diff options
| author | acenteno | 2020-04-21 17:35:34 -0500 |
|---|---|---|
| committer | GitHub | 2020-04-21 17:35:34 -0500 |
| commit | 660589b9c2a507529e8e51ca6ce66ca97ad982c5 (patch) | |
| tree | 27f63957278581bc2fce2b88744bfe20c8a81558 /wqflask/base | |
| parent | d97fdc18359233f07c1a1c7b83fe7e88eb225043 (diff) | |
| parent | f2a3ae13231a7d270a5bb6911c248aa713f1ef91 (diff) | |
| download | genenetwork2-660589b9c2a507529e8e51ca6ce66ca97ad982c5.tar.gz | |
Merge pull request #1 from genenetwork/testing
Updating my testing branch
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/anon_collection.py | 21 | ||||
| -rw-r--r-- | wqflask/base/data_set.py | 349 | ||||
| -rw-r--r-- | wqflask/base/mrna_assay_tissue_data.py | 66 | ||||
| -rw-r--r-- | wqflask/base/species.py | 107 | ||||
| -rw-r--r-- | wqflask/base/template.py | 123 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 356 | ||||
| -rw-r--r-- | wqflask/base/trait_collection.py | 53 | ||||
| -rw-r--r-- | wqflask/base/webqtlCaseData.py | 17 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 59 | ||||
| -rw-r--r-- | wqflask/base/webqtlFormData.py | 352 |
10 files changed, 313 insertions, 1190 deletions
diff --git a/wqflask/base/anon_collection.py b/wqflask/base/anon_collection.py deleted file mode 100644 index 8ee73296..00000000 --- a/wqflask/base/anon_collection.py +++ /dev/null @@ -1,21 +0,0 @@ -class AnonCollection(TraitCollection): - - def __init__(self, anon_id) - self.anon_id = anon_id - self.collection_members = Redis.smembers(self.anon_id) - print("self.collection_members is:", self.collection_members) - self.num_members = len(self.collection_members) - - - @app.route("/collections/remove", methods=('POST',)) - def remove_traits(traits_to_remove): - print("traits_to_remove:", traits_to_remove) - for trait in traits_to_remove: - Redis.srem(self.anon_id, trait) - members_now = self.collection_members - traits_to_remove - print("members_now:", members_now) - print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now))) - - # We need to return something so we'll return this...maybe in the future - # we can use it to check the results - return str(len(members_now)) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 54dd3c4b..ebf3f021 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -26,10 +26,10 @@ import collections import codecs import json +import requests import gzip import cPickle as pickle import itertools -from operator import itemgetter from redis import Redis Redis = Redis() @@ -44,8 +44,11 @@ from db import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench 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 @@ -61,18 +64,21 @@ logger = getLogger(__name__ ) # Each subclass will add to this DS_NAME_MAP = {} -def create_dataset(dataset_name, dataset_type = None, get_samplelist = True): +def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None): if not dataset_type: dataset_type = Dataset_Getter(dataset_name) logger.debug("dataset_type", dataset_type) dataset_ob = DS_NAME_MAP[dataset_type] dataset_class = globals()[dataset_ob] - return dataset_class(dataset_name, get_samplelist) + if dataset_type == "Temp": + return dataset_class(dataset_name, get_samplelist, group_name) + else: + return dataset_class(dataset_name, get_samplelist) class Dataset_Types(object): - def __init__(self): + def __init__(self, rebuild=False): """Create a dictionary of samples where the value is set to Geno, Publish or ProbeSet. E.g. @@ -88,8 +94,10 @@ Publish or ProbeSet. E.g. """ self.datasets = {} - if USE_GN_SERVER: - data = menu_main() + if rebuild: #ZS: May make this the only option + data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content) + logger.debug("THE DATA:", data) + #data = gen_menu.gen_dropdown_json() else: file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: @@ -107,8 +115,9 @@ Publish or ProbeSet. E.g. else: new_type = "ProbeSet" self.datasets[short_dataset_name] = new_type + # Set LOG_LEVEL_DEBUG=5 to see the following: - logger.debugf(5,"datasets",self.datasets) + logger.debugf(5, "datasets",self.datasets) def __call__(self, name): return self.datasets[name] @@ -166,20 +175,31 @@ def mescape(*items): class Markers(object): """Todo: Build in cacheing so it saves us reading the same file more than once""" def __init__(self, name): - json_data_fh = open(locate(name + '.json','genotype/json')) - try: - markers = json.load(json_data_fh) - except: - markers = [] + json_data_fh = open(locate(name + ".json",'genotype/json')) + + markers = [] + with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh: + if len(bimbam_fh.readline().split(", ")) > 2: + delimiter = ", " + elif len(bimbam_fh.readline().split(",")) > 2: + delimiter = "," + elif len(bimbam_fh.readline().split("\t")) > 2: + delimiter = "\t" + else: + delimiter = " " + for line in bimbam_fh: + marker = {} + marker['name'] = line.split(delimiter)[0].rstrip() + marker['Mb'] = float(line.split(delimiter)[1].rstrip())/1000000 + marker['chr'] = line.split(delimiter)[2].rstrip() + markers.append(marker) for marker in markers: - if (marker['chr'] != "X") and (marker['chr'] != "Y"): + if (marker['chr'] != "X") and (marker['chr'] != "Y") and (marker['chr'] != "M"): marker['chr'] = int(marker['chr']) marker['Mb'] = float(marker['Mb']) self.markers = markers - #logger.debug("self.markers:", self.markers) - def add_pvalues(self, p_values): logger.debug("length of self.markers:", len(self.markers)) @@ -261,10 +281,12 @@ class DatasetGroup(object): has multiple datasets associated with it. """ - def __init__(self, dataset): + def __init__(self, dataset, name=None): """This sets self.group and self.group_id""" - #logger.debug("DATASET NAME2:", dataset.name) - self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group) + if name == None: + self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group) + else: + self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name) if self.name == 'BXD300': self.name = "BXD" @@ -272,7 +294,6 @@ 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) @@ -282,55 +303,39 @@ 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] if mapping_id == "1": - mapping_names = ["QTLReaper", "PYLMM", "R/qtl"] + mapping_names = ["GEMMA", "QTLReaper", "R/qtl"] elif mapping_id == "2": mapping_names = ["GEMMA"] + elif mapping_id == "3": + mapping_names = ["R/qtl"] elif mapping_id == "4": - mapping_names = ["PLINK"] + mapping_names = ["GEMMA", "PLINK"] else: mapping_names = [] return mapping_id, mapping_names - def get_specified_markers(self, markers = []): - self.markers = HumanMarkers(self.name, markers) - def get_markers(self): - logger.debug("self.species is:", self.species) - def check_plink_gemma(): if flat_file_exists("mapping"): MAPPING_PATH = flat_files("mapping")+"/" - if (os.path.isfile(MAPPING_PATH+self.name+".bed") and - (os.path.isfile(MAPPING_PATH+self.name+".map") or - os.path.isfile(MAPPING_PATH+self.name+".bim"))): + if os.path.isfile(MAPPING_PATH+self.name+".bed"): return True return False if check_plink_gemma(): marker_class = HumanMarkers else: - marker_class = Markers + marker_class = Markers - self.markers = marker_class(self.name) + if self.genofile: + self.markers = marker_class(self.genofile[:-5]) + else: + self.markers = marker_class(self.name) def get_f1_parent_strains(self): try: @@ -344,30 +349,32 @@ class DatasetGroup(object): if maternal and paternal: self.parlist = [maternal, paternal] + def get_genofiles(self): + jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name) + try: + f = open(jsonfile) + except: + return None + jsondata = json.load(f) + return jsondata['genofile'] + def get_samplelist(self): result = None - key = "samplelist:v2:" + self.name + key = "samplelist:v3:" + self.name if USE_REDIS: result = Redis.get(key) if result is not None: - #logger.debug("Sample List Cache hit!!!") - #logger.debug("Before unjsonifying {}: {}".format(type(result), result)) self.samplelist = json.loads(result) - #logger.debug(" type: ", type(self.samplelist)) - #logger.debug(" self.samplelist: ", self.samplelist) else: logger.debug("Cache not hit") genotype_fn = locate_ignore_error(self.name+".geno",'genotype') - mapping_fn = locate_ignore_error(self.name+".fam",'mapping') - if mapping_fn: - self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn) - elif genotype_fn: + if genotype_fn: self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn) else: self.samplelist = None - logger.debug("Sample list: ",self.samplelist) + if USE_REDIS: Redis.set(key, json.dumps(self.samplelist)) Redis.expire(key, 60*5) @@ -378,19 +385,27 @@ 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) - genotype_1 = reaper.Dataset() + #genotype_1 = reaper.Dataset() # reaper barfs on unicode filenames, so here we ensure it's a string if self.genofile: - full_filename = str(locate(self.genofile, 'genotype')) + if "RData" in self.genofile: #ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData + full_filename = str(locate(self.genofile.split(".")