosomes[the_chr].name, + "size": str(dataset.species.chromosomes.chromosomes[the_chr].length) + } + chr_lengths.append(this_chr) + else: + this_chr = 1 + highest_pos = 0 + for i, result in enumerate(qtl_results): + if int(result['chr']) > this_chr or i == (len(qtl_results) - 1): + chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)}) + this_chr = int(result['chr']) + highest_pos = 0 + else: + if float(result['ps']) > highest_pos: + highest_pos = float(result['ps']) + + return chr_lengths
\ No newline at end of file diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 12a69bc3..33515e25 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -25,7 +25,7 @@ from db import webqtlDatabaseFunction from wqflask import user_manager -from flask import render_template +from flask import render_template, Flask, g from utility import formatting from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string @@ -47,6 +47,7 @@ views.py). ########################################### self.uc_id = uuid.uuid4() + self.go_term = None logger.debug("uc_id:", self.uc_id) # contains a unique id logger.debug("kw is:", kw) # dict containing search terms @@ -112,7 +113,7 @@ views.py). trait_dict['hmac'] = user_manager.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) if this_trait.dataset.type == "ProbeSet": trait_dict['symbol'] = this_trait.symbol - trait_dict['description'] = insert_newlines(this_trait.description_display) + trait_dict['description'] = this_trait.description_display.decode('utf-8', 'replace') trait_dict['location'] = this_trait.location_repr trait_dict['mean'] = "N/A" trait_dict['additive'] = "N/A" @@ -157,29 +158,34 @@ views.py). combined_where_clause = "" previous_from_clauses = [] #The same table can't be referenced twice in the from clause for i, a_search in enumerate(self.search_terms): - the_search = self.get_search_ob(a_search) - if the_search != None: - get_from_clause = getattr(the_search, "get_from_clause", None) - if callable(get_from_clause): - from_clause = the_search.get_from_clause() - if from_clause in previous_from_clauses: - pass - else: - previous_from_clauses.append(from_clause) - combined_from_clause += from_clause - where_clause = the_search.get_where_clause() - combined_where_clause += "(" + where_clause + ")" - if (i+1) < len(self.search_terms): - if self.and_or == "and": - combined_where_clause += "AND" - else: - combined_where_clause += "OR" + if a_search['key'] == "GO": + self.go_term = a_search['search_term'][0] + gene_list = get_GO_symbols(a_search) + self.search_terms += gene_list + continue else: - self.search_term_exists = False + the_search = self.get_search_ob(a_search) + if the_search != None: + get_from_clause = getattr(the_search, "get_from_clause", None) + if callable(get_from_clause): + from_clause = the_search.get_from_clause() + if from_clause in previous_from_clauses: + pass + else: + previous_from_clauses.append(from_clause) + combined_from_clause += from_clause + where_clause = the_search.get_where_clause() + combined_where_clause += "(" + where_clause + ")" + if (i+1) < len(self.search_terms): + if self.and_or == "and": + combined_where_clause += "AND" + else: + combined_where_clause += "OR" + else: + self.search_term_exists = False if self.search_term_exists: combined_where_clause = "(" + combined_where_clause + ")" final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause) - # logger.debug("final_query",final_query) results = the_search.execute(final_query) self.results.extend(results) else: @@ -187,11 +193,19 @@ views.py). self.search_term_exists = False else: for a_search in self.search_terms: - the_search = self.get_search_ob(a_search) - if the_search != None: - self.results.extend(the_search.run()) + logger.debug("TERMS:", self.search_terms) + if a_search['key'] == "GO": + self.go_term = a_search['search_term'][0] + gene_list = get_GO_symbols(a_search) + self.search_terms += gene_list + self.search_terms.pop(0) + continue else: - self.search_term_exists = False + the_search = self.get_search_ob(a_search) + if the_search != None: + self.results.extend(the_search.run()) + else: + self.search_term_exists = False if self.search_term_exists: if the_search != None: @@ -205,6 +219,8 @@ views.py). search_type['dataset_type'] = self.dataset.type if a_search['key']: search_type['key'] = a_search['key'].upper() + else: + search_type['key'] = None logger.debug("search_type is:", pf(search_type)) search_ob = do_search.DoSearch.get_search(search_type) @@ -214,14 +230,33 @@ views.py). the_search = search_class(search_term, search_operator, self.dataset, + search_type['key'] ) return the_search else: return None +def get_GO_symbols(a_search): + query = """SELECT genes + FROM GORef + WHERE goterm='{0}:{1}'""".format(a_search['key'], a_search['search_term'][0]) + + gene_list = g.db.execute(query).fetchone()[0].strip().split() + + new_terms = [] + for gene in gene_list: + this_term = dict(key=None, + separator=None, + search_term=[gene]) + + new_terms.append(this_term) + + return new_terms + def insert_newlines(string, every=64): """ This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """ lines = [] for i in xrange(0, len(string), every): lines.append(string[i:i+every]) return '\n'.join(lines) + diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 66d3a448..3b057427 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -107,7 +107,7 @@ class ShowTrait(object): blatsequence += '%3EProbe_' + string.strip(seqt[1]) + '%0A' + string.strip(seqt[0]) + '%0A' if self.dataset.group.species == "rat": - self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence) + self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn6', blatsequence) self.UTHSC_BLAT_URL = "" elif self.dataset.group.species == "mouse": self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm10', blatsequence) @@ -142,40 +142,6 @@ class ShowTrait(object): self.qnorm_vals = quantile_normalize_vals(self.sample_groups) self.z_scores = get_z_scores(self.sample_groups) - # Todo: Add back in the ones we actually need from below, as we discover we need them - hddn = OrderedDict() - - if self.dataset.group.allsamples: - hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ') - - hddn['trait_id'] = self.trait_id - hddn['dataset'] = self.dataset.name - hddn['temp_trait'] = False - if self.temp_trait: - hddn['temp_trait'] = True - hddn['group'] = self.temp_group - hddn['species'] = self.temp_species - hddn['use_outliers'] = False - hddn['method'] = "gemma" - hddn['selected_chr'] = -1 - hddn['mapping_display_all'] = True - hddn['suggestive'] = 0 - hddn['num_perm'] = 0 - hddn['manhattan_plot'] = "" - hddn['control_marker'] = "" - if not self.temp_trait: - if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish": - hddn['control_marker'] = self.nearest_marker - #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2 - hddn['do_control'] = False - hddn['maf'] = 0.01 - hddn['compare_traits'] = [] - hddn['export_data'] = "" - hddn['export_format'] = "excel" - - # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self - self.hddn = hddn - self.temp_uuid = uuid.uuid4() self.sample_group_types = OrderedDict() @@ -216,18 +182,61 @@ class ShowTrait(object): sample_column_width = max_samplename_width * 8 - if self.num_values >= 500: + if self.num_values >= 5000: self.maf = 0.01 else: self.maf = 0.05 trait_symbol = None + short_description = None if not self.temp_trait: if self.this_trait.symbol: trait_symbol = self.this_trait.symbol + short_description = trait_symbol + + elif hasattr(self.this_trait, 'post_publication_abbreviation'): + short_description = self.this_trait.post_publication_abbreviation + + elif hasattr(self.this_trait, 'pre_publication_abbreviation'): + short_description = self.this_trait.pre_publication_abbreviation + + # Todo: Add back in the ones we actually need from below, as we discover we need them + hddn = OrderedDict() + + if self.dataset.group.allsamples: + hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ') + hddn['primary_samples'] = string.join(self.primary_sample_names, ',') + hddn['trait_id'] = self.trait_id + hddn['dataset'] = self.dataset.name + hddn['temp_trait'] = False + if self.temp_trait: + hddn['temp_trait'] = True + hddn['group'] = self.temp_group + hddn['species'] = self.temp_species + hddn['use_outliers'] = False + hddn['method'] = "gemma" + hddn['selected_chr'] = -1 + hddn['mapping_display_all'] = True + hddn['suggestive'] = 0 + hddn['num_perm'] = 0 + hddn['manhattan_plot'] = "" + hddn['control_marker'] = "" + if not self.temp_trait: + if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish": + hddn['control_marker'] = self.nearest_marker + #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2 + hddn['do_control'] = False + hddn['maf'] = 0.05 + hddn['compare_traits'] = [] + hddn['export_data'] = "" + hddn['export_format'] = "excel" + + # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self + self.hddn = hddn js_data = dict(trait_id = self.trait_id, trait_symbol = trait_symbol, + short_description = short_description, unit_type = trait_units, dataset_type = self.dataset.type, data_scale = self.dataset.data_scale, @@ -246,7 +255,6 @@ class ShowTrait(object): self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.this_trait.pubmed_id if check_if_attr_exists(self.this_trait, 'pubmed_id') else None self.ncbi_gene_link = webqtlConfig.NCBI_LOCUSID % self.this_trait.geneid if check_if_attr_exists(self.this_trait, 'geneid') else None self.omim_link = webqtlConfig.OMIM_ID % self.this_trait.omim if check_if_attr_exists(self.this_trait, 'omim') else None - self.unigene_link = webqtlConfig.UNIGEN_ID % tuple(string.split(self.this_trait.unigeneid, '.')[:2]) if check_if_attr_exists(self.this_trait, 'unigeneid') else None self.homologene_link = webqtlConfig.HOMOLOGENE_ID % self.this_trait.homologeneid if check_if_attr_exists(self.this_trait, 'homologeneid') else None self.genbank_link = None @@ -256,17 +264,22 @@ class ShowTrait(object): genbank_id = genbank_id[0:-1] self.genbank_link = webqtlConfig.GENBANK_ID % genbank_id - self.genotation_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = None - self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = None + self.genotation_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = self.protein_atlas_link = None + self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = self.genemania_link = self.ensembl_link = None if self.this_trait.symbol: self.genotation_link = webqtlConfig.GENOTATION_URL % self.this_trait.symbol self.gtex_link = webqtlConfig.GTEX_URL % self.this_trait.symbol self.string_link = webqtlConfig.STRING_URL % self.this_trait.symbol self.panther_link = webqtlConfig.PANTHER_URL % self.this_trait.symbol self.ebi_gwas_link = webqtlConfig.EBIGWAS_URL % self.this_trait.symbol + self.protein_atlas_link = webqtlConfig.PROTEIN_ATLAS_URL % self.this_trait.symbol + #self.open_targets_link = webqtlConfig.OPEN_TARGETS_URL % self.this_trait.symbol if self.dataset.group.species == "mouse" or self.dataset.group.species == "human": - self.genebridge_link = webqtlConfig.GENEBRIDGE_URL % (self.this_trait.symbol, self.dataset.group.species) + if self.dataset.group.species == "mouse": + self.genemania_link = webqtlConfig.GENEMANIA_URL % ("mus-musculus", self.this_trait.symbol) + else: + self.genemania_link = webqtlConfig.GENEMANIA_URL % ("homo-sapiens", self.this_trait.symbol) if self.dataset.group.species == "mouse": self.aba_link = webqtlConfig.ABA_URL % self.this_trait.symbol @@ -275,22 +288,34 @@ class ShowTrait(object): FROM GeneList WHERE geneSymbol = '{}'""".format(self.this_trait.symbol) - chr, transcript_start, transcript_end = g.db.execute(query).fetchall()[0] if len(g.db.execute(query).fetchall()) > 0 else None + results = g.db.execute(query).fetchone() + if results: + chr, transcript_start, transcript_end = results + else: + chr = transcript_start = transcript_end = None + if chr and transcript_start and transcript_end and self.this_trait.refseq_transcriptid: transcript_start = int(transcript_start*1000000) transcript_end = int(transcript_end*1000000) self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('mm10', self.this_trait.refseq_transcriptid, chr, transcript_start, transcript_end) if self.dataset.group.species == "rat": + self.genemania_link = webqtlConfig.GENEMANIA_URL % ("rattus-norvegicus", self.this_trait.symbol) + query = """SELECT kgID, chromosome, txStart, txEnd - FROM GeneLink_rn33 + FROM GeneList_rn33 WHERE geneSymbol = '{}'""".format(self.this_trait.symbol) - kgId, chr, transcript_start, transcript_end = g.db.execute(query).fetchall()[0] if len(g.db.execute(query).fetchall()) > 0 else None + results = g.db.execute(query).fetchone() + if results: + kgId, chr, transcript_start, transcript_end = results + else: + kgId = chr = transcript_start = transcript_end = None + if chr and transcript_start and transcript_end and kgId: transcript_start = int(transcript_start*1000000) # Convert to bases from megabases transcript_end = int(transcript_end*1000000) - self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('rn3', kgId, chr, transcript_start, transcript_end) + self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('rn6', kgId, chr, transcript_start, transcript_end) if self.this_trait.geneid and (self.dataset.group.species == "mouse" or self.dataset.group.species == "rat" or self.dataset.group.species == "human"): self.biogps_link = webqtlConfig.BIOGPS_URL % (self.dataset.group.species, self.this_trait.geneid) @@ -381,6 +406,8 @@ class ShowTrait(object): sample_group_type='primary', header="%s Only" % (self.dataset.group.name)) self.sample_groups = (primary_samples,) + + self.primary_sample_names = primary_sample_names self.dataset.group.allsamples = all_samples_ordered def quantile_normalize_vals(sample_groups): @@ -478,7 +505,7 @@ def get_genofiles(this_dataset): return jsondata['genofile'] def get_table_widths(sample_groups, has_num_cases=False): - stats_table_width = 200 + stats_table_width = 250 if len(sample_groups) > 1: stats_table_width = 450 diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index 9a980cb1..7f0a0a31 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -477,8 +477,8 @@ class SnpBrowser(object): the_bases = [] for j, item in enumerate(allele_value_list): - if item and isinstance(item, str): - this_base = [item, base_color_dict[item]] + if item and isinstance(item, basestring): + this_base = [str(item), base_color_dict[item]] else: this_base = "" @@ -486,24 +486,24 @@ class SnpBrowser(object): this_row = { "index": i + 1, - "rs": rs, - "snp_url": snp_url, - "snp_name": snp_name, - "chr": chr, + "rs": str(rs), + "snp_url": str(snp_url), + "snp_name": str(snp_name), + "chr": str(chr), "mb_formatted": mb_formatted, - "alleles": alleles, - "snp_source": snp_source, + "alleles": str(alleles), + "snp_source": str(snp_source), "source_urls": source_urls, - "conservation_score": conservation_score, - "gene_name": gene_name, - "gene_link": gene_link, - "transcript": transcript, - "transcript_link": transcript_link, - "exon": exon, - "domain_1": domain_1, - "domain_2": domain_2, - "function": function, - "function_details": function_details, + "conservation_score": str(conservation_score), + "gene_name": str(gene_name), + "gene_link": str(gene_link), + "transcript": str(transcript), + "transcript_link": str(transcript_link), + "exon": str(exon), + "domain_1": str(domain_1), + "domain_2": str(domain_2), + "function": str(function), + "function_details": str(function_details), "allele_value_list": the_bases } @@ -511,15 +511,15 @@ class SnpBrowser(object): indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name = result this_row = { "index": i, - "indel_name": indel_name, - "indel_chr": indel_chr, - "indel_mb_s": indel_mb_s, - "indel_mb_e": indel_mb_e, - "indel_strand": indel_strand, - "indel_type": indel_type, - "indel_size": indel_size, - "indel_sequence": indel_sequence, - "source_name": source_name + "indel_name": str(indel_name), + "indel_chr": str(indel_chr), + "indel_mb_s": str(indel_mb_s), + "indel_mb_e": str(indel_mb_e), + "indel_strand": str(indel_strand), + "indel_type": str(indel_type), + "indel_size": str(indel_size), + "indel_sequence": str(indel_sequence), + "source_name": str(source_name) } #this_row = [indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name] else: @@ -612,7 +612,7 @@ class SnpBrowser(object): this_allele_list = [] for item in self.allele_list: - if item and isinstance(item, str) and (item.lower() not in this_allele_list) and (item != "-"): + if item and isinstance(item, basestring) and (item.lower() not in this_allele_list) and (item != "-"): this_allele_list.append(item.lower()) total_allele_count = len(this_allele_list) diff --git a/wqflask/wqflask/static/gif/89.gif b/wqflask/wqflask/static/gif/89.gif Binary files differnew file mode 100644 index 00000000..e9b3279d --- /dev/null +++ b/wqflask/wqflask/static/gif/89.gif diff --git a/wqflask/wqflask/static/new/javascript/create_corr_matrix.js b/wqflask/wqflask/static/new/javascript/create_corr_matrix.js index fe89a672..c0c39fbc 100644 --- a/wqflask/wqflask/static/new/javascript/create_corr_matrix.js +++ b/wqflask/wqflask/static/new/javascript/create_corr_matrix.js @@ -1,5 +1,5 @@ -var neg_color_scale = chroma.scale(['#FF0000', '#FFFFFF']).domain([-1, -0.4]); -var pos_color_scale = chroma.scale(['#FFFFFF', '#00FFFF']).domain([0.4, 1]) +var neg_color_scale = chroma.scale(['#91bfdb', '#ffffff']).domain([-1, -0.4]); +var pos_color_scale = chroma.scale(['#ffffff', '#fc8d59']).domain([0.4, 1]) $('.corr_cell').each( function () { corr_value = parseFloat($(this).find('span.corr_value').text()) if (corr_value >= 0.5){ @@ -14,6 +14,11 @@ $('.corr_cell').each( function () { }); $('#short_labels').click( function (){ + if ($('.short_check').css("display") == "none"){ + $('.short_check').css("display", "inline-block") + } else { + $('.short_check').css("display", "none") + } $('.shortName').each( function() { if ($(this).css("display") == "none"){ $(this).css("display", "block"); @@ -25,6 +30,11 @@ $('#short_labels').click( function (){ }); $('#long_labels').click( function (){ + if ($('.long_check').css("display") == "none"){ + $('.long_check').css("display", "inline-block") + } else { + $('.long_check').css("display", "none") + } $('.verboseName').each( function() { if ($(this).css("display") == "none"){ $(this).css("display", "block"); diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index b2354f70..6531f5a0 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -1335,7 +1335,7 @@ [ "None", "HCPPublish", - "HCP Phenotypes" + "HCP Private Phenotypes" ] ] }, @@ -1347,14 +1347,14 @@ "GSE9588 Human Liver Normal (Mar11) Both Sexes" ], [ - "383", - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], - [ "384", "HLCF_0311", "GSE9588 Human Liver Normal (Mar11) Females" + ], + [ + "383", + "HLCM_0311", + "GSE9588 Human Liver Normal (Mar11) Males" ] ], "Phenotypes": [ @@ -1440,7 +1440,7 @@ [ "None", "HSBPublish", - "HSB Phenotypes" + "HSB Published Phenotypes" ] ], "Posterior Inferior Parietal Cortex mRNA": [ @@ -1530,6 +1530,11 @@ "AIL": { "Hippocampus mRNA": [ [ + "874", + "UCSD_AIL_HIP_RNA-Seq_log2_0418", + "UCSD AIL Hippocampus (Apr18) RNA-Seq Log2" + ], + [ "844", "UCSD_AIL_HIP_RNA-Seq_0418", "UCSD AIL Hippocampus (Apr18) RNA-Seq" @@ -1544,6 +1549,11 @@ ], "Prefrontal Cortex mRNA": [ [ + "876", + "UCSD_AIL_PFC_RNA-Seq_log2_0418", + "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq Log2" + ], + [ "846", "UCSD_AIL_PFC_RNA-Seq_0418", "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq" @@ -1551,6 +1561,11 @@ ], "Striatum mRNA": [ [ + "875", + "UCSD_AIL_STR_RNA-Seq_log2_0418", + "UCSD AIL Striatum (Apr18) RNA-Seq Log2" + ], + [ "845", "UCSD_AIL_STR_RNA-Seq_0418", "UCSD AIL Striatum (Apr18) RNA-Seq" @@ -1706,7 +1721,7 @@ [ "None", "B6D2Publish", - "B6D2 Phenotypes" + "UTHSC-Glaucoma-Aged-Retina Phenotypes" ] ] }, @@ -1819,6 +1834,11 @@ ], "Striatum mRNA": [ [ + "85", + "SA_M2_0905_P", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" + ], + [ "84", "SA_M2_0905_R", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" @@ -1827,27 +1847,22 @@ "83", "SA_M2_0905_M", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" - ], - [ - "85", - "SA_M2_0905_P", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" ] ] }, "BHF2": { "Adipose mRNA": [ [ - "196", - "UCLA_BHF2_ADIPOSE_MALE", - "UCLA BHF2 Adipose Male mlratio" - ], - [ "197", "UCLA_BHF2_ADIPOSE_FEMALE", "UCLA BHF2 Adipose Female mlratio" ], [ + "196", + "UCLA_BHF2_ADIPOSE_MALE", + "UCLA BHF2 Adipose Male mlratio" + ], + [ "165", "UCLA_BHF2_ADIPOSE_0605", "UCLA BHF2 Adipose (June05) mlratio" @@ -1855,16 +1870,16 @@ ], "Brain mRNA": [ [ - "198", - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], - [ "199", "UCLA_BHF2_BRAIN_FEMALE", "UCLA BHF2 Brain Female mlratio" ], [ + "198", + "UCLA_BHF2_BRAIN_MALE", + "UCLA BHF2 Brain Male mlratio" + ], + [ "166", "UCLA_BHF2_BRAIN_0605", "UCLA BHF2 Brain (June05) mlratio" @@ -1879,16 +1894,16 @@ ], "Liver mRNA": [ [ - "200", - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ "201", "UCLA_BHF2_LIVER_FEMALE", "UCLA BHF2 Liver Female mlratio" ], [ + "200", + "UCLA_BHF2_LIVER_MALE", + "UCLA BHF2 Liver Male mlratio" + ], + [ "167", "UCLA_BHF2_LIVER_0605", "UCLA BHF2 Liver (June05) mlratio" @@ -2122,6 +2137,11 @@ "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], [ + "81", + "BR_U_0805_P", + "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" + ], + [ "80", "BR_U_0805_M", "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" @@ -2132,11 +2152,6 @@ "UTHSC Brain mRNA U74Av2 (Aug05) RMA" ], [ - "81", - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], - [ "42", "CB_M_0204_P", "INIA Brain mRNA M430 (Feb04) PDNN" @@ -2233,6 +2248,11 @@ "Eye M430v2 WT Gpnmb (Sep08) RMA" ], [ + "382", + "Eye_M2_0908_WTWT", + "Eye M430v2 WT WT (Sep08) RMA" + ], + [ "279", "Eye_M2_0908_R_WT", "Eye M430v2 WT Tyrp1 (Sep08) RMA" @@ -2243,11 +2263,6 @@ "Eye M430v2 Mutant Tyrp1 (Sep08) RMA" ], [ - "382", - "Eye_M2_0908_WTWT", - "Eye M430v2 WT WT (Sep08) RMA" - ], - [ "400", "DBA2J-ONH-1212", "Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA" @@ -2485,6 +2500,11 @@ "245", "UT_ILM_BXD_hipp_RSE_0909", "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" + ], + [ + "711", + "UTHSC_BXD_AgeHipp0515", + "UTHSC BXD Aged Hippocampus Affy MoGene1.0 ST (May15) RMA Gene Level" ] ], "Hypothalamus mRNA": [ @@ -2682,6 +2702,11 @@ "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" ], [ + "848", + "EPFLMouseLiverHFCEx0413", + "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" + ], + [ "432", "EPFLMouseLiverCDRMA0413", "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" @@ -2692,11 +2717,6 @@ "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" ], [ - "848", - "EPFLMouseLiverHFCEx0413", - "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" - ], - [ "433", "EPFLMouseLiverBothExRMA0413", "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" @@ -2850,14 +2870,14 @@ "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv" ], [ - "274", - "DevNeocortex_ILM6.2P3RInv_1110", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" - ], - [ "275", "DevNeocortex_ILM6.2P14RInv_1110", "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" + ], + [ + "274", + "DevNeocortex_ILM6.2P3RInv_1110", + "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" ] ], "Nucleus Accumbens mRNA": [ @@ -3014,16 +3034,6 @@ ], "Striatum mRNA": [ [ - "376", - "DevStriatum_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv" - ], - [ - "377", - "DevStriatum_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv" - ], - [ "399", "Striatum_Exon_1212", "HQF Striatum Affy Mouse Exon 1.0ST Gene Level (Dec09) RMA" @@ -3034,6 +3044,16 @@ "HQF Striatum Affy Mouse Exon 1.0ST Exon Level (Dec09) RMA" ], [ + "376", + "DevStriatum_ILM6.2P3RInv_1111", + "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv" + ], + [ + "377", + "DevStriatum_ILM6.2P14RInv_1111", + "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv" + ], + [ "285", "UTHSC_Striatum_RankInv_1210", "HQF BXD Striatum ILM6.1 (Dec10v2) RankInv" @@ -3090,6 +3110,11 @@ ], "Ventral Tegmental Area mRNA": [ [ + "230", + "VCUEtvsSal_0609_R", + "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA" + ], + [ "229", "VCUEtOH_0609_R", "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA" @@ -3098,11 +3123,6 @@ "228", "VCUSal_0609_R", "VCU BXD VTA Sal M430 2.0 (Jun09) RMA" - ], - [ - "230", - "VCUEtvsSal_0609_R", - "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA" ] ] }, @@ -3134,7 +3154,7 @@ [ "None", "BXD-HarvestedPublish", - "BXD-Harvested Phenotypes" + "BXD-NIA-Longevity Phenotypes" ] ] }, @@ -3540,6 +3560,11 @@ ], "Hippocampus mRNA": [ [ + "211", + "Illum_LXS_Hipp_RSS_1008", + "Hippocampus Illumina RSS (Oct08) RankInv beta" + ], + [ "213", "Illum_LXS_Hipp_NOS_1008", "Hippocampus Illumina NOS (Oct08) RankInv beta" @@ -3560,11 +3585,6 @@ "Hippocampus Illumina NOE (Oct08) RankInv beta" ], [ - "211", - "Illum_LXS_Hipp_RSS_1008", - "Hippocampus Illumina RSS (Oct08) RankInv beta" - ], - [ "143", "Illum_LXS_Hipp_loess0807", "Hippocampus Illumina (Aug07) LOESS" @@ -3820,7 +3840,7 @@ [ "None", "HSNIH-RGSMCPublish", - "HSNIH-RGSMC Phenotypes" + "HSNIH Published Phenotypes" ] ] }, diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js index 9bca1517..b80539bd 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -6,10 +6,11 @@ process_json = function(data) { return apply_default(); } }; -$.ajax('/static/new/javascript/dataset_menu_structure.json', { +$.ajax('/api/v_pre1/gen_dropdown', { dataType: 'json', success: process_json }); + populate_species = function() { var species_list; species_list = this.jdata.species; diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js index a74c99d3..8fdbad35 100644 --- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js +++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js @@ -1,30 +1,120 @@ var chart; var srchart; +x_val_range = js_data.x_range[1] - js_data.x_range[0] +y_val_range = js_data.y_range[1] - js_data.y_range[0] + +if (x_val_range >= 2 && x_val_range < 9){ + x_tick_digits = '.1f' +} else if (x_val_range >= 0.8 && x_val_range < 2) { + x_tick_digits = '.2f' +} else if (x_val_range < 0.8) { + x_tick_digits = '.3f' +} else { + x_tick_digits = 'f' +} + +if (y_val_range >= 2 && y_val_range < 8){ + y_tick_digits = '.1f' +} else if (y_val_range >= 0.8 && y_val_range < 2) { + y_tick_digits = '.2f' +} else if (y_val_range < 0.8) { + y_tick_digits = '.3f' +} else { + y_tick_digits = 'f' +} + +console.log("y_digits:", y_tick_digits) + var layout = { height: 700, width: 800, margin: { - l: 60, + l: 70, r: 30, - t: 80, + t: 90, b: 50 }, xaxis: { + range: [js_data.x_range[0], js_data.x_range[1]], title: js_data.trait_1, zeroline: false, visible: true, linecolor: 'black', linewidth: 1, + ticklen: 4, + tickformat: x_tick_digits }, yaxis: { + range: [js_data.y_range[0], js_data.y_range[1]], title: js_data.trait_2, zeroline: false, visible: true, linecolor: 'black', linewidth: 1, + ticklen: 4, + tickformat: y_tick_digits, + automargin: true }, - hovermode: "closest" + hovermode: "closest", + showlegend: false, + annotations:[{ + xref: 'paper', + yref: 'paper', + x: 1, + xanchor: 'right', + y: 1.05, + yanchor: 'top', + text: '<i>r</i> = ' + js_data.r_value.toFixed(3) + ', <i>p</i> = ' + js_data.p_value.toExponential(3) + ', <i>n</i> = ' + js_data.num_overlap, + showarrow: false, + font: { + size: 14 + }, + } + ] +} + +var sr_layout = { + height: 700, + width: 800, + margin: { + l: 60, + r: 30, + t: 80, + b: 50 + }, + xaxis: { + range: [js_data.sr_range[0], js_data.sr_range[1]], + title: js_data.trait_1, + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + }, + yaxis: { + range: [js_data.sr_range[0], js_data.sr_range[1]], + title: js_data.trait_2, + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + }, + hovermode: "closest", + showlegend: false, + annotations:[{ + xref: 'paper', + yref: 'paper', + x: 1, + xanchor: 'right', + y: 1.05, + yanchor: 'top', + text: '<i>r</i> = ' + js_data.srr_value.toFixed(3) + ', <i>P</i> = ' + js_data.srp_value.toExponential(3) + ', <i>n</i> = ' + js_data.num_overlap, + showarrow: false, + font: { + size: 14 + }, + } +] } cofactor1_dict = {} @@ -48,14 +138,23 @@ function drawg() { sample_names.push(js_data.indIDs[j]) } - var trace = { + var trace1 = { x: x_values, y: y_values, mode: 'markers', text: sample_names } - Plotly.newPlot('scatterplot2', [trace], layout) + var trace2 = { + x: [js_data.intercept_coords[0][0], js_data.intercept_coords[1][0]], + y: [js_data.intercept_coords[0][1], js_data.intercept_coords[1][1]], + mode: 'lines', + line: { + color: 'rgb(250, 60, 73)' + } + } + + Plotly.newPlot('scatterplot2', [trace2, trace1], layout) } @@ -69,14 +168,14 @@ function srdrawg() { sample_names.push(js_data.indIDs[j]) } - var trace = { + var trace1 = { x: x_values, y: y_values, mode: 'markers', text: sample_names } - Plotly.newPlot('srscatterplot2', [trace], layout) + Plotly.newPlot('srscatterplot2', [trace1], sr_layout) } function getdata() { @@ -256,32 +355,41 @@ function getdata() { point_text.push(this_text) } - console.log("symbol list:", symbol_list) - if (symbol_list.length > 0) { - var trace = { + var trace1 = { x: x_values, y: y_values, mode: 'markers', text: point_text, marker: { + color: 'rgb(66, 66, 245)', symbol: symbol_list, size: sizes } } } else { - var trace = { + var trace1 = { x: x_values, y: y_values, mode: 'markers', text: point_text, marker: { + color: 'rgb(66, 66, 245)', size: sizes } } } - return [trace]; + var trace2 = { + x: [js_data.intercept_coords[0][0], js_data.intercept_coords[1][0]], + y: [js_data.intercept_coords[0][1], js_data.intercept_coords[1][1]], + mode: 'lines', + line: { + color: 'rgb(250, 60, 73)' + } + } + + return [trace2, trace1]; } function map1to2 (min1, max1, min2, max2, v1) { @@ -465,18 +573,28 @@ function srgetdata() { point_text.push(this_text) } - var trace = { + var trace1 = { x: x_values, y: y_values, mode: 'markers', text: point_text, marker: { + color: 'rgb(66, 66, 245)', symbol: symbol_list, size: sizes } } - return [trace]; + var trace2 = { + x: [js_data.sr_intercept_coords[0][0], js_data.sr_intercept_coords[1][0]], + y: [js_data.sr_intercept_coords[0][1], js_data.sr_intercept_coords[1][1]], + mode: 'lines', + line: { + color: 'rgb(250, 60, 73)' + } + } + + return [trace2, trace1]; } function chartupdatewh() { @@ -490,7 +608,8 @@ function chartupdatewh() { Plotly.newPlot('scatterplot2', getdata(), layout) Plotly.relayout('scatterplot2', width_height_update) - Plotly.newPlot('srscatterplot2', srgetdata(), layout) + + Plotly.newPlot('srscatterplot2', srgetdata(), sr_layout) Plotly.relayout('srscatterplot2', width_height_update) } @@ -567,7 +686,7 @@ function chartupdatedata() { Plotly.newPlot('scatterplot2', getdata(), layout) Plotly.relayout('scatterplot2', pearson_title_update) - Plotly.newPlot('srscatterplot2', srgetdata(), layout) + Plotly.newPlot('srscatterplot2', srgetdata(), sr_layout) Plotly.relayout('srscatterplot2', spearman_title_update) if ($('#cofactor1_type option:selected').val() == "color"){ diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js new file mode 100644 index 00000000..2552fb04 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js @@ -0,0 +1,84 @@ +console.log("THE FILES:", js_data.browser_files) + +snps_filename = "/browser_input?filename=" + js_data.browser_files[0] +annot_filename = "/browser_input?filename=" + js_data.browser_files[1] + +localUrls = +{ + snps: snps_filename, + annotations: annot_filename +}; + +var coordinateSystem = js_data.chr_lengths + +var vscaleWidth = 90.0; +var legendWidth = 150.0; + +if ('significant' in js_data) { + var significant_score = parseFloat(js_data.significant) +} else { + var significant_score = js_data.max_score * 0.75 +} +var score = { min: 0.0, max: js_data.max_score, sig: significant_score }; +var gwasPadding = { top: 35.0, + bottom: 35.0, + left: vscaleWidth, + right: legendWidth }; +var gwasHeight = 500.0; +var config = +{ score: score, + urls: localUrls, + tracks: { + gwas: { + trackHeight: gwasHeight, + padding: gwasPadding, + snps: { + radius: 3.75, + lineWidth: 1.0, + color: { outline: "#FFFFFF", + fill: "#00008B" }, + pixelOffset: {x: 0.0, y: 0.0} + }, + annotations: { + urls: { + url: "GeneNetwork" + }, + radius: 5.5, + outline: "#000000", + snpColor: "#0074D9", + geneColor: "#FF4136" + }, + score: score, + legend: { + fontSize: 14, + hPad: 0.1, + vPad: 0.2 + }, + vscale: { + color: "#000000", + hPad: 0.125, + numSteps: 3, + fonts: { labelSize: 18, scaleSize: 16 } + }, + }, + }, + chrs: { + chrBG1: "#FFFFFF", + chrBG2: "#EEEEEE", + chrLabels: { fontSize: 16 }, + }, + // initialChrs: { left: "1", right: "5" } + coordinateSystem: coordinateSystem, +}; + +if (js_data.selected_chr != -1) { + config['initialChrs'] = {left: js_data.selected_chr, right: js_data.selected_chr} +} + +$('#browser_tab').click(function() { + if ($('#gwas').length == 0){ + GenomeBrowser.main(config)(); + } +}); + +document.getElementById("controls").style.visibility = "visible";
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js index d52cb100..e8b7ab83 100644 --- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js +++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js @@ -161,29 +161,33 @@ intercept_line['samples_all'] = [[first_x, last_x], [first_value, last_value]] } - if (Math.max(y_values['samples_all']) - Math.min(y_values['samples_all']) < 6){ + val_range = Math.max(...y_values['samples_all']) - Math.min(...y_values['samples_all']) + if (val_range < 4){ tick_digits = '.1f' + } else if (val_range < 0.4) { + tick_digits = '.2f' } else { tick_digits = 'f' } var layout = { - title: js_data.trait_id, + title: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>", margin: { - l: 65, + l: 100, r: 30, t: 80, - b: 80 + b: 60 }, xaxis: { - title: "Normal Theoretical Quantiles", + title: "<b>Normal Theoretical Quantiles</b>", range: [first_x, last_x], zeroline: false, visible: true, linecolor: 'black', linewidth: 1, titlefont: { - size: 16 + family: "arial", + size: 20 }, ticklen: 4, tickfont: { @@ -191,19 +195,20 @@ } }, yaxis: { - title: "Data Quantiles", zeroline: false, visible: true, linecolor: 'black', linewidth: 1, titlefont: { - size: 16 + family: "arial", + size: 20 }, ticklen: 4, tickfont: { size: 16 }, - tickformat: tick_digits + tickformat: tick_digits, + automargin: true }, hovermode: "closest" } diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 50765eda..830dbf7f 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -30,11 +30,11 @@ Stat_Table_Rows = [ }, { vn: "min", pretty: "Minimum", - digits: 2 + digits: 3 }, { vn: "max", pretty: "Maximum", - digits: 2 + digits: 3 } ] @@ -67,7 +67,7 @@ Stat_Table_Rows.push( digits: 3 }, { vn: "interquartile", - pretty: "<font color='blue'>Interquartile Range</font>", + pretty: "<font color='black'>Interquartile Range</font>", url: "http://www.genenetwork.org/glossary.html#Interquartile", digits: 3 }, { @@ -334,9 +334,9 @@ update_prob_plot = function() { make_table = function() { var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1; if (js_data.trait_symbol != null) { - header = "<thead><tr><th style=\"text-align: center;\" colspan=\"100%\">Trait: " + js_data.trait_id + " - " + js_data.trait_symbol + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>"; + header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + " - " + js_data.trait_symbol + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>"; } else { - header = "<thead><tr><th style=\"text-align: center;\" colspan=\"100%\">Trait: " + js_data.trait_id + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>"; + header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + ": " + js_data.short_description + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>"; } _ref = js_data.sample_group_types; for (key in _ref) { @@ -921,8 +921,12 @@ get_bar_range = function(sample_list){ } root.chart_range = get_bar_range(sample_lists[0]) -if (root.chart_range[1] - root.chart_range[0] < 4){ +val_range = root.chart_range[1] - root.chart_range[0] + +if (val_range < 4){ tick_digits = '.1f' +} else if (val_range < 0.4) { + tick_digits = '.2f' } else { tick_digits = 'f' } @@ -934,8 +938,9 @@ if (js_data.num_values < 256) { bottom_margin = get_bar_bottom_margin(sample_lists[0]) root.bar_layout = { - title: js_data.trait_id, + title: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>", xaxis: { + type: 'category', titlefont: { size: 16 }, @@ -943,7 +948,7 @@ if (js_data.num_values < 256) { ticklen: 4, tickfont: { size: 16 - } + }, }, yaxis: { title: js_data.unit_type, @@ -986,12 +991,13 @@ var hist_trace = { root.histogram_data = [hist_trace]; root.histogram_layout = { bargap: 0.05, - title: js_data.trait_id, + title: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>", xaxis: { autorange: true, - title: "Value", + title: "<b>Value</b>", titlefont: { - size: 16 + family: "arial", + size: 20 }, ticklen: 4, tickfont: { @@ -1000,23 +1006,25 @@ root.histogram_layout = { }, yaxis: { autorange: true, - title: "Count", + title: "<b>Count</b>", titlefont: { - size: 16 + family: "arial", + size: 20 }, showline: true, ticklen: 4, tickfont: { size: 16 - } + }, + automargin: true }, width: 500, height: 600, margin: { - l: 50, + l: 70, r: 30, t: 100, - b: 60 + b: 50 } }; @@ -1032,25 +1040,34 @@ $('.histogram_samples_group').change(function() { }); root.box_layout = { - title: js_data.trait_id, xaxis: { showline: true, + titlefont: { + family: "arial", + size: 20 + }, tickfont: { size: 16 }, }, yaxis: { - title: js_data.unit_type, + title: "<b>" + js_data.unit_type +"</b>", autorange: true, showline: true, + titlefont: { + family: "arial", + size: 20 + }, ticklen: 4, tickfont: { size: 16 }, - tickformat: tick_digits + tickformat: tick_digits, + zeroline: false, + automargin: true }, margin: { - l: 50, + l: 90, r: 30, t: 30, b: 80 @@ -1118,7 +1135,7 @@ if (full_sample_lists.length > 1) { { type: 'box', y: get_sample_vals(full_sample_lists[0]), - name: sample_group_list[0], + name: "<b>Trait " + js_data.trait_id + "</b>", boxpoints: 'Outliers', jitter: 0.5, whiskerwidth: 0.2, @@ -1146,28 +1163,36 @@ $('.box_plot_tab').click(function() { // Violin Plot root.violin_layout = { - title: js_data.trait_id, xaxis: { showline: true, + titlefont: { + family: "arial", + size: 20 + }, tickfont: { size: 16 } }, yaxis: { - title: js_data.unit_type, + title: "<b>"+js_data.unit_type+"</b>", autorange: true, showline: true, + titlefont: { + family: "arial", + size: 20 + }, ticklen: 4, tickfont: { size: 16 }, tickformat: tick_digits, - zeroline: false + zeroline: false, + automargin: true }, margin: { - l: 50, + l: 90, r: 30, - t: 80, + t: 30, b: 80 } }; @@ -1235,14 +1260,11 @@ if (full_sample_lists.length > 1) { box: { visible: true }, - line: { - color: 'green', - }, meanline: { visible: true }, - name: sample_group_list[0], - x0: sample_group_list[0] + name: "<b>Trait " + js_data.trait_id + "</b>", + x0: "<b>Trait " + js_data.trait_id + "</b>" } ] } diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index 95d3a537..8db9522c 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -156,7 +156,7 @@ 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', - 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species'] + 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples'] $("#rqtl_geno_compute").on("click", (function(_this) { return function() { diff --git a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css index d352390f..36affd72 100644 --- a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css +++ b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css @@ -6,7 +6,7 @@ /* Account for fixed navbar */ body { - min-width: 1200px; + //min-width: 1200px; padding-top: 70px; padding-bottom: 30px; } @@ -28,7 +28,7 @@ body { /* Reset the container */ .container { - width: 1400px; + width: 100%; max-width: none !important; } diff --git a/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css b/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css new file mode 100644 index 00000000..135292ac --- /dev/null +++ b/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css @@ -0,0 +1 @@ +body,html{max-width:100%;overflow-x:hidden}#browser{position:absolute;margin:0}#info-line{border:1px solid #aaa;padding:2px;position:absolute;right:0;top:1px;min-width:14%;font-size:9pt}#controls{visibility:hidden;position:absolute;top:4px;left:100px;z-index:1000}#controls>button{border:1px solid #aaa;border-radius:2px;padding-left:6px;padding-right:6px;height:23px;min-width:20px}button#scrollRight,button#zoomIn{margin-left:-2px;margin-right:4px}#infoBox{position:absolute;display:inline-block;z-index:10000;visibility:hidden;padding:5px;border:2px solid grey;border-radius:5%;background-color:#fff;min-height:100px;min-width:10px;max-width:80%;margin-top:9.7em;font-family:sans-serif}#infoBox>div{float:left;margin:1em 1.2em}#infoBox>div>p{margin:.1em}
\ No newline at end of file diff --git a/wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js b/wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js new file mode 100644 index 00000000..26fd2d99 --- /dev/null +++ b/wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js @@ -0,0 +1,659 @@ +parcelRequire=function(e,r,t,n){var i,o="function"==typeof parcelRequire&&parcelRequire,u="function"==typeof require&&require;function f(t,n){if(!r[t]){if(!e[t]){var i="function"==typeof parcelRequire&&parcelRequire;if(!n&&i)return i(t,!0);if(o)return o(t,!0);if(u&&"string"==typeof t)return u(t);var c=new Error("Cannot find module '"+t+"'");throw c.code="MODULE_NOT_FOUND",c}p.resolve=function(r){return e[t][1][r]||r},p.cache={};var l=r[t]=new f.Module(t);e[t][0].call(l.exports,p,l,l.exports,this)}return r[t].exports;function p(e){return 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i=require("../Control.Semigroupoid/index.js"),t=function(i,t){this.Semigroupoid0=i,this.identity=t},n=function(i){return i.identity},e=new t(function(){return i.semigroupoidFn},function(i){return i});module.exports={Category:t,identity:n,categoryFn:e}; +},{"../Control.Semigroupoid/index.js":"/riR"}],"ObQr":[function(require,module,exports) { +"use strict";var e=!0;module.exports={otherwise:e}; +},{}],"ImXJ":[function(require,module,exports) { +"use strict";var n=require("../Data.Boolean/index.js"),r=function(n){return function(r){return function(t){return function(u){return n(r(t))(r(u))}}}},t=function(n){return function(r){return function(t){return n(t)(r)}}},u=function(n){return function(r){return n}},e=function(r){return function(t){return function(u){var e,o=t,i=!1;function c(t,e){if(t<=0)return i=!0,e;if(n.otherwise)return o=t-1|0,void(u=r(e));throw new Error("Failed pattern match at Data.Function (line 94, column 3 - line 96, column 37): 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strict";exports.unsafeCoerce=function(e){return e}; +},{}],"4oJQ":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),n=function(){function e(){}return e.value=new e,e}(),r=function(e){this.reflectSymbol=e},t=function(r){return function(t){return e.unsafeCoerce(function(e){return t(e)})({reflectSymbol:function(e){return r}})(n.value)}},u=function(e){return e.reflectSymbol};module.exports={IsSymbol:r,reflectSymbol:u,reifySymbol:t,SProxy:n}; +},{"./foreign.js":"AvJb"}],"CHMS":[function(require,module,exports) { +"use strict";exports.unsafeHas=function(n){return function(r){return{}.hasOwnProperty.call(r,n)}},exports.unsafeGet=function(n){return function(r){return r[n]}},exports.unsafeSet=function(n){return function(r){return function(t){var e={};for(var u in t)({}).hasOwnProperty.call(t,u)&&(e[u]=t[u]);return e[n]=r,e}}},exports.unsafeDelete=function(n){return function(r){var t={};for(var e in r)e!==n&&{}.hasOwnProperty.call(r,e)&&(t[e]=r[e]);return t}}; +},{}],"KG04":[function(require,module,exports) { +"use strict";var e=require("./foreign.js");module.exports={unsafeHas:e.unsafeHas,unsafeGet:e.unsafeGet,unsafeSet:e.unsafeSet,unsafeDelete:e.unsafeDelete}; +},{"./foreign.js":"CHMS"}],"XaXP":[function(require,module,exports) { +"use strict";var e=function(){function e(){}return e.value=new e,e}();module.exports={RLProxy:e}; +},{}],"mFY7":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),e=require("../Data.Symbol/index.js"),r=require("../Record.Unsafe/index.js"),o=require("../Type.Data.RowList/index.js"),t=function(n){this.showRecordFields=n},u=function(n){this.show=n},i=new u(n.showStringImpl),s=new t(function(n){return function(n){return[]}}),w=function(n){return n.showRecordFields},c=function(e){return function(e){return new u(function(r){var t=w(e)(o.RLProxy.value)(r);return 0===t.length?"{}":n.join(" ")(["{",n.join(", ")(t),"}"])})}},h=new u(n.showNumberImpl),l=new u(n.showIntImpl),a=new u(n.showCharImpl),f=new u(function(n){if(n)return"true";if(!n)return"false";throw new Error("Failed pattern match at Data.Show (line 20, column 1 - line 22, column 23): "+[n.constructor.name])}),d=function(n){return n.show},m=function(e){return new u(n.showArrayImpl(d(e)))},R=function(u){return function(i){return function(s){return new t(function(t){return function(t){var c=w(i)(o.RLProxy.value)(t),h=e.reflectSymbol(u)(e.SProxy.value),l=r.unsafeGet(h)(t);return n.cons(n.join(": ")([h,d(s)(l)]))(c)}})}}};module.exports={Show:u,show:d,ShowRecordFields:t,showRecordFields:w,showBoolean:f,showInt:l,showNumber:h,showChar:a,showString:i,showArray:m,showRecord:c,showRecordFieldsNil:s,showRecordFieldsCons:R}; +},{"./foreign.js":"qgjE","../Data.Symbol/index.js":"4oJQ","../Record.Unsafe/index.js":"KG04","../Type.Data.RowList/index.js":"XaXP"}],"NhVk":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),i=require("../Data.Show/index.js"),n=new i.Show(function(e){return"unit"});module.exports={showUnit:n,unit:e.unit}; +},{"./foreign.js":"Nqls","../Data.Show/index.js":"mFY7"}],"+0AE":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Control.Semigroupoid/index.js"),t=require("../Data.Function/index.js"),u=require("../Data.Unit/index.js"),i=function(n){this.map=n},e=function(n){return n.map},o=function(n){return function(r){return function(t){return e(n)(t)(r)}}},c=function(n){return e(n)(t.const(u.unit))},f=function(n){return function(r){return function(u){return e(n)(t.const(u))(r)}}},a=function(n){return function(r){return e(n)(t.const(r))}},s=new i(r.compose(r.semigroupoidFn)),p=new i(n.arrayMap),d=function(n){return function(r){return function(t){return e(n)(function(n){return n(t)})(r)}}};module.exports={Functor:i,map:e,mapFlipped:o,void:c,voidRight:a,voidLeft:f,flap:d,functorFn:s,functorArray:p}; 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function(o){return function(e){return c(n)(c(n)(u.map(n.Functor0())(r)(t))(o))(e)}}}}},y=function(n){return function(r){return function(t){return function(o){return function(e){return function(i){return c(n)(c(n)(c(n)(u.map(n.Functor0())(r)(t))(o))(e))(i)}}}}}},F=function(n){return function(r){return function(t){return function(o){return function(e){return function(i){return function(f){return c(n)(c(n)(c(n)(c(n)(u.map(n.Functor0())(r)(t))(o))(e))(i))(f)}}}}}}};module.exports={Apply:o,apply:c,applyFirst:f,applySecond:p,lift2:a,lift3:l,lift4:y,lift5:F,applyFn:e,applyArray:i}; +},{"./foreign.js":"7nyB","../Control.Category/index.js":"IAi2","../Data.Function/index.js":"ImXJ","../Data.Functor/index.js":"+0AE"}],"qYya":[function(require,module,exports) { +"use strict";var n=require("../Control.Apply/index.js"),r=require("../Data.Unit/index.js"),t=function(n,r){this.Apply0=n,this.pure=r},e=function(n){return n.pure},u=function(n){return function(t){return function(u){if(!t)return u;if(t)return e(n)(r.unit);throw new Error("Failed pattern match at Control.Applicative (line 62, column 1 - line 62, column 65): "+[t.constructor.name,u.constructor.name])}}},i=function(n){return function(t){return function(u){if(t)return u;if(!t)return e(n)(r.unit);throw new Error("Failed pattern match at Control.Applicative (line 57, column 1 - line 57, column 63): "+[t.constructor.name,u.constructor.name])}}},o=function(r){return function(t){return function(u){return n.apply(r.Apply0())(e(r)(t))(u)}}},c=new t(function(){return n.applyFn},function(n){return function(r){return n}}),p=new t(function(){return n.applyArray},function(n){return[n]});module.exports={Applicative:t,pure:e,liftA1:o,unless:u,when:i,applicativeFn:c,applicativeArray:p}; +},{"../Control.Apply/index.js":"QcLv","../Data.Unit/index.js":"NhVk"}],"S3W+":[function(require,module,exports) { +"use strict";exports.arrayBind=function(r){return function(t){for(var n=[],e=0,o=r.length;e<o;e++)Array.prototype.push.apply(n,t(r[e]));return n}}; +},{}],"7VcT":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Control.Apply/index.js"),t=require("../Control.Category/index.js"),i=require("../Data.Function/index.js"),u=function(n){this.discard=n},e=function(n,r){this.Apply0=n,this.bind=r},o=function(n){return n.discard},c=new e(function(){return r.applyFn},function(n){return function(r){return function(t){return r(n(t))(t)}}}),f=new e(function(){return r.applyArray},n.arrayBind),d=function(n){return n.bind},s=function(n){return i.flip(d(n))},a=function(n){return function(r){return function(t){return function(i){return s(n)(r)(t(i))}}}},p=function(n){return function(r){return function(t){return function(i){return d(n)(r(i))(t)}}}},l=new u(function(n){return d(n)}),y=function(n){return function(r){return function(t){return function(i){return d(n)(r)(function(n){return n?t:i})}}}},b=function(n){return function(r){return d(n)(r)(t.identity(t.categoryFn))}};module.exports={Bind:e,bind:d,bindFlipped:s,Discard:u,discard:o,join:b,composeKleisli:p,composeKleisliFlipped:a,ifM:y,bindFn:c,bindArray:f,discardUnit:l}; +},{"./foreign.js":"S3W+","../Control.Apply/index.js":"QcLv","../Control.Category/index.js":"IAi2","../Data.Function/index.js":"ImXJ"}],"phTL":[function(require,module,exports) { +"use strict";exports.concatString=function(n){return function(t){return n+t}},exports.concatArray=function(n){return function(t){return 0===n.length?t:0===t.length?n:n.concat(t)}}; +},{}],"bncE":[function(require,module,exports) { +"use strict";var r=require("../Data.Show/index.js"),n=function(r){return r},o=function(r){return function(r){var n;for(;;)n=void(r=r);return n}(r)},e=new r.Show(o);module.exports={absurd:o,showVoid:e}; +},{"../Data.Show/index.js":"mFY7"}],"EsAJ":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Data.Symbol/index.js"),e=require("../Data.Unit/index.js"),u=require("../Data.Void/index.js"),t=require("../Record.Unsafe/index.js"),i=require("../Type.Data.RowList/index.js"),o=function(n){this.appendRecord=n},c=function(n){this.append=n},f=new c(function(n){return u.absurd}),a=new c(function(n){return function(n){return e.unit}}),s=new c(n.concatString),p=new o(function(n){return function(n){return function(n){return{}}}}),d=new c(n.concatArray),g=function(n){return n.appendRecord},m=function(n){return function(n){return new c(g(n)(i.RLProxy.value))}},R=function(n){return n.append},w=function(n){return new c(function(r){return function(e){return function(u){return R(n)(r(u))(e(u))}}})},x=function(n){return function(e){return function(e){return function(u){return new o(function(o){return function(o){return function(c){var f=g(e)(i.RLProxy.value)(o)(c),a=r.reflectSymbol(n)(r.SProxy.value),s=t.unsafeSet(a),p=t.unsafeGet(a);return s(R(u)(p(o))(p(c)))(f)}}})}}}};module.exports={Semigroup:c,append:R,SemigroupRecord:o,appendRecord:g,semigroupString:s,semigroupUnit:a,semigroupVoid:f,semigroupFn:w,semigroupArray:d,semigroupRecord:m,semigroupRecordNil:p,semigroupRecordCons:x}; +},{"./foreign.js":"phTL","../Data.Symbol/index.js":"4oJQ","../Data.Unit/index.js":"NhVk","../Data.Void/index.js":"bncE","../Record.Unsafe/index.js":"KG04","../Type.Data.RowList/index.js":"XaXP"}],"lN+m":[function(require,module,exports) { +"use strict";var r=require("../Data.Functor/index.js"),t=require("../Data.Semigroup/index.js"),e=function(r,t){this.Functor0=r,this.alt=t},n=new e(function(){return r.functorArray},t.append(t.semigroupArray)),u=function(r){return r.alt};module.exports={Alt:e,alt:u,altArray:n}; +},{"../Data.Functor/index.js":"+0AE","../Data.Semigroup/index.js":"EsAJ"}],"oMBg":[function(require,module,exports) { +"use strict";var t=require("../Control.Alt/index.js"),r=function(t,r){this.Alt0=t,this.empty=r},e=new r(function(){return t.altArray},[]),n=function(t){return t.empty};module.exports={Plus:r,empty:n,plusArray:e}; +},{"../Control.Alt/index.js":"lN+m"}],"aHia":[function(require,module,exports) { +"use strict";var r=require("../Control.Applicative/index.js"),e=require("../Control.Plus/index.js"),t=function(r,e){this.Applicative0=r,this.Plus1=e},i=new t(function(){return r.applicativeArray},function(){return e.plusArray});module.exports={Alternative:t,alternativeArray:i}; +},{"../Control.Applicative/index.js":"qYya","../Control.Plus/index.js":"oMBg"}],"U/Ix":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),i=require("../Control.Bind/index.js"),r=function(n,i){this.Applicative0=n,this.Bind1=i},t=function(r){return function(t){return function(u){return i.bind(r.Bind1())(t)(function(i){return n.when(r.Applicative0())(i)(u)})}}},u=function(r){return function(t){return function(u){return i.bind(r.Bind1())(t)(function(i){return n.unless(r.Applicative0())(i)(u)})}}},e=new r(function(){return n.applicativeFn},function(){return i.bindFn}),c=new r(function(){return n.applicativeArray},function(){return i.bindArray}),o=function(r){return function(t){return function(u){return i.bind(r.Bind1())(u)(function(i){return n.pure(r.Applicative0())(t(i))})}}},f=function(r){return function(t){return function(u){return i.bind(r.Bind1())(t)(function(t){return i.bind(r.Bind1())(u)(function(i){return n.pure(r.Applicative0())(t(i))})})}}};module.exports={Monad:r,liftM1:o,ap:f,whenM:t,unlessM:u,monadFn:e,monadArray:c}; +},{"../Control.Applicative/index.js":"qYya","../Control.Bind/index.js":"7VcT"}],"IpNh":[function(require,module,exports) { +"use strict";var t=function(t,n){this.Monad0=t,this.callCC=n},n=function(t){return t.callCC};module.exports={MonadCont:t,callCC:n}; +},{}],"YFBA":[function(require,module,exports) { +"use strict";exports.arrayExtend=function(n){return function(r){return r.map(function(r,t,e){return n(e.slice(t))})}}; +},{}],"JIoJ":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Control.Category/index.js"),t=require("../Data.Functor/index.js"),e=require("../Data.Semigroup/index.js"),u=function(n,r){this.Functor0=n,this.extend=r},i=function(n){return new u(function(){return t.functorFn},function(r){return function(t){return function(u){return r(function(r){return t(e.append(n)(u)(r))})}}})},o=new u(function(){return t.functorArray},n.arrayExtend),c=function(n){return n.extend},f=function(n){return function(r){return function(t){return c(n)(t)(r)}}},d=function(n){return c(n)(r.identity(r.categoryFn))},a=function(n){return function(r){return function(t){return function(e){return r(c(n)(t)(e))}}}},s=function(n){return function(r){return function(t){return function(e){return t(c(n)(r)(e))}}}};module.exports={Extend:u,extend:c,extendFlipped:f,composeCoKleisli:s,composeCoKleisliFlipped:a,duplicate:d,extendFn:i,extendArray:o}; +},{"./foreign.js":"YFBA","../Control.Category/index.js":"IAi2","../Data.Functor/index.js":"+0AE","../Data.Semigroup/index.js":"EsAJ"}],"kY6E":[function(require,module,exports) { +"use strict";exports.foldrArray=function(r){return function(n){return function(t){for(var u=n,o=t.length-1;o>=0;o--)u=r(t[o])(u);return u}}},exports.foldlArray=function(r){return function(n){return function(t){for(var u=n,o=t.length,e=0;e<o;e++)u=r(u)(t[e]);return u}}}; +},{}],"h7nC":[function(require,module,exports) { +"use strict";var r=function(r){return function(e){return r===e}};exports.eqBooleanImpl=r,exports.eqIntImpl=r,exports.eqNumberImpl=r,exports.eqCharImpl=r,exports.eqStringImpl=r,exports.eqArrayImpl=function(r){return function(e){return function(t){if(e===t)return!0;if(e.length!==t.length)return!1;for(var n=0;n<e.length;n++)if(!r(e[n])(t[n]))return!1;return!0}}}; +},{}],"Pq4F":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),e=require("../Data.Symbol/index.js"),r=require("../Record.Unsafe/index.js"),t=require("../Type.Data.RowList/index.js"),u=function(n){this.eqRecord=n},o=function(n){this.eq1=n},i=function(n){this.eq=n},c=new i(function(n){return function(n){return!0}}),q=new i(function(n){return function(n){return!0}}),f=new i(n.eqStringImpl),a=new u(function(n){return function(n){return function(n){return!0}}}),l=function(n){return n.eqRecord},w=function(n){return function(n){return new i(l(n)(t.RLProxy.value))}},s=new i(n.eqNumberImpl),m=new i(n.eqIntImpl),R=new i(n.eqCharImpl),d=new i(n.eqBooleanImpl),y=function(n){return n.eq1},p=function(n){return n.eq},I=function(e){return new i(n.eqArrayImpl(p(e)))},x=new o(function(n){return p(I(n))}),h=function(n){return function(o){return function(o){return function(i){return new u(function(u){return function(u){return function(c){var q=l(n)(t.RLProxy.value)(u)(c),f=e.reflectSymbol(o)(e.SProxy.value),a=r.unsafeGet(f);return 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n=require("./foreign.js"),r=require("../Data.Symbol/index.js"),t=require("../Data.Unit/index.js"),e=require("../Record.Unsafe/index.js"),u=require("../Type.Data.Row/index.js"),o=require("../Type.Data.RowList/index.js"),i=function(n,r,t,e,u,o){this.conjRecord=n,this.disjRecord=r,this.ffRecord=t,this.impliesRecord=e,this.notRecord=u,this.ttRecord=o},c=function(n,r,t,e,u,o){this.conj=n,this.disj=r,this.ff=t,this.implies=e,this.not=u,this.tt=o},f=function(n){return n.ttRecord},a=function(n){return n.tt},l=function(n){return n.notRecord},s=function(n){return n.not},R=function(n){return n.impliesRecord},y=function(n){return n.implies},d=new c(function(n){return function(n){return t.unit}},function(n){return function(n){return t.unit}},t.unit,function(n){return function(n){return t.unit}},function(n){return t.unit},t.unit),v=new i(function(n){return function(n){return function(n){return{}}}},function(n){return function(n){return function(n){return{}}}},function(n){return 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function(i){var c=f(t)(o.RLProxy.value)(i),l=r.reflectSymbol(n)(r.SProxy.value);return e.unsafeSet(l)(a(u))(c)}})}}}};module.exports={HeytingAlgebra:c,tt:a,ff:j,implies:y,conj:m,disj:S,not:s,HeytingAlgebraRecord:i,ffRecord:x,ttRecord:f,impliesRecord:R,conjRecord:h,disjRecord:P,notRecord:l,heytingAlgebraBoolean:b,heytingAlgebraUnit:d,heytingAlgebraFunction:L,heytingAlgebraRecord:g,heytingAlgebraRecordNil:v,heytingAlgebraRecordCons:p}; +},{"./foreign.js":"7fWM","../Data.Symbol/index.js":"4oJQ","../Data.Unit/index.js":"NhVk","../Record.Unsafe/index.js":"KG04","../Type.Data.Row/index.js":"ukdD","../Type.Data.RowList/index.js":"XaXP"}],"lD5R":[function(require,module,exports) { +"use strict";var r=require("../Control.Alternative/index.js"),e=require("../Control.Applicative/index.js"),n=require("../Control.Monad/index.js"),t=require("../Control.Plus/index.js"),i=require("../Data.Unit/index.js"),o=function(r,e){this.Alternative1=r,this.Monad0=e},a=new o(function(){return 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function(e){return o<e?r:o===e?n:t}}}}};exports.ordBooleanImpl=r,exports.ordIntImpl=r,exports.ordNumberImpl=r,exports.ordStringImpl=r,exports.ordCharImpl=r,exports.ordArrayImpl=function(r){return function(n){return function(t){for(var o=0,e=n.length,u=t.length;o<e&&o<u;){var p=n[o],i=t[o],f=r(p)(i);if(0!==f)return f;o++}return e===u?0:e>u?-1:1}}}; +},{}],"5Eun":[function(require,module,exports) { +"use strict";var n=require("../Data.Eq/index.js"),e=require("../Data.Semigroup/index.js"),r=require("../Data.Show/index.js"),t=function(){function n(){}return n.value=new n,n}(),i=function(){function n(){}return n.value=new n,n}(),o=function(){function n(){}return n.value=new n,n}(),u=new r.Show(function(n){if(n instanceof t)return"LT";if(n instanceof i)return"GT";if(n instanceof o)return"EQ";throw new Error("Failed pattern match at Data.Ordering (line 26, column 1 - line 29, column 17): "+[n.constructor.name])}),a=new e.Semigroup(function(n){return function(e){if(n instanceof t)return t.value;if(n instanceof i)return i.value;if(n instanceof o)return e;throw new Error("Failed pattern match at Data.Ordering (line 21, column 1 - line 24, column 18): "+[n.constructor.name,e.constructor.name])}}),c=function(n){if(n instanceof i)return t.value;if(n instanceof o)return o.value;if(n instanceof t)return i.value;throw new Error("Failed pattern match at Data.Ordering (line 33, column 1 - line 33, column 31): "+[n.constructor.name])},f=new n.Eq(function(n){return function(e){return n instanceof t&&e instanceof t||(n instanceof i&&e instanceof i||n instanceof o&&e instanceof o)}});module.exports={LT:t,GT:i,EQ:o,invert:c,eqOrdering:f,semigroupOrdering:a,showOrdering:u}; +},{"../Data.Eq/index.js":"Pq4F","../Data.Semigroup/index.js":"EsAJ","../Data.Show/index.js":"mFY7"}],"+BUG":[function(require,module,exports) { +"use strict";exports.intSub=function(n){return function(t){return n-t|0}},exports.numSub=function(n){return function(t){return n-t}}; +},{}],"Vm8y":[function(require,module,exports) { +"use strict";exports.intAdd=function(n){return function(t){return n+t|0}},exports.intMul=function(n){return function(t){return n*t|0}},exports.numAdd=function(n){return function(t){return n+t}},exports.numMul=function(n){return function(t){return n*t}}; +},{}],"11NF":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Data.Symbol/index.js"),e=require("../Data.Unit/index.js"),u=require("../Record.Unsafe/index.js"),t=require("../Type.Data.Row/index.js"),o=require("../Type.Data.RowList/index.js"),i=function(n,r,e,u){this.addRecord=n,this.mulRecord=r,this.oneRecord=e,this.zeroRecord=u},c=function(n,r,e,u){this.add=n,this.mul=r,this.one=e,this.zero=u},f=function(n){return n.zeroRecord},a=function(n){return n.zero},d=new c(function(n){return function(n){return e.unit}},function(n){return function(n){return e.unit}},e.unit,e.unit),l=new i(function(n){return function(n){return 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f=P(e)(o.RLProxy.value)(t)(i),a=r.reflectSymbol(n)(r.SProxy.value),d=u.unsafeSet(a),l=u.unsafeGet(a);return d(g(c)(l(t))(l(i)))(f)}}},function(t){return function(t){return function(i){var f=x(e)(o.RLProxy.value)(t)(i),a=r.reflectSymbol(n)(r.SProxy.value),d=u.unsafeSet(a),l=u.unsafeGet(a);return d(v(c)(l(t))(l(i)))(f)}}},function(i){return function(i){var f=m(e)(o.RLProxy.value)(t.RProxy.value),a=r.reflectSymbol(n)(r.SProxy.value);return u.unsafeSet(a)(y(c))(f)}},function(i){return function(i){var d=f(e)(o.RLProxy.value)(t.RProxy.value),l=r.reflectSymbol(n)(r.SProxy.value);return u.unsafeSet(l)(a(c))(d)}})}}}};module.exports={Semiring:c,add:g,zero:a,mul:v,one:y,SemiringRecord:i,addRecord:P,mulRecord:x,oneRecord:m,zeroRecord:f,semiringInt:R,semiringNumber:s,semiringFn:w,semiringUnit:d,semiringRecord:S,semiringRecordNil:l,semiringRecordCons:L}; +},{"./foreign.js":"Vm8y","../Data.Symbol/index.js":"4oJQ","../Data.Unit/index.js":"NhVk","../Record.Unsafe/index.js":"KG04","../Type.Data.Row/index.js":"ukdD","../Type.Data.RowList/index.js":"XaXP"}],"E2qH":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Data.Semiring/index.js"),e=require("../Data.Symbol/index.js"),i=require("../Data.Unit/index.js"),u=require("../Record.Unsafe/index.js"),t=require("../Type.Data.RowList/index.js"),o=function(n,r){this.SemiringRecord0=n,this.subRecord=r},c=function(n,r){this.Semiring0=n,this.sub=r},f=function(n){return n.subRecord},s=function(n){return n.sub},g=new c(function(){return r.semiringUnit},function(n){return function(n){return i.unit}}),m=new o(function(){return r.semiringRecordNil},function(n){return function(n){return function(n){return{}}}}),d=function(n){return function(i){return function(c){return function(g){return new o(function(){return 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+},{"./foreign.js":"+BUG","../Data.Semiring/index.js":"11NF","../Data.Symbol/index.js":"4oJQ","../Data.Unit/index.js":"NhVk","../Record.Unsafe/index.js":"KG04","../Type.Data.RowList/index.js":"XaXP"}],"r4Vb":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Data.Eq/index.js"),e=require("../Data.Ordering/index.js"),t=require("../Data.Ring/index.js"),u=require("../Data.Semiring/index.js"),o=require("../Data.Symbol/index.js"),i=require("../Record.Unsafe/index.js"),c=require("../Type.Data.RowList/index.js"),a=function(n,r){this.EqRecord0=n,this.compareRecord=r},f=function(n,r){this.Eq10=n,this.compare1=r},l=function(n,r){this.Eq0=n,this.compare=r},s=new l(function(){return r.eqVoid},function(n){return function(n){return e.EQ.value}}),d=new l(function(){return r.eqUnit},function(n){return function(n){return e.EQ.value}}),m=new l(function(){return r.eqString},n.ordStringImpl(e.LT.value)(e.EQ.value)(e.GT.value)),T=new a(function(){return r.eqRowNil},function(n){return function(n){return function(n){return e.EQ.value}}}),v=new l(function(){return e.eqOrdering},function(n){return function(r){if(n instanceof e.LT&&r instanceof e.LT)return e.EQ.value;if(n instanceof e.EQ&&r instanceof e.EQ)return e.EQ.value;if(n instanceof e.GT&&r instanceof e.GT)return e.EQ.value;if(n instanceof e.LT)return e.LT.value;if(n instanceof e.EQ&&r instanceof e.LT)return e.GT.value;if(n instanceof e.EQ&&r instanceof e.GT)return e.LT.value;if(n instanceof e.GT)return e.GT.value;throw new Error("Failed pattern match at Data.Ord (line 112, column 1 - line 119, column 21): "+[n.constructor.name,r.constructor.name])}}),E=new l(function(){return r.eqNumber},n.ordNumberImpl(e.LT.value)(e.EQ.value)(e.GT.value)),q=new l(function(){return r.eqInt},n.ordIntImpl(e.LT.value)(e.EQ.value)(e.GT.value)),w=new l(function(){return r.eqChar},n.ordCharImpl(e.LT.value)(e.EQ.value)(e.GT.value)),p=new l(function(){return r.eqBoolean},n.ordBooleanImpl(e.LT.value)(e.EQ.value)(e.GT.value)),h=function(n){return n.compareRecord},g=function(n){return function(e){return new l(function(){return r.eqRec(n)(e.EqRecord0())},h(e)(c.RLProxy.value))}},L=function(n){return n.compare1},Q=function(n){return n.compare},G=function(n){return function(r){return function(e){return function(t){return Q(n)(r(e))(r(t))}}}},R=function(n){return function(r){return function(t){return Q(n)(r)(t)instanceof e.GT}}},O=function(n){return function(r){return function(t){return!(Q(n)(r)(t)instanceof e.LT)}}},x=function(n){return function(r){return function(e){return O(n)(e)(u.zero(r.Semiring0()))?u.one(r.Semiring0()):t.negate(r)(u.one(r.Semiring0()))}}},y=function(n){return function(r){return function(t){return Q(n)(r)(t)instanceof e.LT}}},S=function(n){return function(r){return function(t){return!(Q(n)(r)(t)instanceof e.GT)}}},D=function(n){return function(r){return function(t){var u=Q(n)(r)(t);if(u instanceof e.LT)return t;if(u instanceof e.EQ)return r;if(u instanceof e.GT)return r;throw new Error("Failed pattern match at Data.Ord (line 167, column 3 - line 170, column 12): "+[u.constructor.name])}}},I=function(n){return function(r){return function(t){var u=Q(n)(r)(t);if(u instanceof e.LT)return r;if(u instanceof e.EQ)return r;if(u instanceof e.GT)return t;throw new Error("Failed pattern match at Data.Ord (line 158, column 3 - line 161, column 12): "+[u.constructor.name])}}},j=function(t){return new l(function(){return r.eqArray(t.Eq0())},(u=function(n){return function(r){var u=Q(t)(n)(r);if(u instanceof e.EQ)return 0;if(u instanceof e.LT)return 1;if(u instanceof e.GT)return-1;throw new Error("Failed pattern match at Data.Ord (line 65, column 7 - line 68, column 17): "+[u.constructor.name])}},function(r){return function(e){return Q(q)(0)(n.ordArrayImpl(u)(r)(e))}}));var u},b=new f(function(){return r.eq1Array},function(n){return Q(j(n))}),A=function(n){return function(t){return function(u){return function(f){return new a(function(){return r.eqRowCons(n.EqRecord0())(t)(u)(f.Eq0())},function(t){return function(t){return function(a){var l=o.reflectSymbol(u)(o.SProxy.value),s=Q(f)(i.unsafeGet(l)(t))(i.unsafeGet(l)(a));return r.notEq(e.eqOrdering)(s)(e.EQ.value)?s:h(n)(c.RLProxy.value)(t)(a)}}})}}}},C=function(n){return function(r){return function(e){return function(t){return I(n)(e)(D(n)(r)(t))}}}},N=function(n){return function(r){return function(e){return function(t){return!y(n)(t)(r)&&!R(n)(t)(e)}}}},F=function(n){return function(r){return function(e){return O(n)(e)(u.zero(r.Semiring0()))?e:t.negate(r)(e)}}};module.exports={Ord:l,compare:Q,Ord1:f,compare1:L,lessThan:y,lessThanOrEq:S,greaterThan:R,greaterThanOrEq:O,comparing:G,min:I,max:D,clamp:C,between:N,abs:F,signum:x,OrdRecord:a,compareRecord:h,ordBoolean:p,ordInt:q,ordNumber:E,ordString:m,ordChar:w,ordUnit:d,ordVoid:s,ordArray:j,ordOrdering:v,ord1Array:b,ordRecordNil:T,ordRecordCons:A,ordRecord:g}; +},{"./foreign.js":"m7Aq","../Data.Eq/index.js":"Pq4F","../Data.Ordering/index.js":"5Eun","../Data.Ring/index.js":"E2qH","../Data.Semiring/index.js":"11NF","../Data.Symbol/index.js":"4oJQ","../Record.Unsafe/index.js":"KG04","../Type.Data.RowList/index.js":"XaXP"}],"kcUU":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),t=require("../Data.Ord/index.js"),r=require("../Data.Ordering/index.js"),e=require("../Data.Unit/index.js"),o=function(n,t,r){this.Ord0=n,this.bottom=t,this.top=r},u=function(n){return n.top},d=new o(function(){return t.ordUnit},e.unit,e.unit),i=new o(function(){return t.ordOrdering},r.LT.value,r.GT.value),b=new o(function(){return t.ordNumber},n.bottomNumber,n.topNumber),a=new o(function(){return t.ordInt},n.bottomInt,n.topInt),m=new o(function(){return t.ordChar},n.bottomChar,n.topChar),c=new o(function(){return t.ordBoolean},!1,!0),f=function(n){return n.bottom};module.exports={Bounded:o,bottom:f,top:u,boundedBoolean:c,boundedInt:a,boundedChar:m,boundedOrdering:i,boundedUnit:d,boundedNumber:b}; +},{"./foreign.js":"0C+G","../Data.Ord/index.js":"r4Vb","../Data.Ordering/index.js":"5Eun","../Data.Unit/index.js":"NhVk"}],"AXkC":[function(require,module,exports) { +"use strict";var n=require("../Data.Functor/index.js"),r=function(n){this.imap=n},t=new r(function(n){return function(r){return function(r){return n(r)}}}),i=new r(function(n){return function(r){return function(t){return function(i){return n(t(r(i)))}}}}),u=new r(function(n){return function(r){return function(r){return n(r)}}}),e=new r(function(n){return function(r){return function(r){return n(r)}}}),o=new r(function(n){return function(r){return function(r){return n(r)}}}),a=new r(function(n){return function(r){return function(r){return n(r)}}}),c=function(r){return function(t){return function(i){return n.map(r)(t)}}},f=new r(c(n.functorArray)),v=new r(c(n.functorFn)),w=function(n){return n.imap};module.exports={imap:w,Invariant:r,imapF:c,invariantFn:v,invariantArray:f,invariantAdditive:a,invariantConj:o,invariantDisj:e,invariantDual:u,invariantEndo:i,invariantMultiplicative:t}; +},{"../Data.Functor/index.js":"+0AE"}],"8EBw":[function(require,module,exports) { +"use strict";exports.intDegree=function(t){return Math.min(Math.abs(t),2147483647)},exports.intDiv=function(t){return function(n){return 0===n?0:n>0?Math.floor(t/n):-Math.floor(t/-n)}},exports.intMod=function(t){return function(n){if(0===n)return 0;var r=Math.abs(n);return(t%r+r)%r}},exports.numDiv=function(t){return function(n){return t/n}}; +},{}],"60TQ":[function(require,module,exports) { +"use strict";var n=require("../Data.Ring/index.js"),t=function(n){this.RingRecord0=n},i=function(n){this.Ring0=n},r=new i(function(){return n.ringUnit}),e=new t(function(){return n.ringRecordNil}),u=function(i){return function(r){return function(e){return function(u){return new t(function(){return n.ringRecordCons(i)(r)(e.RingRecord0())(u.Ring0())})}}}},o=function(t){return function(r){return new i(function(){return n.ringRecord(t)(r.RingRecord0())})}},c=new i(function(){return n.ringNumber}),R=new i(function(){return n.ringInt}),g=function(t){return new i(function(){return n.ringFn(t.Ring0())})};module.exports={CommutativeRing:i,CommutativeRingRecord:t,commutativeRingInt:R,commutativeRingNumber:c,commutativeRingUnit:r,commutativeRingFn:g,commutativeRingRecord:o,commutativeRingRecordNil:e,commutativeRingRecordCons:u}; +},{"../Data.Ring/index.js":"E2qH"}],"2IRB":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),i=require("../Data.CommutativeRing/index.js"),e=require("../Data.Eq/index.js"),t=require("../Data.Semiring/index.js"),r=function(n,i,e,t){this.CommutativeRing0=n,this.degree=i,this.div=e,this.mod=t},u=function(n){return n.mod},o=function(n){return function(i){return function(r){return function(o){var m,g=n,c=i,f=r,a=!1;function d(n,i,r,m){if(e.eq(n)(m)(t.zero(i.CommutativeRing0().Ring0().Semiring0())))return a=!0,r;g=n,c=i,f=m,o=u(i)(r)(m)}for(;!a;)m=d(g,c,f,o);return m}}}},m=new r(function(){return i.commutativeRingNumber},function(n){return 1},n.numDiv,function(n){return function(n){return 0}}),g=new r(function(){return i.commutativeRingInt},n.intDegree,n.intDiv,n.intMod),c=function(n){return n.div},f=function(n){return function(i){return function(r){return function(u){return e.eq(n)(r)(t.zero(i.CommutativeRing0().Ring0().Semiring0()))||e.eq(n)(u)(t.zero(i.CommutativeRing0().Ring0().Semiring0()))?t.zero(i.CommutativeRing0().Ring0().Semiring0()):c(i)(t.mul(i.CommutativeRing0().Ring0().Semiring0())(r)(u))(o(n)(i)(r)(u))}}}},a=function(n){return n.degree};module.exports={EuclideanRing:r,degree:a,div:c,mod:u,gcd:o,lcm:f,euclideanRingInt:g,euclideanRingNumber:m}; 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n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),e=require("../Control.Monad/index.js"),t=require("../Data.Eq/index.js"),i=require("../Data.Functor/index.js"),o=require("../Data.Monoid/index.js"),a=require("../Data.Ord/index.js"),c=require("../Data.Semigroup/index.js"),d=require("../Data.Show/index.js"),f=function(n){return n},l=function(n){return new d.Show(function(r){return"(Dual "+d.show(n)(r)+")"})},p=function(n){return new c.Semigroup(function(r){return function(u){return c.append(n)(u)(r)}})},D=function(n){return n},s=function(n){return new o.Monoid(function(){return p(n.Semigroup0())},o.mempty(n))},q=new i.Functor(function(n){return function(r){return n(r)}}),w=function(n){return n},x=new t.Eq1(function(n){return t.eq(w(n))}),j=new a.Ord1(function(){return x},function(n){return a.compare(D(n))}),m=function(n){return n},S=new r.Apply(function(){return q},function(n){return function(r){return n(r)}}),g=new 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n=require("../Control.Applicative/index.js"),e=require("../Control.Apply/index.js"),i=require("../Control.Bind/index.js"),r=require("../Control.Monad/index.js"),t=require("../Data.Eq/index.js"),u=require("../Data.Functor/index.js"),d=require("../Data.Monoid/index.js"),o=require("../Data.Ord/index.js"),c=require("../Data.Semigroup/index.js"),f=require("../Data.Semiring/index.js"),a=require("../Data.Show/index.js"),v=function(n){return n},A=function(n){return new a.Show(function(e){return"(Additive "+a.show(n)(e)+")"})},p=function(n){return new c.Semigroup(function(e){return function(i){return f.add(n)(e)(i)}})},s=function(n){return n},q=function(n){return new d.Monoid(function(){return p(n)},f.zero(n))},w=new u.Functor(function(n){return function(e){return n(e)}}),x=function(n){return n},j=new t.Eq1(function(n){return t.eq(x(n))}),l=new o.Ord1(function(){return j},function(n){return o.compare(s(n))}),m=function(n){return n},D=new e.Apply(function(){return w},function(n){return 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n=require("../Control.Applicative/index.js"),i=require("../Control.Apply/index.js"),t=require("../Control.Bind/index.js"),e=require("../Control.Monad/index.js"),r=require("../Data.Eq/index.js"),u=require("../Data.Functor/index.js"),o=require("../Data.Monoid/index.js"),c=require("../Data.Ord/index.js"),l=require("../Data.Semigroup/index.js"),a=require("../Data.Semiring/index.js"),p=require("../Data.Show/index.js"),d=function(n){return n},f=function(n){return new p.Show(function(i){return"(Multiplicative "+p.show(n)(i)+")"})},v=function(n){return new l.Semigroup(function(i){return function(t){return a.mul(n)(i)(t)}})},M=function(n){return n},s=function(n){return new o.Monoid(function(){return v(n)},a.one(n))},q=new u.Functor(function(n){return function(i){return n(i)}}),w=function(n){return n},x=new r.Eq1(function(n){return r.eq(w(n))}),j=new c.Ord1(function(){return x},function(n){return c.compare(M(n))}),m=function(n){return n},D=new i.Apply(function(){return q},function(n){return 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M(n)(r)(t.identity(t.categoryFn))(t.identity(t.categoryFn))}},h=function(n){return function(r){return function(t){return function(u){var e=d.unwrap(d.newtypeDisj),i=M(n)(f.monoidDisj(r.HeytingAlgebra0()))(function(n){return f.Disj(t(n))})(function(n){return f.Disj(u(n))});return function(n){return e(i(n))}}}}},_=function(n){return function(r){return function(t){return function(u){var e=d.unwrap(d.newtypeConj),i=M(n)(o.monoidConj(r.HeytingAlgebra0()))(function(n){return o.Conj(t(n))})(function(n){return o.Conj(u(n))});return function(n){return e(i(n))}}}}};module.exports={bifoldMap:M,bifoldl:g,bifoldr:y,Bifoldable:b,bifoldrDefault:F,bifoldlDefault:E,bifoldMapDefaultR:q,bifoldMapDefaultL:x,bifold:A,bitraverse_:s,bifor_:D,bisequence_:j,biany:h,biall:_,bifoldableClown:m,bifoldableJoker:w,bifoldableFlip:v,bifoldableProduct:S,bifoldableWrap:C}; 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i.bipure};module.exports={bipure:t,Biapplicative:i}; +},{}],"X0ga":[function(require,module,exports) { +"use strict";var n=require("../Control.Category/index.js"),t=require("../Data.Bifunctor/index.js"),i=require("../Data.Function/index.js"),r=function(n,t){this.Bifunctor0=n,this.biapply=t},u=function(n){return n.biapply},e=function(r){return function(e){return function(o){return u(r)(n.identity(n.categoryFn)(t.bimap(r.Bifunctor0())(i.const(n.identity(n.categoryFn)))(i.const(n.identity(n.categoryFn))))(e))(o)}}},o=function(r){return function(e){return function(o){return u(r)(n.identity(n.categoryFn)(t.bimap(r.Bifunctor0())(i.const)(i.const))(e))(o)}}},c=function(i){return function(r){return function(e){return function(o){return function(c){return u(i)(n.identity(n.categoryFn)(t.bimap(i.Bifunctor0())(r)(e))(o))(c)}}}}},f=function(i){return function(r){return function(e){return function(o){return function(c){return function(f){return u(i)(u(i)(n.identity(n.categoryFn)(t.bimap(i.Bifunctor0())(r)(e))(o))(c))(f)}}}}}};module.exports={biapply:u,Biapply:r,biapplyFirst:e,biapplySecond:o,bilift2:c,bilift3:f}; +},{"../Control.Category/index.js":"IAi2","../Data.Bifunctor/index.js":"e2Wc","../Data.Function/index.js":"ImXJ"}],"Wuz6":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),e=require("../Control.Biapplicative/index.js"),t=require("../Control.Biapply/index.js"),u=require("../Data.Bifunctor/index.js"),i=require("../Data.Functor/index.js"),o=require("../Data.Newtype/index.js"),c=require("../Data.Show/index.js"),p=function(n){return n},l=function(n){return new c.Show(function(r){return"(Clown "+c.show(n)(r)+")"})},f=function(n){return n},w=new o.Newtype(function(n){return n},p),a=new i.Functor(function(n){return function(n){return n}}),C=function(n){return n},s=function(n){return new u.Bifunctor(function(r){return function(e){return 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n=require("../Control.Biapplicative/index.js"),r=require("../Control.Biapply/index.js"),i=require("../Data.Bifunctor/index.js"),t=require("../Data.Functor/index.js"),e=require("../Data.Newtype/index.js"),u=require("../Data.Show/index.js"),o=function(n){return n},p=function(n){return new u.Show(function(r){return"(Flip "+u.show(n)(r)+")"})},c=function(n){return n},f=new e.Newtype(function(n){return n},o),a=function(n){return new t.Functor(function(r){return function(t){return i.lmap(n)(r)(t)}})},l=function(n){return n},w=function(n){return new i.Bifunctor(function(r){return function(t){return function(e){return i.bimap(n)(t)(r)(e)}}})},F=function(n){return new r.Biapply(function(){return w(n.Bifunctor0())},function(i){return function(t){return r.biapply(n)(i)(t)}})},s=function(r){return new n.Biapplicative(function(){return F(r.Biapply0())},function(i){return function(t){return n.bipure(r)(t)(i)}})};module.exports={Flip:o,newtypeFlip:f,eqFlip:l,ordFlip:c,showFlip:p,functorFlip:a,bifunctorFlip:w,biapplyFlip:F,biapplicativeFlip:s}; +},{"../Control.Biapplicative/index.js":"Sd0N","../Control.Biapply/index.js":"X0ga","../Data.Bifunctor/index.js":"e2Wc","../Data.Functor/index.js":"+0AE","../Data.Newtype/index.js":"lz8k","../Data.Show/index.js":"mFY7"}],"O/Oh":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),e=require("../Control.Biapplicative/index.js"),t=require("../Control.Biapply/index.js"),u=require("../Data.Bifunctor/index.js"),i=require("../Data.Functor/index.js"),o=require("../Data.Newtype/index.js"),c=require("../Data.Show/index.js"),p=function(n){return n},f=function(n){return new c.Show(function(r){return"(Joker "+c.show(n)(r)+")"})},a=function(n){return n},l=new o.Newtype(function(n){return n},p),s=function(n){return new i.Functor(function(r){return 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n=require("../Control.Biapplicative/index.js"),u=require("../Control.Biapply/index.js"),r=require("../Data.Bifunctor/index.js"),e=require("../Data.Eq/index.js"),t=require("../Data.Ord/index.js"),i=require("../Data.Ordering/index.js"),o=require("../Data.Show/index.js"),c=function(){function n(n,u){this.value0=n,this.value1=u}return n.create=function(u){return function(r){return new n(u,r)}},n}(),a=function(n){return function(u){return new o.Show(function(r){return"(Product "+o.show(n)(r.value0)+" "+o.show(u)(r.value1)+")"})}},f=function(n){return function(u){return new e.Eq(function(r){return function(t){return e.eq(n)(r.value0)(t.value0)&&e.eq(u)(r.value1)(t.value1)}})}},l=function(n){return function(u){return new t.Ord(function(){return f(n.Eq0())(u.Eq0())},function(r){return function(e){var o=t.compare(n)(r.value0)(e.value0);return o instanceof i.LT?i.LT.value:o instanceof i.GT?i.GT.value:t.compare(u)(r.value1)(e.value1)}})}},p=function(n){return function(u){return new r.Bifunctor(function(e){return function(t){return function(i){return new c(r.bimap(n)(e)(t)(i.value0),r.bimap(u)(e)(t)(i.value1))}}})}},v=function(n){return function(r){return new u.Biapply(function(){return p(n.Bifunctor0())(r.Bifunctor0())},function(e){return function(t){return new c(u.biapply(n)(e.value0)(t.value0),u.biapply(r)(e.value1)(t.value1))}})}},d=function(u){return function(r){return new n.Biapplicative(function(){return v(u.Biapply0())(r.Biapply0())},function(e){return function(t){return new c(n.bipure(u)(e)(t),n.bipure(r)(e)(t))}})}};module.exports={Product:c,eqProduct:f,ordProduct:l,showProduct:a,bifunctorProduct:p,biapplyProduct:v,biapplicativeProduct:d}; +},{"../Control.Biapplicative/index.js":"Sd0N","../Control.Biapply/index.js":"X0ga","../Data.Bifunctor/index.js":"e2Wc","../Data.Eq/index.js":"Pq4F","../Data.Ord/index.js":"r4Vb","../Data.Ordering/index.js":"5Eun","../Data.Show/index.js":"mFY7"}],"U78Q":[function(require,module,exports) { +"use strict";var n=require("../Control.Biapplicative/index.js"),r=require("../Control.Biapply/index.js"),t=require("../Data.Bifunctor/index.js"),e=require("../Data.Functor/index.js"),u=require("../Data.Newtype/index.js"),i=require("../Data.Show/index.js"),o=function(n){return n},p=function(n){return new i.Show(function(r){return"(Wrap "+i.show(n)(r)+")"})},a=function(n){return n},c=new u.Newtype(function(n){return n},o),f=function(n){return new e.Functor(function(r){return function(e){return t.rmap(n)(r)(e)}})},w=function(n){return n},l=function(n){return new t.Bifunctor(function(r){return function(e){return function(u){return t.bimap(n)(r)(e)(u)}}})},s=function(n){return new r.Biapply(function(){return l(n.Bifunctor0())},function(t){return function(e){return r.biapply(n)(t)(e)}})},W=function(r){return new n.Biapplicative(function(){return s(r.Biapply0())},function(t){return function(e){return n.bipure(r)(t)(e)}})};module.exports={Wrap:o,newtypeWrap:c,eqWrap:w,ordWrap:a,showWrap:p,functorWrap:f,bifunctorWrap:l,biapplyWrap:s,biapplicativeWrap:W}; +},{"../Control.Biapplicative/index.js":"Sd0N","../Control.Biapply/index.js":"X0ga","../Data.Bifunctor/index.js":"e2Wc","../Data.Functor/index.js":"+0AE","../Data.Newtype/index.js":"lz8k","../Data.Show/index.js":"mFY7"}],"oRQn":[function(require,module,exports) { +"use strict";exports.traverseArrayImpl=function(){function n(n){return[n]}function r(n){return function(r){return[n,r]}}function t(n){return function(r){return function(t){return[n,r,t]}}}function u(n){return function(r){return n.concat(r)}}return function(e){return function(c){return function(o){return function(f){return function(i){return function a(s,l){switch(l-s){case 0:return o([]);case 1:return c(n)(f(i[s]));case 2:return e(c(r)(f(i[s])))(f(i[s+1]));case 3:return e(e(c(t)(f(i[s])))(f(i[s+1])))(f(i[s+2]));default:var h=s+2*Math.floor((l-s)/4);return e(c(u)(a(s,h)))(a(h,l))}}(0,i.length)}}}}}}(); +},{}],"W/l6":[function(require,module,exports) { +"use strict";var e=require("../Control.Alt/index.js"),n=require("../Control.Alternative/index.js"),r=require("../Control.MonadZero/index.js"),t=require("../Control.Plus/index.js"),i=require("../Data.Maybe/index.js"),o=require("../Data.Monoid/index.js"),u=require("../Data.Newtype/index.js"),a=require("../Data.Semigroup/index.js"),s=require("../Data.Show/index.js"),d=function(e){return e},c=function(e){return new s.Show(function(n){return"First ("+s.show(i.showMaybe(e))(n)+")"})},F=new a.Semigroup(function(e){return function(n){return e instanceof i.Just?e:n}}),y=function(e){return i.ordMaybe(e)},f=i.ord1Maybe,l=new u.Newtype(function(e){return e},d),p=new o.Monoid(function(){return F},i.Nothing.value),b=i.monadMaybe,M=i.invariantMaybe,w=i.functorMaybe,q=i.extendMaybe,x=function(e){return i.eqMaybe(e)},m=i.eq1Maybe,j=function(e){return i.boundedMaybe(e)},v=i.bindMaybe,h=i.applyMaybe,D=i.applicativeMaybe,g=new e.Alt(function(){return w},a.append(F)),A=new t.Plus(function(){return g},o.mempty(p)),C=new n.Alternative(function(){return D},function(){return A}),S=new r.MonadZero(function(){return C},function(){return