[0] + ".geno", 'genotype')) + else: + full_filename = str(locate(self.genofile, 'genotype')) else: full_filename = str(locate(self.name + '.geno', 'genotype')) - genotype_1.read(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) @@ -419,13 +434,16 @@ def datasets(group_name, this_group = None): FROM PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s' - and PublishFreeze.public > %s) + and PublishFreeze.public > %s + and PublishFreeze.confidentiality < 1 + ORDER BY PublishFreeze.Id ASC) UNION (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze, InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s' - and GenoFreeze.public > %s) + and GenoFreeze.public > %s + and GenoFreeze.confidentiality < 1) UNION (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue @@ -434,27 +452,34 @@ def datasets(group_name, this_group = None): and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like %s and ProbeSetFreeze.public > %s - ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId) + and ProbeSetFreeze.confidentiality < 1 + ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC) ''' % (group_name, webqtlConfig.PUBLICTHRESH, group_name, webqtlConfig.PUBLICTHRESH, "'" + group_name + "'", webqtlConfig.PUBLICTHRESH)) - #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)): - for dataset_item in the_results: + sorted_results = sorted(the_results, key=lambda kv: kv[0]) + + pheno_inserted = False #ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown + geno_inserted = False + for dataset_item in sorted_results: tissue_name = dataset_item[0] dataset = dataset_item[1] dataset_short = dataset_item[2] if tissue_name in ['#PublishFreeze', '#GenoFreeze']: - dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)])) + if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'): + dataset_menu.insert(0, dict(tissue=None, datasets=[(dataset, dataset_short)])) + pheno_inserted = True + elif pheno_inserted and tissue_name == '#GenoFreeze': + dataset_menu.insert(1, dict(tissue=None, datasets=[(dataset, dataset_short)])) + geno_inserted = True + else: + dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)])) else: - dataset_sub_menu = [item[1:] for item in dataset] - tissue_already_exists = False - tissue_position = None for i, tissue_dict in enumerate(dataset_menu): if tissue_dict['tissue'] == tissue_name: tissue_already_exists = True - tissue_position = i break if tissue_already_exists: @@ -481,7 +506,7 @@ class DataSet(object): """ - def __init__(self, name, get_samplelist = True): + def __init__(self, name, get_samplelist = True, group_name = None): assert name, "Need a name" self.name = name @@ -493,11 +518,13 @@ class DataSet(object): self.setup() - self.check_confidentiality() - - self.retrieve_other_names() - - self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype + if self.type == "Temp": #Need to supply group name as input if temp trait + self.group = DatasetGroup(self, name=group_name) # sets self.group and self.group_id and gets genotype + else: + 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) @@ -512,6 +539,31 @@ 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. @@ -658,6 +710,7 @@ class PhenotypeDataSet(DataSet): 'Phenotype.Pre_publication_description', 'Phenotype.Pre_publication_abbreviation', 'Phenotype.Post_publication_abbreviation', + 'PublishXRef.mean', 'Phenotype.Lab_code', 'Publication.PubMed_ID', 'Publication.Abstract', @@ -666,13 +719,14 @@ class PhenotypeDataSet(DataSet): 'PublishXRef.Id'] # Figure out what display_fields is - self.display_fields = ['name', + self.display_fields = ['name', 'group_code', 'pubmed_id', 'pre_publication_description', 'post_publication_description', 'original_description', 'pre_publication_abbreviation', 'post_publication_abbreviation', + 'mean', 'lab_code', 'submitter', 'owner', 'authorized_users', @@ -708,20 +762,6 @@ class PhenotypeDataSet(DataSet): # (Urgently?) Need to write this pass - def get_trait_list(self): - query = """ - select PublishXRef.Id - from PublishXRef, PublishFreeze - where PublishFreeze.InbredSetId=PublishXRef.InbredSetId - and PublishFreeze.Id = {} - """.format(escape(str(self.id))) - logger.sql(query) - results = g.db.execute(query).fetchall() - trait_data = {} - for trait in results: - trait_data[trait[0]] = self.retrieve_sample_data(trait[0]) - return trait_data - def get_trait_info(self, trait_list, species = ''): for this_trait in trait_list: @@ -735,7 +775,7 @@ class