b});module.exports={First:d,newtypeFirst:l,eqFirst:x,eq1First:m,ordFirst:y,ord1First:f,boundedFirst:j,functorFirst:w,invariantFirst:M,applyFirst:h,applicativeFirst:D,bindFirst:v,monadFirst:b,extendFirst:q,showFirst:c,semigroupFirst:F,monoidFirst:p,altFirst:g,plusFirst:A,alternativeFirst:C,monadZeroFirst:S}; +},{"../Control.Alt/index.js":"lN+m","../Control.Alternative/index.js":"aHia","../Control.MonadZero/index.js":"lD5R","../Control.Plus/index.js":"oMBg","../Data.Maybe/index.js":"5mN7","../Data.Monoid/index.js":"TiEB","../Data.Newtype/index.js":"lz8k","../Data.Semigroup/index.js":"EsAJ","../Data.Show/index.js":"mFY7"}],"aQky":[function(require,module,exports) { +"use strict";var e=require("../Control.Alt/index.js"),n=require("../Control.Alternative/index.js"),t=require("../Control.MonadZero/index.js"),r=require("../Control.Plus/index.js"),a=require("../Data.Maybe/index.js"),o=require("../Data.Monoid/index.js"),i=require("../Data.Newtype/index.js"),u=require("../Data.Semigroup/index.js"),s=require("../Data.Show/index.js"),d=function(e){return e},c=function(e){return new s.Show(function(n){return"(Last "+s.show(a.showMaybe(e))(n)+")"})},l=new u.Semigroup(function(e){return function(n){if(n instanceof a.Just)return n;if(n instanceof a.Nothing)return e;throw new Error("Failed pattern match at Data.Maybe.Last (line 52, column 1 - line 54, column 36): "+[e.constructor.name,n.constructor.name])}}),L=function(e){return a.ordMaybe(e)},f=a.ord1Maybe,y=new i.Newtype(function(e){return e},d),p=new o.Monoid(function(){return l},a.Nothing.value),b=a.monadMaybe,M=a.invariantMaybe,w=a.functorMaybe,m=a.extendMaybe,q=function(e){return a.eqMaybe(e)},x=a.eq1Maybe,h=function(e){return a.boundedMaybe(e)},j=a.bindMaybe,v=a.applyMaybe,D=a.applicativeMaybe,g=new e.Alt(function(){return w},u.append(l)),A=new r.Plus(function(){return g},o.mempty(p)),C=new n.Alternative(function(){return D},function(){return A}),N=new t.MonadZero(function(){return C},function(){return b});module.exports={Last:d,newtypeLast:y,eqLast:q,eq1Last:x,ordLast:L,ord1Last:f,boundedLast:h,functorLast:w,invariantLast:M,applyLast:v,applicativeLast:D,bindLast:j,monadLast:b,extendLast:m,showLast:c,semigroupLast:l,monoidLast:p,altLast:g,plusLast:A,alternativeLast:C,monadZeroLast:N}; +},{"../Control.Alt/index.js":"lN+m","../Control.Alternative/index.js":"aHia","../Control.MonadZero/index.js":"lD5R","../Control.Plus/index.js":"oMBg","../Data.Maybe/index.js":"5mN7","../Data.Monoid/index.js":"TiEB","../Data.Newtype/index.js":"lz8k","../Data.Semigroup/index.js":"EsAJ","../Data.Show/index.js":"mFY7"}],"LbSr":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),t=require("../Control.Apply/index.js"),u=require("../Data.Functor/index.js"),e=function(n){return n},r=function(n){return n},c=function(n){return n},a=function(n){return n},i=new u.Functor(function(n){return function(t){return function(u){var e=c(t)(u);return{accum:e.accum,value:n(e.value)}}}}),o=new u.Functor(function(n){return function(t){return function(u){var e=a(t)(u);return{accum:e.accum,value:n(e.value)}}}}),f=new t.Apply(function(){return i},function(n){return function(t){return function(u){var e=c(t)(u),r=c(n)(e.accum);return{accum:r.accum,value:r.value(e.value)}}}}),l=new t.Apply(function(){return o},function(n){return function(t){return function(u){var e=a(n)(u),r=a(t)(e.accum);return{accum:r.accum,value:e.value(r.value)}}}}),v=new n.Applicative(function(){return f},function(n){return function(t){return{accum:t,value:n}}}),p=new n.Applicative(function(){return l},function(n){return function(t){return{accum:t,value:n}}});module.exports={StateL:r,stateL:a,StateR:e,stateR:c,functorStateL:o,applyStateL:l,applicativeStateL:p,functorStateR:i,applyStateR:f,applicativeStateR:v}; +},{"../Control.Applicative/index.js":"qYya","../Control.Apply/index.js":"QcLv","../Data.Functor/index.js":"+0AE"}],"n7EE":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Control.Applicative/index.js"),t=require("../Control.Apply/index.js"),u=require("../Control.Category/index.js"),e=require("../Data.Foldable/index.js"),i=require("../Data.Functor/index.js"),o=require("../Data.Maybe/index.js"),c=require("../Data.Maybe.First/index.js"),a=require("../Data.Maybe.Last/index.js"),f=require("../Data.Monoid.Additive/index.js"),l=require("../Data.Monoid.Conj/index.js"),p=require("../Data.Monoid.Disj/index.js"),s=require("../Data.Monoid.Dual/index.js"),d=require("../Data.Monoid.Multiplicative/index.js"),v=require("../Data.Traversable.Accum.Internal/index.js"),m=function(n,r,t,u){this.Foldable1=n,this.Functor0=r,this.sequence=t,this.traverse=u},y=function(n){return n.traverse},A=new m(function(){return e.foldableMultiplicative},function(){return d.functorMultiplicative},function(n){return function(r){return i.map(n.Apply0().Functor0())(d.Multiplicative)(r)}},function(n){return function(r){return function(t){return 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n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),t=require("../Control.Category/index.js"),u=require("../Data.Bifoldable/index.js"),e=require("../Data.Bifunctor/index.js"),i=require("../Data.Bifunctor.Clown/index.js"),o=require("../Data.Bifunctor.Flip/index.js"),c=require("../Data.Bifunctor.Joker/index.js"),f=require("../Data.Bifunctor.Product/index.js"),a=require("../Data.Bifunctor.Wrap/index.js"),l=require("../Data.Functor/index.js"),p=require("../Data.Traversable/index.js"),b=function(n,r,t,u){this.Bifoldable1=n,this.Bifunctor0=r,this.bisequence=t,this.bitraverse=u},s=function(n){return n.bitraverse},d=function(r){return function(t){return function(u){return function(e){return s(r)(t)(e)(n.pure(t))(u)}}}},F=function(r){return function(t){return function(u){return s(r)(t)(u)(n.pure(t))}}},v=function(r){return function(t){return function(u){return function(e){return s(r)(t)(n.pure(t))(e)(u)}}}},y=function(r){return function(t){return 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n=require("../Data.FoldableWithIndex/index.js"),t=require("../Data.Function/index.js"),r=require("../Data.FunctorWithIndex/index.js"),e=require("../Data.Traversable/index.js"),u=require("../Data.Traversable.Accum.Internal/index.js"),i=require("../Data.Unit/index.js"),a=function(n,t,r,e){this.FoldableWithIndex1=n,this.FunctorWithIndex0=t,this.Traversable2=r,this.traverseWithIndex=e},c=function(n){return function(t){return function(u){var i=e.sequence(n.Traversable2())(t),a=r.mapWithIndex(n.FunctorWithIndex0())(u);return function(n){return i(a(n))}}}},o=function(n){return n.traverseWithIndex},f=function(n){return function(r){return function(e){return o(n)(r)(t.const(e))}}},l=new a(function(){return n.foldableWithIndexMultiplicative},function(){return r.functorWithIndexMultiplicative},function(){return e.traversableMultiplicative},function(n){return function(t){return e.traverse(e.traversableMultiplicative)(n)(t(i.unit))}}),s=new a(function(){return 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function(t){return e.traverse(e.traversableDisj)(n)(t(i.unit))}}),h=new a(function(){return n.foldableWithIndexConj},function(){return r.functorWithIndexConj},function(){return e.traversableConj},function(n){return function(t){return e.traverse(e.traversableConj)(n)(t(i.unit))}}),I=new a(function(){return n.foldableWithIndexArray},function(){return r.functorWithIndexArray},function(){return e.traversableArray},function(n){return c(I)(n)}),W=new a(function(){return n.foldableWithIndexAdditive},function(){return r.functorWithIndexAdditive},function(){return e.traversableAdditive},function(n){return function(t){return e.traverse(e.traversableAdditive)(n)(t(i.unit))}}),D=function(n){return function(t){return function(r){return function(e){return u.stateR(o(n)(u.applicativeStateR)(function(n){return function(r){return function(e){return t(n)(e)(r)}}})(e))(r)}}}},j=function(n){return function(t){return function(r){return function(e){return D(n)(function(n){return function(r){return 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instanceof I)return new I(t(e.value0));throw new Error("Failed pattern match at Data.Either (line 46, column 1 - line 48, column 36): "+[n.constructor.name,t.constructor.name,e.constructor.name])}}}),$=new i.Bifoldable(function(n){return function(n){return function(t){return function(e){if(e instanceof A)return n(e.value0);if(e instanceof I)return t(e.value0);throw new Error("Failed pattern match at Data.Either (line 203, column 1 - line 209, column 32): "+[n.constructor.name,t.constructor.name,e.constructor.name])}}}},function(n){return function(t){return function(e){return function(r){if(r instanceof A)return n(e)(r.value0);if(r instanceof I)return t(e)(r.value0);throw new Error("Failed pattern match at Data.Either (line 203, column 1 - line 209, column 32): "+[n.constructor.name,t.constructor.name,e.constructor.name,r.constructor.name])}}}},function(n){return function(t){return function(e){return function(r){if(r instanceof A)return n(r.value0)(e);if(r instanceof I)return t(r.value0)(e);throw new Error("Failed pattern match at Data.Either (line 203, column 1 - line 209, column 32): "+[n.constructor.name,t.constructor.name,e.constructor.name,r.constructor.name])}}}}),_=new c.Bitraversable(function(){return $},function(){return Z},function(n){return function(t){if(t instanceof A)return d.map(n.Apply0().Functor0())(A.create)(t.value0);if(t instanceof I)return d.map(n.Apply0().Functor0())(I.create)(t.value0);throw new Error("Failed pattern match at Data.Either (line 221, column 1 - line 225, column 37): "+[t.constructor.name])}},function(n){return function(t){return function(e){return function(r){if(r instanceof A)return d.map(n.Apply0().Functor0())(A.create)(t(r.value0));if(r instanceof I)return d.map(n.Apply0().Functor0())(I.create)(e(r.value0));throw new Error("Failed pattern match at Data.Either (line 221, column 1 - line 225, column 37): "+[t.constructor.name,e.constructor.name,r.constructor.name])}}}}),nn=new e.Apply(function(){return C},function(n){return function(t){if(n instanceof A)return new A(n.value0);if(n instanceof I)return d.map(C)(n.value0)(t);throw new Error("Failed pattern match at Data.Either (line 82, column 1 - line 84, column 30): "+[n.constructor.name,t.constructor.name])}}),tn=new r.Bind(function(){return nn},K(function(n){return function(t){return new A(n)}})(function(n){return function(t){return t(n)}})),en=function(n){return new x.Semigroup(function(t){return function(r){return e.apply(nn)(d.map(C)(x.append(n))(t))(r)}})},rn=new t.Applicative(function(){return nn},I.create),un=new o.Monad(function(){return rn},function(){return tn}),on=new n.Alt(function(){return C},function(n){return function(t){return n instanceof 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strict";exports.pureE=function(n){return function(){return n}},exports.bindE=function(n){return function(r){return function(){return r(n())()}}},exports.untilE=function(n){return function(){for(;!n(););return{}}},exports.whileE=function(n){return function(r){return function(){for(;n();)r();return{}}}},exports.forE=function(n){return function(r){return function(t){return function(){for(var u=n;u<r;u++)t(u)()}}}},exports.foreachE=function(n){return function(r){return function(){for(var t=0,u=n.length;t<u;t++)r(n[t])()}}}; +},{}],"oTWB":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),i=require("../Control.Bind/index.js"),t=require("../Control.Monad/index.js"),o=require("../Data.Functor/index.js"),u=require("../Data.Monoid/index.js"),f=require("../Data.Semigroup/index.js"),c=new t.Monad(function(){return d},function(){return p}),p=new i.Bind(function(){return 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r.message},exports.name=function(r){return r.name||"Error"},exports.stackImpl=function(r){return function(t){return function(n){return n.stack?r(n.stack):t}}},exports.throwException=function(r){return function(){throw r}},exports.catchException=function(r){return function(t){return function(){try{return t()}catch(n){return n instanceof Error||"[object Error]"===Object.prototype.toString.call(n)?r(n)():r(new Error(n.toString()))()}}}}; +},{}],"0OCW":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),r=require("../Control.Applicative/index.js"),t=require("../Data.Either/index.js"),i=require("../Data.Functor/index.js"),o=require("../Data.Maybe/index.js"),n=require("../Data.Show/index.js"),a=require("../Effect/index.js"),c=function(o){return e.catchException((n=r.pure(a.applicativeEffect),function(e){return n(t.Left.create(e))}))(i.map(a.functorEffect)(t.Right.create)(o));var n},u=function(r){return e.throwException(e.error(r))},s=e.stackImpl(o.Just.create)(o.Nothing.value),p=new n.Show(e.showErrorImpl);module.exports={stack:s,throw:u,try:c,showError:p,error:e.error,message:e.message,name:e.name,throwException:e.throwException,catchException:e.catchException}; +},{"./foreign.js":"OvLS","../Control.Applicative/index.js":"qYya","../Data.Either/index.js":"B2JL","../Data.Functor/index.js":"+0AE","../Data.Maybe/index.js":"5mN7","../Data.Show/index.js":"mFY7","../Effect/index.js":"oTWB"}],"L8Lk":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Bind/index.js"),t=require("../Data.Either/index.js"),o=require("../Data.Function/index.js"),e=require("../Data.Functor/index.js"),i=require("../Data.Maybe/index.js"),u=require("../Data.Unit/index.js"),a=require("../Effect/index.js"),c=require("../Effect.Exception/index.js"),f=function(n,r){this.Monad0=n,this.throwError=r},d=function(n,r){this.MonadThrow0=n,this.catchError=r},h=function(n){return n.throwError},s=new f(function(){return i.monadMaybe},o.const(i.Nothing.value)),l=new f(function(){return t.monadEither},t.Left.create),w=new f(function(){return a.monadEffect},c.throwException),E=new d(function(){return s},function(n){return function(r){if(n instanceof i.Nothing)return r(u.unit);if(n instanceof i.Just)return new i.Just(n.value0);throw new Error("Failed pattern match at Control.Monad.Error.Class (line 79, column 1 - line 81, column 33): "+[n.constructor.name,r.constructor.name])}}),m=new d(function(){return l},function(n){return function(r){if(n instanceof t.Left)return r(n.value0);if(n instanceof t.Right)return new t.Right(n.value0);throw new Error("Failed pattern match at Control.Monad.Error.Class (line 72, column 1 - line 74, column 35): "+[n.constructor.name,r.constructor.name])}}),M=new d(function(){return w},o.flip(c.catchException)),p=function(n){return n.catchError},x=function(n){return function(r){return function(t){return function(o){return p(n)(t)(function(t){var e=r(t);if(e instanceof i.Nothing)return h(n.MonadThrow0())(t);if(e instanceof i.Just)return o(e.value0);throw new Error("Failed pattern match at Control.Monad.Error.Class (line 57, column 5 - line 59, column 26): "+[e.constructor.name])})}}}},T=function(r){return function(o){return p(r)(e.map(r.MonadThrow0().Monad0().Bind1().Apply0().Functor0())(t.Right.create)(o))((i=n.pure(r.MonadThrow0().Monad0().Applicative0()),function(n){return i(t.Left.create(n))}));var i}},v=function(o){return function(e){return function(i){return function(u){return r.bind(o.MonadThrow0().Monad0().Bind1())(e)(function(e){return r.bind(o.MonadThrow0().Monad0().Bind1())(T(o)(u(e)))(function(u){return r.discard(r.discardUnit)(o.MonadThrow0().Monad0().Bind1())(i(e))(function(){return t.either(h(o.MonadThrow0()))(n.pure(o.MonadThrow0().Monad0().Applicative0()))(u)})})})}}}};module.exports={catchError:p,throwError:h,MonadThrow:f,MonadError:d,catchJust:x,try:T,withResource:v,monadThrowEither:l,monadErrorEither:m,monadThrowMaybe:s,monadErrorMaybe:E,monadThrowEffect:w,monadErrorEffect:M}; +},{"../Control.Applicative/index.js":"qYya","../Control.Bind/index.js":"7VcT","../Data.Either/index.js":"B2JL","../Data.Function/index.js":"ImXJ","../Data.Functor/index.js":"+0AE","../Data.Maybe/index.js":"5mN7","../Data.Unit/index.js":"NhVk","../Effect/index.js":"oTWB","../Effect.Exception/index.js":"0OCW"}],"c2ZJ":[function(require,module,exports) { +"use strict";var n=require("../Control.Category/index.js"),o=require("../Control.Monad/index.js"),e=require("../Control.Semigroupoid/index.js"),r=require("../Data.Functor/index.js"),t=function(n,o){this.Monad0=n,this.ask=o},i=function(n,o){this.MonadAsk0=n,this.local=o},u=new t(function(){return o.monadFn},n.identity(n.categoryFn)),a=new i(function(){return u},e.composeFlipped(e.semigroupoidFn)),d=function(n){return n.local},s=function(n){return n.ask},c=function(n){return function(o){return r.map(n.Monad0().Bind1().Apply0().Functor0())(o)(s(n))}};module.exports={ask:s,local:d,MonadAsk:t,asks:c,MonadReader:i,monadAskFun:u,monadReaderFun:a}; +},{"../Control.Category/index.js":"IAi2","../Control.Monad/index.js":"U/Ix","../Control.Semigroupoid/index.js":"/riR","../Data.Functor/index.js":"+0AE"}],"U0zO":[function(require,module,exports) { +"use strict";var t=function(t,e){this.Extend0=t,this.extract=e},e=function(t){return t.extract};module.exports={Comonad:t,extract:e}; +},{}],"fhx3":[function(require,module,exports) { +"use strict";var n=require("../Data.Bounded/index.js"),e=require("../Data.Monoid/index.js"),r=require("../Data.Newtype/index.js"),t=require("../Data.Ord/index.js"),u=require("../Data.Semigroup/index.js"),o=require("../Data.Show/index.js"),i=function(n){return n},a=function(n){return new o.Show(function(e){return"(Max "+o.show(n)(e)+")"})},c=function(n){return new u.Semigroup(function(e){return function(r){return t.max(n)(e)(r)}})},d=new r.Newtype(function(n){return n},i),x=function(r){return new e.Monoid(function(){return c(r.Ord0())},n.bottom(r))},f=function(n){return n},s=function(n){return new t.Ord(function(){return f(n.Eq0())},function(e){return function(r){return t.compare(n)(e)(r)}})};module.exports={Max:i,newtypeMax:d,eqMax:f,ordMax:s,semigroupMax:c,monoidMax:x,showMax:a}; 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i.compare(n)(e)(r)}})};module.exports={Min:o,newtypeMin:a,eqMin:s,ordMin:w,semigroupMin:d,monoidMin:f,showMin:c}; +},{"../Data.Bounded/index.js":"kcUU","../Data.Monoid/index.js":"TiEB","../Data.Newtype/index.js":"lz8k","../Data.Ord/index.js":"r4Vb","../Data.Semigroup/index.js":"EsAJ","../Data.Show/index.js":"mFY7"}],"ht+A":[function(require,module,exports) { +"use strict";var n=require("../Control.Apply/index.js"),t=require("../Control.Category/index.js"),r=require("../Data.Foldable/index.js"),u=require("../Data.Function/index.js"),e=require("../Data.Functor/index.js"),i=require("../Data.Newtype/index.js"),o=require("../Data.Ord.Max/index.js"),f=require("../Data.Ord.Min/index.js"),c=require("../Data.Semigroup/index.js"),a=require("../Data.Unit/index.js"),l=function(n){return n},d=function(n){return n},p=function(n,t,r){this.Foldable0=n,this.fold1=t,this.foldMap1=r},s=function(n){return new c.Semigroup(function(t){return function(r){return l(function(u){return 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n=require("../Control.Alt/index.js"),t=require("../Control.Applicative/index.js"),e=require("../Control.Apply/index.js"),r=require("../Control.Bind/index.js"),u=require("../Control.Comonad/index.js"),i=require("../Control.Extend/index.js"),o=require("../Control.Monad/index.js"),c=require("../Data.Eq/index.js"),d=require("../Data.Foldable/index.js"),f=require("../Data.FoldableWithIndex/index.js"),a=require("../Data.Functor/index.js"),l=require("../Data.Functor.Invariant/index.js"),y=require("../Data.FunctorWithIndex/index.js"),I=require("../Data.Newtype/index.js"),s=require("../Data.Ord/index.js"),x=require("../Data.Semigroup.Foldable/index.js"),p=require("../Data.Semigroup.Traversable/index.js"),w=require("../Data.Show/index.js"),q=require("../Data.Traversable/index.js"),b=require("../Data.TraversableWithIndex/index.js"),j=require("../Data.Unit/index.js"),m=function(n){return n},v=function(n){return new w.Show(function(t){return"(Identity "+w.show(n)(t)+")"})},F=function(n){return 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n.value}},exports["modify'"]=function(n){return function(t){return function(){var r=n(t.value);return t.value=r.state,r.value}}},exports.write=function(n){return function(t){return function(){return t.value=n,{}}}}; +},{}],"/Jaj":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),r=require("../Data.Functor/index.js"),t=require("../Effect/index.js"),i=function(r){return e["modify'"](function(e){var t=r(e);return{state:t,value:t}})},n=function(e){return function(n){return r.void(t.functorEffect)(i(e)(n))}};module.exports={modify:i,modify_:n,new:e.new,read:e.read,"modify'":e["modify'"],write:e.write}; +},{"./foreign.js":"bagd","../Data.Functor/index.js":"+0AE","../Effect/index.js":"oTWB"}],"UVIy":[function(require,module,exports) { +"use strict";var n=require("../Control.Bind/index.js"),t=require("../Control.Monad/index.js"),e=require("../Data.Bifunctor/index.js"),r=require("../Data.Either/index.js"),u=require("../Data.Functor/index.js"),o=require("../Data.Identity/index.js"),i=require("../Data.Maybe/index.js"),c=require("../Data.Unit/index.js"),a=require("../Effect/index.js"),f=require("../Effect.Ref/index.js"),l=function(){function n(n){this.value0=n}return n.create=function(t){return new n(t)},n}(),s=function(){function n(n){this.value0=n}return n.create=function(t){return new n(t)},n}(),d=function(n,t){this.Monad0=n,this.tailRecM=t},m=function(n){return n.tailRecM},w=function(n){return function(t){return function(e){return function(r){return m(n)(function(n){return t(n.a)(n.b)})({a:e,b:r})}}}},v=function(n){return function(t){return function(e){return function(r){return function(u){return m(n)(function(n){return t(n.a)(n.b)(n.c)})({a:e,b:r,c:u})}}}}},h=function(n){return function(t){return function(t){var e,r=!1;function 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r.monadEither},function(n){return function(t){return h(function(t){if(t instanceof r.Left)return new s(new r.Left(t.value0));if(t instanceof r.Right&&t.value0 instanceof l)return new l(n(t.value0.value0));if(t instanceof r.Right&&t.value0 instanceof s)return new s(new r.Right(t.value0.value0));throw new Error("Failed pattern match at Control.Monad.Rec.Class (line 119, column 7 - line 119, column 33): "+[t.constructor.name])})(n(t))}}),E=new d(function(){return a.monadEffect},function(t){return function(e){var r=function(n){if(n instanceof s)return n.value0;throw new Error("Failed pattern match at Control.Monad.Rec.Class (line 111, column 30 - line 111, column 44): "+[n.constructor.name])};return function(){var o=n.bindFlipped(a.bindEffect)(f.new)(t(e))();return function(){for(;!function(){var n=f.read(o)();if(n instanceof l){var e=t(n.value0)();f.write(e)(o)();return!1}if(n instanceof s)return!0;throw new Error("Failed pattern match at Control.Monad.Rec.Class (line 102, column 22 - line 107, column 28): "+[n.constructor.name])}(););}(),u.map(a.functorEffect)(r)(f.read(o))()}}}),F=new u.Functor(function(n){return function(t){if(t instanceof l)return new l(t.value0);if(t instanceof s)return new s(n(t.value0));throw new Error("Failed pattern match at Control.Monad.Rec.Class (line 25, column 1 - line 25, column 48): "+[t.constructor.name])}}),x=function(n){return function(t){return m(n)(function(e){return u.voidRight(n.Monad0().Bind1().Apply0().Functor0())(new l(e))(t)})(c.unit)}},b=new e.Bifunctor(function(n){return function(t){return function(e){if(e instanceof l)return new l(n(e.value0));if(e instanceof s)return new s(t(e.value0));throw new Error("Failed pattern match at Control.Monad.Rec.Class (line 27, column 1 - line 29, column 34): 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r}};module.exports={defer:u,Lazy:t,fix:i,lazyFn:e,lazyUnit:r}; +},{"../Data.Unit/index.js":"NhVk"}],"e7y+":[function(require,module,exports) { +"use strict";var n=require("../Data.HeytingAlgebra/index.js"),e=function(n){this.HeytingAlgebraRecord0=n},r=function(n){this.HeytingAlgebra0=n},o=new r(function(){return n.heytingAlgebraUnit}),t=new e(function(){return n.heytingAlgebraRecordNil}),i=function(r){return function(o){return function(t){return function(i){return new e(function(){return n.heytingAlgebraRecordCons(r)(o)(t.HeytingAlgebraRecord0())(i.HeytingAlgebra0())})}}}},a=function(e){return function(o){return new r(function(){return n.heytingAlgebraRecord(e)(o.HeytingAlgebraRecord0())})}},g=function(e){return new r(function(){return n.heytingAlgebraFunction(e.HeytingAlgebra0())})},l=new r(function(){return 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n=require("../Control.Applicative/index.js"),e=require("../Control.Bind/index.js"),t=require("../Data.Tuple/index.js"),i=function(n,e){this.Monad0=n,this.tell=e},r=function(n,e,t){this.MonadTell0=n,this.listen=e,this.pass=t},u=function(n){return n.tell},l=function(n){return n.pass},o=function(n){return n.listen},a=function(i){return function(r){return function(u){return e.bind(i.MonadTell0().Monad0().Bind1())(o(i)(u))(function(e){return n.pure(i.MonadTell0().Monad0().Applicative0())(new t.Tuple(e.value0,r(e.value1)))})}}},s=function(i){return function(r){return function(u){return l(i)(e.bind(i.MonadTell0().Monad0().Bind1())(u)(function(e){return n.pure(i.MonadTell0().Monad0().Applicative0())(new t.Tuple(e,r))}))}}};module.exports={listen:o,pass:l,tell:u,MonadTell:i,MonadWriter:r,listens:a,censor:s}; +},{"../Control.Applicative/index.js":"qYya","../Control.Bind/index.js":"7VcT","../Data.Tuple/index.js":"II/O"}],"HkJx":[function(require,module,exports) { +"use strict";var r=require("../Control.MonadZero/index.js"),o=function(r){this.MonadZero0=r},n=new o(function(){return r.monadZeroArray});module.exports={MonadPlus:o,monadPlusArray:n}; +},{"../Control.MonadZero/index.js":"lD5R"}],"dWtH":[function(require,module,exports) { +"use strict";var t=require("../Control.Category/index.js"),e=require("../Effect/index.js"),f=function(t,e){this.Monad0=t,this.liftEffect=e},n=new f(function(){return e.monadEffect},t.identity(t.categoryFn)),i=function(t){return t.liftEffect};module.exports={liftEffect:i,MonadEffect:f,monadEffectEffect:n}; +},{"../Control.Category/index.js":"IAi2","../Effect/index.js":"oTWB"}],"gr8B":[function(require,module,exports) { +"use strict";var n=require("../Control.Alt/index.js"),e=require("../Control.Alternative/index.js"),t=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),o=require("../Control.Category/index.js"),i=require("../Control.Monad/index.js"),a=require("../Control.Monad.Cont.Class/index.js"),c=require("../Control.Monad.Error.Class/index.js"),f=require("../Control.Monad.Reader.Class/index.js"),l=require("../Control.Monad.Rec.Class/index.js"),d=require("../Control.Monad.State.Class/index.js"),p=require("../Control.Monad.Trans.Class/index.js"),s=require("../Control.Monad.Writer.Class/index.js"),x=require("../Control.MonadPlus/index.js"),w=require("../Control.MonadZero/index.js"),M=require("../Control.Plus/index.js"),v=require("../Data.Either/index.js"),E=require("../Data.Functor/index.js"),T=require("../Data.Monoid/index.js"),m=require("../Data.Newtype/index.js"),C=require("../Data.Semigroup/index.js"),h=require("../Data.Tuple/index.js"),j=require("../Effect.Class/index.js"),q=function(n){return 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+},{"../Control.Alt/index.js":"lN+m","../Control.Alternative/index.js":"aHia","../Control.Applicative/index.js":"qYya","../Control.Apply/index.js":"QcLv","../Control.Bind/index.js":"7VcT","../Control.Category/index.js":"IAi2","../Control.Monad/index.js":"U/Ix","../Control.Monad.Cont.Class/index.js":"IpNh","../Control.Monad.Error.Class/index.js":"L8Lk","../Control.Monad.Reader.Class/index.js":"c2ZJ","../Control.Monad.Rec.Class/index.js":"UVIy","../Control.Monad.State.Class/index.js":"u1pL","../Control.Monad.Trans.Class/index.js":"5tIR","../Control.Monad.Writer.Class/index.js":"gxgA","../Control.MonadPlus/index.js":"HkJx","../Control.MonadZero/index.js":"lD5R","../Control.Plus/index.js":"oMBg","../Data.Either/index.js":"B2JL","../Data.Functor/index.js":"+0AE","../Data.Monoid/index.js":"TiEB","../Data.Newtype/index.js":"lz8k","../Data.Semigroup/index.js":"EsAJ","../Data.Tuple/index.js":"II/O","../Effect.Class/index.js":"dWtH"}],"Fye2":[function(require,module,exports) { +"use strict";var t=require("../Control.Monad.Except.Trans/index.js"),e=require("../Data.Identity/index.js"),n=require("../Data.Newtype/index.js"),r=t.withExceptT(e.functorIdentity),i=function(){var r=n.unwrap(e.newtypeIdentity);return function(e){return r(t.runExceptT(e))}}(),u=function(r){return t.mapExceptT((i=n.unwrap(e.newtypeIdentity),function(t){return e.Identity(r(i(t)))}));var i};module.exports={runExcept:i,mapExcept:u,withExcept:r}; +},{"../Control.Monad.Except.Trans/index.js":"gr8B","../Data.Identity/index.js":"2OKT","../Data.Newtype/index.js":"lz8k"}],"TZDL":[function(require,module,exports) { +"use strict";exports.range=function(n){return function(r){for(var t=n>r?-1:1,e=new Array(t*(r-n)+1),u=n,o=0;u!==r;)e[o++]=u,u+=t;return e[o]=u,e}};var n=function(n){return function(r){return n<1?[]:new Array(n).fill(r)}},r=function(n){return function(r){for(var t=[],e=0,u=0;u<n;u++)t[e++]=r;return t}};exports.replicate="function"==typeof 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n=require("./foreign.js"),r=require("../Control.Applicative/index.js"),t=require("../Control.Bind/index.js"),e=require("../Control.Monad.ST.Internal/index.js"),u=require("../Data.Maybe/index.js"),i=require("../Data.Ord/index.js"),o=require("../Data.Ordering/index.js"),a=function(r){return n.unshiftAll([r])},c=function(){var n=r.pure(e.applicativeST);return function(r){return n(r)}}(),s=function(){var n=r.pure(e.applicativeST);return function(r){return n(r)}}(),l=n.copyImpl,f=function(n){return function(r){return function(){var t=l(r)();n(t)();return s(t)()}}},p=function(r){return n.sortByImpl(function(n){return function(t){var e=r(n)(t);if(e instanceof o.GT)return 1;if(e instanceof o.EQ)return 0;if(e instanceof o.LT)return-1;throw new Error("Failed pattern match at Data.Array.ST (line 109, column 15 - line 112, column 13): "+[e.constructor.name])}})},h=function(n){return function(r){return p(i.comparing(n)(r))}},m=function(n){return p(i.compare(n))},d=n.shiftImpl(u.Just.create)(u.Nothing.value),A=function(n){return t.bind(e.bindST)(n)(s)()},v=function(r){return n.pushAll([r])},y=n.popImpl(u.Just.create)(u.Nothing.value),T=n.peekImpl(u.Just.create)(u.Nothing.value),g=function(r){return function(t){return function(e){return function(){var i=T(r)(e)();if(i instanceof u.Just)return n.poke(r)(t(i.value0))(e)();if(i instanceof u.Nothing)return!1;throw new Error("Failed pattern match at Data.Array.ST (line 195, column 3 - line 197, column 26): "+[i.constructor.name])}}}},j=n.copyImpl;module.exports={run:A,withArray:f,peek:T,modify:g,pop:y,push:v,shift:d,unshift:a,sort:m,sortBy:p,sortWith:h,freeze:j,thaw:l,unsafeFreeze:s,unsafeThaw:c,empty:n.empty,poke:n.poke,pushAll:n.pushAll,unshiftAll:n.unshiftAll,splice:n.splice,toAssocArray:n.toAssocArray}; +},{"./foreign.js":"pEQc","../Control.Applicative/index.js":"qYya","../Control.Bind/index.js":"7VcT","../Control.Monad.ST.Internal/index.js":"Sedc","../Data.Maybe/index.js":"5mN7","../Data.Ord/index.js":"r4Vb","../Data.Ordering/index.js":"5Eun"}],"Wi7L":[function(require,module,exports) { +"use strict";var n=require("../Control.Monad.ST.Internal/index.js"),r=require("../Data.Array.ST/index.js"),t=require("../Data.Function/index.js"),e=require("../Data.Functor/index.js"),u=require("../Data.HeytingAlgebra/index.js"),a=require("../Data.Maybe/index.js"),i=function(){function n(n,r){this.value0=n,this.value1=r}return n.create=function(r){return function(t){return new n(r,t)}},n}(),o=function(r){return function(){var t=n.read(r.value1)();return r.value0(t)}},c=function(r){return function(){var t=n.read(r.value1)();n.modify(function(n){return n+1|0})(r.value1)();return r.value0(t)}},f=function(t){return function(i){return function(f){return function(){for(var l=n.new(!1)();e.map(n.functorST)(u.not(u.heytingAlgebraBoolean))(n.read(l))();)!function(){var u=o(i)();if(u instanceof a.Just&&t(u.value0)){r.push(u.value0)(f)();return e.void(n.functorST)(c(i))()}e.void(n.functorST)(n.write(!0)(l))()}();return{}}}}},l=f(t.const(!0)),s=function(r){return e.map(n.functorST)(i.create(r))(n.new(0))},v=function(r){return function(t){return function(){for(var i=n.new(!1)();e.map(n.functorST)(u.not(u.heytingAlgebraBoolean))(n.read(i))();)!function(){var u=c(r)();if(u instanceof a.Just)return t(u.value0)();if(u instanceof a.Nothing)return e.void(n.functorST)(n.write(!0)(i))();throw new Error("Failed pattern match at Data.Array.ST.Iterator (line 42, column 5 - line 44, column 47): "+[u.constructor.name])}();return{}}}},d=function(){var r=e.map(n.functorST)(a.isNothing);return function(n){return r(o(n))}}();module.exports={iterator:s,iterate:v,next:c,peek:o,exhausted:d,pushWhile:f,pushAll:l}; +},{"../Control.Monad.ST.Internal/index.js":"Sedc","../Data.Array.ST/index.js":"s8si","../Data.Function/index.js":"ImXJ","../Data.Functor/index.js":"+0AE","../Data.HeytingAlgebra/index.js":"paZe","../Data.Maybe/index.js":"5mN7"}],"v/61":[function(require,module,exports) { +"use strict";exports.unfoldrArrayImpl=function(r){return function(n){return function(t){return function(u){return function(f){return function(o){for(var e=[],i=o;;){var c=f(i);if(r(c))return e;var a=n(c);e.push(t(a)),i=u(a)}}}}}}}; +},{}],"rpkt":[function(require,module,exports) { +"use strict";exports.unfoldr1ArrayImpl=function(r){return function(n){return function(t){return function(u){return function(f){return function(o){for(var e=[],i=o;;){var c=f(i);e.push(t(c));var a=u(c);if(r(a))return e;i=n(a)}}}}}}}; +},{}],"S0Nl":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Data.Boolean/index.js"),e=require("../Data.Maybe/index.js"),t=require("../Data.Semigroup.Traversable/index.js"),u=require("../Data.Tuple/index.js"),i=function(n){this.unfoldr1=n},o=function(n){return n.unfoldr1},a=new i(n.unfoldr1ArrayImpl(e.isNothing)(e.fromJust())(u.fst)(u.snd)),f=function(n){return function(t){return function(i){return o(n)(function(n){if(n<=0)return new u.Tuple(i,e.Nothing.value);if(r.otherwise)return new u.Tuple(i,new e.Just(n-1|0));throw new Error("Failed pattern match at Data.Unfoldable1 (line 64, column 5 - line 64, column 39): "+[n.constructor.name])})(t-1|0)}}},l=function(n){return function(r){return function(e){return function(u){return function(i){return t.sequence1(e)(n)(f(r)(u)(i))}}}}},c=function(n){return f(n)(1)},s=function(n){return function(r){return function(t){var i=t>=r?1:-1;return o(n)(function(n){return function(r){var i=r+n|0;return new u.Tuple(r,r===t?e.Nothing.value:new e.Just(i))}}(i))(r)}}};module.exports={Unfoldable1:i,unfoldr1:o,replicate1:f,replicate1A:l,singleton:c,range:s,unfoldable1Array:a}; +},{"./foreign.js":"rpkt","../Data.Boolean/index.js":"ObQr","../Data.Maybe/index.js":"5mN7","../Data.Semigroup.Traversable/index.js":"qkfi","../Data.Tuple/index.js":"II/O"}],"77+Z":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),e=require("../Data.Function/index.js"),r=require("../Data.Functor/index.js"),u=require("../Data.Maybe/index.js"),t=require("../Data.Traversable/index.js"),i=require("../Data.Tuple/index.js"),o=require("../Data.Unfoldable1/index.js"),a=require("../Data.Unit/index.js"),f=function(n,e){this.Unfoldable10=n,this.unfoldr=e},l=function(n){return n.unfoldr},c=new f(function(){return o.unfoldable1Array},n.unfoldrArrayImpl(u.isNothing)(u.fromJust())(i.fst)(i.snd)),s=function(n){return function(e){return function(r){return l(n)(function(n){return n<=0?u.Nothing.value:new u.Just(new i.Tuple(r,n-1|0))})(e)}}},d=function(n){return function(e){return function(r){return function(u){return function(i){return t.sequence(r)(n)(s(e)(u)(i))}}}}},b=function(n){return l(n)(e.const(u.Nothing.value))(a.unit)},p=function(n){return l(n)(function(n){return r.map(u.functorMaybe)(e.flip(i.Tuple.create)(u.Nothing.value))(n)})};module.exports={Unfoldable:f,unfoldr:l,replicate:s,replicateA:d,none:b,fromMaybe:p,unfoldableArray:c}; +},{"./foreign.js":"v/61","../Data.Function/index.js":"ImXJ","../Data.Functor/index.js":"+0AE","../Data.Maybe/index.js":"5mN7","../Data.Traversable/index.js":"n7EE","../Data.Tuple/index.js":"II/O","../Data.Unfoldable1/index.js":"S0Nl","../Data.Unit/index.js":"NhVk"}],"4t4C":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Control.Alt/index.js"),t=require("../Control.Applicative/index.js"),e=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),i=require("../Control.Category/index.js"),o=require("../Control.Lazy/index.js"),a=require("../Control.Monad.Rec.Class/index.js"),c=require("../Control.Monad.ST.Internal/index.js"),f=require("../Data.Array.ST/index.js"),l=require("../Data.Array.ST.Iterator/index.js"),s=require("../Data.Boolean/index.js"),p=require("../Data.Eq/index.js"),d=require("../Data.Foldable/index.js"),h=require("../Data.Function/index.js"),m=require("../Data.Functor/index.js"),v=require("../Data.HeytingAlgebra/index.js"),y=require("../Data.Maybe/index.js"),g=require("../Data.Ord/index.js"),A=require("../Data.Ordering/index.js"),q=require("../Data.Semigroup/index.js"),x=require("../Data.Traversable/index.js"),w=require("../Data.Tuple/index.js"),b=require("../Data.Unfoldable/index.js"),F=function(r){return function(t){return 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function(e){try{var o=n(e,u);return r(o)}catch(i){return t}}}}},exports["fromNumber'"]=function(t){return function(u){return function(e){try{var o=n(r(e));return t(o)}catch(i){return u}}}},exports.fromInt=function(r){return n(r)},exports.toBase=function(n){return function(r){return r.toString(n)}},exports.toNumber=function(n){return n.toJSNumber()},exports.biAdd=function(n){return function(r){return n.add(r)}},exports.biMul=function(n){return function(r){return n.multiply(r)}},exports.biSub=function(n){return function(r){return n.minus(r)}},exports.biMod=function(n){return function(r){return n.mod(r)}},exports.biDiv=function(n){return function(r){return n.divide(r)}},exports.biEquals=function(n){return function(r){return n.equals(r)}},exports.biCompare=function(n){return function(r){return n.compare(r)}},exports.abs=function(n){return n.abs()},exports.even=function(n){return n.isEven()},exports.odd=function(n){return n.isOdd()},exports.prime=function(n){return 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s.foldMap1(n(e))(r)(t.identity(t.categoryFn))},function(n){return function(r){return function(t){return i.foldl(e)(function(e){return function(t){return v.append(n)(e)(r(t))}})(r(t.value0))(t.value1)}}})},U=function(n){return function(e){return new o.Eq(function(r){return function(t){return o.eq(e)(r.value0)(t.value0)&&o.eq1(n)(e)(r.value1)(t.value1)}})}},G=function(n){return function(e){return new d.Ord(function(){return U(n.Eq10())(e.Eq0())},function(r){return function(t){var u=d.compare(e)(r.value0)(t.value0);return u instanceof p.LT?p.LT.value:u instanceof p.GT?p.GT.value:d.compare1(n)(e)(r.value1)(t.value1)}})}},L=function(n){return new o.Eq1(function(e){return o.eq(U(n)(e))})},P=function(n){return new d.Ord1(function(){return L(n.Eq10())},function(e){return 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n=require("../Control.Alt/index.js"),e=require("../Control.Alternative/index.js"),t=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),i=require("../Control.Category/index.js"),o=require("../Control.Comonad/index.js"),a=require("../Control.Extend/index.js"),l=require("../Control.Monad/index.js"),c=require("../Control.MonadPlus/index.js"),f=require("../Control.MonadZero/index.js"),v=require("../Control.Plus/index.js"),s=require("../Data.Eq/index.js"),d=require("../Data.Foldable/index.js"),p=require("../Data.FoldableWithIndex/index.js"),m=require("../Data.Function/index.js"),w=require("../Data.Functor/index.js"),y=require("../Data.FunctorWithIndex/index.js"),x=require("../Data.Maybe/index.js"),E=require("../Data.Monoid/index.js"),L=require("../Data.Newtype/index.js"),h=require("../Data.NonEmpty/index.js"),N=require("../Data.Ord/index.js"),b=require("../Data.Ordering/index.js"),q=require("../Data.Semigroup/index.js"),j=require("../Data.Semigroup.Traversable/index.js"),I=require("../Data.Semiring/index.js"),D=require("../Data.Show/index.js"),W=require("../Data.Traversable/index.js"),F=require("../Data.TraversableWithIndex/index.js"),T=require("../Data.Tuple/index.js"),g=require("../Data.Unfoldable/index.js"),C=require("../Data.Unfoldable1/index.js"),A=function(){function 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function(e){return function(t){var r;return(r=e,function(e){return function(t){for(var u,i,o,a,l=r,c=e,f=!1;!f;)i=l,o=c,u=(a=t)?i instanceof A&&o instanceof A?(f=!0,a):i instanceof M&&o instanceof M?(l=i.value1,c=o.value1,void(t=a&&s.eq(n)(o.value0)(i.value0))):(f=!0,!1):(f=!0,!1);return u}})(t)(!0)}}}),vn=function(n){return new s.Eq(s.eq1(fn)(n))},sn=function(n){return h.eqNonEmpty(fn)(n)},dn=new N.Ord1(function(){return fn},function(n){return function(e){return function(t){var r;return(r=e,function(e){var t,u=r,i=!1;function o(t,r){if(t instanceof A&&r instanceof A)return i=!0,b.EQ.value;if(t instanceof A)return i=!0,b.LT.value;if(r instanceof A)return i=!0,b.GT.value;if(t instanceof M&&r instanceof M){var o=N.compare(n)(t.value0)(r.value0);return o instanceof b.EQ?(u=t.value1,void(e=r.value1)):(i=!0,o)}throw new Error("Failed pattern match at Data.List.Types (line 61, column 5 - line 61, column 20): "+[t.constructor.name,r.constructor.name])}for(;!i;)t=o(u,e);return t})(t)}}}),pn=function(n){return new N.Ord(function(){return vn(n.Eq0())},N.compare1(dn)(n))},mn=function(n){return h.ordNonEmpty(dn)(n)},wn=new o.Comonad(function(){return ln},function(n){return n.value0}),yn=new r.Apply(function(){return Z},function(n){return function(e){if(n instanceof A)return A.value;if(n instanceof M)return q.append(R)(w.map(Z)(n.value0)(e))(r.apply(yn)(n.value1)(e));throw new Error("Failed pattern match at Data.List.Types (line 155, column 1 - line 157, column 48): "+[n.constructor.name,e.constructor.name])}}),xn=new r.Apply(function(){return J},function(n){return function(e){return new h.NonEmpty(n.value0(e.value0),q.append(R)(r.apply(yn)(n.value1)(new M(e.value0,A.value)))(r.apply(yn)(new M(n.value0,n.value1))(e.value1)))}}),En=new u.Bind(function(){return yn},function(n){return function(e){if(n instanceof A)return A.value;if(n instanceof M)return q.append(R)(e(n.value0))(u.bind(En)(n.value1)(e));throw new Error("Failed pattern match at Data.List.Types (line 162, column 1 - line 164, column 37): "+[n.constructor.name,e.constructor.name])}}),Ln=new u.Bind(function(){return xn},function(n){return function(e){var t=e(n.value0);return new h.NonEmpty(t.value0,q.append(R)(t.value1)(u.bind(En)(n.value1)(function(n){return P(e(n))})))}}),hn=new t.Applicative(function(){return yn},function(n){return new M(n,A.value)}),Nn=new l.Monad(function(){return hn},function(){return En}),bn=new n.Alt(function(){return J},q.append(X)),qn=new n.Alt(function(){return Z},q.append(R)),jn=new v.Plus(function(){return qn},A.value),In=new e.Alternative(function(){return hn},function(){return jn}),Dn=new f.MonadZero(function(){return In},function(){return Nn}),Wn=new c.MonadPlus(function(){return Dn}),Fn=new t.Applicative(function(){return xn},function(){var n=h.singleton(jn);return function(e){return S(n(e))}}()),Tn=new l.Monad(function(){return Fn},function(){return Ln}),gn=new j.Traversable1(function(){return an},function(){return nn},function(n){return j.traverse1(gn)(n)(i.identity(i.categoryFn))},function(n){return function(e){return function(u){return w.mapFlipped(n.Functor0())(d.foldl(Q)(function(t){var u=r.lift2(n)(m.flip(U))(t);return function(n){return u(e(n))}})(w.map(n.Functor0())(t.pure(Fn))(e(u.value0)))(u.value1))(function(n){return d.foldl(Q)(m.flip(U))(t.pure(Fn)(n.value0))(n.value1)})}}});module.exports={Nil:A,Cons:M,NonEmptyList:S,toList:P,nelCons:U,showList:Y,eqList:vn,eq1List:fn,ordList:pn,ord1List:dn,semigroupList:R,monoidList:V,functorList:Z,functorWithIndexList:H,foldableList:Q,foldableWithIndexList:k,unfoldable1List:rn,unfoldableList:un,traversableList:_,traversableWithIndexList:en,applyList:yn,applicativeList:hn,bindList:En,monadList:Nn,altList:qn,plusList:jn,alternativeList:In,monadZeroList:Dn,monadPlusList:Wn,extendList:cn,newtypeNonEmptyList:O,eqNonEmptyList:sn,ordNonEmptyList:mn,showNonEmptyList:$,functorNonEmptyList:J,applyNonEmptyList:xn,applicativeNonEmptyList:Fn,bindNonEmptyList:Ln,monadNonEmptyList:Tn,altNonEmptyList:bn,extendNonEmptyList:ln,comonadNonEmptyList:wn,semigroupNonEmptyList:X,foldableNonEmptyList:G,traversableNonEmptyList:nn,foldable1NonEmptyList:an,unfoldable1NonEmptyList:on,functorWithIndexNonEmptyList:K,foldableWithIndexNonEmptyList:z,traversableWithIndexNonEmptyList:tn,traversable1NonEmptyList:gn}; 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{ +"use strict";var 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In});module.exports={List:C,Nil:M,Cons:S,step:Z,nil:U,cons:tn,NonEmptyList:P,toList:dn,newtypeList:B,showList:Q,eqList:X,eq1List:V,ordList:_,ord1List:$,lazyList:H,semigroupList:J,monoidList:k,functorList:K,functorWithIndexList:fn,foldableList:en,foldableWithIndexList:an,unfoldable1List:wn,unfoldableList:Ln,traversableList:pn,traversableWithIndexList:mn,applyList:Nn,applicativeList:qn,bindList:bn,monadList:En,altList:Fn,plusList:Wn,alternativeList:Tn,monadZeroList:zn,monadPlusList:gn,extendList:rn,newtypeNonEmptyList:O,eqNonEmptyList:Y,ordNonEmptyList:nn,showNonEmptyList:G,functorNonEmptyList:R,applyNonEmptyList:jn,applicativeNonEmptyList:An,bindNonEmptyList:In,monadNonEmptyList:Cn,altNonEmptyList:Dn,extendNonEmptyList:un,comonadNonEmptyList:hn,semigroupNonEmptyList:sn,foldableNonEmptyList:on,traversableNonEmptyList:vn,unfoldable1NonEmptyList:xn,functorWithIndexNonEmptyList:ln,foldableWithIndexNonEmptyList:cn,traversableWithIndexNonEmptyList:yn}; 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{ +"use strict";var n=require("../Control.Alt/index.js"),t=require("../Control.Applicative/index.js"),e=require("../Control.Apply/index.js"),r=require("../Control.Bind/index.js"),u=require("../Control.Category/index.js"),i=require("../Control.Lazy/index.js"),o=require("../Control.Monad.Rec.Class/index.js"),a=require("../Data.Boolean/index.js"),c=require("../Data.Eq/index.js"),l=require("../Data.Foldable/index.js"),f=require("../Data.Function/index.js"),s=require("../Data.Functor/index.js"),p=require("../Data.HeytingAlgebra/index.js"),m=require("../Data.Lazy/index.js"),v=require("../Data.List.Lazy.Types/index.js"),d=require("../Data.Maybe/index.js"),w=require("../Data.Newtype/index.js"),L=require("../Data.NonEmpty/index.js"),y=require("../Data.Ord/index.js"),h=require("../Data.Ordering/index.js"),z=require("../Data.Semigroup/index.js"),C=require("../Data.Show/index.js"),N=require("../Data.Traversable/index.js"),D=require("../Data.Tuple/index.js"),b=require("../Data.Unfoldable/index.js"),q=function(n){return 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t=require("../Control.Alt/index.js"),e=require("../Control.Alternative/index.js"),n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),a=require("../Control.Bind/index.js"),i=require("../Control.Plus/index.js"),u=require("../Data.Array/index.js"),o=require("../Data.Either/index.js"),l=require("../Data.Foldable/index.js"),c=require("../Data.Function/index.js"),f=require("../Data.Functor/index.js"),s=require("../Data.List/index.js"),m=require("../Data.List.Types/index.js"),p=require("../Data.Map.Internal/index.js"),h=require("../Data.Maybe/index.js"),v=require("../Data.Monoid/index.js"),d=require("../Data.Unit/index.js"),w=function(t,e){this.compact=t,this.separate=e},g=function(e){return function(r){return function(a){return l.foldl(r)(function(r){return function(a){if(a instanceof o.Left)return{left:t.alt(e.Plus1().Alt0())(r.left)(n.pure(e.Applicative0())(a.value0)),right:r.right};if(a instanceof 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t=require("../Control.Bind/index.js"),n=require("../Data.Array/index.js"),e=require("../Data.Compactable/index.js"),r=require("../Data.Either/index.js"),i=require("../Data.Foldable/index.js"),u=require("../Data.Function/index.js"),a=require("../Data.Functor/index.js"),o=require("../Data.HeytingAlgebra/index.js"),l=require("../Data.List/index.js"),f=require("../Data.List.Types/index.js"),c=require("../Data.Map.Internal/index.js"),s=require("../Data.Maybe/index.js"),h=require("../Data.Monoid/index.js"),m=require("../Data.Semigroup/index.js"),p=function(t,n,e,r,i,u){this.Compactable0=t,this.Functor1=n,this.filter=e,this.filterMap=r,this.partition=i,this.partitionMap=u},g=function(t){return function(n){var r=e.separate(t.Compactable0()),i=a.map(t.Functor1())(n);return function(t){return r(i(t))}}},b=function(t){return t.partitionMap},d=function(t){return t.partition},v=function(t){return function(n){return t(n)?new s.Just(n):s.Nothing.value}},w=new p(function(){return 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function(n){return t(n)?new r.Right(n):new r.Left(n)}},A=function(t){return function(n){return function(e){return b(t)(E(n))(e).right}}},N=function(t){return function(n){return function(e){var r=b(t)(E(n))(e);return{no:r.left,yes:r.right}}}},R=function t(n){return new p(function(){return e.compactableEither(n)},function(){return r.functorEither},function(e){return x(t(n))(e)},function(t){return function(e){if(e instanceof r.Left)return new r.Left(e.value0);if(e instanceof r.Right){var i=t(e.value0);if(i instanceof s.Nothing)return new r.Left(h.mempty(n));if(i instanceof s.Just)return new r.Right(i.value0);throw new Error("Failed pattern match at Data.Filterable (line 180, column 27 - line 182, column 22): "+[i.constructor.name])}throw new Error("Failed pattern match at Data.Filterable (line 171, column 1 - line 184, column 29): "+[t.constructor.name,e.constructor.name])}},function(e){return N(t(n))(e)},function(t){return function(e){if(e instanceof r.Left)return{left:new r.Left(e.value0),right:new r.Left(e.value0)};if(e instanceof r.Right){var i=t(e.value0);if(i instanceof r.Left)return{left:new r.Right(i.value0),right:new r.Left(h.mempty(n))};if(i instanceof r.Right)return{left:new r.Left(h.mempty(n)),right:new r.Right(i.value0)};throw new Error("Failed pattern match at Data.Filterable (line 173, column 30 - line 175, column 53): "+[i.constructor.name])}throw new Error("Failed pattern match at Data.Filterable (line 171, column 1 - line 184, column 29): "+[t.constructor.name,e.constructor.name])}})},C=function t(n){return new p(function(){return e.compactableMap(n)},function(){return c.functorMap},function(e){return x(t(n))(e)},function(t){return function(e){var r=c.toUnfoldable(f.unfoldableList);return i.foldr(f.foldableList)(function(e){return function(r){return c.alter(n)(u.const(t(e.value1)))(e.value0)(r)}})(c.empty)(r(e))}},function(e){return N(t(n))(e)},function(t){return function(e){var u=c.toUnfoldable(f.unfoldableList);return i.foldr(f.foldableList)(function(e){return function(i){var u=t(e.value1);if(u instanceof r.Left)return{left:c.insert(n)(e.value0)(u.value0)(i.left),right:i.right};if(u instanceof r.Right)return{left:i.left,right:c.insert(n)(e.value0)(u.value0)(i.right)};throw new Error("Failed pattern match at Data.Filterable (line 215, column 44 - line 217, column 57): "+[u.constructor.name])}})({left:c.empty,right:c.empty})(u(e))}})},B=new p(function(){return e.compactableMaybe},function(){return s.functorMaybe},function(t){return x(B)(t)},t.bindFlipped(s.bindMaybe),function(t){return N(B)(t)},function(t){return function(n){if(n instanceof s.Nothing)return{left:s.Nothing.value,right:s.Nothing.value};if(n instanceof s.Just){var e=t(n.value0);if(e instanceof r.Left)return{left:new s.Just(e.value0),right:s.Nothing.value};if(e instanceof r.Right)return{left:s.Nothing.value,right:new s.Just(e.value0)};throw new Error("Failed pattern match at Data.Filterable (line 161, column 29 - line 163, column 48): "+[e.constructor.name])}throw new Error("Failed pattern match at Data.Filterable (line 159, column 1 - line 169, column 29): "+[t.constructor.name,n.constructor.name])}}),J=function(t){return F(t)(u.const(s.Nothing.value))};module.exports={Filterable:p,partitionMap:b,partition:d,filterMap:F,filter:j,eitherBool:E,partitionDefault:N,partitionDefaultFilter:q,partitionDefaultFilterMap:L,partitionMapDefault:g,maybeBool:v,filterDefault:x,filterDefaultPartition:M,filterDefaultPartitionMap:A,filterMapDefault:D,cleared:J,filterableArray:y,filterableMaybe:B,filterableEither:R,filterableList:w,filterableMap:C}; 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n=require("../Data.Foldable/index.js"),e=require("../Data.Generic.Rep/index.js"),r=require("../Data.Monoid/index.js"),t=require("../Data.Semigroup/index.js"),o=require("../Data.Show/index.js"),i=require("../Data.Symbol/index.js"),u=function(n){this.genericShowArgs=n},c=function(n){this["genericShow'"]=n},a=new u(function(n){return[]}),s=function(n){return new u(function(e){return[o.show(n)(e)]})},f=function(n){return n.genericShowArgs},g=function(n){return function(e){return new u(function(r){return t.append(t.semigroupArray)(f(n)(r.value0))(f(e)(r.value1))})}},w=function(e){return function(o){return new c(function(u){var c=i.reflectSymbol(o)(i.SProxy.value),a=f(e)(u);return 0===a.length?c:"("+n.intercalate(n.foldableArray)(r.monoidString)(" ")(t.append(t.semigroupArray)([c])(a))+")"})}},h=function(n){return n["genericShow'"]},S=new c(function(n){return h(S)(n)}),l=function(n){return function(r){return new c(function(t){if(t instanceof e.Inl)return h(n)(t.value0);if(t instanceof 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n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),t=require("../Control.Semigroupoid/index.js"),e=require("../Data.Bifoldable/index.js"),u=require("../Data.Bifunctor/index.js"),i=require("../Data.Bitraversable/index.js"),o=require("../Data.Eq/index.js"),c=require("../Data.Foldable/index.js"),f=require("../Data.FoldableWithIndex/index.js"),a=require("../Data.Functor/index.js"),s=require("../Data.Functor.Contravariant/index.js"),d=require("../Data.Functor.Invariant/index.js"),l=require("../Data.FunctorWithIndex/index.js"),p=require("../Data.Monoid/index.js"),C=require("../Data.Newtype/index.js"),x=require("../Data.Ord/index.js"),q=require("../Data.Semigroup/index.js"),b=require("../Data.Show/index.js"),w=require("../Data.Traversable/index.js"),m=require("../Data.TraversableWithIndex/index.js"),j=function(n){return n},v=function(n){return new b.Show(function(r){return"(Const "+b.show(n)(r)+")"})},D=function(n){return n},h=new 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n=require("../Control.Alt/index.js"),r=require("../Control.Alternative/index.js"),t=require("../Control.Applicative/index.js"),e=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),i=require("../Control.Category/index.js"),o=require("../Control.Monad/index.js"),c=require("../Control.MonadPlus/index.js"),a=require("../Control.MonadZero/index.js"),f=require("../Control.Plus/index.js"),l=require("../Control.Semigroupoid/index.js"),p=require("../Data.Distributive/index.js"),d=require("../Data.Either/index.js"),s=require("../Data.Functor/index.js"),v=require("../Data.Functor.Invariant/index.js"),S=require("../Data.Newtype/index.js"),w=require("../Data.Profunctor/index.js"),x=require("../Data.Profunctor.Choice/index.js"),j=require("../Data.Profunctor.Closed/index.js"),q=require("../Data.Profunctor.Strong/index.js"),A=require("../Data.Tuple/index.js"),C=function(n){return n},m=function(n){return new l.Semigroupoid(function(r){return function(t){return function(e){return 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n=require("../Data.Functor/index.js"),t=require("../Data.Identity/index.js"),r=require("../Data.Newtype/index.js"),e=require("../Data.Profunctor.Choice/index.js"),i=require("../Data.Profunctor.Star/index.js"),u=require("../Data.Profunctor.Strong/index.js"),o=function(n,t,r){this.Choice1=n,this.Strong0=t,this.wander=r},a=function(n){return new o(function(){return i.choiceStar(n)},function(){return i.strongStar(n.Apply0().Functor0())},function(t){return function(r){return t(n)(r)}})},c=new o(function(){return e.choiceFn},function(){return u.strongFn},function(e){return r.alaF(n.functorFn)(n.functorFn)(t.newtypeIdentity)(t.newtypeIdentity)(t.Identity)(e(t.applicativeIdentity))}),d=function(n){return n.wander};module.exports={wander:d,Wander:o,wanderFunction:c,wanderStar:a}; 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n=require("../Data.Const/index.js"),r=require("../Data.Either/index.js"),e=require("../Data.Functor/index.js"),t=require("../Data.Lens.Internal.Wander/index.js"),o=require("../Data.Monoid/index.js"),u=require("../Data.Newtype/index.js"),i=require("../Data.Profunctor/index.js"),c=require("../Data.Profunctor.Choice/index.js"),f=require("../Data.Profunctor.Cochoice/index.js"),a=require("../Data.Profunctor.Strong/index.js"),s=require("../Data.Semigroup/index.js"),d=require("../Data.Tuple/index.js"),F=function(n){return n},g=function(n){return s.semigroupFn(n)},p=new i.Profunctor(function(n){return function(r){return function(r){return function(e){return r(n(e))}}}}),x=new a.Strong(function(){return p},function(n){return function(r){return n(d.fst(r))}},function(n){return function(r){return n(d.snd(r))}}),j=new u.Newtype(function(n){return n},F),m=function(n){return o.monoidFn(n)},q=new f.Cochoice(function(){return p},function(n){return function(e){return 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n=require("../Control.Category/index.js"),e=require("../Control.Monad.State.Class/index.js"),t=require("../Data.Lens.Internal.Forget/index.js"),r=require("../Data.Lens.Internal.Indexed/index.js"),u=require("../Data.Newtype/index.js"),o=require("../Data.Profunctor.Strong/index.js"),i=function(e){return u.unwrap(t.newtypeForget)(e(n.identity(n.categoryFn)))},a=function(n){return function(e){return i(e)(n)}},c=function(n){return function(t){return e.gets(n)(function(n){return a(n)(t)})}},s=function(n){return function(e){var r=u.unwrap(t.newtypeForget)(e);return function(e){return r(n(e))}}},f=function(e){return function(t){return s(o.fanout(n.categoryFn)(o.strongFn)(i(e))(i(t)))}},d=function(e){return u.unwrap(t.newtypeForget)(e(r.Indexed(n.identity(n.categoryFn))))},g=function(n){return function(t){return e.gets(n)(d(t))}},w=function(n){return s(i(n))};module.exports={viewOn:a,view:i,to:s,takeBoth:f,use:c,iview:d,iuse:g,cloneGetter:w}; 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n=require("../Control.Applicative/index.js"),e=require("../Control.Bind/index.js"),t=require("../Control.Monad.Gen.Class/index.js"),r=require("../Control.Monad.Rec.Class/index.js"),u=require("../Data.Boolean/index.js"),i=require("../Data.Foldable/index.js"),o=require("../Data.Function/index.js"),a=require("../Data.Functor/index.js"),c=require("../Data.Maybe/index.js"),l=require("../Data.Monoid.Additive/index.js"),d=require("../Data.Newtype/index.js"),f=require("../Data.Semigroup/index.js"),s=require("../Data.Semigroup.Foldable/index.js"),p=require("../Data.Semiring/index.js"),v=require("../Data.Tuple/index.js"),m=require("../Data.Unfoldable/index.js"),w=require("../Data.Unit/index.js"),M=function(){function n(n,e){this.value0=n,this.value1=e}return n.create=function(e){return function(t){return new n(e,t)}},n}(),h=function(){function n(){}return n.value=new n,n}(),F=function(n){return n},q=function(n){return n},x=function(i){return function(o){return function(l){return function(d){var 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n=require("../Data.Array.NonEmpty/index.js"),r=require("../Data.Maybe/index.js"),t=require("../Data.Semigroup.Foldable/index.js"),e=require("../Data.String.CodeUnits/index.js"),u=require("../Data.String.NonEmpty.Internal/index.js"),o=require("../Data.String.Unsafe/index.js"),i=require("../Unsafe.Coerce/index.js"),a=i.unsafeCoerce,f=function(n){return function(r){return a(r+e.singleton(n))}},c=function(n){return a(e.singleton(n))},s=i.unsafeCoerce,l=function(n){var r=s(e.takeWhile(n));return function(n){return u.fromString(r(n))}},h=function(n){var r=e["lastIndexOf'"](n);return function(n){return s(r(n))}},g=function(n){return s(e.lastIndexOf(n))},d=function(n){var r=e["indexOf'"](n);return function(n){return s(r(n))}},m=function(n){return s(e.indexOf(n))},v=i.unsafeCoerce,x=function(n){return e.length(v(n))},p=function(n){return function(r){var t=e.splitAt(n)(v(r));return{before:u.fromString(t.before),after:u.fromString(t.after)}}},y=function(n){return function(t){var u=v(t);return 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n)({}).hasOwnProperty.call(n,o)&&(a[o]=n[o]);for(var t in r)({}).hasOwnProperty.call(r,t)&&(a[t]=r[t]);return a}; +},{}],"cB+g":[function(require,module,exports) { +"use strict";exports.mkFn0=function(n){return function(){return n({})}},exports.mkFn2=function(n){return function(r,t){return n(r)(t)}},exports.mkFn3=function(n){return function(r,t,u){return n(r)(t)(u)}},exports.mkFn4=function(n){return function(r,t,u,e){return n(r)(t)(u)(e)}},exports.mkFn5=function(n){return function(r,t,u,e,o){return n(r)(t)(u)(e)(o)}},exports.mkFn6=function(n){return function(r,t,u,e,o,c){return n(r)(t)(u)(e)(o)(c)}},exports.mkFn7=function(n){return function(r,t,u,e,o,c,i){return n(r)(t)(u)(e)(o)(c)(i)}},exports.mkFn8=function(n){return function(r,t,u,e,o,c,i,f){return n(r)(t)(u)(e)(o)(c)(i)(f)}},exports.mkFn9=function(n){return function(r,t,u,e,o,c,i,f,s){return n(r)(t)(u)(e)(o)(c)(i)(f)(s)}},exports.mkFn10=function(n){return function(r,t,u,e,o,c,i,f,s,p){return n(r)(t)(u)(e)(o)(c)(i)(f)(s)(p)}},exports.runFn0=function(n){return n()},exports.runFn2=function(n){return function(r){return function(t){return n(r,t)}}},exports.runFn3=function(n){return function(r){return function(t){return function(u){return n(r,t,u)}}}},exports.runFn4=function(n){return function(r){return function(t){return function(u){return function(e){return n(r,t,u,e)}}}}},exports.runFn5=function(n){return function(r){return function(t){return function(u){return function(e){return function(o){return n(r,t,u,e,o)}}}}}},exports.runFn6=function(n){return function(r){return function(t){return function(u){return function(e){return function(o){return function(c){return n(r,t,u,e,o,c)}}}}}}},exports.runFn7=function(n){return function(r){return function(t){return function(u){return function(e){return function(o){return function(c){return function(i){return n(r,t,u,e,o,c,i)}}}}}}}},exports.runFn8=function(n){return function(r){return function(t){return function(u){return function(e){return function(o){return function(c){return function(i){return function(f){return n(r,t,u,e,o,c,i,f)}}}}}}}}},exports.runFn9=function(n){return function(r){return function(t){return function(u){return function(e){return function(o){return function(c){return function(i){return function(f){return function(s){return n(r,t,u,e,o,c,i,f,s)}}}}}}}}}},exports.runFn10=function(n){return function(r){return function(t){return function(u){return function(e){return function(o){return function(c){return function(i){return function(f){return function(s){return function(p){return n(r,t,u,e,o,c,i,f,s,p)}}}}}}}}}}}; +},{}],"TowT":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),F=function(n){return n},r=function(n){return n};module.exports={mkFn1:r,runFn1:F,mkFn0:n.mkFn0,mkFn2:n.mkFn2,mkFn3:n.mkFn3,mkFn4:n.mkFn4,mkFn5:n.mkFn5,mkFn6:n.mkFn6,mkFn7:n.mkFn7,mkFn8:n.mkFn8,mkFn9:n.mkFn9,mkFn10:n.mkFn10,runFn0:n.runFn0,runFn2:n.runFn2,runFn3:n.runFn3,runFn4:n.runFn4,runFn5:n.runFn5,runFn6:n.runFn6,runFn7:n.runFn7,runFn8:n.runFn8,runFn9:n.runFn9,runFn10:n.runFn10}; +},{"./foreign.js":"cB+g"}],"WmUk":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),e=require("../Data.Function.Uncurried/index.js"),i=e.runFn2(n.unsafeUnionFn);module.exports={unsafeUnion:i,unsafeUnionFn:n.unsafeUnionFn}; +},{"./foreign.js":"3koD","../Data.Function.Uncurried/index.js":"TowT"}],"0gG4":[function(require,module,exports) { +"use strict";var n=require("../Data.Eq/index.js"),r=require("../Data.Symbol/index.js"),u=require("../Record.Unsafe/index.js"),t=require("../Record.Unsafe.Union/index.js"),e=require("../Type.Data.RowList/index.js"),i=require("../Unsafe.Coerce/index.js"),o=function(n){this.equalFields=n},f=function(n){return function(n){return function(r){return t.unsafeUnionFn(n,r)}}},c=function(n){return function(t){return function(t){return function(t){return function(e){return function(i){return u.unsafeSet(r.reflectSymbol(n)(t))(e)(i)}}}}}},s=function(n){return i.unsafeCoerce},a=function(n){return function(n){return function(n){return function(r){return t.unsafeUnionFn(n,r)}}}},l=function(n){return function(t){return function(t){return function(t){return function(e){return function(i){return u.unsafeSet(r.reflectSymbol(n)(t))(e)(i)}}}}}},d=function(n){return function(t){return function(t){return function(e){return u.unsafeGet(r.reflectSymbol(n)(t))(e)}}}},q=function(n){return function(r){return function(u){return function(t){return function(e){return function(i){return c(n)(r)(u)(t)(e(d(n)(r)(t)(i)))(i)}}}}}},x=new o(function(n){return function(n){return function(n){return!0}}}),y=function(n){return n.equalFields},m=function(u){return function(t){return function(i){return function(f){return new o(function(o){return function(o){return function(c){var s=d(u)(i)(r.SProxy.value),a=y(f)(e.RLProxy.value);return n.eq(t)(s(o))(s(c))&&a(o)(c)}}})}}}},F=function(n){return function(n){return function(r){return function(u){return y(n)(e.RLProxy.value)(r)(u)}}}},S=function(n){return function(n){return function(n){return function(r){return t.unsafeUnionFn(n,r)}}}},U=function(n){return function(t){return function(t){return function(t){return function(e){return u.unsafeDelete(r.reflectSymbol(n)(t))(e)}}}}},j=function(n){return function(r){return function(u){return function(t){return function(e){return function(i){return function(o){return function(f){return function(c){return l(r)(i)(e)(f)(d(n)(u)(o)(c))(U(n)(t)(u)(o)(c))}}}}}}}}};module.exports={get:d,set:c,modify:q,insert:l,delete:U,rename:j,equal:F,merge:a,union:f,disjointUnion:S,nub:s,EqualFields:o,equalFields:y,equalFieldsCons:m,equalFieldsNil:x}; +},{"../Data.Eq/index.js":"Pq4F","../Data.Symbol/index.js":"4oJQ","../Record.Unsafe/index.js":"KG04","../Record.Unsafe.Union/index.js":"WmUk","../Type.Data.RowList/index.js":"XaXP","../Unsafe.Coerce/index.js":"ETUV"}],"/s47":[function(require,module,exports) { +"use strict";exports.float32ToInt32=function(r){var t=new ArrayBuffer(4),n=new Float32Array(t),e=new Int32Array(t);return n[0]=r,e[0]}; +},{}],"34Kp":[function(require,module,exports) { +"use strict";var n=require("../Control.Alt/index.js"),t=require("../Control.Alternative/index.js"),e=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),o=require("../Control.Lazy/index.js"),i=require("../Control.Monad/index.js"),a=require("../Control.Monad.Cont.Class/index.js"),c=require("../Control.Monad.Error.Class/index.js"),l=require("../Control.Monad.Reader.Class/index.js"),f=require("../Control.Monad.Rec.Class/index.js"),d=require("../Control.Monad.State.Class/index.js"),s=require("../Control.Monad.Trans.Class/index.js"),p=require("../Control.Monad.Writer.Class/index.js"),T=require("../Control.MonadPlus/index.js"),M=require("../Control.MonadZero/index.js"),v=require("../Control.Plus/index.js"),w=require("../Data.Functor/index.js"),S=require("../Data.Newtype/index.js"),C=require("../Data.Tuple/index.js"),m=require("../Data.Unit/index.js"),x=require("../Effect.Class/index.js"),j=function(n){return n},q=function(n){return function(t){return function(e){return t(n(e))}}},A=function(n){return n},y=new S.Newtype(function(n){return n},j),E=new s.MonadTrans(function(n){return function(t){return function(r){return u.bind(n.Bind1())(t)(function(t){return e.pure(n.Applicative0())(new C.Tuple(t,r))})}}}),h=function(n){return function(t){return function(e){return n(t(e))}}},B=new o.Lazy(function(n){return function(t){return n(m.unit)(t)}}),R=function(n){return new w.Functor(function(t){return function(e){return function(r){return w.map(n)(function(n){return new C.Tuple(t(n.value0),n.value1)})(e(r))}}})},b=function(n){return function(t){return function(e){return w.map(n)(C.snd)(t(e))}}},D=function(n){return function(t){return function(e){return w.map(n)(C.fst)(t(e))}}},P=function(n){return new i.Monad(function(){return L(n)},function(){return F(n)})},F=function(n){return new u.Bind(function(){return k(n)},function(t){return function(e){return function(r){return u.bind(n.Bind1())(t(r))(function(n){return e(n.value0)(n.value1)})}}})},k=function(n){return new r.Apply(function(){return R(n.Bind1().Apply0().Functor0())},i.ap(P(n)))},L=function(n){return new e.Applicative(function(){return k(n)},function(t){return function(r){return e.pure(n.Applicative0())(new C.Tuple(t,r))}})},Z=function(n){return new l.MonadAsk(function(){return P(n.Monad0())},s.lift(E)(n.Monad0())(l.ask(n)))},z=function(n){return new l.MonadReader(function(){return Z(n.MonadAsk0())},(t=l.local(n),function(n){return h(t(n))}));var t},W=function(n){return new a.MonadCont(function(){return P(n.Monad0())},function(t){return function(e){return a.callCC(n)(function(n){return t(function(t){return function(e){return n(new C.Tuple(t,e))}})(e)})}})},N=function(n){return new x.MonadEffect(function(){return P(n.Monad0())},(t=s.lift(E)(n.Monad0()),e=x.liftEffect(n),function(n){return t(e(n))}));var t,e},U=function(n){return new f.MonadRec(function(){return P(n.Monad0())},function(t){return function(r){var o=function(r){var o=t(r.value0);return u.bind(n.Monad0().Bind1())(o(r.value1))(function(t){return e.pure(n.Monad0().Applicative0())(function(){if(t.value0 instanceof f.Loop)return new f.Loop(new C.Tuple(t.value0.value0,t.value1));if(t.value0 instanceof f.Done)return new f.Done(new C.Tuple(t.value0.value0,t.value1));throw new Error("Failed pattern match at Control.Monad.State.Trans (line 87, column 16 - line 89, column 40): "+[t.value0.constructor.name])}())})};return function(t){return f.tailRecM(n)(o)(new C.Tuple(r,t))}}})},g=function(n){return new d.MonadState(function(){return P(n)},function(t){return j((r=e.pure(n.Applicative0()),function(n){return r(t(n))}));var r})},G=function(n){return new p.MonadTell(function(){return P(n.Monad0())},(t=s.lift(E)(n.Monad0()),e=p.tell(n),function(n){return t(e(n))}));var t,e},H=function(n){return new p.MonadWriter(function(){return G(n.MonadTell0())},function(t){return function(r){return u.bind(n.MonadTell0().Monad0().Bind1())(p.listen(n)(t(r)))(function(t){return e.pure(n.MonadTell0().Monad0().Applicative0())(new C.Tuple(new C.Tuple(t.value0.value0,t.value1),t.value0.value1))})}},function(t){return function(r){return p.pass(n)(u.bind(n.MonadTell0().Monad0().Bind1())(t(r))(function(t){return e.pure(n.MonadTell0().Monad0().Applicative0())(new C.Tuple(new C.Tuple(t.value0.value0,t.value1),t.value0.value1))}))}})},I=function(n){return new c.MonadThrow(function(){return P(n.Monad0())},function(t){return s.lift(E)(n.Monad0())(c.throwError(n)(t))})},J=function(n){return new c.MonadError(function(){return I(n.MonadThrow0())},function(t){return function(e){return function(r){return c.catchError(n)(t(r))(function(n){return e(n)(r)})}}})},K=function(t){return function(t){return new n.Alt(function(){return R(t.Functor0())},function(e){return function(r){return function(u){return n.alt(t)(e(u))(r(u))}}})}},O=function(n){return function(t){return new v.Plus(function(){return K(n)(t.Alt0())},function(n){return v.empty(t)})}},Q=function(n){return function(e){return new t.Alternative(function(){return L(n)},function(){return O(n)(e.Plus1())})}},V=function(n){return new M.MonadZero(function(){return Q(n.Monad0())(n.Alternative1())},function(){return P(n.Monad0())})},X=function(n){return new T.MonadPlus(function(){return V(n.MonadZero0())})};module.exports={StateT:j,runStateT:A,evalStateT:D,execStateT:b,mapStateT:h,withStateT:q,newtypeStateT:y,functorStateT:R,applyStateT:k,applicativeStateT:L,altStateT:K,plusStateT:O,alternativeStateT:Q,bindStateT:F,monadStateT:P,monadRecStateT:U,monadZeroStateT:V,monadPlusStateT:X,monadTransStateT:E,lazyStateT:B,monadEffectState:N,monadContStateT:W,monadThrowStateT:I,monadErrorStateT:J,monadAskStateT:Z,monadReaderStateT:z,monadStateStateT:g,monadTellStateT:G,monadWriterStateT:H}; 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t=require("../Control.Monad.State.Trans/index.js"),e=require("../Data.Identity/index.js"),n=require("../Data.Newtype/index.js"),r=t.withStateT,u=function(t){var r=n.unwrap(e.newtypeIdentity);return function(e){return r(t(e))}},a=function(r){return t.mapStateT((u=n.unwrap(e.newtypeIdentity),function(t){return e.Identity(r(u(t)))}));var u},i=function(t){return function(e){return t(e).value1}},o=function(t){return function(e){return t(e).value0}};module.exports={runState:u,evalState:o,execState:i,mapState:a,withState:r}; +},{"../Control.Monad.State.Trans/index.js":"34Kp","../Data.Identity/index.js":"2OKT","../Data.Newtype/index.js":"lz8k"}],"7S1u":[function(require,module,exports) { +"use strict";exports.random=Math.random; +},{}],"V+tx":[function(require,module,exports) { +"use strict";var r=require("./foreign.js"),n=require("../Data.Functor/index.js"),e=require("../Data.Int/index.js"),t=require("../Effect/index.js"),o=function(n){return function(e){return function(){return 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n=require("./foreign.js"),e=require("../Control.Applicative/index.js"),t=require("../Control.Apply/index.js"),r=require("../Control.Bind/index.js"),u=require("../Control.Monad.Gen.Class/index.js"),i=require("../Control.Monad.Rec.Class/index.js"),a=require("../Control.Monad.State/index.js"),o=require("../Control.Monad.State.Class/index.js"),d=require("../Control.Monad.State.Trans/index.js"),c=require("../Data.Array/index.js"),f=require("../Data.Bounded/index.js"),l=require("../Data.Enum/index.js"),s=require("../Data.Foldable/index.js"),m=require("../Data.Functor/index.js"),p=require("../Data.Identity/index.js"),v=require("../Data.Int/index.js"),S=require("../Data.List/index.js"),y=require("../Data.List.Types/index.js"),b=require("../Data.Maybe/index.js"),x=require("../Data.Monoid.Additive/index.js"),w=require("../Data.Newtype/index.js"),q=require("../Data.NonEmpty/index.js"),j=require("../Data.Ord/index.js"),T=require("../Data.Semiring/index.js"),I=require("../Data.Tuple/index.js"),N=require("../Data.Unfoldable/index.js"),D=require("../Data.Unit/index.js"),G=require("../Math/index.js"),M=require("../Random.LCG/index.js"),C=function(n){return 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n=require("../Control.Alt/index.js"),r=require("../Control.Alternative/index.js"),e=require("../Control.Applicative/index.js"),t=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),o=require("../Control.Monad/index.js"),i=require("../Control.Monad.Cont.Class/index.js"),a=require("../Control.Monad.Error.Class/index.js"),c=require("../Control.Monad.Reader.Class/index.js"),d=require("../Control.Monad.Rec.Class/index.js"),f=require("../Control.Monad.State.Class/index.js"),l=require("../Control.Monad.Trans.Class/index.js"),s=require("../Control.Monad.Writer.Class/index.js"),p=require("../Control.MonadPlus/index.js"),M=require("../Control.MonadZero/index.js"),T=require("../Control.Plus/index.js"),R=require("../Data.Distributive/index.js"),w=require("../Data.Function/index.js"),C=require("../Data.Functor/index.js"),m=require("../Data.Monoid/index.js"),x=require("../Data.Newtype/index.js"),j=require("../Data.Semigroup/index.js"),q=require("../Effect.Class/index.js"),v=function(n){return 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n=require("../Control.Alt/index.js"),r=require("../Control.Alternative/index.js"),e=require("../Control.Applicative/index.js"),t=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),o=require("../Control.Monad/index.js"),i=require("../Control.Monad.Cont.Class/index.js"),a=require("../Control.Monad.Error.Class/index.js"),c=require("../Control.Monad.Reader.Class/index.js"),l=require("../Control.Monad.Rec.Class/index.js"),f=require("../Control.Monad.State.Class/index.js"),d=require("../Control.Monad.Trans.Class/index.js"),p=require("../Control.Monad.Writer.Class/index.js"),s=require("../Control.MonadPlus/index.js"),v=require("../Control.MonadZero/index.js"),T=require("../Control.Plus/index.js"),w=require("../Data.Functor/index.js"),M=require("../Data.Monoid/index.js"),m=require("../Data.Newtype/index.js"),C=require("../Data.Semigroup/index.js"),W=require("../Data.Tuple/index.js"),x=require("../Data.Unit/index.js"),j=require("../Effect.Class/index.js"),q=function(n){return 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n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),e=require("../Data.Eq/index.js"),t=require("../Data.Monoid/index.js"),u=require("../Data.Newtype/index.js"),p=require("../Data.Ord/index.js"),o=require("../Data.Semigroup/index.js"),i=require("../Data.Show/index.js"),c=require("../Unsafe.Coerce/index.js"),f=function(n){return n},a=function(n){return n},A=function(n){return n},d=function(n){return new i.Show(function(r){return"(App "+i.show(n)(r)+")"})},s=function(n){return function(e){return new o.Semigroup(function(t){return function(u){return r.lift2(n)(o.append(e))(t)(u)}})}},l=function(n){return n},q=new u.Newtype(function(n){return n},f),w=function(r){return function(e){return new t.Monoid(function(){return s(r.Apply0())(e.Semigroup0())},n.pure(r)(t.mempty(e)))}},m=function(n){return n},x=function(n){return n},h=function(n){return n},j=function(n){return n},y=c.unsafeCoerce,v=c.unsafeCoerce,D=function(n){return function(r){return 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Fn});module.exports={Canceler:_,launchAff:z,launchAff_:U,launchSuspendedAff:W,runAff:pn,runAff_:sn,runSuspendedAff:dn,forkAff:R,suspendAff:P,supervise:vn,attempt:ln,apathize:Cn,delay:N,never:yn,finally:V,invincible:X,killFiber:fn,joinFiber:en,cancelWith:Q,bracket:T,nonCanceler:jn,effectCanceler:nn,fiberCanceler:on,functorAff:L,applyAff:K,applicativeAff:O,bindAff:J,monadAff:I,semigroupAff:Z,monoidAff:qn,altAff:gn,plusAff:kn,monadRecAff:hn,monadThrowAff:cn,monadErrorAff:an,monadEffectAff:$,lazyAff:Y,functorParAff:S,applyParAff:G,applicativeParAff:An,semigroupParAff:H,monoidParAff:wn,altParAff:bn,plusParAff:Fn,alternativeParAff:_n,parallelAff:mn,functorFiber:rn,applyFiber:tn,applicativeFiber:un,newtypeCanceler:M,semigroupCanceler:En,monoidCanceler:xn,makeAff:n.makeAff,generalBracket:n.generalBracket}; +},{"./foreign.js":"idq0","../Control.Alt/index.js":"lN+m","../Control.Alternative/index.js":"aHia","../Control.Applicative/index.js":"qYya","../Control.Apply/index.js":"QcLv","../Control.Bind/index.js":"7VcT","../Control.Lazy/index.js":"y9cE","../Control.Monad/index.js":"U/Ix","../Control.Monad.Error.Class/index.js":"L8Lk","../Control.Monad.Rec.Class/index.js":"UVIy","../Control.Parallel/index.js":"LNK1","../Control.Parallel.Class/index.js":"NR5l","../Control.Plus/index.js":"oMBg","../Data.Either/index.js":"B2JL","../Data.Foldable/index.js":"eVDl","../Data.Function/index.js":"ImXJ","../Data.Functor/index.js":"+0AE","../Data.Monoid/index.js":"TiEB","../Data.Newtype/index.js":"lz8k","../Data.Semigroup/index.js":"EsAJ","../Data.Unit/index.js":"NhVk","../Effect/index.js":"oTWB","../Effect.Class/index.js":"dWtH","../Effect.Exception/index.js":"0OCW","../Effect.Unsafe/index.js":"tPW2","../Partial.Unsafe/index.js":"aoR+","../Unsafe.Coerce/index.js":"ETUV"}],"89Lg":[function(require,module,exports) { +"use strict";var e=function(){function e(){this.head=null,this.last=null,this.size=0}function n(e,n){this.queue=e,this.value=n,this.next=null,this.prev=null}function t(n){this.draining=!1,this.error=null,this.value=n,this.takes=new e,this.reads=new e,this.puts=new e}var r={};function u(e){try{e()}catch(n){setTimeout(function(){throw n},0)}}function a(e){var n;switch(e.size){case 0:return null;case 1:n=e.head,e.head=null;break;case 2:n=e.last,e.head.next=null,e.last=null;break;default:n=e.last,e.last=n.prev,e.last.next=null}return n.prev=null,n.queue=null,e.size--,n.value}function l(e){var n;switch(e.size){case 0:return null;case 1:n=e.head,e.head=null;break;case 2:n=e.head,e.last.prev=null,e.head=e.last,e.last=null;break;default:n=e.head,e.head=n.next,e.head.prev=null}return n.next=null,n.queue=null,e.size--,n.value}return t.EMPTY=r,t.putLast=function(e,t){var r=new n(e,t);switch(e.size){case 0:e.head=r;break;case 1:r.prev=e.head,e.head.next=r,e.last=r;break;default:r.prev=e.last,e.last.next=r,e.last=r}return e.size++,r},t.takeLast=a,t.takeHead=l,t.deleteCell=function(e){null!==e.queue&&(e.queue.last!==e?e.queue.head!==e?(e.prev&&(e.prev.next=e.next),e.next&&(e.next.prev=e.prev),e.queue.size--,e.queue=null,e.value=null,e.next=null,e.prev=null):l(e.queue):a(e.queue))},t.drainVar=function(e,n){if(!n.draining){var t,a,i,s,o,c=n.puts,f=n.takes,v=n.reads;for(n.draining=!0;;){if(t=null,a=null,i=null,s=n.value,o=v.size,null!==n.error){for(s=e.left(n.error);t=l(c);)u(t.cb(s));for(;a=l(v);)u(a(s));for(;i=l(f);)u(i(s));break}if(s===r&&(t=l(c))&&(n.value=s=t.value),s!==r){for(i=l(f);o--&&(a=l(v));)u(a(e.right(s)));null!==i&&(n.value=r,u(i(e.right(s))))}if(null!==t&&u(t.cb(e.right(void 0))),n.value===r&&0===c.size||n.value!