PhenotypeDataSet(DataSet): #of the post-publication description if this_trait.confidential: this_trait.description_display = "" - continue # for now + continue # for now, because no authorization features if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( privilege=self.privilege, @@ -759,9 +799,7 @@ class PhenotypeDataSet(DataSet): #LRS and its location this_trait.LRS_score_repr = "N/A" - this_trait.LRS_score_value = 0 this_trait.LRS_location_repr = "N/A" - this_trait.LRS_location_value = 1000000 if this_trait.lrs: query = """ @@ -778,17 +816,7 @@ class PhenotypeDataSet(DataSet): LRS_Chr = result[0] LRS_Mb = result[1] - #XZ: LRS_location_value is used for sorting - try: - LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb) - except: - if LRS_Chr.upper() == 'X': - LRS_location_value = 20*1000 + float(LRS_Mb) - else: - LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb) - this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs - this_trait.LRS_score_value = LRS_score_value = this_trait.lrs this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb)) def retrieve_sample_data(self, trait): @@ -850,45 +878,18 @@ class GenotypeDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - def get_trait_list(self): - query = """ - select Geno.Name - from Geno, GenoXRef - where GenoXRef.GenoId = Geno.Id - and GenoFreezeId = {} - """.format(escape(str(self.id))) - logger.sql(query) - results = g.db.execute(query).fetchall() - trait_data = {} - for trait in results: - trait_data[trait[0]] = self.retrieve_sample_data(trait[0]) - return trait_data - def get_trait_info(self, trait_list, species=None): for this_trait in trait_list: if not this_trait.haveinfo: this_trait.retrieveInfo() - #XZ: trait_location_value is used for sorting - trait_location_repr = 'N/A' - trait_location_value = 1000000 - if this_trait.chr and this_trait.mb: - try: - trait_location_value = int(this_trait.chr)*1000 + this_trait.mb - except: - if this_trait.chr.upper() == 'X': - trait_location_value = 20*1000 + this_trait.mb - else: - trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb - this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) ) - this_trait.location_value = trait_location_value def retrieve_sample_data(self, trait): query = """ SELECT - Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Sample.Name2 + Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2 FROM (GenoData, GenoFreeze, Strain, Geno, GenoXRef) left join GenoSE on @@ -940,6 +941,7 @@ class MrnaAssayDataSet(DataSet): 'blatseq', 'targetseq', 'chipid', 'comments', 'strand_probe', 'strand_gene', + 'proteinid', 'uniprotid', 'probe_set_target_region', 'probe_set_specificity', 'probe_set_blat_score', @@ -978,20 +980,6 @@ class MrnaAssayDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - def get_trait_list_1(self): - query = """ - select ProbeSet.Name - from ProbeSet, ProbeSetXRef - where ProbeSetXRef.ProbeSetId = ProbeSet.Id - and ProbeSetFreezeId = {} - """.format(escape(str(self.id))) - logger.sql(query) - results = g.db.execute(query).fetchall() - trait_data = {} - for trait in results: - trait_data[trait[0]] = self.retrieve_sample_data(trait[0]) - return trait_data - def get_trait_info(self, trait_list=None, species=''): # Note: setting trait_list to [] is probably not a great idea. @@ -1023,27 +1011,8 @@ class MrnaAssayDataSet(DataSet): # Save it for the jinja2 template this_trait.description_display = description_display - #XZ: trait_location_value is used for sorting - trait_location_repr = 'N/A' - trait_location_value = 1000000 - if this_trait.chr and this_trait.mb: - #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") - #This is so we can convert the location to a number used for sorting - trait_location_value = self.convert_location_to_value(this_trait.chr, this_trait.mb) - #try: - # trait_location_value = int(this_trait.chr)*1000 + this_trait.mb - #except ValueError: - # if this_trait.chr.upper() == 'X': - # trait_location_value = 20*1000 + this_trait.mb - # else: - # trait_location_value = (ord(str(this_trait.chr).upper()[0])*1000 + - # this_trait.mb) - - #ZS: Put this in function currently called "convert_location_to_value" - this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, - float(this_trait.mb)) - this_trait.location_value = trait_location_value + this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb)) #Get mean expression value query = ( @@ -1065,9 +1034,7 @@ class MrnaAssayDataSet(DataSet): #LRS and