==r&&0===f.size)break}n.draining=!1}},t}();exports.empty=function(){return new e(e.EMPTY)},exports._newVar=function(n){return function(){return new e(n)}},exports._killVar=function(n,t,r){return function(){null===r.error&&(r.error=t,r.value=e.EMPTY,e.drainVar(n,r))}},exports._putVar=function(n,t,r,u){return function(){var a=e.putLast(r.puts,{cb:u,value:t});return e.drainVar(n,r),function(){e.deleteCell(a)}}},exports._takeVar=function(n,t,r){return function(){var u=e.putLast(t.takes,r);return e.drainVar(n,t),function(){e.deleteCell(u)}}},exports._readVar=function(n,t,r){return function(){var u=e.putLast(t.reads,r);return e.drainVar(n,t),function(){e.deleteCell(u)}}},exports._tryPutVar=function(n,t,r){return function(){return r.value===e.EMPTY&&null===r.error&&(r.value=t,e.drainVar(n,r),!0)}},exports._tryTakeVar=function(n,t){return function(){var r=t.value;return r===e.EMPTY?n.nothing:(t.value=e.EMPTY,e.drainVar(n,t),n.just(r))}},exports._tryReadVar=function(n,t){return function(){return t.value===e.EMPTY?n.nothing:n.just(t.value)}},exports._status=function(n,t){return function(){return t.error?n.killed(t.error):t.value===e.EMPTY?n.empty:n.filled(t.value)}}; +},{}],"XiHq":[function(require,module,exports) { +"use strict";var t=require("./foreign.js"),n=require("../Data.Either/index.js"),e=require("../Data.Maybe/index.js"),r=function(){function t(t){this.value0=t}return t.create=function(n){return new t(n)},t}(),u=function(){function t(t){this.value0=t}return t.create=function(n){return new t(n)},t}(),i=function(){function t(){}return t.value=new t,t}(),a=t._newVar,c=function(t){return t instanceof r},o=function(t){return t instanceof u},f=function(t){return t instanceof i},l={left:n.Left.create,right:n.Right.create,nothing:e.Nothing.value,just:e.Just.create,killed:r.create,filled:u.create,empty:i.value},s=function(n){return function(e){return t._killVar(l,n,e)}},d=function(n){return function(e){return function(r){return t._putVar(l,n,e,r)}}},y=function(n){return function(e){return t._readVar(l,n,e)}},_=function(n){return t._status(l,n)},p=function(n){return function(e){return t._takeVar(l,n,e)}},V=function(n){return function(e){return t._tryPutVar(l,n,e)}},h=function(n){return t._tryReadVar(l,n)},k=function(n){return t._tryTakeVar(l,n)};module.exports={Killed:r,Filled:u,Empty:i,new:a,take:p,tryTake:k,put:d,tryPut:V,read:y,tryRead:h,kill:s,status:_,isEmpty:f,isFilled:o,isKilled:c,empty:t.empty}; +},{"./foreign.js":"89Lg","../Data.Either/index.js":"B2JL","../Data.Maybe/index.js":"5mN7"}],"hACG":[function(require,module,exports) { +"use strict";var t=require("../Effect.AVar/index.js"),f=require("../Effect.Aff/index.js"),n=require("../Effect.Class/index.js"),e=function(){var e=n.liftEffect(f.monadEffectAff);return function(f){return e(t.tryTake(f))}}(),r=function(){var e=n.liftEffect(f.monadEffectAff);return function(f){return e(t.tryRead(f))}}(),u=function(e){var r=n.liftEffect(f.monadEffectAff),u=t.tryPut(e);return function(t){return r(u(t))}},c=function(n){return f.makeAff(function(e){return function(){var r=t.take(n)(e)();return f.effectCanceler(r)}})},i=function(){var e=n.liftEffect(f.monadEffectAff);return function(f){return e(t.status(f))}}(),a=function(n){return f.makeAff(function(e){return function(){var r=t.read(n)(e)();return f.effectCanceler(r)}})},o=function(n){return function(e){return f.makeAff(function(r){return function(){var u=t.put(n)(e)(r)();return f.effectCanceler(u)}})}},E=function(){var e=n.liftEffect(f.monadEffectAff);return function(f){return e(t.new(f))}}(),l=function(e){var r=n.liftEffect(f.monadEffectAff),u=t.kill(e);return function(t){return r(u(t))}},d=n.liftEffect(f.monadEffectAff)(t.empty);module.exports={new:E,empty:d,status:i,take:c,tryTake:e,put:o,tryPut:u,read:a,tryRead:r,kill:l}; +},{"../Effect.AVar/index.js":"XiHq","../Effect.Aff/index.js":"I7lu","../Effect.Class/index.js":"dWtH"}],"ty16":[function(require,module,exports) { +"use strict";exports.log=function(n){return function(){return console.log(n),{}}},exports.warn=function(n){return function(){return console.warn(n),{}}},exports.error=function(n){return function(){return console.error(n),{}}},exports.info=function(n){return function(){return console.info(n),{}}},exports.time=function(n){return function(){return console.time(n),{}}},exports.timeEnd=function(n){return function(){return console.timeEnd(n),{}}}; +},{}],"+3bp":[function(require,module,exports) { +"use strict";var r=require("./foreign.js"),n=require("../Data.Show/index.js"),o=function(o){return function(e){return r.warn(n.show(o)(e))}},e=function(o){return function(e){return r.log(n.show(o)(e))}},t=function(o){return function(e){return r.info(n.show(o)(e))}},i=function(o){return function(e){return r.error(n.show(o)(e))}};module.exports={logShow:e,warnShow:o,errorShow:i,infoShow:t,log:r.log,warn:r.warn,error:r.error,info:r.info,time:r.time,timeEnd:r.timeEnd}; +},{"./foreign.js":"ty16","../Data.Show/index.js":"mFY7"}],"3Dts":[function(require,module,exports) { +"use strict";var n=require("../Effect.Class/index.js"),r=require("../Effect.Console/index.js"),t=function(t){return function(f){var e=n.liftEffect(t),u=r.warnShow(f);return function(n){return e(u(n))}}},f=function(t){var f=n.liftEffect(t);return function(n){return f(r.warn(n))}},e=function(t){var f=n.liftEffect(t);return function(n){return f(r.timeEnd(n))}},u=function(t){var f=n.liftEffect(t);return function(n){return f(r.time(n))}},o=function(t){return function(f){var e=n.liftEffect(t),u=r.logShow(f);return function(n){return e(u(n))}}},i=function(t){var f=n.liftEffect(t);return function(n){return f(r.log(n))}},c=function(t){return function(f){var e=n.liftEffect(t),u=r.infoShow(f);return function(n){return e(u(n))}}},l=function(t){var f=n.liftEffect(t);return function(n){return f(r.info(n))}},a=function(t){return function(f){var e=n.liftEffect(t),u=r.errorShow(f);return function(n){return e(u(n))}}},E=function(t){var f=n.liftEffect(t);return function(n){return f(r.error(n))}};module.exports={log:i,logShow:o,warn:f,warnShow:t,error:E,errorShow:a,info:l,infoShow:c,time:u,timeEnd:e}; +},{"../Effect.Class/index.js":"dWtH","../Effect.Console/index.js":"+3bp"}],"kKQF":[function(require,module,exports) { +"use strict";function t(o){return(t="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(o)}exports.unsafeToForeign=function(t){return t},exports.unsafeFromForeign=function(t){return t},exports.typeOf=function(o){return t(o)},exports.tagOf=function(t){return Object.prototype.toString.call(t).slice(8,-1)},exports.isNull=function(t){return null===t},exports.isUndefined=function(t){return void 0===t},exports.isArray=Array.isArray||function(t){return"[object Array]"===Object.prototype.toString.call(t)}; +},{}],"XAY7":[function(require,module,exports) { +"use strict";var n=require("../Control.Bind/index.js"),t=require("../Control.Category/index.js"),e=require("../Data.Boolean/index.js"),r=require("../Data.Eq/index.js"),u=require("../Data.Function/index.js"),o=require("../Data.Functor/index.js"),i=require("../Data.FunctorWithIndex/index.js"),a=require("../Data.List/index.js"),c=require("../Data.List.Types/index.js"),l=require("../Data.Maybe/index.js"),f=require("../Data.NonEmpty/index.js"),s=require("../Data.Ord/index.js"),m=require("../Data.Semigroup/index.js"),p=require("../Data.Semigroup.Traversable/index.js"),v=require("../Data.Tuple/index.js"),d=require("../Data.Unfoldable/index.js"),y=require("../Partial.Unsafe/index.js"),w=function(n){return function(t){return function(e){return new f.NonEmpty(n(t.value0)(e.value0),a.zipWith(n)(t.value1)(e.value1))}}},h=function(n){return function(t){return function(e){return function(r){return p.sequence1(c.traversable1NonEmptyList)(n.Apply0())(w(t)(e)(r))}}}},E=w(v.Tuple.create),N=function(n){return function(t){return function(e){return function(r){var u=t(new c.Cons(e.value0,e.value1))(new c.Cons(r.value0,r.value1));if(u instanceof c.Cons)return new f.NonEmpty(u.value0,u.value1);if(u instanceof c.Nil)return y.unsafeCrashWith("Impossible: empty list in NonEmptyList "+n);throw new Error("Failed pattern match at Data.List.NonEmpty (line 104, column 3 - line 106, column 81): "+[u.constructor.name])}}}},b=function(n){return function(t){return function(e){var r=t(new c.Cons(e.value0,e.value1));if(r instanceof c.Cons)return new f.NonEmpty(r.value0,r.value1);if(r instanceof c.Nil)return y.unsafeCrashWith("Impossible: empty list in NonEmptyList "+n);throw new Error("Failed pattern match at Data.List.NonEmpty (line 91, column 3 - line 93, column 81): "+[r.constructor.name])}}},L=function(n){return function(t){return function(r){if(0===n)return new l.Just(new f.NonEmpty(t,r.value1));if(e.otherwise)return o.map(l.functorMaybe)(function(n){return c.NonEmptyList((t=n,new f.NonEmpty(r.value0,t)));var t})(a.updateAt(n-1|0)(t)(r.value1));throw new Error("Failed pattern match at Data.List.NonEmpty (line 197, column 1 - line 197, column 75): "+[n.constructor.name,t.constructor.name,r.constructor.name])}}},x=function(n){return new v.Tuple(o.map(c.functorNonEmptyList)(v.fst)(n),o.map(c.functorNonEmptyList)(v.snd)(n))},D=function(n){var t=a.unsnoc(n.value1);if(t instanceof l.Nothing)return{init:c.Nil.value,last:n.value0};if(t instanceof l.Just)return{init:new c.Cons(n.value0,t.value0.init),last:t.value0.last};throw new Error("Failed pattern match at Data.List.NonEmpty (line 159, column 35 - line 161, column 50): "+[t.constructor.name])},g=function(){var n=N("unionBy");return function(t){return n(a.unionBy(t))}}(),q=function(n){return N("union")(a.union(n))},F=function(n){return{head:n.value0,tail:n.value1}},B=function(n){return new c.Cons(n.value0,n.value1)},C=function(n){var t=d.unfoldr(n)(function(n){return o.map(l.functorMaybe)(function(n){return new v.Tuple(n.head,n.tail)})(a.uncons(n))});return function(n){return t(B(n))}},j=function(n){return n.value1},M=function(){var n=b("sortBy");return function(t){return n(a.sortBy(t))}}(),W=function(n){return function(t){return M(s.compare(n))(t)}},I=function(n){return function(t){return new f.NonEmpty(n.value0,a.snoc(n.value1)(t))}},J=function(){var n=f.singleton(c.plusList);return function(t){return c.NonEmptyList(n(t))}}(),A=function(n){return function(t){if(n instanceof c.Cons)return new f.NonEmpty(n.value0,a.snoc(n.value1)(t));if(n instanceof c.Nil)return J(t);throw new Error("Failed pattern match at Data.List.NonEmpty (line 139, column 1 - line 139, column 51): "+[n.constructor.name,t.constructor.name])}},T=b("reverse")(a.reverse),z=function(){var n=b("nubBy");return function(t){return n(a.nubBy(t))}}(),k=function(n){return b("nub")(a.nub(n))},U=function(n){return function(t){return function(r){if(0===n)return new l.Just(new f.NonEmpty(t(r.value0),r.value1));if(e.otherwise)return o.map(l.functorMaybe)(function(n){return c.NonEmptyList((t=n,new f.NonEmpty(r.value0,t)));var t})(a.modifyAt(n-1|0)(t)(r.value1));throw new Error("Failed pattern match at Data.List.NonEmpty (line 202, column 1 - line 202, column 82): "+[n.constructor.name,t.constructor.name,r.constructor.name])}}},S=i.mapWithIndex(c.functorWithIndexNonEmptyList),O=function(n){return function(t){return n(new c.Cons(t.value0,t.value1))}},P=function(n){return O(a.mapMaybe(n))},G=function(n){return O(a.partition(n))},H=function(n){return O(a.span(n))},K=function(n){return O(a.take(n))},Q=function(n){return O(a.takeWhile(n))},R=function(n){return 1+a.length(n.value1)|0},V=function(n){return l.fromMaybe(n.value0)(a.last(n.value1))},X=function(){var n=N("intersectBy");return function(t){return n(a.intersectBy(t))}}(),Y=function(n){return N("intersect")(a.intersect(n))},Z=function(n){return function(t){return function(r){if(0===n)return new l.Just(new f.NonEmpty(t,new c.Cons(r.value0,r.value1)));if(e.otherwise)return o.map(l.functorMaybe)(function(n){return c.NonEmptyList((t=n,new f.NonEmpty(r.value0,t)));var t})(a.insertAt(n-1|0)(t)(r.value1));throw new Error("Failed pattern match at Data.List.NonEmpty (line 192, column 1 - line 192, column 75): "+[n.constructor.name,t.constructor.name,r.constructor.name])}}},$=function(n){return l.maybe(c.Nil.value)(function(t){return new c.Cons(n.value0,t)})(a.init(n.value1))},_=function(n){return function(t){if(0===t)return new l.Just(n.value0);if(e.otherwise)return a.index(n.value1)(t-1|0);throw new Error("Failed pattern match at Data.List.NonEmpty (line 166, column 1 - line 166, column 52): "+[n.constructor.name,t.constructor.name])}},nn=function(n){return n.value0},tn=function(){var n=b("groupBy");return function(t){return n(a.groupBy(t))}}(),en=function(n){return b("group'")(a["group'"](n))},rn=function(n){return b("group")(a.group(n))},un=function(n){if(n instanceof c.Nil)return l.Nothing.value;if(n instanceof c.Cons)return new l.Just(new f.NonEmpty(n.value0,n.value1));throw new Error("Failed pattern match at Data.List.NonEmpty (line 120, column 1 - line 120, column 57): "+[n.constructor.name])},on=function(n){var t=a.fromFoldable(n);return function(n){return un(t(n))}},an=function(t){return function(e){return function(r){return function(u){return n.bind(t.Bind1())(e(r)(u.value0))(function(n){return a.foldM(t)(e)(n)(u.value1)})}}}},cn=function(n){return function(t){var r=a.findLastIndex(n)(t.value1);if(r instanceof l.Just)return new l.Just(r.value0+1|0);if(r instanceof l.Nothing){if(n(t.value0))return new l.Just(0);if(e.otherwise)return l.Nothing.value}throw new Error("Failed pattern match at Data.List.NonEmpty (line 186, column 3 - line 190, column 29): "+[r.constructor.name])}},ln=function(n){return function(t){if(n(t.value0))return new l.Just(0);if(e.otherwise)return o.map(l.functorMaybe)(function(n){return n+1|0})(a.findIndex(n)(t.value1));throw new Error("Failed pattern match at Data.List.NonEmpty (line 179, column 1 - line 179, column 69): "+[n.constructor.name,t.constructor.name])}},fn=function(n){var t=a.filterM(n);return function(n){return O(t(n))}},sn=function(n){return O(a.filter(n))},mn=function(n){return function(t){return cn(function(e){return r.eq(n)(e)(t)})}},pn=function(n){return function(t){return ln(function(e){return r.eq(n)(e)(t)})}},vn=function(n){return O(a.dropWhile(n))},dn=function(n){return O(a.drop(n))},yn=function(n){return function(t){return new f.NonEmpty(n,t)}},wn=function(n){return function(t){return new f.NonEmpty(n,new c.Cons(t.value0,t.value1))}},hn=u.flip(n.bind(c.bindNonEmptyList)),En=function(e){return n.bind(c.bindNonEmptyList)(e)(t.identity(t.categoryFn))},Nn=O(a.catMaybes),bn=function(n){return function(t){return function(e){return new f.NonEmpty(t.value0,m.append(c.semigroupList)(t.value1)(a.fromFoldable(n)(e)))}}};module.exports={toUnfoldable:C,fromFoldable:on,fromList:un,toList:B,singleton:J,length:R,cons:wn,"cons'":yn,snoc:I,"snoc'":A,head:nn,last:V,tail:j,init:$,uncons:F,unsnoc:D,index:_,elemIndex:pn,elemLastIndex:mn,findIndex:ln,findLastIndex:cn,insertAt:Z,updateAt:L,modifyAt:U,reverse:T,concat:En,concatMap:hn,filter:sn,filterM:fn,mapMaybe:P,catMaybes:Nn,appendFoldable:bn,mapWithIndex:S,sort:W,sortBy:M,take:K,takeWhile:Q,drop:dn,dropWhile:vn,span:H,group:rn,"group'":en,groupBy:tn,partition:G,nub:k,nubBy:z,union:q,unionBy:g,intersect:Y,intersectBy:X,zipWith:w,zipWithA:h,zip:E,unzip:x,foldM:an}; +},{"../Control.Bind/index.js":"7VcT","../Control.Category/index.js":"IAi2","../Data.Boolean/index.js":"ObQr","../Data.Eq/index.js":"Pq4F","../Data.Function/index.js":"ImXJ","../Data.Functor/index.js":"+0AE","../Data.FunctorWithIndex/index.js":"OHRN","../Data.List/index.js":"ezw6","../Data.List.Types/index.js":"Xxuc","../Data.Maybe/index.js":"5mN7","../Data.NonEmpty/index.js":"qF8i","../Data.Ord/index.js":"r4Vb","../Data.Semigroup/index.js":"EsAJ","../Data.Semigroup.Traversable/index.js":"qkfi","../Data.Tuple/index.js":"II/O","../Data.Unfoldable/index.js":"77+Z","../Partial.Unsafe/index.js":"aoR+"}],"pu1p":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),n=require("../Control.Applicative/index.js"),r=require("../Control.Monad.Error.Class/index.js"),t=require("../Control.Monad.Except/index.js"),a=require("../Control.Monad.Except.Trans/index.js"),i=require("../Data.Boolean/index.js"),o=require("../Data.Either/index.js"),u=require("../Data.Eq/index.js"),c=require("../Data.Function/index.js"),l=require("../Data.Identity/index.js"),s=require("../Data.Int/index.js"),f=require("../Data.List.NonEmpty/index.js"),d=require("../Data.Maybe/index.js"),v=require("../Data.Ord/index.js"),p=require("../Data.Ordering/index.js"),m=require("../Data.Show/index.js"),h=require("../Data.String.CodeUnits/index.js"),w=function(){function e(e){this.value0=e}return e.create=function(n){return new e(n)},e}(),g=function(){function e(e,n){this.value0=e,this.value1=n}return e.create=function(n){return function(r){return new e(n,r)}},e}(),E=function(){function e(e,n){this.value0=e,this.value1=n}return e.create=function(n){return function(r){return new e(n,r)}},e}(),T=function(){function e(e,n){this.value0=e,this.value1=n}return e.create=function(n){return function(r){return new e(n,r)}},e}(),x=new m.Show(function(e){if(e instanceof w)return"(ForeignError "+m.show(m.showString)(e.value0)+")";if(e instanceof E)return"(ErrorAtIndex "+m.show(m.showInt)(e.value0)+" "+m.show(x)(e.value1)+")";if(e instanceof T)return"(ErrorAtProperty "+m.show(m.showString)(e.value0)+" "+m.show(x)(e.value1)+")";if(e instanceof g)return"(TypeMismatch "+m.show(m.showString)(e.value0)+" "+m.show(m.showString)(e.value1)+")";throw new Error("Failed pattern match at Foreign (line 63, column 1 - line 67, column 89): "+[e.constructor.name])}),F=function e(n){if(n instanceof w)return n.value0;if(n instanceof E)return"Error at array index "+m.show(m.showInt)(n.value0)+": "+e(n.value1);if(n instanceof T)return"Error at property "+m.show(m.showString)(n.value0)+": "+e(n.value1);if(n instanceof g)return"Type mismatch: expected "+n.value0+", found "+n.value1;throw new Error("Failed pattern match at Foreign (line 72, column 1 - line 72, column 45): "+[n.constructor.name])},y=function(r){if(e.isUndefined(r))return n.pure(a.applicativeExceptT(l.monadIdentity))(d.Nothing.value);if(i.otherwise)return n.pure(a.applicativeExceptT(l.monadIdentity))(new d.Just(r));throw new Error("Failed pattern match at Foreign (line 157, column 1 - line 157, column 46): "+[r.constructor.name])},q=function(r){if(e.isNull(r)||e.isUndefined(r))return n.pure(a.applicativeExceptT(l.monadIdentity))(d.Nothing.value);if(i.otherwise)return n.pure(a.applicativeExceptT(l.monadIdentity))(new d.Just(r));throw new Error("Failed pattern match at Foreign (line 162, column 1 - line 162, column 52): "+[r.constructor.name])},I=function(r){if(e.isNull(r))return n.pure(a.applicativeExceptT(l.monadIdentity))(d.Nothing.value);if(i.otherwise)return n.pure(a.applicativeExceptT(l.monadIdentity))(new d.Just(r));throw new Error("Failed pattern match at Foreign (line 152, column 1 - line 152, column 41): "+[r.constructor.name])},j=function(){var e=r.throwError(a.monadThrowExceptT(l.monadIdentity));return function(n){return e(f.singleton(n))}}(),S=function(r){if(e.isArray(r))return n.pure(a.applicativeExceptT(l.monadIdentity))(e.unsafeFromForeign(r));if(i.otherwise)return j(new g("array",e.tagOf(r)));throw new Error("Failed pattern match at Foreign (line 147, column 1 - line 147, column 42): "+[r.constructor.name])},N=function(r){return function(t){if(e.tagOf(t)===r)return n.pure(a.applicativeExceptT(l.monadIdentity))(e.unsafeFromForeign(t));if(i.otherwise)return j(new g(r,e.tagOf(t)));throw new Error("Failed pattern match at Foreign (line 106, column 1 - line 106, column 55): "+[r.constructor.name,t.constructor.name])}},O=N("Boolean"),D=N("Number"),L=function(r){var a,i=o.Left.create(f.singleton(new g("Int",e.tagOf(r)))),u=(a=d.maybe(i)(n.pure(o.applicativeEither)),function(e){return a(s.fromNumber(e))});return t.mapExcept(o.either(c.const(i))(u))(D(r))},A=N("String"),C=function(r){var a,i=o.Left.create(f.singleton(new g("Char",e.tagOf(r)))),u=(a=d.maybe(i)(n.pure(o.applicativeEither)),function(e){return a(h.toChar(e))});return t.mapExcept(o.either(c.const(i))(u))(A(r))},G=new u.Eq(function(e){return function(n){return e instanceof w&&n instanceof w?e.value0===n.value0:e instanceof g&&n instanceof g?e.value0===n.value0&&e.value1===n.value1:e instanceof E&&n instanceof E?e.value0===n.value0&&u.eq(G)(e.value1)(n.value1):e instanceof T&&n instanceof T&&(e.value0===n.value0&&u.eq(G)(e.value1)(n.value1))}}),U=new v.Ord(function(){return G},function(e){return function(n){if(e instanceof w&&n instanceof w)return v.compare(v.ordString)(e.value0)(n.value0);if(e instanceof w)return p.LT.value;if(n instanceof w)return p.GT.value;var r;if(e instanceof g&&n instanceof g)return(r=v.compare(v.ordString)(e.value0)(n.value0))instanceof p.LT?p.LT.value:r instanceof p.GT?p.GT.value:v.compare(v.ordString)(e.value1)(n.value1);if(e instanceof g)return p.LT.value;if(n instanceof g)return p.GT.value;if(e instanceof E&&n instanceof E)return(r=v.compare(v.ordInt)(e.value0)(n.value0))instanceof p.LT?p.LT.value:r instanceof p.GT?p.GT.value:v.compare(U)(e.value1)(n.value1);if(e instanceof E)return p.LT.value;if(n instanceof E)return p.GT.value;if(e instanceof T&&n instanceof T)return(r=v.compare(v.ordString)(e.value0)(n.value0))instanceof p.LT?p.LT.value:r instanceof p.GT?p.GT.value:v.compare(U)(e.value1)(n.value1);throw new Error("Failed pattern match at Foreign (line 61, column 1 - line 61, column 52): "+[e.constructor.name,n.constructor.name])}});module.exports={ForeignError:w,TypeMismatch:g,ErrorAtIndex:E,ErrorAtProperty:T,renderForeignError:F,unsafeReadTagged:N,readString:A,readChar:C,readBoolean:O,readNumber:D,readInt:L,readArray:S,readNull:I,readUndefined:y,readNullOrUndefined:q,fail:j,eqForeignError:G,ordForeignError:U,showForeignError:x,unsafeToForeign:e.unsafeToForeign,unsafeFromForeign:e.unsafeFromForeign,typeOf:e.typeOf,tagOf:e.tagOf,isNull:e.isNull,isUndefined:e.isUndefined,isArray:e.isArray}; +},{"./foreign.js":"kKQF","../Control.Applicative/index.js":"qYya","../Control.Monad.Error.Class/index.js":"L8Lk","../Control.Monad.Except/index.js":"Fye2","../Control.Monad.Except.Trans/index.js":"gr8B","../Data.Boolean/index.js":"ObQr","../Data.Either/index.js":"B2JL","../Data.Eq/index.js":"Pq4F","../Data.Function/index.js":"ImXJ","../Data.Identity/index.js":"2OKT","../Data.Int/index.js":"xNJb","../Data.List.NonEmpty/index.js":"XAY7","../Data.Maybe/index.js":"5mN7","../Data.Ord/index.js":"r4Vb","../Data.Ordering/index.js":"5Eun","../Data.Show/index.js":"mFY7","../Data.String.CodeUnits/index.js":"6c6X"}],"t65A":[function(require,module,exports) { +"use strict";var n="function"==typeof Array.from,t="undefined"!=typeof Symbol&&null!=Symbol&&void 0!==Symbol.iterator&&"function"==typeof String.prototype[Symbol.iterator],r="function"==typeof String.prototype.fromCodePoint,o="function"==typeof String.prototype.codePointAt;exports._unsafeCodePointAt0=function(n){return o?function(n){return n.codePointAt(0)}:n},exports._codePointAt=function(n){return function(r){return function(o){return function(e){return function(u){return function(i){var f=i.length;if(u<0||u>=f)return o;if(t)for(var c=i[Symbol.iterator](),a=u;;--a){var p=c.next();if(p.done)return o;if(0===a)return r(e(p.value))}return n(u)(i)}}}}}},exports._countPrefix=function(n){return function(r){return t?function(n){return function(t){for(var o=t[Symbol.iterator](),e=0;;++e){var u=o.next();if(u.done)return e;var i=r(u.value);if(!n(i))return e}}}:n}},exports._fromCodePointArray=function(n){return r?function(t){return t.length<1e4?String.fromCodePoint.apply(String,t):t.map(n).join("")}:function(t){return t.map(n).join("")}},exports._singleton=function(n){return r?String.fromCodePoint:n},exports._take=function(n){return function(r){return t?function(n){for(var t="",o=n[Symbol.iterator](),e=0;e<r;++e){var u=o.next();if(u.done)return t;t+=u.value}return t}:n(r)}},exports._toCodePointArray=function(t){return function(r){return n?function(n){return Array.from(n,r)}:t}}; +},{}],"mAJY":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Data.Array/index.js"),t=require("../Data.Boolean/index.js"),e=require("../Data.Bounded/index.js"),u=require("../Data.Enum/index.js"),o=require("../Data.Eq/index.js"),i=require("../Data.EuclideanRing/index.js"),a=require("../Data.Functor/index.js"),f=require("../Data.Int/index.js"),d=require("../Data.Maybe/index.js"),c=require("../Data.Ord/index.js"),l=require("../Data.Show/index.js"),s=require("../Data.String.CodeUnits/index.js"),m=require("../Data.String.Common/index.js"),h=require("../Data.String.Unsafe/index.js"),v=require("../Data.Tuple/index.js"),x=require("../Data.Unfoldable/index.js"),E=function(n){return n},g=function(n){return function(r){return 65536+((1024*(n-55296|0)|0)+(r-56320|0)|0)|0}},C=new l.Show(function(n){return"(CodePoint 0x"+m.toUpper(f.toStringAs(f.hexadecimal)(n))+")"}),b=function(n){return 56320<=n&&n<=57343},p=function(n){return 55296<=n&&n<=56319},q=function(n){var r=s.length(n);if(0===r)return d.Nothing.value;if(1===r)return new d.Just({head:u.fromEnum(u.boundedEnumChar)(h.charAt(0)(n)),tail:""});var t=u.fromEnum(u.boundedEnumChar)(h.charAt(1)(n)),e=u.fromEnum(u.boundedEnumChar)(h.charAt(0)(n));return p(e)&&b(t)?new d.Just({head:g(e)(t),tail:s.drop(2)(n)}):new d.Just({head:e,tail:s.drop(1)(n)})},w=function(n){return a.map(d.functorMaybe)(function(n){return new v.Tuple(n.head,n.tail)})(q(n))},P=function(n){return x.unfoldr(x.unfoldableArray)(w)(n)},D=function(n){var r=u.fromEnum(u.boundedEnumChar)(h.charAt(0)(n));if(p(r)&&s.length(n)>1){var t=u.fromEnum(u.boundedEnumChar)(h.charAt(1)(n));return b(t)?g(r)(t):r}return r},j=n._unsafeCodePointAt0(D),A=n._toCodePointArray(P)(j),y=function(n){return r.length(A(n))},J=function(n){return function(r){return a.map(d.functorMaybe)(function(n){return y(s.take(n)(r))})(s.lastIndexOf(n)(r))}},O=function(n){return function(r){return a.map(d.functorMaybe)(function(n){return y(s.take(n)(r))})(s.indexOf(n)(r))}},I=function(){var n=u.toEnumWithDefaults(u.boundedEnumChar)(e.bottom(e.boundedChar))(e.top(e.boundedChar));return function(r){return s.singleton(n(r))}}(),S=function(n){if(n<=65535)return I(n);var r=i.div(i.euclideanRingInt)(n-65536|0)(1024)+55296|0,t=i.mod(i.euclideanRingInt)(n-65536|0)(1024)+56320|0;return I(r)+I(t)},k=n._fromCodePointArray(S),_=n._singleton(S),M=function n(r){return function(t){if(r<1)return"";var e=q(t);return e instanceof d.Just?_(e.value0.head)+n(r-1|0)(e.value0.tail):t}},N=n._take(M),B=function(n){return function(r){return function(t){var e=s.length(N(r)(t));return a.map(d.functorMaybe)(function(n){return y(s.take(n)(t))})(s["lastIndexOf'"](n)(e)(t))}}},U=function(n){return function(r){var t=N(n)(r);return{before:t,after:s.drop(s.length(t))(r)}}},F=new o.Eq(function(n){return function(r){return n===r}}),R=new c.Ord(function(){return F},function(n){return function(r){return c.compare(c.ordInt)(n)(r)}}),W=function(n){return function(r){return s.drop(s.length(N(n)(r)))(r)}},T=function(n){return function(r){return function(t){var e=W(r)(t);return a.map(d.functorMaybe)(function(n){return r+y(s.take(n)(e))|0})(s.indexOf(n)(e))}}},z=function(n){return function(r){return function(t){var e,u,o,i,a=n,f=r,c=!1;for(;!c;)u=a,o=t,i=void 0,e=(i=q(f))instanceof d.Just&&u(i.value0.head)?(a=u,f=i.value0.tail,void(t=o+1|0)):(c=!0,o);return e}}},G=function(n){return function(r){return z(n)(r)(0)}},H=n._countPrefix(G)(j),K=function(n){return function(r){return W(H(n)(r))(r)}},L=function(n){return function(r){return N(H(n)(r))(r)}},Q=function(){var n=u.fromEnum(u.boundedEnumChar);return function(r){return E(n(r))}}(),V=function(n){return function(r){var t,e,u,o=n,i=!1;for(;!i;)e=o,u=void 0,t=(u=q(r))instanceof d.Just?0===e?(i=!0,new d.Just(u.value0.head)):(o=e-1|0,void(r=u.value0.tail)):(i=!0,d.Nothing.value);return t}},X=function(r){return function(t){return r<0?d.Nothing.value:0===r&&""===t?d.Nothing.value:0===r?new d.Just(j(t)):n._codePointAt(V)(d.Just.create)(d.Nothing.value)(j)(r)(t)}},Y=new e.Bounded(function(){return R},0,1114111),Z=new u.BoundedEnum(function(){return Y},function(){return $},1114112,function(n){return n},function(n){if(n>=0&&n<=1114111)return new d.Just(n);if(t.otherwise)return d.Nothing.value;throw new Error("Failed pattern match at Data.String.CodePoints (line 63, column 1 - line 68, column 26): "+[n.constructor.name])}),$=new u.Enum(function(){return R},u.defaultPred(u.toEnum(Z))(u.fromEnum(Z)),u.defaultSucc(u.toEnum(Z))(u.fromEnum(Z)));module.exports={codePointFromChar:Q,singleton:_,fromCodePointArray:k,toCodePointArray:A,codePointAt:X,uncons:q,length:y,countPrefix:H,indexOf:O,"indexOf'":T,lastIndexOf:J,"lastIndexOf'":B,take:N,takeWhile:L,drop:W,dropWhile:K,splitAt:U,eqCodePoint:F,ordCodePoint:R,showCodePoint:C,boundedCodePoint:Y,enumCodePoint:$,boundedEnumCodePoint:Z}; +},{"./foreign.js":"t65A","../Data.Array/index.js":"4t4C","../Data.Boolean/index.js":"ObQr","../Data.Bounded/index.js":"kcUU","../Data.Enum/index.js":"oOsU","../Data.Eq/index.js":"Pq4F","../Data.EuclideanRing/index.js":"2IRB","../Data.Functor/index.js":"+0AE","../Data.Int/index.js":"xNJb","../Data.Maybe/index.js":"5mN7","../Data.Ord/index.js":"r4Vb","../Data.Show/index.js":"mFY7","../Data.String.CodeUnits/index.js":"6c6X","../Data.String.Common/index.js":"OSrc","../Data.String.Unsafe/index.js":"5UWM","../Data.Tuple/index.js":"II/O","../Data.Unfoldable/index.js":"77+Z"}],"rsyP":[function(require,module,exports) { +"use strict";exports["showRegex'"]=function(n){return""+n},exports["regex'"]=function(n){return function(r){return function(t){return function(e){try{return r(new RegExp(t,e))}catch(u){return n(u.message)}}}}},exports.source=function(n){return n.source},exports["flags'"]=function(n){return{multiline:n.multiline,ignoreCase:n.ignoreCase,global:n.global,sticky:!!n.sticky,unicode:!!n.unicode}},exports.test=function(n){return function(r){var t=n.lastIndex,e=n.test(r);return n.lastIndex=t,e}},exports._match=function(n){return function(r){return function(t){return function(e){var u=e.match(t);if(null==u||0===u.length)return r;for(var o=0;o<u.length;o++)u[o]=null==u[o]?r:n(u[o]);return n(u)}}}},exports.replace=function(n){return function(r){return function(t){return t.replace(n,r)}}},exports["replace'"]=function(n){return function(r){return function(t){return t.replace(n,function(n){return r(n)(Array.prototype.splice.call(arguments,1,arguments.length-3))})}}},exports._search=function(n){return function(r){return function(t){return function(e){var u=e.search(t);return-1===u?r:n(u)}}}},exports.split=function(n){return function(r){return r.split(n)}}; +},{}],"W1/V":[function(require,module,exports) { + +"use strict";var e=require("../Control.MonadZero/index.js"),i=require("../Data.Eq/index.js"),n=require("../Data.Functor/index.js"),r=require("../Data.Monoid/index.js"),a=require("../Data.Semigroup/index.js"),o=require("../Data.Show/index.js"),u=require("../Data.String.Common/index.js"),l=function(){function e(e){this.value0=e}return e.create=function(i){return new e(i)},e}(),t=new l({global:!1,ignoreCase:!1,multiline:!1,sticky:!1,unicode:!0}),g=new l({global:!1,ignoreCase:!1,multiline:!1,sticky:!0,unicode:!1}),s=new o.Show(function(r){var o=a.append(a.semigroupArray)([])(a.append(a.semigroupArray)(n.voidLeft(n.functorArray)(e.guard(e.monadZeroArray)(r.value0.global))("global"))(a.append(a.semigroupArray)(n.voidLeft(n.functorArray)(e.guard(e.monadZeroArray)(r.value0.ignoreCase))("ignoreCase"))(a.append(a.semigroupArray)(n.voidLeft(n.functorArray)(e.guard(e.monadZeroArray)(r.value0.multiline))("multiline"))(a.append(a.semigroupArray)(n.voidLeft(n.functorArray)(e.guard(e.monadZeroArray)(r.value0.sticky))("sticky"))(n.voidLeft(n.functorArray)(e.guard(e.monadZeroArray)(r.value0.unicode))("unicode"))))));return i.eq(i.eqArray(i.eqString))(o)([])?"noFlags":"("+u.joinWith(" <> ")(o)+")"}),d=new a.Semigroup(function(e){return function(i){return new l({global:e.value0.global||i.value0.global,ignoreCase:e.value0.ignoreCase||i.value0.ignoreCase,multiline:e.value0.multiline||i.value0.multiline,sticky:e.value0.sticky||i.value0.sticky,unicode:e.value0.unicode||i.value0.unicode})}}),c=new l({global:!1,ignoreCase:!1,multiline:!1,sticky:!1,unicode:!1}),v=new l({global:!1,ignoreCase:!1,multiline:!0,sticky:!1,unicode:!1}),m=new r.Monoid(function(){return d},c),y=new l({global:!1,ignoreCase:!0,multiline:!1,sticky:!1,unicode:!1}),f=new l({global:!0,ignoreCase:!1,multiline:!1,sticky:!1,unicode:!1}),p=new i.Eq(function(e){return function(i){return e.value0.global===i.value0.global&&e.value0.ignoreCase===i.value0.ignoreCase&&e.value0.multiline===i.value0.multiline&&e.value0.sticky===i.value0.sticky&&e.value0.unicode===i.value0.unicode}});module.exports={RegexFlags:l,noFlags:c,global:f,ignoreCase:y,multiline:v,sticky:g,unicode:t,semigroupRegexFlags:d,monoidRegexFlags:m,eqRegexFlags:p,showRegexFlags:s}; +},{"../Control.MonadZero/index.js":"lD5R","../Data.Eq/index.js":"Pq4F","../Data.Functor/index.js":"+0AE","../Data.Monoid/index.js":"TiEB","../Data.Semigroup/index.js":"EsAJ","../Data.Show/index.js":"mFY7","../Data.String.Common/index.js":"OSrc"}],"lBFq":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),t=require("../Data.Either/index.js"),a=require("../Data.Maybe/index.js"),r=require("../Data.Show/index.js"),n=require("../Data.String.CodeUnits/index.js"),i=require("../Data.String.Regex.Flags/index.js"),s=new r.Show(e["showRegex'"]),u=e._search(a.Just.create)(a.Nothing.value),c=function(e){return(e.value0.global?"g":"")+(e.value0.ignoreCase?"i":"")+(e.value0.multiline?"m":"")+(e.value0.sticky?"y":"")+(e.value0.unicode?"u":"")},l=function(a){return function(r){return e["regex'"](t.Left.create)(t.Right.create)(a)(c(r))}},o=function(e){return new i.RegexFlags({global:n.contains("g")(e),ignoreCase:n.contains("i")(e),multiline:n.contains("m")(e),sticky:n.contains("y")(e),unicode:n.contains("u")(e)})},g=e._match(a.Just.create)(a.Nothing.value),x=function(t){return i.RegexFlags.create(e["flags'"](t))};module.exports={regex:l,flags:x,renderFlags:c,parseFlags:o,match:g,search:u,showRegex:s,source:e.source,test:e.test,replace:e.replace,"replace'":e["replace'"],split:e.split}; +},{"./foreign.js":"rsyP","../Data.Either/index.js":"B2JL","../Data.Maybe/index.js":"5mN7","../Data.Show/index.js":"mFY7","../Data.String.CodeUnits/index.js":"6c6X","../Data.String.Regex.Flags/index.js":"W1/V"}],"f3ma":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Bind/index.js"),t=require("../Data.Array.NonEmpty/index.js"),e=require("../Data.Boolean/index.js"),u=require("../Data.Either/index.js"),o=require("../Data.Eq/index.js"),i=require("../Data.Foldable/index.js"),a=require("../Data.Function/index.js"),c=require("../Data.Functor/index.js"),f=require("../Data.Int/index.js"),l=require("../Data.Maybe/index.js"),s=require("../Data.Ord/index.js"),v=require("../Data.Show/index.js"),m=require("../Data.String.CodePoints/index.js"),b=require("../Data.String.Regex/index.js"),h=require("../Math/index.js"),d=function(n){return n},w=function(){function n(){}return n.value=new n,n}(),g=function(){function n(){}return n.value=new n,n}(),p=function(){function n(){}return n.value=new n,n}(),x=function(){function n(){}return n.value=new n,n}(),y=function(){function n(n,r,t,e){this.value0=n,this.value1=r,this.value2=t,this.value3=e}return n.create=function(r){return function(t){return function(e){return function(u){return new n(r,t,e,u)}}}},n}(),q=function(n){return function(r){return h.remainder(h.remainder(n)(r)+r)(r)}},j=function(n){return function(r){return function(t){return function(u){var o=s.clamp(s.ordInt)(0)(255)(n),i=f.toNumber(o)/255,a=s.clamp(s.ordInt)(0)(255)(r),c=f.toNumber(a)/255,l=s.clamp(s.ordInt)(0)(255)(t),v=s.max(s.ordInt)(s.max(s.ordInt)(o)(a))(l),m=s.min(s.ordInt)(s.min(s.ordInt)(o)(a))(l),b=v-m|0,d=f.toNumber(b)/255,w=f.toNumber(v+m|0)/510,g=function(){if(0===b)return 0;if(e.otherwise)return d/(1-h.abs(2*w-1));throw new Error("Failed pattern match at Color (line 157, column 5 - line 158, column 75): "+[])}(),p=f.toNumber(l)/255,x=60*function(n){if(0===n)return 0;if(v===o)return q((c-p)/d)(6);if(v===a)return(p-i)/d+2;if(e.otherwise)return(i-c)/d+4;throw new Error("Failed pattern match at Color (line 148, column 5 - line 148, column 17): "+[n.constructor.name])}(b);return new y(x,g,w,u)}}}},C=function(n){return function(r){return function(t){return j(n)(r)(t)(1)}}},I=function(n){return function(r){return function(t){return function(e){return j(f.round(255*n))(f.round(255*r))(f.round(255*t))(e)}}}},M=function(n){return function(r){return function(t){return I(n)(r)(t)(1)}}},N=function(n){return function(r){return function(t){var u=function(n){if(n<=.0031308)return 12.92*n;if(e.otherwise)return 1.055*h.pow(n)(1/2.4)-.055;throw new Error("Failed pattern match at Color (line 224, column 5 - line 225, column 65): "+[n.constructor.name])},o=u(-.9689*n+1.8758*r+.0415*t),i=u(3.2406*n-1.5372*r-.4986*t),a=u(.0557*n-.204*r+1.057*t);return M(i)(o)(a)}}},E=function(n){return function(r){return function(t){return r+n*(t-r)}}},F=function(n){return function(r){return function(t){var e=[{from:r,to:t},{from:r,to:t+360},{from:r+360,to:t}],u=l.fromJust()(i.minimumBy(i.foldableArray)(s.comparing(s.ordNumber)(function(n){return h.abs(n.to-n.from)}))(e));return E(n)(u.from)(u.to)}}},S=function(n){return function(r){return function(t){var e=h.pi/180,u=t.value1-r.value1,o=t.value2-r.value2,i=(r.value0+120)*e,a=(t.value0+120)*e-i;return function(e){var c=h.pow(r.value2+o*e)(n),f=i+a*e,l=(r.value1+u*e)*c*(1-c),s=c+l*(1.97294*h.cos(f)),v=c+l*(-.29227*h.cos(f)-.90649*h.sin(f)),m=c+l*(-.14861*h.cos(f)+1.78277*h.sin(f)),b=E(e)(r.value3)(t.value3);return I(m)(v)(s)(b)}}}},D=function(n){return function(r){return function(t){return function(e){var u=s.clamp(s.ordNumber)(0)(1)(r),o=s.clamp(s.ordNumber)(0)(1)(t),i=s.clamp(s.ordNumber)(0)(1)(e);return new y(n,u,o,i)}}}},A=function(n){return function(r){return function(t){return function(e){var u=r;if(0===t)return D(n)(u/(2-u))(0)(e);if(0===r&&1===t)return D(n)(0)(1)(e);var o=(2-r)*t,i=(u=r*t/(o<1?o:2-o),o/2);return D(n)(u)(i)(e)}}}},L=function(n){return function(r){return function(t){return A(n)(r)(t)(1)}}},B=function(n){return function(r){return D(r.value0)(r.value1)(r.value2+n)(r.value3)}},H=function(n){return function(r){return D(r.value0+n)(r.value1)(r.value2)(r.value3)}},z=function(n){return function(r){return D(r.value0)(r.value1+n)(r.value2)(r.value3)}},R=function(n){return function(r){return function(t){return D(n)(r)(t)(1)}}},G=R(0)(0)(1),k=function(n){return R(0)(0)(n)},J=function(n){var r=s.clamp(s.ordInt)(0)(16777215)(n),t=r>>8&255,e=255&r;return C(r>>16&255)(t)(e)},O=function(e){var o,i,s=(o=l.fromMaybe(0),i=f.fromStringAs(f.hexadecimal),function(n){return o(i(n))}),v=4===m.length(e),h=u.either(a.const(l.Nothing.value))(l.Just.create),d="([0-9a-f][0-9a-f])",w=v?"([0-9a-f])([0-9a-f])([0-9a-f])":d+(d+d),g=b.regex("^#(?:"+w+")$")(b.parseFlags("i"));return r.bind(l.bindMaybe)(h(g))(function(u){return r.bind(l.bindMaybe)(b.match(u)(e))(function(e){return r.bind(l.bindMaybe)(c.map(l.functorMaybe)(s)(r.join(l.bindMaybe)(t.index(e)(1))))(function(u){return r.bind(l.bindMaybe)(c.map(l.functorMaybe)(s)(r.join(l.bindMaybe)(t.index(e)(2))))(function(o){return r.bind(l.bindMaybe)(c.map(l.functorMaybe)(s)(r.join(l.bindMaybe)(t.index(e)(3))))(function(r){return v?n.pure(l.applicativeMaybe)(C((16*u|0)+u|0)((16*o|0)+o|0)((16*r|0)+r|0)):n.pure(l.applicativeMaybe)(C(u)(o)(r))})})})})})},P=function(n){return z(-n)},V=function(n){return B(-n)},X={xn:.95047,yn:1,zn:1.08883},Y=function(n){return function(r){return function(t){var u=(n+16)/116,o=function(n){if(n>6/29)return h.pow(n)(3);if(e.otherwise)return 6/29*3*(6/29)*(n-4/29);throw new Error("Failed pattern match at Color (line 249, column 5 - line 250, column 64): "+[n.constructor.name])},i=X.xn*o(u+r/500),a=X.yn*o(u),c=X.zn*o(u-t/200);return N(i)(a)(c)}}},Z=function(n){return function(r){return function(t){var e=h.pi/180,u=r*h.sin(t*e),o=r*h.cos(t*e);return Y(n)(o)(u)}}},$=function(n){var r=function(n){return v.show(v.showNumber)(f.toNumber(f.round(100*n))/100)},t=r(100*n.value1)+"%",e=r(100*n.value2)+"%",u=r(n.value0),o=v.show(v.showNumber)(n.value3);return 1===n.value3?"hsl("+u+", "+t+", "+e+")":"hsla("+u+", "+t+", "+e+", "+o+")"},K=H(180),Q=function(n){return 360===n?n:q(n)(360)},T=function(n){return{h:Q(n.value0),s:n.value1,l:n.value2,a:n.value3}},U=function(n){var r=n.value1;if(0===n.value2)return{h:Q(n.value0),s:2*r/(1+r),v:0,a:n.value3};if(0===n.value1&&1===n.value2)return{h:Q(n.value0),s:0,v:1,a:n.value3};var t=n.value1*(n.value2<.5?n.value2:1-n.value2),e=n.value2+t;r=2*t/(n.value2+t);return{h:Q(n.value0),s:r,v:e,a:n.value3}},W=function(n){var r=Q(n.value0)/60,t=(1-h.abs(2*n.value2-1))*n.value1,u=n.value2-t/2,o=t*(1-h.abs(h.remainder(r)(2)-1)),i=function(){if(r<1)return{r:t,g:o,b:0};if(1<=r&&r<2)return{r:o,g:t,b:0};if(2<=r&&r<3)return{r:0,g:t,b:o};if(3<=r&&r<4)return{r:0,g:o,b:t};if(4<=r&&r<5)return{r:o,g:0,b:t};if(e.otherwise)return{r:t,g:0,b:o};throw new Error("Failed pattern match at Color (line 342, column 5 - line 347, column 61): "+[])}();return{r:i.r+u,g:i.g+u,b:i.b+u,a:n.value3}},_=function(n){var r=W(n),t=function(n){if(n<=.03928)return n/12.92;if(e.otherwise)return h.pow((n+.055)/1.055)(2.4);throw new Error("Failed pattern match at Color (line 604, column 9 - line 605, column 61): "+[n.constructor.name])},u=t(r.g);return.2126*t(r.r)+.7152*u+.0722*t(r.b)},nn=function(n){return function(r){var t=_(r),e=_(n);return e>t?(e+.05)/(t+.05):(t+.05)/(e+.05)}},rn=function(n){return function(r){return nn(n)(r)>4.5}},tn=function(n){var r=W(n),t=f.round(255*r.g);return{r:f.round(255*r.r),g:t,b:f.round(255*r.b),a:r.a}},en=function(n){var r=tn(n),t=v.show(v.showInt)(r.g),e=v.show(v.showInt)(r.r),u=v.show(v.showInt)(r.b),o=v.show(v.showNumber)(r.a);return 1===r.a?"rgb("+e+", "+t+", "+u+")":"rgba("+e+", "+t+", "+u+", "+o+")"},un=new o.Eq(function(n){return function(r){var t=tn(r),e=tn(n);return e.r===t.r&&e.g===t.g&&e.b===t.b&&e.a===t.a}}),on=new v.Show(function(n){var r=tn(n);return"rgba "+v.show(v.showInt)(r.r)+" "+v.show(v.showInt)(r.g)+" "+v.show(v.showInt)(r.b)+" "+v.show(v.showNumber)(r.a)}),an=function(n){var r=function(n){var r=f.toStringAs(f.hexadecimal)(n);return 1===m.length(r)?"0"+r:r},t=tn(n);return"#"+(r(t.r)+(r(t.g)+r(t.b)))},cn=function(n){var r=W(n),t=function(n){if(n<=.04045)return n/12.92;if(e.otherwise)return h.pow((n+.055)/1.055)(2.4);throw new Error("Failed pattern match at Color (line 366, column 5 - line 367, column 63): "+[n.constructor.name])},u=t(r.g),o=t(r.r),i=t(r.b);return{x:.4124*o+.3576*u+.1805*i,y:.2126*o+.7152*u+.0722*i,z:.0193*o+.1192*u+.9505*i}},fn=function(n){var r=cn(n),t=h.pow(6/29)(3),u=function(n){if(n>t)return h.pow(n)(1/3);if(e.otherwise)return 1/3*h.pow(29/6)(2)*n+4/29;throw new Error("Failed pattern match at Color (line 384, column 5 - line 385, column 76): "+[n.constructor.name])},o=u(r.y/X.yn),i=116*o-16,a=200*(o-u(r.z/X.zn));return{l:i,a:500*(u(r.x/X.xn)-o),b:a}},ln=function(n){return function(r){var t=function(n){return h.pow(n)(2)},e=fn(r),u=fn(n);return h.sqrt(t(u.l-e.l)+t(u.a-e.a)+t(u.b-e.b))}},sn=function(n){var r=fn(n),t=180/h.pi,e=h.sqrt(r.a*r.a+r.b*r.b),u=q(h.atan2(r.b)(r.a)*t)(360);return{l:r.l,c:e,h:u}},vn=function(n){return function(r){return function(t){return function(e){if(n instanceof g){var u=T(t),o=T(r);return D(F(e)(o.h)(u.h))(E(e)(o.s)(u.s))(E(e)(o.l)(u.l))(E(e)(o.a)(u.a))}if(n instanceof w){u=W(t),o=W(r);return I(E(e)(o.r)(u.r))(E(e)(o.g)(u.g))(E(e)(o.b)(u.b))(E(e)(o.a)(u.a))}if(n instanceof p){u=sn(t),o=sn(r);return Z(E(e)(o.l)(u.l))(E(e)(o.c)(u.c))(F(e)(o.h)(u.h))}if(n instanceof x){u=fn(t),o=fn(r);return Y(E(e)(o.l)(u.l))(E(e)(o.a)(u.a))(E(e)(o.b)(u.b))}throw new Error("Failed pattern match at Color (line 520, column 1 - line 520, column 34): "+[n.constructor.name,r.constructor.name,t.constructor.name,e.constructor.name])}}}},mn=function(n){var r=sn(n);return P(1)(Z(r.l)(0)(0))},bn=function(n){var r=W(n);return(299*r.r+587*r.g+114*r.b)/1e3},hn=function(n){return bn(n)>.5},dn=R(0)(0)(0),wn=function(n){if(hn(n))return dn;if(e.otherwise)return G;throw new Error("Failed pattern match at Color (line 643, column 1 - line 643, column 28): "+[n.constructor.name])};module.exports={RGB:w,HSL:g,LCh:p,Lab:x,rgba:j,rgb:C,"rgba'":I,"rgb'":M,hsla:D,hsl:R,hsva:A,hsv:L,xyz:N,lab:Y,lch:Z,fromHexString:O,fromInt:J,toHSLA:T,toHSVA:U,toRGBA:tn,"toRGBA'":W,toXYZ:cn,toLab:fn,toLCh:sn,toHexString:an,cssStringHSLA:$,cssStringRGBA:en,black:dn,white:G,graytone:k,rotateHue:H,complementary:K,lighten:B,darken:V,saturate:z,desaturate:P,toGray:mn,mix:vn,mixCubehelix:S,brightness:bn,luminance:_,contrast:nn,isLight:hn,isReadable:rn,textColor:wn,distance:ln,showColor:on,eqColor:un}; +},{"../Control.Applicative/index.js":"qYya","../Control.Bind/index.js":"7VcT","../Data.Array.NonEmpty/index.js":"eTKN","../Data.Boolean/index.js":"ObQr","../Data.Either/index.js":"B2JL","../Data.Eq/index.js":"Pq4F","../Data.Foldable/index.js":"eVDl","../Data.Function/index.js":"ImXJ","../Data.Functor/index.js":"+0AE","../Data.Int/index.js":"xNJb","../Data.Maybe/index.js":"5mN7","../Data.Ord/index.js":"r4Vb","../Data.Show/index.js":"mFY7","../Data.String.CodePoints/index.js":"mAJY","../Data.String.Regex/index.js":"lBFq","../Math/index.js":"Rpaz"}],"rp+n":[function(require,module,exports) { +"use strict";var r=require("../Color/index.js"),o=r.fromInt(16768e3),n=r.fromInt(3787980),t=r.fromInt(14540253),m=r.fromInt(16728374),e=r.fromInt(11603401),f=r.fromInt(16745755),I=r.fromInt(4036976),l=r.fromInt(7999),a=r.fromInt(8721483),i=r.fromInt(130928),u=r.fromInt(3066944),s=r.fromInt(11184810),v=r.fromInt(15733438),c=r.fromInt(29913),d=r.fromInt(1118481),g=r.fromInt(8379391);module.exports={navy:l,blue:c,aqua:g,teal:n,olive:I,green:u,lime:i,yellow:o,orange:f,red:m,maroon:a,fuchsia:v,purple:e,"black'":d,gray:s,silver:t}; +},{"../Color/index.js":"f3ma"}],"BG0s":[function(require,module,exports) { +function t(t){return function(o){return function(e){return t.apply(e,[o])}}}exports.toPrecisionNative=t(Number.prototype.toPrecision),exports.toFixedNative=t(Number.prototype.toFixed),exports.toExponentialNative=t(Number.prototype.toExponential),exports.toString=function(t){return t.toString()}; +},{}],"VX77":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),t=require("../Data.Ord/index.js"),e=function(){function n(n){this.value0=n}return n.create=function(t){return new n(t)},n}(),r=function(){function n(n){this.value0=n}return n.create=function(t){return new n(t)},n}(),i=function(){function n(n){this.value0=n}return n.create=function(t){return new n(t)},n}(),u=function(t){if(t instanceof e)return n.toPrecisionNative(t.value0);if(t instanceof r)return n.toFixedNative(t.value0);if(t instanceof i)return n.toExponentialNative(t.value0);throw new Error("Failed pattern match at Data.Number.Format (line 59, column 1 - line 59, column 40): "+[t.constructor.name])},o=function(){var n=t.clamp(t.ordInt)(1)(21);return function(t){return e.create(n(t))}}(),a=function(){var n=t.clamp(t.ordInt)(0)(20);return function(t){return r.create(n(t))}}(),c=function(){var n=t.clamp(t.ordInt)(0)(20);return function(t){return i.create(n(t))}}();module.exports={precision:o,fixed:a,exponential:c,toStringWith:u,toString:n.toString}; +},{"./foreign.js":"BG0s","../Data.Ord/index.js":"r4Vb"}],"KkC9":[function(require,module,exports) { +"use strict";exports.unsafeCreateElementImpl=function(e,t,n){var o=document.createElement(e);return o.id=t,o.className=n,o},exports.initializeCanvasImpl=function(e,t){e.width=t.width,e.height=t.height;var n=e.getContext("2d");!0===n.imageSmoothingEnabled&&(n.imageSmoothingEnabled=!1)},exports.setElementStyleImpl=function(e,t,n){e.style[t]=n},exports.appendElem=function(e){return function(t){return function(){e.appendChild(t)}}},exports.setContainerStyle=function(e){return function(t){return function(){e.style.position="relative",e.style.border="1px solid black",e.style.display="block",e.style.margin="0",e.style.padding="0",e.style.width=t.width-2+"px",e.style.height=t.height+"px"}}},exports.drawCopies=function(e,t,n,o,i){Math.round(t.width),Math.round(t.height);i.forEach(function(i){o(i)&&n.drawImage(e,Math.floor(i.x-t.width/2),Math.floor(i.y-t.height/2))})},exports.setCanvasTranslation=function(e){return function(t){return function(){t.getContext("2d").setTransform(1,0,0,1,e.x,e.y)}}},exports.elementClickImpl=function(e,t){e.addEventListener("mousedown",function(n){var o=e.getBoundingClientRect(),i=n.clientX-o.left+window.scrollX,r=n.clientY-o.top+window.scrollY;t({x:i,y:r})()})},exports.scrollCanvasImpl=function(e,t,n){var o=e.getContext("2d");o.save(),o.globalCompositeOperation="copy",o.drawImage(t,0,0),o.restore();var i=t.getContext("2d");i.save(),i.globalCompositeOperation="copy",i.setTransform(1,0,0,1,0,0),i.drawImage(e,n.x,n.y),i.restore()},exports.zoomCanvasImpl=function(e,t,n){var 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n=require("../Control.Category/index.js"),t=require("../Control.Monad.Cont.Trans/index.js"),r=require("../Control.Monad.Except.Trans/index.js"),e=require("../Control.Monad.List.Trans/index.js"),f=require("../Control.Monad.Maybe.Trans/index.js"),o=require("../Control.Monad.RWS.Trans/index.js"),a=require("../Control.Monad.Reader.Trans/index.js"),d=require("../Control.Monad.State.Trans/index.js"),i=require("../Control.Monad.Trans.Class/index.js"),u=require("../Control.Monad.Writer.Trans/index.js"),c=require("../Effect.Aff/index.js"),s=function(n,t){this.MonadEffect0=n,this.liftAff=t},M=new s(function(){return c.monadEffectAff},n.identity(n.categoryFn)),E=function(n){return n.liftAff},T=function(n){return new s(function(){return t.monadEffectContT(n.MonadEffect0())},(r=i.lift(t.monadTransContT)(n.MonadEffect0().Monad0()),e=E(n),function(n){return r(e(n))}));var r,e},m=function(n){return new s(function(){return 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function(t,r,u,e,f,c){return n(t)(r)(u)(e)(f)(c)()}},exports.mkEffectFn7=function(n){return function(t,r,u,e,f,c,o){return n(t)(r)(u)(e)(f)(c)(o)()}},exports.mkEffectFn8=function(n){return function(t,r,u,e,f,c,o,i){return n(t)(r)(u)(e)(f)(c)(o)(i)()}},exports.mkEffectFn9=function(n){return function(t,r,u,e,f,c,o,i,s){return n(t)(r)(u)(e)(f)(c)(o)(i)(s)()}},exports.mkEffectFn10=function(n){return function(t,r,u,e,f,c,o,i,s,p){return n(t)(r)(u)(e)(f)(c)(o)(i)(s)(p)()}},exports.runEffectFn1=function(n){return function(t){return function(){return n(t)}}},exports.runEffectFn2=function(n){return function(t){return function(r){return function(){return n(t,r)}}}},exports.runEffectFn3=function(n){return function(t){return function(r){return function(u){return function(){return n(t,r,u)}}}}},exports.runEffectFn4=function(n){return function(t){return function(r){return function(u){return function(e){return function(){return n(t,r,u,e)}}}}}},exports.runEffectFn5=function(n){return function(t){return function(r){return function(u){return function(e){return function(f){return function(){return n(t,r,u,e,f)}}}}}}},exports.runEffectFn6=function(n){return function(t){return function(r){return function(u){return function(e){return function(f){return function(c){return function(){return n(t,r,u,e,f,c)}}}}}}}},exports.runEffectFn7=function(n){return function(t){return function(r){return function(u){return function(e){return function(f){return function(c){return function(o){return function(){return n(t,r,u,e,f,c,o)}}}}}}}}},exports.runEffectFn8=function(n){return function(t){return function(r){return function(u){return function(e){return function(f){return function(c){return function(o){return function(i){return function(){return n(t,r,u,e,f,c,o,i)}}}}}}}}}},exports.runEffectFn9=function(n){return function(t){return function(r){return function(u){return function(e){return function(f){return function(c){return function(o){return function(i){return function(s){return function(){return n(t,r,u,e,f,c,o,i,s)}}}}}}}}}}},exports.runEffectFn10=function(n){return function(t){return function(r){return function(u){return function(e){return function(f){return function(c){return function(o){return function(i){return function(s){return function(p){return function(){return n(t,r,u,e,f,c,o,i,s,p)}}}}}}}}}}}}; +},{}],"qn3Z":[function(require,module,exports) { +"use strict";var f=require("./foreign.js");module.exports={mkEffectFn1:f.mkEffectFn1,mkEffectFn2:f.mkEffectFn2,mkEffectFn3:f.mkEffectFn3,mkEffectFn4:f.mkEffectFn4,mkEffectFn5:f.mkEffectFn5,mkEffectFn6:f.mkEffectFn6,mkEffectFn7:f.mkEffectFn7,mkEffectFn8:f.mkEffectFn8,mkEffectFn9:f.mkEffectFn9,mkEffectFn10:f.mkEffectFn10,runEffectFn1:f.runEffectFn1,runEffectFn2:f.runEffectFn2,runEffectFn3:f.runEffectFn3,runEffectFn4:f.runEffectFn4,runEffectFn5:f.runEffectFn5,runEffectFn6:f.runEffectFn6,runEffectFn7:f.runEffectFn7,runEffectFn8:f.runEffectFn8,runEffectFn9:f.runEffectFn9,runEffectFn10:f.runEffectFn10}; +},{"./foreign.js":"ViyF"}],"61ee":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Bind/index.js"),e=require("../Data.Symbol/index.js"),t=require("../Data.Unit/index.js"),i=require("../Effect.Aff/index.js"),u=require("../Effect.Aff.AVar/index.js"),f=require("../Record/index.js"),c=require("../Type.Data.RowList/index.js"),o=require("../Type.Equality/index.js"),a=function(n){this.compile=n},d=function(n){return n.compile},s=function(n){return function(n){return function(r){return d(n)(c.RLProxy.value)(r)}}},l=function(r){return new a(function(e){return function(e){return n.pure(i.applicativeAff)({run:function(r){return n.pure(i.applicativeAff)(t.unit)},last:o.from(r)({})})}})},p=function(t){return function(o){return function(o){return function(s){return function(l){return function(p){return new a(function(a){return function(a){return r.bind(i.bindAff)(d(p)(c.RLProxy.value)(a))(function(c){return r.bind(i.bindAff)(u.empty)(function(d){var p=f.insert(t)(s)(l)(e.SProxy.value)(u.read(d))(c.last);return n.pure(i.applicativeAff)({last:p,run:function(n){return r.discard(r.discardUnit)(i.bindAff)(c.run(n))(function(){var c=f.get(t)(o)(e.SProxy.value)(a(n));return r.bind(i.bindAff)(u.tryTake(d))(function(n){return u.put(c)(d)})})}})})})}})}}}}}};module.exports={compile:d,CacherAff:a,new:s,cacherAffCons:p,cacherAffNil:l}; +},{"../Control.Applicative/index.js":"qYya","../Control.Bind/index.js":"7VcT","../Data.Symbol/index.js":"4oJQ","../Data.Unit/index.js":"NhVk","../Effect.Aff/index.js":"I7lu","../Effect.Aff.AVar/index.js":"hACG","../Record/index.js":"0gG4","../Type.Data.RowList/index.js":"XaXP","../Type.Equality/index.js":"Uq/R"}],"1Q0x":[function(require,module,exports) { +"use strict";exports.setContextTranslation=function(t){return function(n){return function(){n.setTransform(1,0,0,1,t.x,t.y)}}}; +},{}],"RCTS":[function(require,module,exports) { +"use strict";exports.canvasElementToImageSource=function(n){return n},exports.tryLoadImageImpl=function(n){return function(t){return function(r){return function(){var e=new Image;e.src=n,e.addEventListener("load",function(){r(e)()},!1),e.addEventListener("error",function(n){t()},!1)}}}},exports.getCanvasElementByIdImpl=function(n,t,r){return function(){var e=document.getElementById(n);return e&&e instanceof HTMLCanvasElement?t(e):r}},exports.getContext2D=function(n){return function(){return n.getContext("2d")}},exports.getCanvasWidth=function(n){return function(){return n.width}},exports.getCanvasHeight=function(n){return function(){return n.height}},exports.setCanvasWidth=function(n){return function(t){return function(){n.width=t}}},exports.setCanvasHeight=function(n){return function(t){return function(){n.height=t}}},exports.canvasToDataURL=function(n){return function(){return n.toDataURL()}},exports.setLineWidth=function(n){return function(t){return 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n.setLineCapImpl(e)("round");if(t instanceof D)return n.setLineCapImpl(e)("square");if(t instanceof I)return n.setLineCapImpl(e)("butt");throw new Error("Failed pattern match at Graphics.Canvas (line 234, column 1 - line 234, column 50): "+[e.constructor.name,t.constructor.name])}},on=function(e){return function(t){return n.setGlobalCompositeOperationImpl(e)(function(n){if(n instanceof L)return"source-over";if(n instanceof y)return"source-in";if(n instanceof x)return"source-out";if(n instanceof T)return"source-atop";if(n instanceof A)return"destination-over";if(n instanceof E)return"destination-in";if(n instanceof R)return"destination-out";if(n instanceof F)return"destination-atop";if(n instanceof G)return"lighter";if(n instanceof O)return"copy";if(n instanceof q)return"xor";if(n instanceof b)return"multiply";if(n instanceof k)return"screen";if(n instanceof P)return"overlay";if(n instanceof H)return"darken";if(n instanceof B)return"lighten";if(n instanceof W)return"color-dodge";if(n instanceof J)return"color-burn";if(n instanceof j)return"hard-light";if(n instanceof M)return"soft-light";if(n instanceof X)return"difference";if(n instanceof N)return"exclusion";if(n instanceof Y)return"hue";if(n instanceof U)return"saturation";if(n instanceof z)return"color";if(n instanceof K)return"luminosity";throw new Error("Failed pattern match at Graphics.Canvas (line 318, column 5 - line 318, column 45): "+[n.constructor.name])}(t))}},un=function(t){return function(r){return e.applySecond(o.applyEffect)(n.setCanvasHeight(t)(r.height))(n.setCanvasWidth(t)(r.width))}},cn=function(e){return n.getCanvasElementByIdImpl(e,i.Just.create,i.Nothing.value)},fn=function(e){return function(){return{width:n.getCanvasWidth(e)(),height:n.getCanvasHeight(e)()}}},sn=function(e){return function(t){return function(){n.beginPath(e)();var r=t();n.fill(e)();return r}}},ln=new t.Eq(function(n){return function(e){return n instanceof S&&e instanceof S||(n instanceof D&&e instanceof D||n instanceof I&&e 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c.unwrapSingleConstructors?p.map(o.functorExceptT(m.functorIdentity))(l.Constructor)(y(f)):t.bind(o.bindExceptT(m.monadIdentity))(i.mapExcept(d.lmap(a.bifunctorEither)(p.map(E.functorNonEmptyList)(D.ErrorAtProperty.create(c.sumEncoding.value0.tagFieldName))))(t.bind(o.bindExceptT(m.monadIdentity))(t.bind(o.bindExceptT(m.monadIdentity))(q.index(q.indexString)(f)(c.sumEncoding.value0.tagFieldName))(D.readString))(function(n){var r=c.sumEncoding.value0.constructorTagTransform(w);return t.discard(t.discardUnit)(o.bindExceptT(m.monadIdentity))(e.unless(o.applicativeExceptT(m.monadIdentity))(n===r)(D.fail(new D.ForeignError("Expected "+T.show(T.showString)(r)+" tag"))))(function(){return e.pure(o.applicativeExceptT(m.monadIdentity))(n)})})))(function(n){return t.bind(o.bindExceptT(m.monadIdentity))(i.mapExcept(d.lmap(a.bifunctorEither)(p.map(E.functorNonEmptyList)(D.ErrorAtProperty.create(c.sumEncoding.value0.contentsFieldName))))(t.bind(o.bindExceptT(m.monadIdentity))(q.index(q.indexString)(f)(c.sumEncoding.value0.contentsFieldName))(y)))(function(n){return e.pure(o.applicativeExceptT(m.monadIdentity))(n)})})}})}}},Yn=new z(D.unsafeToForeign),Zn=new H(D.readChar),$n=new z(D.unsafeToForeign),_n=new H(D.readBoolean),ne=function(n){return new z((e=p.map(p.functorArray)(In(n)),function(n){return D.unsafeToForeign(e(n))}));var e},ee=function(n){return new H((e=function(e){return function(t){return i.mapExcept(d.lmap(a.bifunctorEither)(p.map(E.functorNonEmptyList)(D.ErrorAtIndex.create(e))))(Mn(n)(t))}},t.composeKleisli(o.bindExceptT(m.monadIdentity))(D.readArray)(function(n){return h.sequence(h.traversableArray)(o.applicativeExceptT(m.monadIdentity))(c.zipWith(e)(c.range(0)(c.length(n)))(n))})));var e};module.exports={countArgs:Hn,decode:Mn,decodeArgs:Bn,decodeOpts:Gn,decodeRecordWithOptions:Rn,decodeWithOptions:Nn,encode:In,encodeArgs:Tn,encodeOpts:yn,encodeRecordWithOptions:mn,encodeWithOptions:pn,TaggedObject:P,defaultOptions:qn,Decode:H,Encode:z,DecodeWithOptions:V,EncodeWithOptions:M,DecodeRecord:k,EncodeRecord:J,GenericDecode:B,GenericEncode:G,GenericDecodeArgs:U,GenericEncodeArgs:W,GenericCountArgs:K,voidDecode:X,unitDecode:Z,foreignDecode:fn,stringDecode:_,charDecode:Zn,booleanDecode:_n,numberDecode:en,intDecode:rn,identityDecode:zn,arrayDecode:ee,maybeDecode:Vn,objectDecode:kn,recordDecode:Ln,voidEncode:Q,unitEncode:Y,foreignEncode:sn,stringEncode:$,charEncode:Yn,booleanEncode:$n,numberEncode:nn,intEncode:tn,identityEncode:Fn,arrayEncode:ne,maybeEncode:Dn,objectEncode:jn,recordEncode:Sn,decodeWithOptionsRecord:Cn,decodeWithOptionsOther:Jn,encodeWithOptionsRecord:gn,encodeWithOptionsOther:An,decodeRecordNil:Pn,encodeRecordNil:En,decodeRecordCons:Wn,encodeRecordCons:xn,genericDecodeNoConstructors:un,genericEncodeNoConstructors:wn,genericDecodeConstructor:Xn,genericEncodeConstructor:hn,genericDecodeSum:Un,genericEncodeSum:vn,genericDecodeArgsNoArguments:cn,genericEncodeArgsNoArguments:on,genericDecodeArgsArgument:On,genericEncodeArgsArgument:ln,genericDecodeArgsProduct:Kn,genericEncodeArgsProduct:bn,genericCountArgsNoArguments:dn,genericCountArgsArgument:an,genericCountArgsProduct:Qn}; 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{ +"use strict";var e=require("../Data.CommutativeRing/index.js"),n=require("../Data.DivisionRing/index.js"),r=require("../Data.Eq/index.js"),t=require("../Data.EuclideanRing/index.js"),i=require("../Data.Lens.Getter/index.js"),u=require("../Data.Lens.Iso/index.js"),o=require("../Data.Lens.Iso.Newtype/index.js"),a=require("../Data.Maybe/index.js"),c=require("../Data.Newtype/index.js"),d=require("../Data.Number.Format/index.js"),s=require("../Data.Ord/index.js"),p=require("../Data.Ring/index.js"),w=require("../Data.Semiring/index.js"),f=require("../Data.Show/index.js"),g=require("../Data.String.CodeUnits/index.js"),m=require("../Data.String.Common/index.js"),h=require("../Data.String.Pattern/index.js"),x=require("../Foreign.Generic.Class/index.js"),q=require("../Math/index.js"),l=function(e){return e},D=function(e){return e},N=function(e){return e},j=new f.Show(function(e){return e}),B=new f.Show(function(e){return d.toStringWith(d.fixed(0))(e)+" 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a.Just)return c.wrap(S)(r.value0);throw new Error("Failed pattern match at Genetics.Browser.Types (line 47, column 6 - line 49, column 28): "+[r.constructor.name])},U=function(e){return i.to(d.toStringWith(d.precision(e)))},k=function(e){return i.to(d.toStringWith(d.fixed(e)))},z=function(e){return i.to(d.toStringWith(d.exponential(e)))},A=function(e){return u.iso(function(e){return c.wrap(I)(-q.log(e)/q.ln10)})(function(e){return q.pow(10)(-e)})(e)},H=function(e){return o._Newtype(S)(S)(e)},K=function(e){return o._Newtype(R)(R)(e)};module.exports={Bp:N,_Bp:K,ChrId:D,chrId:T,validChrId:b,_ChrId:H,NegLog10:l,_NegLog10:A,_prec:U,_fixed:k,_exp:z,newtypeBp:R,eqBp:P,ordBp:C,semiringBp:y,ringBp:v,divisionRingBp:W,euclideanRingBp:L,commutativeRingBp:O,encodeBp:G,decodeBp:M,showBp:B,newtypeChrId:S,eqChrId:_,ordChrId:E,encodeChrId:F,decodeChrId:J,showChrId:j,newtypeNegLog10:I}; 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e.toExponential(n)}},exports.unsafeToPrecision=function(n){return function(e){return e.toPrecision(n)}},exports.unsafeDecodeURI=decodeURI,exports.unsafeEncodeURI=encodeURI,exports.unsafeDecodeURIComponent=decodeURIComponent,exports.unsafeEncodeURIComponent=encodeURIComponent; +},{}],"qSZP":[function(require,module,exports) { +"use strict";var e=require("./foreign.js");module.exports={unsafeStringify:e.unsafeStringify,unsafeToFixed:e.unsafeToFixed,unsafeToExponential:e.unsafeToExponential,unsafeToPrecision:e.unsafeToPrecision,unsafeDecodeURI:e.unsafeDecodeURI,unsafeEncodeURI:e.unsafeEncodeURI,unsafeDecodeURIComponent:e.unsafeDecodeURIComponent,unsafeEncodeURIComponent:e.unsafeEncodeURIComponent}; +},{"./foreign.js":"7rcn"}],"7bYH":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),e=require("../Control.Bind/index.js"),r=require("../Control.Monad.Except.Trans/index.js"),i=require("../Data.Array/index.js"),t=require("../Data.BigInt/index.js"),u=require("../Data.Boolean/index.js"),a=require("../Data.Either/index.js"),o=require("../Data.Eq/index.js"),d=require("../Data.EuclideanRing/index.js"),c=require("../Data.Foldable/index.js"),l=require("../Data.Functor/index.js"),s=require("../Data.Generic.Rep/index.js"),f=require("../Data.Identity/index.js"),p=require("../Data.Lens.Getter/index.js"),m=require("../Data.Lens.Internal.Forget/index.js"),g=require("../Data.Lens.Iso.Newtype/index.js"),v=require("../Data.List.Types/index.js"),x=require("../Data.Map.Internal/index.js"),w=require("../Data.Maybe/index.js"),b=require("../Data.Monoid.Additive/index.js"),y=require("../Data.Newtype/index.js"),I=require("../Data.Ord/index.js"),q=require("../Data.Pair/index.js"),h=require("../Data.Ring/index.js"),j=require("../Data.Semiring/index.js"),B=require("../Data.Traversable/index.js"),T=require("../Data.Tuple/index.js"),S=require("../Foreign/index.js"),P=require("../Foreign.Index/index.js"),D=require("../Genetics.Browser.Types/index.js"),F=require("../Global.Unsafe/index.js"),E=function(n){return 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q.Pair(h.sub(t.ringBigInt)(e.value0)(i),j.add(t.semiringBigInt)(e.value1)(i))}},V=function(n){return function(e){var r=l.map(l.functorFn)(w.fromJust())(t.fromNumber)(e*t.toNumber(G(t.ringBigInt)(n)));return l.map(q.functorPair)(function(n){return j.add(t.semiringBigInt)(n)(r)})(n)}},_=function(n){return function(e){var r=G(t.ringBigInt)(e);return{pixelWidth:n.width,coordWidth:r}}},J=function(n){return function(e){return function(r){return function(i){return d.div(n)(h.sub(n.CommutativeRing0().Ring0())(i)(e))(h.sub(n.CommutativeRing0().Ring0())(r)(e))}}}},U=new y.Newtype(function(n){return n},N),k=new y.Newtype(function(n){return n},C),H=function(n){return function(e){return function(r){return function(i){return j.add(n.Semiring0())(j.mul(n.Semiring0())(h.sub(n)(j.one(n.Semiring0()))(i))(e))(j.mul(n.Semiring0())(i)(r))}}}},K=new s.Generic(function(n){return n},function(n){return n}),Q=new l.Functor(function(n){return function(e){return C(l.map(x.functorMap)(l.map(q.functorPair)(n))(e))}}),X=new o.Eq(function(n){return function(e){return o.eq(t.eqBigInt)(n.coordWidth)(e.coordWidth)&&n.pixelWidth===e.pixelWidth}}),Y=new y.Newtype(function(n){return n},z),Z=function(n){return function(e){return function(r){var t,u,a=i.unzip(r);return C(x.fromFoldable(n)(c.foldableArray)(i.zip(a.value0)((t=a.value1,u=B.scanl(B.traversableArray)(function(n){return function(r){return j.add(e)(n)(r)}})(j.zero(e))(t),i.zipWith(q.Pair.create)(i.cons(j.zero(e))(u))(u)))))}}},$=function(i){return e.bind(r.bindExceptT(f.monadIdentity))(S.readArray(i))(function(i){return e.bind(r.bindExceptT(f.monadIdentity))(B.traverse(B.traversableArray)(r.applicativeExceptT(f.monadIdentity))(function(i){return e.bind(r.bindExceptT(f.monadIdentity))(l.map(r.functorExceptT(f.functorIdentity))(y.wrap(D.newtypeChrId))(e.bindFlipped(r.bindExceptT(f.monadIdentity))(S.readString)(P.ix(P.indexableForeign)(P.indexString)(i)("chr"))))(function(u){return e.bind(r.bindExceptT(f.monadIdentity))(e.bindFlipped(r.bindExceptT(f.monadIdentity))((o=r.except(f.applicativeIdentity),d=a.note(n.pure(v.applicativeNonEmptyList)(new S.ForeignError("error parsing size for chr"))),function(n){return o(d(t.fromString(n)))}))(e.bindFlipped(r.bindExceptT(f.monadIdentity))(S.readString)(P.ix(P.indexableForeign)(P.indexString)(i)("size"))))(function(e){return n.pure(r.applicativeExceptT(f.monadIdentity))(new T.Tuple(u,e))});var o,d})})(i))(function(e){return n.pure(r.applicativeExceptT(f.monadIdentity))(Z(D.ordChrId)(t.semiringBigInt)(e))})})},nn=function(n){return function(e){return function(r){return new q.Pair(h.sub(n)(r.value0)(e),j.add(n.Semiring0())(r.value1)(e))}}},en=function(n){return g._Newtype(k)(k)(n.Profunctor0())},rn=function(n){var e=en(m.strongForget),r=p.to(y.alaF(l.functorFn)(l.functorFn)(y.newtypeAdditive)(y.newtypeAdditive)(b.Additive)(c.foldMap(x.foldableMap)(b.monoidAdditive(n.Semiring0())))(G(n)));return function(n){return e(r(n))}},tn=function(n){return function(e){return function(r){var i=p.viewOn(n)(rn(t.ringBigInt)),u=y.unwrap(Y)(r),a=h.sub(t.ringBigInt)(u.value1)(u.value0),o=function(){var n=I.greaterThan(t.ordBigInt)(u.value1)(i),e=I.lessThan(t.ordBigInt)(u.value0)(j.zero(t.semiringBigInt));if(e&&!n)return new q.Pair(j.zero(t.semiringBigInt),a);if(!e&&n)return new q.Pair(h.sub(t.ringBigInt)(i)(a),i);if(e&&n)return new q.Pair(j.zero(t.semiringBigInt),i);if(!e&&!n)return new q.Pair(u.value0,u.value1);throw new Error("Failed pattern match at Genetics.Browser.Coordinates (line 207, column 22 - line 211, column 39): "+[e.constructor.name,n.constructor.name])}();return L(I.min(t.ordBigInt)(i)(I.max(t.ordBigInt)(a)(e)))(new q.Pair(o.value0,o.value1))}}},un=function(n){return function(e){return l.map(x.functorMap)(l.map(q.functorPair)(M(e)))(p.viewOn(n)(en(m.strongForget)))}},an=function(n){return function(e){return function(r){return function(i){return x.filter(n)(function(n){if(I.lessThan(e)(n.value0)(i.value0)&&I.greaterThan(e)(n.value1)(i.value1))return!0;if(I.lessThan(e)(n.value0)(i.value0)&&I.lessThan(e)(n.value1)(i.value0))return!1;if(I.greaterThan(e)(n.value0)(i.value1)&&I.greaterThan(e)(n.value1)(i.value1))return!1;if(u.otherwise)return!0;throw new Error("Failed pattern match at Genetics.Browser.Coordinates (line 167, column 9 - line 171, column 29): "+[n.constructor.name])})(p.viewOn(r)(en(m.strongForget)))}}}},on=function(n){return function(e){return function(r){return function(i){return l.map(x.functorMap)(l.map(q.functorPair)(M(i)))(an(n)(t.ordBigInt)(e)(y.unwrap(Y)(r)))}}}};module.exports={CoordSysView:z,pairSize:G,_TotalSize:rn,normalizeView:tn,aroundPair:nn,normalize:J,scalePairBy:O,scaledSegments:un,"scaledSegments'":on,translatePairBy:V,viewScale:_,xPerPixel:A,_Segments:en,pairsOverlap:R,coordSys:Z,parseCoordSys:$,scaleToScreen:M,newtypeNormalized:U,functorCoordSys:Q,newtypeCoordSys:k,genericCoordSys:K,eqViewScale:X,coordsysviewNewtype:Y}; +},{"../Control.Applicative/index.js":"qYya","../Control.Bind/index.js":"7VcT","../Control.Monad.Except.Trans/index.js":"gr8B","../Data.Array/index.js":"4t4C","../Data.BigInt/index.js":"Zx+T","../Data.Boolean/index.js":"ObQr","../Data.Either/index.js":"B2JL","../Data.Eq/index.js":"Pq4F","../Data.EuclideanRing/index.js":"2IRB","../Data.Foldable/index.js":"eVDl","../Data.Functor/index.js":"+0AE","../Data.Generic.Rep/index.js":"AuzG","../Data.Identity/index.js":"2OKT","../Data.Lens.Getter/index.js":"OPOX","../Data.Lens.Internal.Forget/index.js":"mj9z","../Data.Lens.Iso.Newtype/index.js":"CiFJ","../Data.List.Types/index.js":"Xxuc","../Data.Map.Internal/index.js":"RRDs","../Data.Maybe/index.js":"5mN7","../Data.Monoid.Additive/index.js":"fHyj","../Data.Newtype/index.js":"lz8k","../Data.Ord/index.js":"r4Vb","../Data.Pair/index.js":"PpsX","../Data.Ring/index.js":"E2qH","../Data.Semiring/index.js":"11NF","../Data.Traversable/index.js":"n7EE","../Data.Tuple/index.js":"II/O","../Foreign/index.js":"pu1p","../Foreign.Index/index.js":"Ryy1","../Genetics.Browser.Types/index.js":"HhmG","../Global.Unsafe/index.js":"qSZP"}],"BQGe":[function(require,module,exports) { +exports._parseJSON=JSON.parse,exports._undefined=void 0; +},{}],"DqNI":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),n=require("../Control.Alt/index.js"),r=require("../Control.Applicative/index.js"),t=require("../Control.Apply/index.js"),i=require("../Control.Bind/index.js"),u=require("../Control.Category/index.js"),o=require("../Control.Monad.Except/index.js"),a=require("../Control.Monad.Except.Trans/index.js"),c=require("../Control.Semigroupoid/index.js"),f=require("../Data.Bifunctor/index.js"),d=require("../Data.Boolean/index.js"),l=require("../Data.Either/index.js"),p=require("../Data.Function/index.js"),s=require("../Data.Functor/index.js"),m=require("../Data.Identity/index.js"),y=require("../Data.List.Types/index.js"),x=require("../Data.Maybe/index.js"),w=require("../Data.Nullable/index.js"),g=require("../Data.Semigroup/index.js"),F=require("../Data.Symbol/index.js"),v=require("../Data.Traversable/index.js"),b=require("../Data.TraversableWithIndex/index.js"),E=require("../Data.Variant/index.js"),I=require("../Effect.Exception/index.js"),T=require("../Effect.Uncurried/index.js"),h=require("../Effect.Unsafe/index.js"),j=require("../Foreign/index.js"),q=require("../Foreign.Index/index.js"),S=require("../Foreign.Object/index.js"),N=require("../Global.Unsafe/index.js"),L=require("../Partial.Unsafe/index.js"),P=require("../Record/index.js"),R=require("../Record.Builder/index.js"),D=require("../Type.Data.RowList/index.js"),O=function(e){this.writeVariantImpl=e},V=function(e){this.writeImplFields=e},C=function(e){this.writeImpl=e},W=function(e){this.readVariantImpl=e},A=function(e){this.getFields=e},B=function(e){this.readImpl=e},M=function(e){return 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B(i.composeKleisliFlipped(a.bindExceptT(m.monadIdentity))((n=v.sequence(S.traversableObject)(a.applicativeExceptT(m.monadIdentity)),t=S.mapWithKey(p.const(fe(e))),function(e){return n(t(e))}))(function(e){if("Object"===j.tagOf(e))return r.pure(a.applicativeExceptT(m.monadIdentity))(j.unsafeFromForeign(e));if(d.otherwise)return j.fail(new j.TypeMismatch("Object",j.tagOf(e)));throw new Error("Failed pattern match at Simple.JSON (line 188, column 7 - line 188, column 51): "+[e.constructor.name])}));var n,t},se=function(e){return function(e){return new B(function(n){return ue(e)(D.RLProxy.value)(n)})}},me=new B(r.pure(a.applicativeExceptT(m.monadIdentity))),ye=new A(function(e){return function(e){return r.pure(a.applicativeExceptT(m.monadIdentity))(u.identity(R.categoryBuilder))}}),xe=new B(j.readChar),we=new B(j.readBoolean),ge=function(e){return new B(i.composeKleisliFlipped(a.bindExceptT(m.monadIdentity))(b.traverseWithIndex(b.traversableWithIndexArray)(a.applicativeExceptT(m.monadIdentity))(function(n){return function(r){return o.withExcept(s.map(y.functorNonEmptyList)(j.ErrorAtIndex.create(n)))(fe(e)(r))}}))(j.readArray))},Fe=function(e){return fe(e)},ve=function(e){var n=fe(e);return function(e){return o.runExcept(n(e))}},be=function(e){var n=ve(e);return function(e){return n(j.unsafeToForeign(e))}},Ee=function(e){var n=ve(e);return function(e){return l.hush(n(e))}},Ie=function(){var n,t=f.lmap(l.bifunctorEither)((n=r.pure(y.applicativeNonEmptyList),function(e){return n(j.ForeignError.create(I.message(e)))})),i=T.runEffectFn1(e._parseJSON);return function(e){return a.ExceptT(m.Identity(t(h.unsafePerformEffect(I.try(i(e))))))}}(),Te=function(e){var n=i.composeKleisliFlipped(a.bindExceptT(m.monadIdentity))(fe(e))(Ie);return function(e){return o.runExcept(n(e))}},he=function(e){var n=Te(e);return function(e){return l.hush(n(e))}},je=function(e){return i.composeKleisliFlipped(a.bindExceptT(m.monadIdentity))(fe(e))(Ie)},qe=new O(function(e){return function(e){return L.unsafeCrashWith("Variant was not able to be writen row WriteForeign.")}}),Se=new V(function(e){return function(e){return u.identity(R.categoryBuilder)}}),Ne=function(e){return e.getFields},Le=function(e){return function(e){return new B(function(n){return s.map(a.functorExceptT(m.functorIdentity))(p.flip(R.build)({}))(Ne(e)(D.RLProxy.value)(n))})}},Pe=function(e){return function(n){return function(r){return function(t){return new O(function(i){return function(i){return E.on(r)(e)(F.SProxy.value)(function(r){return j.unsafeToForeign({type:F.reflectSymbol(e)(F.SProxy.value),value:K(n)(r)})})(M(t)(D.RLProxy.value))(i)}})}}}},Re=function(e){return function(n){return function(r){return function(t){return function(i){return function(u){return new V(function(o){return function(o){var 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function(d){var l=Ne(t)(D.RLProxy.value)(d),p=F.reflectSymbol(e)(F.SProxy.value),x=o.withExcept(s.map(y.functorNonEmptyList)(j.ErrorAtProperty.create(p))),w=i.bind(a.bindExceptT(m.monadIdentity))(x(i.bindFlipped(a.bindExceptT(m.monadIdentity))(fe(n))(q.readProp(p)(d))))(function(n){return r.pure(a.applicativeExceptT(m.monadIdentity))(R.insert(f)(u)(e)(F.SProxy.value)(n))});return Oe(y.semigroupNonEmptyList)(m.applicativeIdentity)(s.map(a.functorExceptT(m.functorIdentity))(c.compose(R.semigroupoidBuilder))(w))(l)}})}}}}},Ce=function(e){return function(t){return function(u){return function(o){return new W(function(c){return function(c){var f=F.reflectSymbol(e)(F.SProxy.value);return n.alt(a.altExceptT(y.semigroupNonEmptyList)(m.monadIdentity))(i.bind(a.bindExceptT(m.monadIdentity))(fe(Le()(Ve(new F.IsSymbol(function(){return"type"}))(oe)(Ve(new F.IsSymbol(function(){return"value"}))(me)(ye)()())()()))(c))(function(n){return n.type===f?i.bind(a.bindExceptT(m.monadIdentity))(fe(t)(n.value))(function(n){return r.pure(a.applicativeExceptT(m.monadIdentity))(E.inj(u)(e)(F.SProxy.value)(n))}):j.fail(j.ForeignError.create("Did not match variant tag 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e[t]}}};exports.url=t("URL"),exports.documentURI=t("documentURI"),exports.origin=t("origin"),exports.compatMode=t("compatMode"),exports.characterSet=t("characterSet"),exports.contentType=t("contentType"),exports._doctype=t("doctype"),exports._documentElement=t("documentElement"),exports.getElementsByTagName=function(t){return function(e){return function(){return e.getElementsByTagName(t)}}},exports._getElementsByTagNameNS=function(t){return function(e){return function(n){return function(){return n.getElementsByTagNameNS(t,e)}}}},exports.getElementsByClassName=function(t){return function(e){return function(){return e.getElementsByClassName(t)}}},exports.createElement=function(t){return function(e){return function(){return e.createElement(t)}}},exports._createElementNS=function(t){return function(e){return function(n){return function(){return n.createElementNS(t,e)}}}},exports.createDocumentFragment=function(t){return function(){return 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e._createElementNS(n.toNullable(t))};module.exports={fromNode:f,fromParentNode:i,fromNonElementParentNode:l,fromEventTarget:g,toNode:m,toParentNode:c,toNonElementParentNode:u,toEventTarget:d,doctype:E,documentElement:N,getElementsByTagNameNS:s,createElementNS:T,url:e.url,documentURI:e.documentURI,origin:e.origin,compatMode:e.compatMode,characterSet:e.characterSet,contentType:e.contentType,getElementsByTagName:e.getElementsByTagName,getElementsByClassName:e.getElementsByClassName,createElement:e.createElement,createDocumentFragment:e.createDocumentFragment,createTextNode:e.createTextNode,createComment:e.createComment,createProcessingInstruction:e.createProcessingInstruction,importNode:e.importNode,adoptNode:e.adoptNode}; +},{"./foreign.js":"CI3f","../Data.Functor/index.js":"+0AE","../Data.Nullable/index.js":"YQ8o","../Effect/index.js":"oTWB","../Unsafe.Coerce/index.js":"ETUV","../Web.Internal.FFI/index.js":"fdUh"}],"9SEv":[function(require,module,exports) { +"use strict";var e=function(e){return function(t){return function(){return t[e]}}};exports.children=e("children"),exports._firstElementChild=e("firstElementChild"),exports._lastElementChild=e("lastElementChild"),exports.childElementCount=e("childElementCount"),exports._querySelector=function(e){return function(t){return function(){return t.querySelector(e)}}},exports.querySelectorAll=function(e){return function(t){return function(){return t.querySelectorAll(e)}}}; +},{}],"lU5U":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),r=require("../Data.Eq/index.js"),t=require("../Data.Functor/index.js"),n=require("../Data.Newtype/index.js"),u=require("../Data.Nullable/index.js"),i=require("../Data.Ord/index.js"),l=require("../Effect/index.js"),o=function(e){return e},c=function(r){var n=t.map(l.functorEffect)(u.toMaybe),i=e._querySelector(r);return function(e){return n(i(e))}},a=i.ordString,f=new n.Newtype(function(e){return e},o),d=function(){var r=t.map(l.functorEffect)(u.toMaybe);return function(t){return r(e._lastElementChild(t))}}(),q=function(){var r=t.map(l.functorEffect)(u.toMaybe);return function(t){return r(e._firstElementChild(t))}}(),s=r.eqString;module.exports={firstElementChild:q,lastElementChild:d,QuerySelector:o,querySelector:c,eqQuerySelector:s,ordQuerySelector:a,newtypeQuerySelector:f,children:e.children,childElementCount:e.childElementCount,querySelectorAll:e.querySelectorAll}; +},{"./foreign.js":"9SEv","../Data.Eq/index.js":"Pq4F","../Data.Functor/index.js":"+0AE","../Data.Newtype/index.js":"lz8k","../Data.Nullable/index.js":"YQ8o","../Data.Ord/index.js":"r4Vb","../Effect/index.js":"oTWB"}],"UOgE":[function(require,module,exports) { +"use strict";exports.window=function(){return window}; +},{}],"UQRJ":[function(require,module,exports) { +"use strict";var e=require("./foreign.js");module.exports={window:e.window}; +},{"./foreign.js":"UOgE"}],"dln3":[function(require,module,exports) { +"use strict";exports._body=function(t){return function(){return t.body}},exports._readyState=function(t){return function(){return t.readyState}},exports._activeElement=function(t){return function(){return t.activeElement}},exports._currentScript=function(t){return function(){return t.currentScript}},exports.referrer=function(t){return function(){return t.referrer}},exports.title=function(t){return function(){return t.title}},exports.setTitle=function(t){return function(r){return function(){return r.title=t,{}}}}; +},{}],"v4VO":[function(require,module,exports) { +"use strict";var n=require("../Data.Eq/index.js"),e=require("../Data.Maybe/index.js"),t=require("../Data.Ord/index.js"),r=require("../Data.Ordering/index.js"),a=require("../Data.Show/index.js"),i=function(){function n(){}return n.value=new n,n}(),o=function(){function n(){}return n.value=new n,n}(),u=function(){function n(){}return n.value=new n,n}(),c=new a.Show(function(n){if(n instanceof i)return"Loading";if(n instanceof o)return"Interactive";if(n instanceof u)return"Complete";throw new Error("Failed pattern match at Web.HTML.HTMLDocument.ReadyState (line 15, column 10 - line 18, column 27): "+[n.constructor.name])}),f=function(n){if(n instanceof i)return"loading";if(n instanceof o)return"interactive";if(n instanceof u)return"complete";throw new Error("Failed pattern match at Web.HTML.HTMLDocument.ReadyState (line 21, column 9 - line 24, column 25): "+[n.constructor.name])},s=function(n){return"loading"===n?new e.Just(i.value):"interactive"===n?new e.Just(o.value):"complete"===n?new e.Just(u.value):e.Nothing.value},l=new n.Eq(function(n){return function(e){return n instanceof i&&e instanceof i||(n instanceof o&&e instanceof o||n instanceof u&&e instanceof u)}}),d=new t.Ord(function(){return l},function(n){return function(e){if(n instanceof i&&e instanceof i)return r.EQ.value;if(n instanceof i)return r.LT.value;if(e instanceof i)return r.GT.value;if(n instanceof o&&e instanceof o)return r.EQ.value;if(n instanceof o)return r.LT.value;if(e instanceof o)return r.GT.value;if(n instanceof u&&e instanceof u)return r.EQ.value;throw new Error("Failed pattern match at Web.HTML.HTMLDocument.ReadyState (line 12, column 1 - line 12, column 48): "+[n.constructor.name,e.constructor.name])}});module.exports={Loading:i,Interactive:o,Complete:u,print:f,parse:s,eqReadyState:l,ordReadyState:d,showReadyState:c}; +},{"../Data.Eq/index.js":"Pq4F","../Data.Maybe/index.js":"5mN7","../Data.Ord/index.js":"r4Vb","../Data.Ordering/index.js":"5Eun","../Data.Show/index.js":"mFY7"}],"EU5r":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),r=require("../Data.Functor/index.js"),t=require("../Data.Maybe/index.js"),n=require("../Data.Nullable/index.js"),o=require("../Effect/index.js"),a=require("../Unsafe.Coerce/index.js"),u=require("../Web.HTML.HTMLDocument.ReadyState/index.js"),f=require("../Web.Internal.FFI/index.js"),c=a.unsafeCoerce,i=a.unsafeCoerce,d=a.unsafeCoerce,s=a.unsafeCoerce,m=a.unsafeCoerce,T=function(){var n,a=r.map(o.functorEffect)((n=t.fromMaybe(u.Loading.value),function(e){return n(u.parse(e))}));return function(r){return a(e._readyState(r))}}(),g=f.unsafeReadProtoTagged("HTMLDocument"),l=f.unsafeReadProtoTagged("HTMLDocument"),M=f.unsafeReadProtoTagged("HTMLDocument"),D=f.unsafeReadProtoTagged("HTMLDocument"),E=f.unsafeReadProtoTagged("HTMLDocument"),b=function(){var t=r.map(o.functorEffect)(n.toMaybe);return function(r){return t(e._currentScript(r))}}(),v=function(){var t=r.map(o.functorEffect)(n.toMaybe);return function(r){return t(e._body(r))}}(),y=function(){var t=r.map(o.functorEffect)(n.toMaybe);return function(r){return t(e._activeElement(r))}}();module.exports={fromDocument:E,fromNode:M,fromParentNode:g,fromNonElementParentNode:l,fromEventTarget:D,toDocument:m,toNode:d,toParentNode:c,toNonElementParentNode:i,toEventTarget:s,body:v,readyState:T,activeElement:y,currentScript:b,referrer:e.referrer,title:e.title,setTitle:e.setTitle}; +},{"./foreign.js":"dln3","../Data.Functor/index.js":"+0AE","../Data.Maybe/index.js":"5mN7","../Data.Nullable/index.js":"YQ8o","../Effect/index.js":"oTWB","../Unsafe.Coerce/index.js":"ETUV","../Web.HTML.HTMLDocument.ReadyState/index.js":"v4VO","../Web.Internal.FFI/index.js":"fdUh"}],"qu+f":[function(require,module,exports) { +"use strict";exports.document=function(n){return function(){return n.document}},exports.navigator=function(n){return function(){return n.navigator}},exports.location=function(n){return function(){return n.location}},exports.history=function(n){return function(){return n.history}},exports.innerWidth=function(n){return function(){return n.innerWidth}},exports.innerHeight=function(n){return function(){return n.innerHeight}},exports.alert=function(n){return function(r){return function(){return r.alert(n),{}}}},exports.confirm=function(n){return function(r){return function(){return r.confirm(n)}}},exports.moveBy=function(n){return function(r){return function(t){return function(){return t.moveBy(n,r),{}}}}},exports.moveTo=function(n){return function(r){return function(t){return function(){return t.moveTo(n,r),{}}}}},exports._open=function(n){return function(r){return function(t){return function(e){return function(){return e.open(n,r,t)}}}}},exports.outerHeight=function(n){return function(){return n.outerHeight}},exports.outerWidth=function(n){return function(){return n.outerWidth}},exports.print=function(n){return function(){return n.print(),{}}},exports._prompt=function(n){return function(r){return function(t){return function(){return t.prompt(n,r)}}}},exports.resizeBy=function(n){return function(r){return function(t){return function(){return t.resizeBy(n,r),{}}}}},exports.resizeTo=function(n){return function(r){return function(t){return function(){return t.resizeTo(n,r),{}}}}},exports.screenX=function(n){return function(){return n.screenX}},exports.screenY=function(n){return function(){return n.screenY}},exports.scroll=function(n){return function(r){return function(t){return function(){return t.scroll(n,r),{}}}}},exports.scrollBy=function(n){return function(r){return function(t){return function(){return t.scrollBy(n,r),{}}}}},exports.scrollX=function(n){return function(){return n.scrollX}},exports.scrollY=function(n){return function(){return n.scrollY}},exports.localStorage=function(n){return function(){return n.localStorage}},exports.sessionStorage=function(n){return function(){return n.sessionStorage}},exports._requestAnimationFrame=function(n){return function(r){return function(){return r.requestAnimationFrame(n)}}},exports._cancelAnimationFrame=function(n){return function(r){return function(){return r.cancelAnimationFrame(n)}}},exports._requestIdleCallback=function(n){return function(r){return function(t){return function(){return t.requestIdleCallback(r,n)}}}},exports._cancelIdleCallback=function(n){return function(r){return function(){return r.cancelIdleCallback(n)}}},exports.parent=function(n){return function(){return n.parent}},exports._opener=function(n){return function(){return n.opener}}; +},{}],"o+50":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),n=require("../Data.Eq/index.js"),r=require("../Data.Functor/index.js"),t=require("../Data.Newtype/index.js"),o=require("../Data.Nullable/index.js"),u=require("../Data.Ord/index.js"),i=require("../Effect/index.js"),c=require("../Unsafe.Coerce/index.js"),a=function(e){return e},f=function(e){return e},l=c.unsafeCoerce,s=function(n){return function(t){var o=r.map(i.functorEffect)(a),u=e._requestIdleCallback(n)(t);return function(e){return o(u(e))}}},m=function(n){var t=r.map(i.functorEffect)(f),o=e._requestAnimationFrame(n);return function(e){return t(o(e))}},d=function(n){return function(t){return function(u){return r.map(i.functorEffect)(o.toMaybe)(e._prompt(n)(t)(u))}}},p=function(n){return function(t){return r.map(i.functorEffect)(o.toMaybe)(e._prompt(n)("")(t))}},q=function(n){return r.map(i.functorEffect)(o.toMaybe)(e._opener(n))},y=function(n){return function(t){return function(u){return function(c){return r.map(i.functorEffect)(o.toMaybe)(e._open(n)(t)(u)(c))}}}},I=new t.Newtype(function(e){return e},a),w=new t.Newtype(function(e){return e},f),b=new n.Eq(function(e){return function(n){return e===n}}),g=new u.Ord(function(){return b},function(e){return function(n){return u.compare(u.ordInt)(e)(n)}}),E=new n.Eq(function(e){return function(n){return e===n}}),h=new u.Ord(function(){return E},function(e){return function(n){return u.compare(u.ordInt)(e)(n)}}),v=function(n){return e._cancelIdleCallback(t.unwrap(I)(n))},C=function(n){return e._cancelAnimationFrame(t.unwrap(w)(n))};module.exports={toEventTarget:l,open:y,prompt:p,promptDefault:d,requestAnimationFrame:m,cancelAnimationFrame:C,requestIdleCallback:s,cancelIdleCallback:v,opener:q,newtypeRequestAnimationFrameId:w,eqRequestAnimationFrameId:E,ordRequestAnimationFrameId:h,newtypeRequestIdleCallbackId:I,eqRequestIdleCallbackId:b,ordRequestIdleCallbackId:g,document:e.document,navigator:e.navigator,location:e.location,history:e.history,innerWidth:e.innerWidth,innerHeight:e.innerHeight,alert:e.alert,confirm:e.confirm,moveBy:e.moveBy,moveTo:e.moveTo,outerHeight:e.outerHeight,outerWidth:e.outerWidth,print:e.print,resizeBy:e.resizeBy,resizeTo:e.resizeTo,screenX:e.screenX,screenY:e.screenY,scroll:e.scroll,scrollBy:e.scrollBy,scrollX:e.scrollX,scrollY:e.scrollY,localStorage:e.localStorage,sessionStorage:e.sessionStorage,parent:e.parent}; 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e=require("./foreign.js"),n=require("../Data.Bounded/index.js"),t=require("../Data.Enum/index.js"),r=require("../Data.Eq/index.js"),o=require("../Data.Maybe/index.js"),u=require("../Data.Ord/index.js"),a=require("../Data.Ordering/index.js"),i=require("../Unsafe.Coerce/index.js"),c=require("../Web.Internal.FFI/index.js"),f=function(){function e(){}return e.value=new e,e}(),s=function(){function e(){}return e.value=new e,e}(),d=function(){function e(){}return e.value=new e,e}(),l=function(){function e(){}return e.value=new e,e}(),v=i.unsafeCoerce,m=i.unsafeCoerce,E=function(e){return 0===e?new o.Just(f.value):1===e?new o.Just(s.value):2===e?new o.Just(d.value):3===e?new o.Just(l.value):o.Nothing.value},y=c.unsafeReadProtoTagged("KeyboardEvent"),K=c.unsafeReadProtoTagged("KeyboardEvent"),w=function(e){if(e instanceof f)return 0;if(e instanceof s)return 1;if(e instanceof d)return 2;if(e instanceof l)return 3;throw new Error("Failed pattern match at Web.UIEvent.KeyboardEvent (line 107, 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t.bind(D.bindAff)(R.liftEffect(D.monadEffectAff)(Z.browserViewManager(i)(h.wrap(N.newtypeMilliseconds)(200))({initialView:u})(f)))(function(s){return t.bind(D.bindAff)(R.liftEffect(D.monadEffectAff)(L.new({viewManager:s,cmdInfoBox:a,container:f,coordSys:i})))(function(i){return t.discard(t.discardUnit)(D.bindAff)(R.liftEffect(D.monadEffectAff)((a={scrollMod:.1,zoomMod:.15},function(){var n;return ge(a)(function(e){return s.updateView(e)})(),e.buttonEvent("reset")((n=new Z.ModView(c.const(h.unwrap(P.coordsysviewNewtype)(u))),s.updateView(n)))(),be(b.viewOn(f)(V._Container(V.newtypeBrowserContainer)(p.strongForget)))({scrollMod:.075})(function(e){return s.updateView(e)})(),V.wheelZoom(V.newtypeBrowserContainer)(f)(function(e){var n=Z.ZoomView.create(1+.06*e);return s.updateView(n)})()})))(function(){if(o.urls.snps instanceof g.Just)return r.applySecond(D.applyAff)(qe(i)(o))(n.pure(D.applicativeAff)(M.unit));if(o.urls.snps instanceof g.Nothing)return n.pure(D.applicativeAff)(M.unit);throw 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{ +var e=require("./output/Genetics.Browser.UI");window.GenomeBrowser=e; +},{"./output/Genetics.Browser.UI":"JuOH"}]},{},["Focm"], null)
\ No newline at end of file diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 2c1f67d4..42e57523 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -21,10 +21,10 @@ </head> -<body style="width: 100% !important;"> +<body style="width: 100%"> <!-- Navbar ================================================== --> - <div class="navbar navbar-inverse navbar-static-top pull-left" role="navigation" style="width: 100%; white-space: nowrap;"> + <div class="navbar navbar-inverse navbar-static-top pull-left" role="navigation" style="width: 100%; min-width: 770px; white-space: nowrap;"> <!--<div class="navbar navbar-default" style="width: 100%; white-space: nowrap;">--> <div class="container-fluid" style="width: 100%;"> <!-- Brand and toggle get grouped for better mobile display --> @@ -41,13 +41,33 @@ <a href="/" style="font-weight: bold;">GeneNetwork</a> </li> <li class=""> - <a href="/intro">Intro</a> + <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Intro <span class="caret"></a> + <ul class="dropdown-menu"> + <li><a href="/intro">Intro</a></li> + <li><a href="/submit_trait">Submit Trait</a></li> + <li><a href="http://genenetwork.org/webqtl/main.py?FormID=batSubmit">Batch Submission</a></li> + </ul> </li> <li class=""> - <a href="/">Search</a> + <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Help <span class="caret"></a> + <ul class="dropdown-menu"> + <li><a href="/references">References</a></li> + <li><a href="http://genenetwork.org/glossary.html">Glossary of Term</a></li> + <li><a href="http://genenetwork.org/faq.html">FAQ</a></li> + <li><a href="/policies">Policies</a></li> + <li><a href="/links">Links</a></li> + <li><a href="/environments">Environments</a></li> + <li><a href="/news">GN1 News</a></li> + </ul> </li> <li class=""> - <a href="/submit_trait">Submit Trait</a> + <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Tools <span class="caret"></a> + <ul class="dropdown-menu"> + <li><a href="/snp_browser">Variant Browser</a></li> + <li><a href="http://bnw.genenetwork.org/BNW/sourcecodes/home.php">Bayesian Network Webserver</a></li> + <li><a href="https://systems-genetics.org/">Systems Genetics PheWAS</a></li> + <li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a></li> + </ul> </li> <li class=""> <a href="/collections/list">Collections @@ -59,46 +79,32 @@ </a> </li> <li class=""> - <a href="/snp_browser">SNP Browser</a> - </li> - <li class=""> - <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Help <span class="caret"></a> - <ul class="dropdown-menu"> - <li><a href="/news">News</a></li> - <li><a href="/references">References</a></li> - <li><a href="/policies">Policies</a></li> - <li><a href="/links">Links</a></li> - <li><a href="/environments">Environments</a></li> - </ul> - </li> - <li class=""> {% if g.user_session.logged_in %} <a id="login_out" title="Signed in as {{ g.user_session.user_name }}" href="/n/logout">Sign out</a> {% else %} <a id="login_in" href="/n/login">Sign in</a> {% endif %} </li> + <!-- <li style="margin-left: 20px;"> <a href="http://gn2-staging.genenetwork.org" style="font-weight: bold;" >Use Staging Branch</a> </li> - <li style="margin-left: 20px;"> - <a href="http://www.genenetwork.org" style="font-weight: bold;" >Use GeneNetwork 1</a> - </li> + --> </ul> </div> </div> </div> - <div class="container-fluid" style="position: relative; background-color: #d5d5d5; height: 95px;"> + <div class="container-fluid" style="width: 100%; min-width: 650px; position: relative; background-color: #d5d5d5; height: 84px;"> <form method="get" action="/gsearch"> - <div class="row" style="position: absolute; bottom: 0; top: 30px;"> - <select class="form-control col-xs-2" style="width: 170px; margin-top: 15px; margin-left: 10px;" name="type"> + <div class="row" style="width: 100%; position: absolute; bottom: 0; top: 30px;"> + <select style="width: 150px; margin-top: 15px; margin-left: 20px;" name="type"> <option value="gene">Genes / Molecules</option> <option value="phenotype" {% if type=="phenotype" %}selected{% endif %}>Phenotypes</option> </select> - <input class="btn btn-primary form-control col-xs-2" style="width: 100px; margin-top: 15px; margin-left: 10px;" type="submit" value="Search All"> - <input class="form-control col-xs-6" style="width: 600px; margin-top: 15px; margin-left: 10px;" type="text" name="terms" required> + <input class="btn btn-primary" style="width: 100px; margin-left: 10px;" type="submit" value="Search All"> + <input style="width: 50%; margin-top: 15px; margin-left: 10px;" type="text" name="terms" required> </div> </form> </div> @@ -125,27 +131,35 @@ <a href="http://joss.theoj.org/papers/10.21105/joss.00025"><img src="https://camo.githubusercontent.com/846b750f582ae8f1d0b4f7e8fee78bed705c88ba/687474703a2f2f6a6f73732e7468656f6a2e6f72672f7061706572732f31302e32313130352f6a6f73732e30303032352f7374617475732e737667" alt="JOSS" data-canonical-src="http://joss.theoj.org/papers/10.21105/joss.00025/status.svg" style="max-width:100%;"></a> </p> <br /> - <p>GeneNetwork is supported by:</p> - <UL> - <LI> - <a href="http://citg.uthsc.edu"> + <p>GeneNetwork support from:</p> + <ul> + <li> + <a href="http://citg.uthsc.edu"> The UT Center for Integrative and Translational Genomics - </A> + </a> + </li> + <li> + <a href="https://www.nigms.nih.gov/">NIGMS</a> + Systems Genetics and Precision Medicine Project (R01 GM123489, 2017-2021) + </li> + <li> + <a href="https://www.drugabuse.gov/">NIDA</a> + NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022) + </li> + <li> + <a href="http://www.nia.nih.gov/">NIA</a> + Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018) </li> - <LI><a href="http://www.iniastress.org">NIAAA</A> - Integrative Neuroscience Initiative on Alcoholism - (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425) + <li> + <a href="http://www.iniastress.org/">NIAAA</a> + Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017) </li> - <LI> - <a - href="https://www.drugabuse.gov/">NIDA</A>, <a class="smallsize" href="http://www.nimh.nih.gov/">NIMH</A> - , and <a class="smallsize" href="http://www.niaaa.nih.gov/"> - NIAAA</A> (P20-DA 21131) + <li> + <a href="http://www.drugabuse.gov/">NIDA</a>, <a href="http://www.nimh.nih.gov/">NIMH</a>, and <a href="http://www.niaaa.nih.gov/">NIAAA</a> + (P20-DA 21131, 2001-2012) </li> - <LI>NCI <a href="http://emice.nci.nih.gov/">MMHCC</A> (U01CA105417) and - <a href="https://en.wikipedia.org/wiki/National_Center_for_Research_Resources">NCRR</a> - <a href="https://en.wikipedia.org/wiki/Biomedical_Informatics_Research_Network">BIRN</a> - (U24 RR021760) + <li> + NCI <a href="http://emice.nci.nih.gov/">MMHCC</a> (U01CA105417), NCRR, <a href="http://www.birncommunity.org/">BIRN</a>, (U24 RR021760) </li> </UL> <!--</p>--> diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html index 5372fa46..e6e09449 100644 --- a/wqflask/wqflask/templates/collections/list.html +++ b/wqflask/wqflask/templates/collections/list.html @@ -92,8 +92,6 @@ <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script> <script> $('#trait_table').dataTable( { "drawCallback": function( settings ) { @@ -116,12 +114,11 @@ "orderable": false } ], "order": [[1, "asc" ]], - "sDom": "RZtr", + "sDom": "Ztr", "iDisplayLength": -1, - "autoWidth": true, + "autoWidth": false, "bDeferRender": true, "bSortClasses": false, - "scrollY": "600px", "scrollCollapse": true, "paging": false, "orderClasses": true diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 8d22b2a8..a23f3f70 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -8,7 +8,7 @@ {% block content %} <!-- Start of body --> - <div class="container"> + <div class="container" style="min-width: 1250px;"> {% if uc %} <h1>{{ uc.name }}</h1> {% else %} @@ -84,8 +84,8 @@ <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button> <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button> - <button class="btn btn-danger" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Delete From Collection</button> - <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Copy Record to Other Collection</button> + <button class="btn btn-danger" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Delete Rows</button> + <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Copy to Other Collection</button> <br /> <br /> <form id="export_form" method="POST" action="/export_traits_csv"> @@ -182,6 +182,7 @@ { "type": "natural", "width": 50 }, { "type": "natural" }, { "type": "natural", "width": 120 }, + { "type": "natural", "width": 120 }, { "type": "natural" }, { "type": "natural", "width": 130 }, { "type": "natural", "width": 35 }, diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index bcdc499f..34a15c6a 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -2,52 +2,56 @@ {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/corr_matrix.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" /> {% endblock %} {% block content %} -<div class="container"> +<div class="container" width="100%"> <h1>Correlation Matrix</h1> +<div style="width: 100%; max-width: 850px;">Lower left cells list Pearson product-moment correlations; upper right cells list Spearman rank order correlations. Each cell also contains the n of cases. Values ranging from 0.4 to 1.0 range from orange to white, while values ranging from -0.4 to -1.0 range from dark blue to white. Select any cell to generate a scatter plot. Select trait labels for more information.</div> <hr style="height: 1px; background-color: #A9A9A9;"> {% if lowest_overlap < 8 %} -<div style="margin: 20px;" >Caution: This matrix of correlations contains some cells with small sample sizes of fewer than 8.</div> +<div style="margin-bottom: 10px;"><i><font style="color: red;">Caution</font>: This matrix of correlations contains some cells with small sample sizes of fewer than 8.</i></div> {% endif %} -<table class="matrix" border="1" cellpadding="5" cellspacing="1" width="80%"> +<table class="matrix" border="1" cellpadding="5" cellspacing="1" width="100%"> <tbody> <tr> - <td style="background-color: royalblue;" ></td> - <td align="center" colspan="{{traits|length + 1 }}" style="font-weight: Bold; border: 1px solid #999999; padding: 3px; color: #fff; background-color: royalblue;">Spearman Rank Correlation (rho)</td> + <td style="background-color: #369;" ></td> + <td align="center" colspan="{{traits|length + 2 }}" style="font-weight: Bold; border: 1px solid #000000; padding: 3px; color: #fff; background-color: #369;">Spearman Rank Correlation (rho)</td> </tr> <tr> - <td align="center" rowspan="{{traits|length + 1 }}" width="10" style="font-weight: Bold; border: 1px solid #999999; padding: 3px; color: #fff; background-color: royalblue;">P e a r s o n r</td> - <td width="300"></td> + <td align="center" rowspan="{{traits|length + 2 }}" width="10" style="font-weight: Bold; border: 1px solid #000000; padding: 3px; color: #fff; background-color: #369;">P e a r s o n r</td> + <td></td> + <td width="300" align="center" style="white-space: nowrap"><div style="display: inline-block; margin: 4px;"><button class="btn btn-default" id="short_labels" style="display: inline-block"><span style="display: none;" class="short_check glyphicon glyphicon-ok"></span> Short Labels</button> <button class="btn btn-default" id="long_labels" style="display: inline-block;"><span style="display: none;" class="long_check glyphicon glyphicon-ok"></span> Long Labels</button></div></td> {% for trait in traits %} - <td align="center"> - <a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}" style="font-weight: Bold;">Trait{{ loop.index }}</a> + <td align="center" style="padding: 5px;"> + <a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 14px;"><b>{{ loop.index }}</b></font></a> </td> {% endfor %} </tr> {% for trait in traits %} <tr> - <td> - <a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}" style="font-weight: Bold;">Trait {{ loop.index }}: {{ trait.dataset.name }}::{{ trait.name }}</a> - <div class="shortName" style="display:none">{% if trait.dataset.type == "ProbeSet" %}Symbol: {{ trait.symbol }}{% elif trait.dataset.type == "Publish" %}Phenotype: {{ trait.post_publication_abbreviation }}{% else %}Genotype{% endif %} </div> + <td align="center"><input type="checkbox" class="checkbox" style="margin-left: 3px; margin-right: 1px;"></td> + <td align="right" style="padding-right: 4px;" > + <a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 14px; font-style: Bold;"><b>Trait {{ loop.index }}: {{ trait.dataset.name }} {{ trait.name }}</b></font></a> + <div class="shortName" style="display:none">{% if trait.dataset.type == "ProbeSet" %}Gene Symbol: {{ trait.symbol }}{% elif trait.dataset.type == "Publish" %}Trait Symbol: {{ trait.post_publication_abbreviation }}{% elif trait.dataset.type == "Geno" %}Genotype{% endif %} </div> <div class="verboseName" style="display: none;"> {% if trait.dataset.type == "ProbeSet" %} <div>{{ trait.symbol }} on Chr {{ trait.chr }} @ {{ trait.mb }} Mb</div><div>{{ trait.description }}</div><div>{{ trait.probe_target_description }}</div> {% elif trait.dataset.type == "Publish" %} - <div>PubMed {{ trait.pubmed_id }}: RecordID/{{ trait.name }}</div><div>Phenotype: {{ trait.description_display }}</div> - {% else %} + <div>PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term={{ trait.pubmed_id }}">{{ trait.pubmed_id }}</a>, Record ID {{ trait.name }}</div><div>Phenotype: {{ trait.description_display }}</div> + {% elif trait.dataset.type == "Geno" %} <div>Locus {{ trait.name }}</div><div>Chr {{ trait.chr }} @ {{ trait.mb }} Mb</div> {% endif %} </div> </td> {% for result in corr_results[loop.index-1] %} {% if result[0].name == trait.name %} - <td nowrap="ON" align="center" bgcolor="#cccccc" style="line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #000000;" ><em>n</em><br>{{ result[2] }}</font></a></td> + <td nowrap="ON" align="center" bgcolor="#cccccc" style="padding: 3px; line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><em>n</em><br>{{ result[2] }}</font></a></td> {% else %} - <td nowrap="ON" align="middle" class="corr_cell" style="line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #000000;" ><span class="corr_value">{{ '%0.3f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> + <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> {% endif %} {% endfor %} </tr> @@ -55,28 +59,40 @@ </tbody> </table> <br> -<button class="btn btn-default" id="short_labels">Short Labels</button> -<button class="btn btn-default" id="long_labels">Long Labels</button> {% if pca_works == "True" %} -<br> -<br> <h2>PCA Traits</h2> -<ul> +<div style="margin-bottom: 20px; overflow:hidden;"> +<table id="pca_table" class="table-hover table-striped cell-border" id='trait_table' style="float: left;"> + <thead> + <tr> + <th></th> + <th>Index</th> + <th>PCA Trait</th> + </tr> + </tr> + </thead> + <tbody> {% for this_trait_id in pca_trait_ids %} - <li>{{ loop.index }}. <input type="checkbox" class="trait_checkbox" name="pca_trait" value="{{ data_hmac('{}:{}'.format(pca_trait_ids[loop.index - 1], "Temp")) }}"> <a href="{{ url_for('show_trait_page', trait_id = pca_trait_ids[loop.index - 1], dataset = "Temp") }}">{{ pca_trait_ids[loop.index - 1] }}</a></li> + <tr> + <td align="center" style="padding: 0px;"><input type="checkbox" class="trait_checkbox" name="pca_trait" value="{{ data_hmac('{}:{}'.format(pca_trait_ids[loop.index - 1], "Temp")) }}"></td> + <td align="right">{{ loop.index }}</td> + <td><a href="{{ url_for('show_trait_page', trait_id = pca_trait_ids[loop.index - 1], dataset = "Temp") }}">{{ pca_trait_ids[loop.index - 1] }}</a></td> + </tr> {% endfor %} -</ul> + </tbody> +</table> +<br> <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button> <button class="btn btn-default" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> -<br> +</div> <h2>Factor Loadings Plot</h2> <div id="loadings_plot" style="margin-top: 20px; margin-bottom: 20px; width: 980px; border-style: solid; border-width: 1px;"></div> <h2>Factor Loadings Table</h2> -<table class="table table-hover table-striped" border="1" style="margin-top: 20px; margin-bottom: 20px;" width="30%"> +<table id="loadings_table" class="table-hover table-striped cell-border" id='trait_table' style="float: left;"> <thead> <tr> - <th></th> + <th>Trait</th> <th style="text-align: right;" >Factor 1</th> <th style="text-align: right;" >Factor 2</th> {% if trait_list|length > 2 %}<th style="text-align: right;">Factor 3</th>{% endif %} @@ -87,7 +103,7 @@ {% set row_counter = loop.index-1 %} <tr> <td> - <a href="{{ url_for('show_trait_page', trait_id = traits[loop.index-1].name, dataset = traits[loop.index-1].dataset.name) }}"> + <a title="{% if traits[loop.index-1].dataset.type == "ProbeSet" %}{{ traits[loop.index-1].symbol }}{% elif traits[loop.index-1].dataset.type == "Publish" %}{{ traits[loop.index-1].post_publication_abbreviation }}{% endif %}" href="{{ url_for('show_trait_page', trait_id = traits[loop.index-1].name, dataset = traits[loop.index-1].dataset.name) }}"> {{ traits[loop.index-1].name }} </a> </td> @@ -119,5 +135,39 @@ <script language="javascript" type="text/javascript" src="/static/new/js_external/chroma.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/loadings_plot.js"></script> <script type="text/javascript" src="/static/new/javascript/create_corr_matrix.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script> + <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> + + <script> + $('#pca_table').dataTable( { + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "t", + "iDisplayLength": -1, + "autoWidth": true, + "bDeferRender": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true + } ); + + $('#loadings_table').dataTable( { + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "t", + "iDisplayLength": -1, + "autoWidth": true, + "bDeferRender": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true + } ); + </script> {% endblock %} diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 7cc998bb..8b94784f 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -2,9 +2,10 @@ {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css"> {% endblock %} {% block content %} - <div class="container"> + <div class="container" style="min-width: 1250px;"> <div class="page-header"> <h1>Correlation Table</h1> <h2>Trait: {{ this_trait.name }} @@ -12,8 +13,8 @@ <hr style="height: 1px; background-color: #A9A9A9;"> </div> - <p>Values of record {{ this_trait.name }} in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId={{ dataset.group.accession_id }}">{{ dataset.fullname }}</a> - dataset were compared to all records in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId={{ target_dataset.group.accession_id }}">{{ target_dataset.fullname }}</a> + <p>Values of record {{ this_trait.name }} in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a> + dataset were compared to all records in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if target_dataset.accession_id != 'None' %}GN_AccessionId={{ target_dataset.accession_id }}{% else %}InfoPageName={{ target_dataset.name }}{% endif %}">{{ target_dataset.fullname }}</a> dataset. The top {{ return_number }} correlations ranked by the {{ formatted_corr_type }} are displayed. You can resort this list by clicking the headers. Select the Record ID to open the trait data and analysis page. @@ -70,82 +71,50 @@ </button> </form> </div> - <div> - <br /> - <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> - <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button> - <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button> - <button class="btn btn-default" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> - <button id="redraw" class="btn btn-default">Reset Columns</button> - <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ..."> - <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ..."> - <br /> <br /> + <div> + <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> + <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button> + <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button> + <button class="btn btn-default" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> + <button id="redraw" class="btn btn-default">Reset Columns</button> + <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ..."> + <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ..."> + <br /> + <br /> + <button id="more_options" class="btn btn-primary">More Options...</button> + <br /> + <br /> + <div id="filter_options" style="display: none;"> + <span style="border: 1px dashed #999999; padding: 8px; background-color: #ddf; font-size: 12px;"> + <button id="select_traits" class="btn btn-primary" style="font-size: 12px; padding: 2px 3px;">Select Traits</button> with r > + <input type="text" name="r_greater_select" value="-1.0" size="6" maxlength="10"> + <select id="r_and_or" size="1"> + <option value="and" selected>AND</option> + <option value="or">OR</option> + </select> + r < + <input type="text" name="r_less_select" value="1.0" size="6" maxlength="10">, with mean > + <input type="text" name="mean_greater_select" value="0" size="6" maxlength="10"> + <select id="mean_and_or" size="1"> + <option value="and" selected>AND</option> + <option value="or">OR</option> + </select> + mean < + <input type="text" name="mean_less_select" value="100" size="6" maxlength="10"> + </span> + <br /> + <br /> + </div> </div> - <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};"> <table id="trait_table" class="display dataTable nowrap" style="font-size: 12px; float: left;"> <thead> <tr> <th></th> - {% for header in target_dataset.header_fields %} - {% if header == 'Year' %} - <th>{{header}}</th> - {% elif header == 'Max LRS' %} - <th>Max LRS</th> - {% elif header == 'Max LRS Location' %} - <th>{{header}}</th> - {% elif header == 'Location' %} - <th>{{header}}</th> - {% elif header == 'Mean' %} - <th>{{header}}</th> - {% elif header == 'Additive Effect' %} - <th>Additive Effect</th> - {% elif header == 'Index' %} + {% for header in header_fields %} <th>{{header}}</th> - {% elif header == 'N' %} - <th>{{header}}</th> - {% else %} - <th>{{header}}</th> - {% endif %} {% endfor %} - {% if target_dataset.type == "ProbeSet" %} - {% if corr_method == 'pearson' %} - <th>Sample r</th> - <th>N</th> - <th>Sample p(r)</th> - <th>Lit r</th> - <th>Tissue r</th> - <th>Tissue p(r)</th> - {% else %} - <th>Sample rho</th> - <th>N</th> - <th>Sample p(rho)</th> - <th>Lit r</th> - <th>Tissue rho</th> - <th>Tissue p(rho)</th> - {% endif %} - {% elif target_dataset.type == "Publish" %} - {% if corr_method == 'pearson' %} - <th>Sample r</th> - <th> N</th> - <th>Sample p(r)</th> - {% else %} - <th>Sample rho</th> - <th> N</th> - <th>Sample p(rho)</th> - {% endif %} - {% elif target_dataset.type == "Geno" %} - {% if corr_method == 'pearson' %} - <th>Sample r</th> - <th>N</th> - <th>Sample p(r)</th> - {% else %} - <th>Sample rho</th> - <th>N</th> - <th>Sample p(rho)</th> - {% endif %} - {% endif %} </tr> </thead> @@ -167,9 +136,6 @@ <td>{{ trait.description_display }}</TD> <td style="white-space: nowrap;">{{ trait.location_repr }}</td> <td align="right">{{ '%0.3f' % trait.mean|float }}</td> - <td align="right">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td> - <td align="right">{{ trait.LRS_location_repr }}</td> - <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td> <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td> <td align="right">{{ trait.num_overlap }}</td> <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td> @@ -185,6 +151,9 @@ <td align="right">{{'%0.3f'|format(trait.tissue_corr)}}</td> <td align="right">{{'%0.3e'|format(trait.tissue_pvalue)}}</td> {% endif %} + <td align="right">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td> + <td align="right">{{ trait.LRS_location_repr }}</td> + <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td> {% elif target_dataset.type == "Publish" %} <td>{{ trait.description_display }}</td> <td>{{ trait.authors }}</td> @@ -193,12 +162,12 @@ {{ trait.pubmed_text }} </a> </td> - <td align="right">{{ trait.LRS_score_repr }}</td> - <td align="right">{{ trait.LRS_location_repr }}</td> - <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td> <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td> <td align="right">{{ trait.num_overlap }}</td> <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td> + <td align="right">{{ trait.LRS_score_repr }}</td> + <td align="right">{{ trait.LRS_location_repr }}</td> + <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td> {% elif target_dataset.type == "Geno" %} <td align="right">{{ trait.location_repr }}</TD> <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td> @@ -220,10 +189,9 @@ <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script> - <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> - <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script> - <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script> + <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.13/js/jquery.dataTables.min.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/buttons.colVis.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> <script type="text/javascript" charset="utf-8"> @@ -262,6 +230,47 @@ return ((x < y) ? 1 : ((x > y) ? -1 : 0)); }; + //$.fn.dataTableExt.afnFiltering.push( + + $.fn.dataTable.ext.search.push( function( settings, data, dataIndex ) { + var r_column = {{ filter_cols[0] }}; + var r_greater = parseFloat($('input[name=r_greater_select]').val()) + var r_less = parseFloat($('input[name=r_less_select]').val()); + var r_and_or = $('#r_and_or').val(); + + var mean_column = {{ filter_cols[1] }}; + var mean_greater = parseFloat($('input[name=mean_greater_select]').val()); + var mean_less = parseFloat($('input[name=mean_less_select]').val()); + var mean_and_or = $('#mean_and_or').val(); + + if (r_and_or == "and" && mean_and_or == "and"){ + if ( (data[r_column] >= r_greater && data[r_column] <= r_less) && {% if filter_cols[1] != 0 %}(data[mean_column] > mean_greater && data[mean_column] < mean_less){% else %} true{% endif %} ){ + return true + } + else { + return false + } + } else if (r_and_or == "and" && mean_and_or == "or"){ + if ( (data[r_column] >= r_greater && data[r_column] <= r_less) && {% if filter_cols[1] != 0 %}(data[mean_column] >= mean_greater || data[mean_column] <= mean_less){% else %} true{% endif %} ){ + return true + } else { + return false + } + } else if (r_and_or == "or" && mean_and_or == "and") { + if ( (data[r_column] >= r_greater || data[r_column] <= r_less) && {% if filter_cols[1] != 0 %}(data[mean_column] >= mean_greater && data[mean_column] <= mean_less){% else %} true{% endif %} ){ + return true + } else { + return false + } + } else { + if ( (data[r_column] >= r_greater || data[r_column] <= r_less) && {% if filter_cols[1] != 0 %}(data[mean_column] >= mean_greater || data[mean_column] <= mean_less){% else %} true{% endif %} ){ + return true + } else { + return false + } + } + return true + }); $(document).ready( function () { @@ -301,7 +310,7 @@ console.time("Creating table"); {% if target_dataset.type == "ProbeSet" %} - $('#trait_table').dataTable( { + table_conf = { "drawCallback": function( settings ) { $('#trait_table tr').click(function(event) { if (event.target.type !== 'checkbox') { @@ -310,15 +319,17 @@ }); $('.trait_checkbox:checkbox').on("change", change_buttons); }, - "buttons": [ + buttons: [ { - extend: 'csvHtml5', - text: 'Download CSV', - title: 'correlation_results', - fieldBoundary: '"', - exportOptions: { - columns: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] - } + extend: 'columnsToggle', + columns: function( idx, data, node ) { + if (idx != 0) { + return true; + } else { + return false; + } + }, + postfixButtons: [ 'colvisRestore' ] } ], "columnDefs": [ { @@ -333,15 +344,15 @@ { "type": "natural", "width": "15%" }, { "type": "natural" }, { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] }, { "type": "natural" }, { "type": "scientific" }, { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] }, { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] }, - { "type": "scientific" } + { "type": "scientific" }, + { "type": "natural" }, + { "type": "natural" }, + { "type": "natural" } ], "createdRow": function ( row, data, index ) { $('td', row).eq(4).attr('title', $('td', row).eq(4).text()); @@ -350,33 +361,30 @@ $('td', row).eq(4).text($('td', row).eq(4).text() + '...') } }, - "order": [[12, "asc" ]], - "sDom": "BRZtir", + "order": [[9, "asc" ]], + "sDom": "Btir", "iDisplayLength": -1, "autoWidth": false, "deferRender": true, "bSortClasses": false, - "scrollY": "800px", - "scrollCollapse": false, - "scroller": true, "paging": false, "orderClasses": true - } ); - - var table = $('#trait_table').DataTable(); + } {% elif target_dataset.type == "Publish" %} - $('#trait_table').dataTable( { + table_conf = { "paging": false, - "buttons": [ + buttons: [ { - extend: 'csvHtml5', - text: 'Download CSV', - title: 'correlation_results', - fieldBoundary: '"', - exportOptions: { - columns: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11] - } + extend: 'columnsToggle', + columns: function( idx, data, node ) { + if (idx != 0) { + return true; + } else { + return false; + } + }, + postfixButtons: [ 'colvisRestore' ] } ], "columnDefs": [ @@ -390,11 +398,11 @@ { "type": "natural", "width": "12%" }, { "type": "natural" }, { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] }, + { "type": "scientific" }, { "type": "natural" }, - { "type": "scientific" } + { "type": "natural" }, + { "type": "natural" } ], "createdRow": function ( row, data, index ) { $('td', row).eq(3).attr('title', $('td', row).eq(3).text()); @@ -408,25 +416,25 @@ $('td', row).eq(4).text($('td', row).eq(4).text() + '...') } }, - "order": [[11, "asc" ]], + "order": [[8, "asc" ]], "sDom": "Btir", "autoWidth": false, - "bDeferRender": true, - "scrollY": "800px", - "scrollCollapse": false - } ); + "bDeferRender": true + } {% elif target_dataset.type == "Geno" %} - $('#trait_table').dataTable( { + table_conf = { "paging": false, - "buttons": [ + buttons: [ { - extend: 'csvHtml5', - text: 'Download CSV', - title: 'correlation_results', - fieldBoundary: '"', - exportOptions: { - columns: [1, 2, 3, 4, 5, 6] - } + extend: 'columnsToggle', + columns: function( idx, data, node ) { + if (idx != 0) { + return true; + } else { + return false; + } + }, + postfixButtons: [ 'colvisRestore' ] } ], "columnDefs": [ @@ -447,8 +455,11 @@ "bDeferRender": true, "scrollY": "800px", "scrollCollapse": false - } ); + } {% endif %} + + var the_table = $('#trait_table').DataTable(table_conf); + console.timeEnd("Creating table"); submit_special = function(url) { @@ -460,6 +471,15 @@ url = $(this).data("url") return submit_special(url) }); + + $("#more_options").click(function() { + $("div#filter_options").toggle(); + }); + + $("#select_traits").click(function() { + console.log("redrawing") + the_table.draw(); + }); }); </script> {% endblock %} diff --git a/wqflask/wqflask/templates/docs.html b/wqflask/wqflask/templates/docs.html index c485f757..1a241ce7 100644 --- a/wqflask/wqflask/templates/docs.html +++ b/wqflask/wqflask/templates/docs.html @@ -6,9 +6,9 @@ <div class="container"> <h3>{{title}}</h3> <div style="text-align: right;"> - <a href="docedit?entry={{entry}}"> + <!--<a href="docedit?entry={{entry}}">--> <img style="width: 16px;" src="/static/new/images/edit.gif"> - </a> + <!--</a>--> </div> {{content|safe}} </div> diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 4672f161..1a4ff752 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -9,7 +9,8 @@ <div class="container" style="width: 2000px;"> - <p>You searched for {{ terms }}.</p> + <h3>GN searched 754 datasets and 39,765,944 traits across 10 species, and found {{ trait_count }} results that match your query. + You can filter these results by adding key words in the fields below and you can also sort results on most columns.</h3> <p>To study a record, click on its Record ID below.<br />Check records below and click Add button to add to selection.</p> <div> @@ -20,14 +21,13 @@ <button class="btn btn-default" id="add" disabled ><span class="glyphicon glyphicon-plus-sign"></span> Add</button> <input type="text" id="searchbox" class="form-control" style="width: 180px; display: inline;" placeholder="Search This Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 120px; display: inline;" placeholder="Select Top ..."> - <br /> - <br /> - <form id="export_form" method="POST" action="/export_traits_csv"> + <form id="export_form" method="POST" action="/export_traits_csv" style="display: inline;"> <input type="hidden" name="database_name" id="database_name" value="None"> <input type="hidden" name="export_data" id="export_data" value=""> - <button class="btn btn-default" id="export_traits">Download CSV</button> + <button class="btn btn-default" id="export_traits">Download</button> </form> <br /> + <br /> <div style="width: 100%;"> <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;"> <tbody> @@ -78,8 +78,43 @@ } }); + function change_buttons() { + buttons = ["#add", "#remove"]; + num_checked = $('.trait_checkbox:checked').length; + if (num_checked === 0) { + for (_i = 0, _len = buttons.length; _i < _len; _i++) { + button = buttons[_i]; + $(button).prop("disabled", true); + } + } else { + for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) { + button = buttons[_j]; + $(button).prop("disabled", false); + } + } + //}); + if ($(this).is(":checked")) { + if (!$(this).closest('tr').hasClass('selected')) { + $(this).closest('tr').addClass('selected') + } + } + else { + if ($(this).closest('tr').hasClass('selected')) { + $(this).closest('tr').removeClass('selected') + } + } + } + console.time("Creating table"); $('#trait_table').DataTable( { + 'drawCallback': function( settings ) { + $('#trait_table tr').click(function(event) { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { + $(':checkbox', this).trigger('click'); + } + }); + $('.trait_checkbox:checkbox').on("change", change_buttons); + }, 'createdRow': function ( row, data, index ) { $('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;"); $('td', row).eq(1).attr("align", "right"); @@ -158,12 +193,17 @@ 'type': "natural", 'data': null, 'render': function(data, type, row, meta) { - return decodeURIComponent(escape(data.description)) + try { + return decodeURIComponent(escape(data.description)) + } catch(err) { + return escape(data.description) + } } }, { 'title': "Location", - 'type': "natural", + 'type': "natural", + 'width': "100px", 'data': "location_repr" }, { @@ -173,19 +213,21 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'title': "Max<br>LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", 'type': "natural", 'data': "LRS_score_repr", 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS Location", - 'type': "natural", + 'title': "Max LRS<br>Location", + 'type': "natural", + 'width': "100px", 'data': "max_lrs_text" }, { - 'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", - 'type': "natural", + 'title': "Additive<br>Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'type': "natural", + 'width': "50px", 'data': "additive", 'orderSequence': [ "desc", "asc"] } diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index 7dc22a88..4e142846 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -9,7 +9,8 @@ <div class="container"> - <p>You searched for {{ terms }}.</p> + <h3>GN searched 51 datasets and 13763 traits across 10 species, and found {{ trait_count }} results that match your query. + You can filter these results by adding key words in the fields below and you can also sort results on most columns.</h3> <p>To study a record, click on its ID below.<br />Check records below and click Add button to add to selection.</p> <div> @@ -20,16 +21,15 @@ <button class="btn btn-default" id="add" disabled ><span class="glyphicon glyphicon-plus-sign"></span> Add</button> <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ..."> - <br /> - <br /> - <form id="export_form" method="POST" action="/export_traits_csv"> + <form id="export_form" method="POST" action="/export_traits_csv" style="display: inline;"> <input type="hidden" name="database_name" id="database_name" value="None"> <input type="hidden" name="export_data" id="export_data" value=""> <button class="btn btn-default" id="export_traits">Download CSV</button> </form> <br /> - <div> - <table id="trait_table" width="100%" class="table-hover table-striped cell-border" style="float: left;"> + <br /> + <div style="width: 100%;"> + <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;"> <tbody> <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td> </tbody> @@ -78,8 +78,43 @@ } }); + function change_buttons() { + buttons = ["#add", "#remove"]; + num_checked = $('.trait_checkbox:checked').length; + if (num_checked === 0) { + for (_i = 0, _len = buttons.length; _i < _len; _i++) { + button = buttons[_i]; + $(button).prop("disabled", true); + } + } else { + for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) { + button = buttons[_j]; + $(button).prop("disabled", false); + } + } + //}); + if ($(this).is(":checked")) { + if (!$(this).closest('tr').hasClass('selected')) { + $(this).closest('tr').addClass('selected') + } + } + else { + if ($(this).closest('tr').hasClass('selected')) { + $(this).closest('tr').removeClass('selected') + } + } + } + console.time("Creating table"); $('#trait_table').DataTable( { + 'drawCallback': function( settings ) { + $('#trait_table tr').click(function(event) { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { + $(':checkbox', this).trigger('click'); + } + }); + $('.trait_checkbox:checkbox').on("change", change_buttons); + }, "createdRow": function ( row, data, index ) { $('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;"); $('td', row).eq(1).attr("align", "right"); @@ -134,14 +169,26 @@ 'width': "25%", 'data': null, 'render': function(data, type, row, meta) { - return decodeURIComponent(escape(data.description)) + try { + return decodeURIComponent(escape(data.description)) + } catch(err) { + return data.description + } } }, { 'title': "Authors", 'type': "natural", 'width': "25%", - 'data': "authors" + 'data': null, + 'render': function(data, type, row, meta) { + author_list = data.authors.split(",") + if (author_list.length >= 6) { + return author_list.slice(0, 6).join(",") + ", et al." + } else{ + return data.authors + } + } }, { 'title': "Year", diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 4b95e7f9..48ed0ec5 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -17,7 +17,7 @@ </header> --> - <div class="container-fluid"> + <div class="container-fluid" style="min-width: 1200px;"> {{ flash_me() }} @@ -28,7 +28,7 @@ <div class="page-header"> <h1>Select and search</h1> </div> - <form method="get" action="/search" name="SEARCHFORM"> + <form method="get" action="/search" target="_blank" name="SEARCHFORM"> <fieldset> <div style="padding: 20px" class="form-horizontal"> @@ -36,7 +36,7 @@ <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label> <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> <div class="col-8"> - <select name="species" id="species" class="form-control" style="width: 280px !important;"></select> + <select name="species" id="species" class="form-control" style="width: 280px !important;"><option>Loading...</option></select> </div> <div class="col-4" style="margin-left: 10px;"> <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button> @@ -48,7 +48,7 @@ <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label> <div class="col-xs-10 controls input-append" style="padding-left: 20px;"> <div class="col-8"> - <select name="group" id="group" class="form-control" style="width: 280px !important;"></select> + <select name="group" id="group" class="form-control" style="width: 280px !important;"><option>Loading...</option></select> <i class="icon-question-sign"></i> </div> </div> @@ -58,7 +58,7 @@ <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label> <div class="col-xs-10 controls" style="padding-left: 20px;"> <div class="col-8"> - <select name="type" id="type" class="form-control" style="width: 280px !important;"></select> + <select name="type" id="type" class="form-control" style="width: 280px !important;"><option>Loading...</option></select> </div> </div> </div> @@ -67,7 +67,7 @@ <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label> <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> <div class="col-9"> - <select name="dataset" id="dataset" class="form-control" style="width: 340px !important;"></select> + <select name="dataset" id="dataset" class="form-control" style="width: 340px !important;"><option>Loading...</option></select> <i class="icon-question-sign"></i> </div> <div class="col-3" style="margin-left: 10px;"> @@ -138,19 +138,32 @@ <h2>Advanced commands</h2> </div> - <p>You can also use advanced commands. Copy these simple examples into the Get Any or Combined search fields:</p> + <p>You can also use advanced commands. Copy these simple examples into the Get Any field for single term searches and Combined for searches with multiple terms:</p> <ul> <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on chromosome 1 between 25 and 30 Mb.</li> - <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds - highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L">LRS</a> - linkage between 23 and 46.</li> + <li><b>MEAN=(15 16)</b> in the <b>Combined</b> field finds + highly expressed genes (15 to 16 log2 units)</li> <li><b>RANGE=(1.5 2.5)</b> in the <b>Any</b> field finds traits with values with a specified fold-range (minimum = 1). Useful for finding "housekeeping genes" <b>(1.0 1.2)</b> or highly variable molecular assays <b>(10 100)</b>.</li> + <li><b>LRS=(15 1000)</b> or <b>LOD=(2 8)</b> finds all traits with peak LRS or LOD scores between lower and upper limits.</li> + + <li><b>LRS=(9 999 Chr4 122 155)</b> finds all traits on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.</li> + + <li><b>cisLRS=(15 1000 5)</b> or <b>cisLOD=(2 8 5)</b> finds all cis eQTLs with peak LRS or LOD scores between lower and upper limits, + with an <b>inclusion</b> zone of 5 Mb around the parent gene.</li> + + <li><b>transLRS=(15 1000 5)</b> or <b>transLOD=(2 8 5)</b> finds all trans eQTLs with peak LRS or LOD scores between lower and upper limits, + with an <b>exclusion</b> zone of 5 Mb around the parent gene.</li> + + <li><b>POSITION=(Chr4 122 130) cisLRS=(9 999 10)</b> + finds all traits on Chr 4 from 122 and 155 Mb with cisLRS scores + between 9 and 999 and an inclusion zone of 10 Mb.</li> + <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF"> GeneRIF</a> links.</li> @@ -162,11 +175,6 @@ <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202"> Gene Ontology</a>.</li> - <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b> - finds synapse-associated genes with <a href="http://www.genenetwork.org/glossary.html#E"> - cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores - between 9 and 999.</li> - <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b> finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E"> trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS @@ -181,8 +189,9 @@ <h1>Affiliates</h1> <ul> <li><a href="http://ucscbrowser.genenetwork.org/">Genome browser</a> at UTHSC</li> - <li><a href="http://galaxy.genenetwork.org/">Galaxy</a> at UTHSC</li> <li><a href="https://systems-genetics.org/">Systems Genetics</a> @ EPFL</li> + <li>UTHSC <a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a></li> + <li><a href="http://genenetwork.org">GeneNetwork 1</a></li> </ul> </div> </section> @@ -199,9 +208,9 @@ <h1>Github</h1> <ul> <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li> - <li><a href="https://github.com/genenetwork/gn-docs/wiki">GN2 Document Wiki</a></li> - <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li> <li><a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a></li> + <!--<li><a href="https://github.com/genenetwork/gn-docs/wiki">GN2 Document Wiki</a></li>--> + <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li> </ul> </div> </section> @@ -241,13 +250,12 @@ <h3>GeneNetwork v2:</h3> <ul> <li><a href="http://gn2.genenetwork.org/">Main website</a> at UTHSC</li> - <li><a href="http://test-gn2.genenetwork.org/">Testing website</a> at UTHSC</li> + <!--<li><a href="http://test-gn2.genenetwork.org/">Testing website</a> at UTHSC</li>--> </ul> <h3>GeneNetwork v1:</h3> <ul> <li><a href="http://www.genenetwork.org/">Main website</a> at UTHSC</li> - <li><a href="http://genenetwork.helmholtz-hzi.de/">Website</a> at the HZI (Germany)</li> - <li><a href="http://ec2.genenetwork.org/">Amazon + <li><a href="http://artemis.uthsc.edu/">Time Machine</a>: Full GN versions from 2009 to 2016 (mm9)</li> Cloud (EC2)</a></li> </ul> </section> diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 25560249..4c30664b 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -6,13 +6,34 @@ {% endfor %} <div class="container"> <div> - <div style="min-height: 80vh; display: flex; align-items: center;"> - <div style="margin-bottom: 10px; left: 50%; margin-right: -50%; transform: translate(-50%, -50%); position: absolute;"> + <div style="min-height: 80vh; display: flex; align-items: center; text-align: center;"> + <div style="margin-bottom: 5px; left: 50%; margin-right: -50%; margin-top: 10%; transform: translate(-50%, -50%); position: absolute;"> + {% if start_vars.tool_used == "Mapping" %} + <h1>Computing the Map</h1> + <br> + <i>n</i> = {{ start_vars.num_vals }} + <br> + Method = {{ start_vars.method }} + <br> + {% if start_vars.transform != "" %} + transform = {{ start_vars.transform }} + <br> + {% endif %} + MAF = {{ start_vars.maf }} + {% else %} <h1>Loading {{ start_vars.tool_used }} Results...</h1> + {% endif %} + <br><br> + <img align="center" src="/static/gif/89.gif"> </div> - <div class="progress center-block" style="margin-top: 5px; margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;"> + <!--<div style="margin-left: auto; margin-right: auto; display: block; width: 50%; top:50%;"> + <img align="center" src="/static/gif/89.gif"> + </div>--> + <!-- + <div class="progress center-block" style="margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;"> <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div> </div> + --> </div> </div> </div> @@ -22,5 +43,5 @@ <script type="text/javascript"> $("#loading_form").attr("action", "{{ start_vars.form_url }}"); -$("#loading_form").submit(); +setTimeout(function(){ $("#loading_form").submit()}, 350); </script>
\ No newline at end of file diff --git a/wqflask/wqflask/templates/mapping_error.html b/wqflask/wqflask/templates/mapping_error.html index b73a2c31..884d4df8 100644 --- a/wqflask/wqflask/templates/mapping_error.html +++ b/wqflask/wqflask/templates/mapping_error.html @@ -5,7 +5,13 @@ {{ header("An error occurred during mapping") }} <div class="container"> + <h3> <p>There is likely an issue with the genotype file associated with this group/RISet. Please contact Zach Sloan (zachary.a.sloan@gmail.com) or Arthur Centeno (acenteno@gmail.com) about the data set in question.</p> + </h3> + <br> + <h3> + <p>Try mapping using interval mapping instead; some genotype files with many columns of NAs have issues with GEMMA or R/qtl.</p> + </h3> </div> diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index ba4d4d7c..baf2b1ec 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -3,13 +3,15 @@ {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" /> + <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous"> + <link rel="stylesheet" type="text/css" href="/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" /> - <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" /> + {% endblock %} {% from "base_macro.html" import header %} {% block content %} - <div class="container"> + <div class="container" style="min-width: 900px;"> <form method="post" target="_blank" action="/run_mapping" name="marker_regression" id="marker_regression_form"> <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}"> <input type="hidden" name="trait_id" value="{{ this_trait.name }}"> @@ -17,8 +19,11 @@ <input type="hidden" name="genofile" value="{{ genofile_string }}"> <input type="hidden" name="geno_db_exists" value="{{ geno_db_exists }}"> <input type="hidden" name="first_run" value="{{ first_run }}"> - {% if gwa_filename is defined %} - <input type="hidden" name="gwa_filename" value="{{ gwa_filename }}"> + {% if output_files is defined %} + <input type="hidden" name="output_files" value="{{ output_files }}"> + {% endif %} + {% if reaper_version is defined %} + <input type="hidden" name="reaper_version" value="{{ reaper_version }}"> {% endif %} <input type="hidden" name="results_path" value="{{ mapping_results_path }}"> <input type="hidden" name="method" value="{{ mapping_method }}"> @@ -26,6 +31,7 @@ {% for sample in samples %} <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}"> {% endfor %} + <input type="hidden" name="num_vals" value="{{ n_samples }}"> <input type="hidden" name="maf"> <input type="hidden" name="use_loco" value="{{ use_loco }}"> <input type="hidden" name="selected_chr" value="{{ selectedChr }}"> @@ -150,13 +156,11 @@ <li id="gn1_map_tab"> <a href="#gn1_map" data-toggle="tab" aria-expanded="true">GN1 Map</a> </li> - {% if mapping_method != "gemma" and mapping_method != "plink" %} - <li id="vector_map_tab"> - <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" and mapping_method != "plink" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a> + <li id="browser_tab"> + <a href="#browser_holder" data-toggle="tab" aria-expanded="true">Genome Browser</a> </li> - {% endif %} </ul> - <div class="tab-content"> + <div class="tab-content" style="overflow-x: auto;"> <div class="tab-pane active" id="gn1_map"> <div class="qtlcharts"> {{ gifmap|safe }} @@ -165,28 +169,43 @@ <br> <span style="white-space: nowrap;">A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values.</span> {% endif %} - {% if nperm > 0 and permChecked == "ON" %} - <br><br> - <img src="/generated/{{ perm_filename }}.gif"> - <br><br> - Total of {{ nperm }} permutations <a href="javascript:export_perm_data();" target="_blank" >Download Permutation Results</a> - <br> - {% endif %} </div> </div> - {% if mapping_method != "gemma" and mapping_method != "plink" %} - <div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map"> - <div id="chart_container"> - <div class="qtlcharts" id="topchart"></div> - </div> + <div class="tab-pane" id="browser_holder" style="height: 600px;"> + <div id="browser" style="margin-right: 20px; width: 90%;"> + <div id="controls"> + <button id="scrollLeft" type="button" > + <i class="fas fa-arrow-left"></i> + </button> + <button id="scrollRight" type="button" > + <i class="fas fa-arrow-right"></i> + </button> + <button id="zoomOut" type="button" > + <i class="fas fa-search-minus"></i> + </button> + <button id="zoomIn" type="button" > + <i class="fas fa-search-plus"></i> + </button> + <button id="reset" type="button" >Reset</button> + </div> + <div id="infoBox"></div> + </div> </div> - {% endif %} </div> </div> + <div> + {% if nperm > 0 and permChecked == "ON" %} + <br><br> + <img src="/generated/{{ perm_filename }}.gif"> + <br><br> + Total of {{ nperm }} permutations <a href="javascript:export_perm_data();" target="_blank" >Download Permutation Results</a> + <br> + {% endif %} + </div> </form> {% if selectedChr == -1 %} - <div class="container" style="padding-left: 30px;"> + <div class="container" style="padding-left: 30px; margin-top: 50px; position: relative;"> <h2>Mapping Statistics</h2> <br /> <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> @@ -195,7 +214,7 @@ <button class="btn btn-default" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> <br /> <br /> - <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}480{% else %}450{% endif %}px;"> + <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}500{% else %}470{% endif %}px;"> <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer"> <thead> <tr> @@ -231,11 +250,11 @@ {% if 'lod_score' in marker %} <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td> {% else %} - <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.16) }}</td> + <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td> {% endif %} {% else %} {% if 'lod_score' in marker %} - <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.16) }}</td> + <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td> {% else %} <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td> {% endif %} @@ -262,7 +281,7 @@ <div style="width: 100%;"> <h2>Interval Analyst</h2> <div id="table_container"> - <table id="interval_analyst" class="table-hover table-striped cell-border dataTable" style="float: left; width:100%;"> + <table id="trait_table" class="table-hover table-striped cell-border dataTable" style="float: left; width:100%;"> <thead> <tr> {% for header in gene_table_header %} @@ -304,33 +323,28 @@ <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> + <script language="javascript" type="text/javascript" src="/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js"></script> - {% if mapping_method != "gemma" and mapping_method != "plink" %} <script> js_data = {{ js_data | safe }} </script> - {% endif %} <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> - {% if mapping_method != "gemma" and mapping_method != "plink" %} - <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script> - {% endif %} + <script language="javascript" type="text/javascript" src="/static/new/javascript/init_genome_browser.js"></script> <script type="text/javascript" charset="utf-8"> $(document).ready( function () { console.time("Creating table"); + {% if selectedChr == -1 %} $('#trait_table').DataTable( { "columns": [ { "type": "natural", "width": "5%" }, { "type": "natural", "width": "8%" }, { "type": "natural", "width": "25%" }, { "type": "natural" }, - { "type": "natural", "width": "8%" }, - { "type": "natural" }{% if 'additive' in marker %}, - { "type": "natural" }{% endif %}{% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}, + { "type": "natural" }, + { "type": "natural" }{% if 'additive' in qtlresults[0] %}, + { "type": "natural" }{% endif %}{% if 'dominance' in qtlresults[0] and dataset.group.genetic_type != "riset" %}, { "type": "natural" }{% endif %} ], "columnDefs": [ { @@ -346,8 +360,8 @@ "scrollCollapse": false, "paging": false } ); - - $('#interval_analyst').dataTable( { + {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %} + $('#trait_table').dataTable( { "createdRow": function ( row, data, index ) { $('td', row).eq(1).attr("align", "right"); $('td', row).eq(3).attr("align", "right"); @@ -384,6 +398,7 @@ "scrollCollapse": false, "paging": false } ); + {% endif %} $('#vector_map_tab').click(function(){ $('div#gn1_map_options').hide(); @@ -433,6 +448,12 @@ return $('#marker_regression_form').submit(); } + $('#browser_tab').click(function() { + $('#gn1_map_options').css("display", "none") + }) + $('#gn1_map_tab').click(function() { + $('#gn1_map_options').css("display", "block") + }) </script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html index 27b20ebf..c9aaf028 100644 --- a/wqflask/wqflask/templates/new_security/login_user.html +++ b/wqflask/wqflask/templates/new_security/login_user.html @@ -2,53 +2,11 @@ {% block title %}Register{% endblock %} {% block content %} - <div class="container"> + <div class="container" style="min-width: 1250px;"> {{ flash_me() }} - <div class="page-header"> - <h1> Login</h1> - </div> - - - <div class="security_box"> - - <h4>Don't have an account?</h4> - - {% if es_server: %} - <a href="/n/register" class="btn btn-primary modalize">Create a new account</a> - {% else: %} - <div class="alert alert-warning"> - <p>You cannot create an account at this moment.<br /> - Please try again later.</p> - </div> - {% endif %} - - <hr /> - <h4>Login with external services</h4> - - {% if external_login: %} - <div> - {% if external_login["github"]: %} - <a href="{{external_login['github']}}" title="Login with GitHub" class="btn btn-info btn-group">Login with Github</a> - {% else %} - <p>Github login is not available right now</p> - {% endif %} - - {% if external_login["orcid"]: %} - <a href="{{external_login['orcid']}}" title="Login with ORCID" class="btn btn-info btn-group">Login with ORCID</a> - {% else %} - <p>ORCID login is not available right now</p> - {% endif %} - </div> - {% else: %} - <div class="alert alert-warning"> - <p>Sorry, you cannot login with Github or ORCID at this time.</p> - </div> - {% endif %} - <hr /> - - <h4>Already have an account? Sign in here.</h4> + <h4>Already have an account? Sign in here.</h4> {% if es_server: %} <form class="form-horizontal" action="/n/login" method="POST" name="login_user_form" id="loginUserForm"> @@ -69,7 +27,6 @@ </div> </div> - <div class="form-group"> <label class="col-xs-1 control-label" for="remember"></label> <div style="margin-left:20px;" class="col-xs-4 controls"> @@ -87,6 +44,42 @@ </div> </fieldset> + <div class="security_box"> + + <h4>Don't have an account?</h4> + + {% if es_server: %} + <a href="/n/register" class="btn btn-primary modalize">Create a new account</a> + {% else: %} + <div class="alert alert-warning"> + <p>You cannot create an account at this moment.<br /> + Please try again later.</p> + </div> + {% endif %} + + <hr /> + <h4>Login with external services</h4> + + {% if external_login: %} + <div> + {% if external_login["github"]: %} + <a href="{{external_login['github']}}" title="Login with GitHub" class="btn btn-info btn-group">Login with Github</a> + {% else %} + <p>Github login is not available right now</p> + {% endif %} + + {% if external_login["orcid"]: %} + <a href="{{external_login['orcid']}}" title="Login with ORCID" class="btn btn-info btn-group">Login with ORCID</a> + {% else %} + <p>ORCID login is not available right now</p> + {% endif %} + </div> + {% else: %} + <div class="alert alert-warning"> + <p>Sorry, you cannot login with Github or ORCID at this time.</p> + </div> + {% endif %} + </form> {% else: %} <div class="alert alert-warning"> diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index e20ea2d3..2c67f6c3 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -8,13 +8,16 @@ {% endblock %} {% block content %} <!-- Start of body --> - <div style="padding-left: 10px;"> + <div style="padding-left: 10px; min-width: 1200px;"> <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}"> <div style="padding-top: 10px; padding-bottom: 10px; font-size: 16px;"> <!-- Need to customize text more for other types of searches --> - <p>We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId={{dataset.id}}">{{ dataset.fullname }}</a> + <p><b>Search Results:</b> We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a> to find all records + {% if go_term is not none %} + with <u>Gene Ontology ID</u> <strong>GO:{{ go_term }}</strong>. + {% else %} {% for word in search_terms %} {% if word.key|lower == "rif" %} with <u>GeneRIF</u> containing <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %} @@ -24,28 +27,33 @@ with <u>GeneWiki</u> containing <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %} {% elif word.key|lower == "mean" %} with <u>MEAN</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}.{% else %} and {% endif %} - {% elif word.key|lower == "lrs" or word.key|lower == "translrs" or word.key|lower == "cislrs" %} + {% elif word.key|lower == "lrs" or word.key|lower == "lod" or word.key|lower == "translrs" or word.key|lower == "cislrs" or word.key|lower == "translod" or word.key|lower == "cislod" %} {% if word.search_term|length == 1 %} with {% if word.key|lower == "translrs" %}trans{% elif word.key|lower == "cislrs" %}cis{% endif %}LRS {% if word.separator == ">" %} greater than {% elif word.separator == "<" %} less than {% elif word.separator == ">=" %} greater than or equal to {% elif word.separator == "<=" %} less than or equal to {% endif %} <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %} {% elif word.search_term|length == 2 %} - with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}.{% else %} and {% endif %} + with <u>{{ word.key|upper }}</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}.{% else %} and {% endif %} {% elif word.search_term|length == 3 %} - with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong>{% if loop.last %}.{% else %} and {% endif %} + with <u>{{ word.key|upper }}</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong>{% if loop.last %}.{% else %} and {% endif %} {% elif word.search_term|length == 5 %} - with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong> between <strong>{{ word.search_term[3] }}</strong> and <strong>{{ word.search_term[4] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %} + with <u>{{ word.key|upper }}</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong> between <strong>{{ word.search_term[3] }}</strong> and <strong>{{ word.search_term[4] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %} {% endif %} {% elif word.key|lower == "position" %} with <u>target genes</u> on chromosome <strong>{% if word.search_term[0].split('chr')|length > 1 %}{{ word.search_term[0].split('chr')[1] }}{% elif word.search_term[0].split('CHR')|length > 1 %}{{ word.search_term[0].split('CHR')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %} {% else %} - that match the <u>TERM</u> <b>{{ word.search_term[0] }}</b>{% if loop.last %},{% else %} and {% endif %} + {% if word.search_term[0] == "*" %} in the dataset.{% else %}{% if loop.first %}that match:<br>{% endif %}<b>"{{ word.search_term[0] }}"</b>{% if loop.last %}{% else %} and {% endif %}{% endif %} {% endif %} {% endfor %} - and found {{ results|count }} records. + {% endif %} + <br> + {{ results|count }} records are shown below. </p> + {% if go_term is not none %} + <p><b>The associated genes include:</b><br><br>{% for word in search_terms %}{{ word.search_term[0] }}{% endfor %}</p> + {% endif %} - <p>To study a record click on its ID below, and to view the whole description {% if dataset.type == "Publish" %}or list of authors {% endif %} hover over the table cell. Check records below and click Add button to add to selection.</p> + <!--<p>To study a record click on its ID below, and to view the whole description {% if dataset.type == "Publish" %}or list of authors {% endif %} hover over the table cell. Check records below and click Add button to add to selection.</p>--> - <hr style="height: 1px; background-color: #A9A9A9;"> + <!--<hr style="height: 1px; background-color: #A9A9A9;">--> </div> @@ -104,22 +112,20 @@ <div> <br /> - <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> - <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button> + <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select</button> + <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect</button> <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button> <button class="btn btn-default" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ..."> - <br /> - <br /> - <form id="export_form" method="POST" action="/export_traits_csv"> + <form id="export_form" method="POST" action="/export_traits_csv" style="display: inline;"> <input type="hidden" name="database_name" id="database_name" value="{{ dataset.fullname }}"> <input type="hidden" name="export_data" id="export_data" value=""> - <button class="btn btn-default" id="export_traits">Download CSV</button> + <button class="btn btn-default" id="export_traits">Download</button> </form> <br /> - - <div id="table_container" style="width: 1200px;"> + <br /> + <div id="table_container"> <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;"> <tbody> <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td> @@ -206,7 +212,7 @@ $('#trait_table').DataTable( { 'drawCallback': function( settings ) { $('#trait_table tr').click(function(event) { - if (event.target.type !== 'checkbox') { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { $(':checkbox', this).trigger('click'); } }); @@ -250,6 +256,7 @@ 'columns': [ { 'data': null, + 'width': "30px", 'orderDataType': "dom-checkbox", 'orderSequence': [ "desc", "asc"], 'render': function(data, type, row, meta) { @@ -259,12 +266,14 @@ { 'title': "Index", 'type': "natural", + 'width': "30px", 'data': "index" }, { 'title': "Record", 'type': "natural", 'data': null, + 'width': "60px", 'orderDataType': "dom-inner-text", 'render': function(data, type, row, meta) { return '<a href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.name + '</a>' @@ -278,12 +287,11 @@ { 'title': "Description", 'type': "natural", - 'width': "300px", 'data': null, 'render': function(data, type, row, meta) { try { return decodeURIComponent(escape(data.description)) - } catch { + } catch(err){ return escape(data.description) } } @@ -291,12 +299,13 @@ { 'title': "Location", 'type': "natural", - 'width': "140px", + 'width': "120px", 'data': "location" }, { 'title': "Mean", 'type': "natural", + 'width': "40px", 'data': "mean", 'orderSequence': [ "desc", "asc"] }, @@ -309,7 +318,7 @@ { 'title': "Max LRS Location", 'type': "natural", - 'width': "140px", + 'width': "120px", 'data': "lrs_location" }, { @@ -321,17 +330,29 @@ { 'title': "Description", 'type': "natural", - 'width': "500px", + 'width': "25%", 'data': null, 'render': function(data, type, row, meta) { - return decodeURIComponent(escape(data.description)) + try { + return decodeURIComponent(escape(data.description)) + } catch(err){ + return data.description + } } }, { 'title': "Authors", 'type': "natural", - 'width': "300px", - 'data': "authors" + 'width': "25%", + 'data': null, + 'render': function(data, type, row, meta) { + author_list = data.authors.split(",") + if (author_list.length >= 6) { + return author_list.slice(0, 6).join(",") + ", et al." + } else{ + return data.authors + } + } }, { 'title': "Year", @@ -387,7 +408,7 @@ postfixButtons: [ 'colvisRestore' ] } ], - 'sDom': "Btir", + 'sDom': "Bitir", 'autoWidth': false, 'deferRender': true, 'paging': false, @@ -399,25 +420,6 @@ } } ); - if (trait_list.length > 20) { - $('#trait_table').append( - '<tfoot>' + - '<tr>' + - '<th></th>' + - '<th>Index</th>' + - '<th>Record</th>' + - '<th>Symbol</th> ' + - '<th>Description</th>' + - '<th>Location</th>' + - '<th>Mean</th>' + - '<th>Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th>' + - '<th>Max LRS Location</th>' + - '<th>Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th>' + - '</tr>' + - '</tfoot>' - ); - } - console.timeEnd("Creating table"); $('#redraw').click(function() { diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 378f91b1..ff000ced 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -18,7 +18,7 @@ <div class="container"> <h2>Trait Data and Analysis for <b>{{ this_trait.name }}</b></h2> {% if this_trait.dataset.type != 'Publish' %} - <h3>{{ this_trait.description_fmt }}</h3> + <h3>{{ this_trait.description_fmt[0]|upper }}{{ this_trait.description_fmt[1:] }}</h3> {% endif %} </div> @@ -39,7 +39,7 @@ <input type="hidden" name="covariates" value=""> <input type="hidden" name="transform" value=""> - <div class="container"> + <div class="container" style="min-width: 1450px;"> <div class="panel-group" id="accordion"> <div class="panel panel-default"> <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true"> @@ -183,10 +183,10 @@ var x = getValue(a); var y = getValue(b); - if (x == 'x' || x == '') { + if (x == 'x' || x === '') { return 1; } - else if (y == 'x' || y == '') { + else if (y == 'x' || y === '') { return -1; } else { @@ -296,7 +296,7 @@ if (data.value == null) { return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>' } else { - return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id)] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>' + return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>' } } }{% if sample_groups[0].se_exists() %}, diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 09f36021..63a87825 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -1,62 +1,68 @@ <table class="table"> <tr> - <td>Species and Group</td> + <td width="150px"><b>Species and Group</b></td> <td>{{ this_trait.dataset.group.species }}, {{ this_trait.dataset.group.name }}</td> </tr> {% if this_trait.dataset.type == 'Publish' %} <tr> - <td>Phenotype</td> + <td><b>Phenotype</b></td> <td><div style="width:40%;">{{ this_trait.description_fmt }}</div></td> </tr> <tr> - <td>Authors</td> + <td><b>Authors</b></td> <td><div style="width:40%;">{{ this_trait.authors }}</div></td> </tr> <tr> - <td>Title</td> + <td><b>Title</b></td> <td><div style="width:40%;">{{ this_trait.title }}</div></td> </tr> <tr> - <td>Journal</td> - <td>{{ this_trait.journal }} (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed">{{ this_trait.year }}</a>)</td> + <td><b>Journal</b></td> + <td>{{ this_trait.journal }} ({% if this_trait.pubmed_id %}<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" target="_blank" title="PubMed">{{ this_trait.year }}</a>{% else %}{{ this_trait.year }}{% endif %})</td> </tr> {% else %} <tr> - <td>Tissue</td> + <td><b>Tissue</b></td> <td>{{ this_trait.dataset.tissue }}</td> </tr> {% endif %} {% if this_trait.dataset.type == 'ProbeSet' %} {% if this_trait.symbol != None %} <tr> - <td>Gene Symbol</td> + <td><b>Gene Symbol</b></td> <td>{{ this_trait.symbol }}</td> </tr> {% endif %} <tr> - <td>Aliases</td> - <td>{{ this_trait.alias_fmt|replace(",",";") }}</td> + <td><b>Aliases</b></td> + <td>Wikidata: {{ this_trait.wikidata_alias_fmt|replace(",",";") }}</td> + </tr> + {% if this_trait.alias_fmt != "Not Available" %} + <tr> + <td></td> + <td>GeneNetwork: {{ this_trait.alias_fmt|replace(",",";") }}</td> </tr> {% endif %} + {% endif %} {% if this_trait.dataset.type != 'Publish' %} <tr> - <td>Location</td> + <td><b>Location</b></td> <td>{{ this_trait.location_fmt }}</td> </tr> {% endif %} <tr> - <td>Database</td> + <td><b>Database</b></td> <td> - <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName={{ dataset.name }}"> + <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName={{ dataset.name }}" target="_blank"> {{ dataset.fullname }} </a> </td> </tr> {% if this_trait.probe_set_specificity %} <tr> - <td>Target Score</td> + <td><b>Target Score</b></td> <td> - <a href="http://genenetwork.org/blatInfo.html" title="Values higher than 2 for the specificity are good"> + <a href="http://genenetwork.org/blatInfo.html" target="_blank" title="Values higher than 2 for the specificity are good"> BLAT Specificity </a>: {{ "%0.3f" | format(this_trait.probe_set_specificity|float) }} @@ -69,103 +75,109 @@ {% endif %} {% if this_trait.pubmed_id or this_trait.geneid or this_trait.omim or this_trait.symbol %} <tr> - <td>Resource Links</td> + <td><b>Resource Links</b></td> <td> {% if pubmed_link %} - <a href="{{ pubmed_link }}" title="PubMed"> + <a href="{{ pubmed_link }}" target="_blank" title="PubMed"> PubMed </a> {% endif %} {% if ncbi_gene_link %} - <a href="{{ ncbi_gene_link }}" title="Info from NCBI Entrez Gene"> + <a href="{{ ncbi_gene_link }}" target="_blank" title="Info from NCBI Entrez Gene"> Gene </a> {% endif %} {% if omim_link %} - <a href="{{ omim_link }}" title="Summary from On Mendelion Inheritance in Man"> + <a href="{{ omim_link }}" target="_blank" title="Summary from On Mendelion Inheritance in Man"> OMIM </a> {% endif %} - {% if unigene_link %} - <a href="{{ unigene_link }}" title="NCBI UniGene"> - UniGene + {% if genemania_link %} + <a href="{{ genemania_link }}" target="_blank" title="GeneMANIA"> + GeneMANIA </a> {% endif %} - {% if genbank_link %} - <a href="{{ genbank_link }}" title="Find the original GenBank sequence used to design the probes"> - GenBank + {% if protein_atlas_link %} + <a href="{{ protein_atlas_link }}" target="_blank" title="Human Protein Atlas"> + Protein Atlas + </a> + + {% endif %} + {% if open_targets_link %} + <a href="{{ open_targets_link }}" target="_blank" title="Open Targets"> + Open Targets </a> {% endif %} {% if homologene_link %} - <a href="{{ homologene_link }}" title="Find similar genes in other species"> + <a href="{{ homologene_link }}" target="_blank" title="Find similar genes in other species"> HomoloGene </a> {% endif %} {% if this_trait.symbol %} - <a href="{{ genotation_link }}" title="Related descriptive, genomic, clinical, functional and drug-therapy information"> + <a href="{{ genotation_link }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information"> Genotation </a> - <a href="{{ gtex_link }}" title="GTEx Portal"> + <a href="{{ gtex_link }}" target="_blank" title="GTEx Portal"> GTEx Portal </a> {% if genebridge_link %} - <a href="{{ genebridge_link }}"> + <a href="{{ genebridge_link }}" target="_blank"> GeneBridge </a> {% endif %} {% endif %} <br> {% if ucsc_blat_link %} - <a href="{{ ucsc_blat_link }}" title="Info from UCSC Genome Browser"> + <a href="{{ ucsc_blat_link }}" target="_blank" title="Info from UCSC Genome Browser"> UCSC </a> {% endif %} {% if biogps_link %} - <a href="{{ biogps_link }}" title="Expression across many tissues and cell types"> + <a href="{{ biogps_link }}" target="_blank" title="Expression across many tissues and cell types"> BioGPS </a> {% endif %} {% if string_link %} - <a href="{{ string_link }}" title="Protein interactions: known and inferred"> + <a href="{{ string_link }}" target="_blank" title="Protein interactions: known and inferred"> STRING </a> {% endif %} {% if panther_link %} - <a href="{{ panther_link }}" title="Gene and protein data resources from Celera-ABI"> + <a href="{{ panther_link }}" target="_blank" title="Gene and protein data resources from Celera-ABI"> PANTHER </a> {% endif %} {% if gemma_link %} - <a href="{{ gemma_link }}" title="Meta-analysis of gene expression data"> + <a href="{{ gemma_link }}" target="_blank" title="Meta-analysis of gene expression data"> Gemma </a> {% endif %} {% if aba_link %} - <a href="{{ aba_link }}" title="Allen Brain Atlas"> + <a href="{{ aba_link }}" target="_blank" title="Allen Brain Atlas"> ABA </a> {% endif %} {% if ebi_gwas_link %} - <a href="{{ ebi_gwas_link }}" title="EBI GWAS"> + <a href="{{ ebi_gwas_link }}" target="_blank" title="EBI GWAS"> EBI GWAS </a> {% endif %} {% if wiki_pi_link %} - <a href="{{ wiki_pi_link }}" title="Wiki-Pi"> + <a href="{{ wiki_pi_link }}" target="_blank" title="Wiki-Pi"> Wiki-Pi </a> @@ -207,6 +219,9 @@ </a> {% endif %} {% endif %} + <a target="_blank" href="http://www.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}"> + <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button> + </a> </div> </div> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index b5c37b8b..1a67dce8 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -1,6 +1,6 @@ <div> {% if dataset.group.mapping_names|length > 0 %} - <div class="col-xs-5"> + <div class="col-xs-4" style="min-width: 600px;"> <div class="tabbable"> <!-- Only required for left/right tabs --> <ul class="nav nav-pills"> @@ -9,7 +9,7 @@ <a href="#gemma" data-toggle="tab">GEMMA</a> </li> <li class="mapping_tab"> - <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a> + <a href="#interval_mapping" data-toggle="tab">Haley-Knott Regression</a> </li> <li class="mapping_tab rqtl"> <a href="#rqtl_geno" data-toggle="tab">R/qtl</a> @@ -116,6 +116,15 @@ <div class="tab-pane" id="interval_mapping"> <div style="margin-top: 20px" class="form-horizontal"> <div class="mapping_method_fields form-group"> + <label for="reaper_version" style="text-align: right;" class="col-xs-3 control-label">Version<sup><a title="'New' is the new qtlreaper implementation written in RUST by Christian Fischer. 'Original' corresponds to the original version written in C.">?</a></sup></label> + <div style="margin-left:20px;" class="col-xs-3 controls"> + <select name="reaper_version" class="form-control"> + <option value="new">New</option> + <option value="original">Original</option> + </select> + </div> + </div> + <div class="mapping_method_fields form-group"> <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label> <div style="margin-left:20px;" class="col-xs-2 controls"> <select id="chr_reaper" class="form-control"> @@ -150,13 +159,15 @@ </div> </div> <div class="mapping_method_fields form-group"> - <label style="text-align: right;" for="control_for" class="col-xs-3 control-label">Control for</label> + <label style="text-align: right;" for="control_for" class="col-xs-3 control-label">Control for<br>Cofactors</label> <div style="margin-left:20px;" class="col-xs-6 controls"> {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} - <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" /> + <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px; display: inline-block;" class="form-control" /> {% else %} - <input name="control_reaper" value="" type="text" class="form-control" /> + <input name="control_reaper" value="" type="text" style="display: inline-block; padding-right: 10px;" class="form-control" /> {% endif %} + <input type="radio" name="do_control_reaper" value="true"> Yes <input type="radio" name="do_control_reaper" value="false" checked="" style="margin-left: 10px;"> No</span> + <!-- <label class="radio-inline"> <input type="radio" name="do_control_reaper" value="true"> Yes @@ -165,6 +176,7 @@ <input type="radio" name="do_control_reaper" value="false" checked=""> No </label> + --> </div> </div> @@ -193,14 +205,14 @@ </div> --> <div class="mapping_method_fields form-group"> - <label style="text-align: right;" class="col-xs-3 control-label">Marker<br>Regression</label> + <label style="text-align: right;" class="col-xs-3 control-label">Interval Map</label> <div style="margin-left:20px;" class="col-xs-6 controls"> <label class="radio-inline"> - <input type="radio" name="manhattan_plot_reaper" value="True"> + <input type="radio" name="manhattan_plot_reaper" value="False" checked=""> Yes </label> <label class="radio-inline"> - <input type="radio" name="manhattan_plot_reaper" value="False" checked=""> + <input type="radio" name="manhattan_plot_reaper" value="True"> No </label> </div> @@ -342,14 +354,15 @@ </div> </div> </div> - <div class="col-xs-5"> + <div class="col-xs-6"> <dl> <dt>GEMMA</dt> <dd>GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).</dd> {% if dataset.group.mapping_id == "1" %} - <dt>Interval Mapping</dt> - <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd> - <dt>R/qtl</dt> + <dt style="margin-top: 20px;">Haley-Knott Regression</dt> + <dd>This method is implementing using the tool QTLReaper. Interval mapping (the last option) is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.<br><br> + The default option is a version of QTLReaper rewritten in RUST that should fix some of the issues the original had. You can still use the original with the Version option.</dd> + <dt style="margin-top: 20px;">R/qtl</dt> <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd> {% endif %} </dl> diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html index 9d85f767..4422ba73 100644 --- a/wqflask/wqflask/templates/snp_browser.html +++ b/wqflask/wqflask/templates/snp_browser.html @@ -383,6 +383,8 @@ return '<input type="checkbox" name="trait_check">' } }, { + 'data': 'index' + }, { 'data': 'indel_name' }, { 'data': 'indel_type' @@ -393,11 +395,11 @@ }, { 'data': 'indel_mb_e' }, { - 'data': 'strand' + 'data': 'indel_strand' }, { - 'data': 'size' + 'data': 'indel_size' }, { - 'data': 'sequence' + 'data': 'indel_sequence' }, { 'data': 'source_name' } diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html index c9f716bf..0dd38fe5 100644 --- a/wqflask/wqflask/templates/submit_trait.html +++ b/wqflask/wqflask/templates/submit_trait.html @@ -8,7 +8,7 @@ {{ flash_me() }} <div class="row" style="width: 1400px !important;"> - <div class="col-xs-5"> + <div class="col-xs-3"> <section id="description"> <div> <h2 style="color: #5a5a5a;">Introduction</h2> @@ -33,7 +33,7 @@ <h2 style="color: #5a5a5a;">Trait Submission Form</h2> <hr> <div style="padding-bottom: 50px;" class="form-horizontal"> - <h3>1. Choose cross or RI set:</h3> + <h3>1. Choose Species and Group:</h3> <br> <div class="col-xs-2" style="min-height: 15vh; display: flex; align-items: center;"> <img src="/static/new/images/step1.gif"> @@ -52,7 +52,6 @@ </div> </div> </div> - <div class="form-horizontal"><img src="/static/new/images/arrowdown.gif" style="display:block; margin-left: 50%; margin-right: 50%;"></div> </div> <div style="padding-bottom: 50px;" class="form-horizontal"> <h3>2. Enter Trait Data:</h3> @@ -66,9 +65,9 @@ <div class="form-group" style="padding-left: 15px;"> <p> <b>From a File:</b> You can enter data by entering a file name here. The file should contain a series of numbers representing trait values. - The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual - or recombinant inbred line. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set, - when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name here, any data that + The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual + or recombinant inbred line. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set, + when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name here, any data that you paste into the next section will be ignored. </p> <input type="file" name="trait_file" style="border-width: 1px; border-style: solid; border-color: #999999;"> @@ -77,10 +76,10 @@ <div class="form-group" style="padding-left: 15px;"> <p> <b>Paste or Type Multiple Values:</b> You can enter data by pasting a series of numbers representing trait values into this area. - The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual - or recombinant inbredline. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set, - when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name in the previous section, - any data that you paste here will be ignored. Check sample data for the correct format. + The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each individual + or line. Use an "x" for missing values. If you have chosen a set of inbred strains, then your data will be displayed in a form in + which you can confirm and/or edit. If you enter a file name in the previous section, + any data that you paste here will be ignored. Check <a href="http://genenetwork.org/RIsample.html">sample data</a> for the correct format. </p> <textarea name="trait_paste" rows="6" cols="70"></textarea> </div> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 109e30cc..cef5f8ec 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -80,7 +80,7 @@ def connect_db(): db = getattr(g, '_database', None) if db is None: logger.debug("Get new database connector") - g.db = g._database = sqlalchemy.create_engine(SQL_URI) + g.db = g._database = sqlalchemy.create_engine(SQL_URI, encoding="latin1") logger.debug(g.db) @app.teardown_appcontext @@ -560,6 +560,7 @@ def loading_page(): logger.info(request.url) initial_start_vars = request.form start_vars_container = {} + num_vals = 0 #ZS: So it can be displayed on loading page if 'wanted_inputs' in initial_start_vars: wanted = initial_start_vars['wanted_inputs'].split(",") start_vars = {} @@ -567,6 +568,15 @@ def loading_page(): if key in wanted or key.startswith(('value:')): start_vars[key] = value + if 'primary_samples' in start_vars: + samples = start_vars['primary_samples'].split(",") + for sample in samples: + value = start_vars.get('value:' + sample) + if value != "x": + num_vals += 1 + + start_vars['num_vals'] = num_vals + start_vars_container['start_vars'] = start_vars else: start_vars_container['start_vars'] = initial_start_vars @@ -588,7 +598,7 @@ def mapping_results_page(): 'samples', 'vals', 'first_run', - 'gwa_filename', + 'output_files', 'geno_db_exists', 'method', 'mapping_results_path', @@ -628,7 +638,9 @@ def mapping_results_page(): 'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', - 'temp_trait' + 'temp_trait', + 'reaper_version', + 'num_vals' ) start_vars = {} for key, value in initial_start_vars.iteritems(): @@ -659,36 +671,36 @@ def mapping_results_page(): if template_vars.no_results: rendered_template = render_template("mapping_error.html") else: - if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink": - template_vars.js_data = json.dumps(template_vars.js_data, - default=json_default_handler, - indent=" ") - - result = template_vars.__dict__ - - if result['pair_scan']: - with Bench("Rendering template"): - img_path = result['pair_scan_filename'] - logger.info("img_path:", img_path) - initial_start_vars = request.form - logger.info("initial_start_vars:", initial_start_vars) - imgfile = open(TEMPDIR + img_path, 'rb') - imgdata = imgfile.read() - imgB64 = imgdata.encode("base64") - bytesarray = array.array('B', imgB64) - result['pair_scan_array'] = bytesarray - rendered_template = render_template("pair_scan_results.html", **result) - else: - gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__ - #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) - #logger.info("pickled result length:", len(pickled_result)) - #Redis.set(key, pickled_result) - #Redis.expire(key, 1*60) - - with Bench("Rendering template"): - if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"): - gn1_template_vars.pop('qtlresults', None) - rendered_template = render_template("mapping_results.html", **gn1_template_vars) + #if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink": + template_vars.js_data = json.dumps(template_vars.js_data, + default=json_default_handler, + indent=" ") + + result = template_vars.__dict__ + + if result['pair_scan']: + with Bench("Rendering template"): + img_path = result['pair_scan_filename'] + logger.info("img_path:", img_path) + initial_start_vars = request.form + logger.info("initial_start_vars:", initial_start_vars) + imgfile = open(TEMPDIR + img_path, 'rb') + imgdata = imgfile.read() + imgB64 = imgdata.encode("base64") + bytesarray = array.array('B', imgB64) + result['pair_scan_array'] = bytesarray + rendered_template = render_template("pair_scan_results.html", **result) + else: + gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__ + #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) + #logger.info("pickled result length:", len(pickled_result)) + #Redis.set(key, pickled_result) + #Redis.expire(key, 1*60) + + with Bench("Rendering template"): + #if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"): + #gn1_template_vars.pop('qtlresults', None) + rendered_template = render_template("mapping_results.html", **gn1_template_vars) return rendered_template @@ -797,6 +809,17 @@ def get_temp_data(): temp_uuid = request.args['key'] return flask.jsonify(temp_data.TempData(temp_uuid).get_all()) +@app.route("/browser_input", methods=('GET',)) +def browser_inputs(): + """ Returns JSON from tmp directory for the purescript genome browser""" + + filename = request.args['filename'] + + with open("{}/gn2/".format(TEMPDIR) + filename + ".json", "r") as the_file: + file_contents = json.load(the_file) + + return flask.jsonify(file_contents) + ########################################################################## def json_default_handler(obj): |