its location this_trait.LRS_score_repr = 'N/A' - this_trait.LRS_score_value = 0 this_trait.LRS_location_repr = 'N/A' - this_trait.LRS_location_value = 1000000 #Max LRS and its Locus location if this_trait.lrs and this_trait.locus: @@ -1082,40 +1049,10 @@ class MrnaAssayDataSet(DataSet): if result: lrs_chr, lrs_mb = result - #XZ: LRS_location_value is used for sorting - lrs_location_value = self.convert_location_to_value(lrs_chr, lrs_mb) this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs - this_trait.LRS_score_value = this_trait.lrs this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb)) - - def convert_location_to_value(self, chromosome, mb): - try: - location_value = int(chromosome)*1000 + float(mb) - except ValueError: - if chromosome.upper() == 'X': - location_value = 20*1000 + float(mb) - else: - location_value = (ord(str(chromosome).upper()[0])*1000 + - float(mb)) - - return location_value - - def get_sequence(self): - query = """ - SELECT - ProbeSet.BlatSeq - FROM - ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSet.Id=ProbeSetXRef.ProbeSetId and - ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and - ProbeSet.Name = %s - ProbeSetFreeze.Name = %s - """ % (escape(self.name), escape(self.dataset.name)) - logger.sql(query) - results = g.db.execute(query).fetchone() - return results[0] + return trait_list def retrieve_sample_data(self, trait): query = """ @@ -1139,7 +1076,6 @@ class MrnaAssayDataSet(DataSet): #logger.debug("RETRIEVED RESULTS HERE:", results) return results - def retrieve_genes(self, column_name): query = """ select ProbeSet.Name, ProbeSet.%s @@ -1156,6 +1092,8 @@ class MrnaAssayDataSet(DataSet): class TempDataSet(DataSet): '''Temporary user-generated data set''' + DS_NAME_MAP['Temp'] = 'TempDataSet' + def setup(self): self.search_fields = ['name', 'description'] @@ -1191,19 +1129,6 @@ class TempDataSet(DataSet): desc = self.handle_pca(desc) return desc - def get_group(self): - query = """ - SELECT - InbredSet.Name, InbredSet.Id - FROM - InbredSet, Temp - WHERE - Temp.InbredSetId = InbredSet.Id AND - Temp.Name = "%s" - """ % self.name - logger.sql(query) - self.group, self.group_id = g.db.execute(query).fetchone() - def retrieve_sample_data(self, trait): query = """ SELECT diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index eb836e6c..6fec5dcd 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -18,21 +18,11 @@ class MrnaAssayTissueData(object): def __init__(self, gene_symbols=None): self.gene_symbols = gene_symbols - self.have_data = False if self.gene_symbols == None: self.gene_symbols = [] - #print("self.gene_symbols:", self.gene_symbols) - self.data = collections.defaultdict(Bunch) - #self.gene_id_dict ={} - #self.data_id_dict = {} - #self.chr_dict = {} - #self.mb_dict = {} - #self.desc_dict = {} - #self.probe_target_desc_dict = {} - query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description from ( select Symbol, max(Mean) as maxmean @@ -52,7 +42,6 @@ class MrnaAssayTissueData(object): in_clause = db_tools.create_in_clause(gene_symbols) #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower - query += ''' Symbol in {} group by Symbol) as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol and t.Mean = x.maxmean; @@ -67,9 +56,7 @@ class MrnaAssayTissueData(object): for result in results: symbol = result[0] - #if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]: if symbol.lower() in lower_symbols: - #gene_symbols.append(symbol) symbol = symbol.lower() self.data[symbol].gene_id = result.GeneId @@ -79,8 +66,6 @@ class MrnaAssayTissueData(object): self.data[symbol].description = result.description self.data[symbol].probe_target_description = result.Probe_Target_Description - print("self.data: ", pf(self.data)) - ########################################################################### #Input: cursor, symbolList (list), dataIdDict(Dict) #output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair, @@ -107,53 +92,4 @@ class MrnaAssayTissueData(object): else: symbol_values_dict[result.Symbol.lower()].append(result.value) - #for symbol in self.data: - # data_id = self.data[symbol].data_id - # symbol_values_dict[symbol] = self.get_tissue_values(data_id) - - - return symbol_values_dict - - - #def get_tissue_values(self, data_id): - # """Gets the tissue values for a particular gene""" - # - # tissue_values=[] - # - # query = """SELECT value, id - # FROM TissueProbeSetData - # WHERE Id IN {}""".format(db_tools.create_in_clause(data_id)) - # - # #try : - # results = g.db.execute(query).fetchall() - # for result in results: - # tissue_values.append(result.value) - # #symbol_values_dict[symbol] = value_list - # #except: - # # symbol_values_pairs[symbol] = None - # - # return tissue_values - -######################################################################################################## -#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol -#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair. -# key is symbol, value is one list of expression values of one probeSet. -#function: wrapper function for getSymbolValuePairDict function -# build gene symbol list if necessary, cut it into small lists if necessary, -# then call getSymbolValuePairDict function and merge the results. -######################################################################################################## - -#def get_trait_symbol_and_tissue_values(symbol_list=None): -# tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list) -# -# #symbolList, -# #geneIdDict, -# #dataIdDict, -# #ChrDict, -# #MbDict, -# #descDict, -# #pTargetDescDict = getTissueProbeSetXRefInfo( -# # GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId) -# -# if len(tissue_data.gene_symbols): -# return get_symbol_values_pairs(tissue_data) + return symbol_values_dict \ No newline at end of file diff --git a/wqflask/base/species.py b/wqflask/base/species.py index ce763fc3..6d99af65 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -14,23 +14,13 @@ from utility.logger import getLogger logger = getLogger(__name__ ) class TheSpecies(object): - def __init__(self, dataset): - self.dataset = dataset - #print("self.dataset is:", pf(self.dataset.__dict__)) - self.chromosomes = Chromosomes(self.dataset) - self.genome_mb_length = self.chromosomes.get_genome_mb_length() - - #@property - #def chromosomes(self): - # chromosomes = [("All", -1)] - # - # for counter, genotype in enumerate(self.dataset.group.genotype): - # if len(genotype) > 1: - # chromosomes.append((genotype.name, counter)) - # - # print("chromosomes is: ", pf(chromosomes)) - # - # return chromosomes + def __init__(self, dataset=None, species_name=None): + if species_name != None: + self.name = species_name + self.chromosomes = Chromosomes(species=self.name) + else: + self.dataset = dataset + self.chromosomes = Chromosomes(dataset=self.dataset) class IndChromosome(object): def __init__(self, name, length): @@ -42,17 +32,22 @@ class IndChromosome(object): """Chromosome length in megabases""" return self.length / 1000000 - def set_cm_length(self, genofile_chr): - self.cm_length = genofile_chr[-1].cM - genofile_chr[0].cM - - class Chromosomes(object): - def __init__(self, dataset): - self.dataset = dataset + def __init__(self, dataset=None, species=None): self.chromosomes = collections.OrderedDict() + if species != None: + query = """ + Select + Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species + where + Chr_Length.SpeciesId = Species.SpeciesId AND + Species.Name = '%s' + Order by OrderId + """ % species.capitalize() + else: + self.dataset = dataset - - query = """ + query = """ Select Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet where @@ -64,64 +59,4 @@ class Chromosomes(object): results = g.db.execute(query).fetchall() for item in results: - self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) - - self.set_mb_graph_interval() - #self.get_cm_length_list() - - - def set_mb_graph_interval(self): - """Empirical megabase interval""" - - if self.chromosomes: - self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) - else: - self.mb_graph_interval = 1 - - #if self.chromosomes: - #assert self.chromosomes, "Have to add some code back in apparently to set it to 1" - #self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) - #else: - #self.mb_graph_interval = 1 - - - def get_genome_mb_length(self): - """Gets the sum of each chromosome's length in megabases""" - - return sum([ind_chromosome.mb_length for ind_chromosome in self.chromosomes.values()]) - - - def get_genome_cm_length(self): - """Gets the sum of each chromosome's length in centimorgans""" - - return sum([ind_chromosome.cm_length for ind_chromosome in self.chromosomes.values()]) - - def get_cm_length_list(self): - """Chromosome length in centimorgans - - Calculates the length in centimorgans by subtracting the centimorgan position - of the last marker in a chromosome by the position of the first marker - - """ - - self.dataset.group.read_genotype_file() - - self.cm_length_list = [] - - for chromosome in self.dataset.group.genotype: - self.cm_length_list.append(chromosome[-1].cM - chromosome[0].cM) - - print("self.cm_length_list:", pf(self.cm_length_list)) - - assert len(self.cm_length_list) == len(self.chromosomes), "Uh-oh lengths should be equal!" - for counter, chromosome in enumerate(self.chromosomes.values()): - chromosome.cm_length = self.cm_length_list[counter] - #self.chromosomes[counter].cm_length = item - - for key, value in self.chromosomes.items(): - print("bread - %s: %s" % (key, pf(vars(value)))) - - -# Testing -#if __name__ == '__main__': -# foo = dict(bar=dict(length)) + self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) \ No newline at end of file diff --git a/wqflask/base/template.py b/wqflask/base/template.py deleted file mode 100644 index aa8f90dc..00000000 --- a/wqflask/base/template.py +++ /dev/null @@ -1,123 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -template = """ -<?XML VERSION="1.0" ENCODING="UTF-8"> -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> -<HTML> -<HEAD> -<TITLE>%s</TITLE> - -<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> -<META NAME="keywords" CONTENT="genetics, bioinformatics, genome, phenome, gene expression, complex trait analysis, gene mapping, SNP, quantitative trait locus QTL, expression eQTL, WebQTL, Traitnet, Traitnetwork, personalized medicine"> -<META NAME="description" CONTENT ="GeneNetwork is a free scientific web resource used to study relationships between differences in genes, environmental factors, phenotypes, and disease risk." > -<META NAME="author" CONTENT ="GeneNetwork developers" > -<META NAME="geo.placename" CONTENT ="Memphis, TN" > -<META NAME="geo.region" CONTENT="US-TN"> -%s -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> -<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" /> -<LINK REL="apple-touch-icon" href="/images/ipad_icon3.png" /> -<link type="text/css" href='/css/custom-theme/jquery-ui-1.8.12.custom.css' rel='Stylesheet' /> -<link type="text/css" href='/css/tab_style.css' rel='Stylesheet' /> - -<script type="text/javascript" src="/javascript/jquery-1.5.2.min.js"></script> -<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> -<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT> -<SCRIPT SRC="/javascript/tablesorter.js"></SCRIPT> -<SCRIPT SRC="/javascript/jqueryFunction.js"></SCRIPT> -<script src="/javascript/tabbed_pages.js" type="text/javascript"></script> -<script src="/javascript/jquery-ui-1.8.12.custom.min.js" type="text/javascript"></script> -%s - -<script type="text/javascript"> - var _gaq = _gaq || []; - _gaq.push(['_setAccount', 'UA-3782271-1']); - _gaq.push(['_trackPageview']); - (function() { - var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; - ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; - var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); - })(); -</script> -</HEAD> -<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff %s> -%s -<TABLE cellSpacing=5 cellPadding=4 width="100%%" border=0> - <TBODY> - <!-- Start of header --> - <TR> - %s - </TR> - <!-- End of header --> - - <!-- Start of body --> - <TR> - <TD bgColor=#eeeeee class="solidBorder"> - <Table width= "100%%" cellSpacing=0 cellPadding=5> - <TR> - %s - </TR> - </TABLE> - </TD> - </TR> - <!-- End of body --> - - <!-- Start of footer --> - <TR> - <TD align=center bgColor=#ddddff class="solidBorder"> - <TABLE width="90%%">%s</table> - </td> - </TR> - <!-- End of footer --> -</TABLE> - -<!-- menu script itself. you should not modify this file --> -<script language="JavaScript" src="/javascript/menu_new.js"></script> -<!-- items structure. menu hierarchy and links are stored there --> -<script language="JavaScript" src="/javascript/menu_items.js"></script> -<!-- files with geometry and styles structures --> -<script language="JavaScript" src="/javascript/menu_tpl.js"></script> -<script language="JavaScript"> - <!--// - // Note where menu initialization block is located in HTML document. - // Don't try to position menu locating menu initialization block in - // some table cell or other HTML element. Always put it before </body> - // each menu gets two parameters (see demo files) - // 1. items structure - // 2. geometry structure - new menu (MENU_ITEMS, MENU_POS); - // make sure files containing definitions for these variables are linked to the document - // if you got some javascript error like "MENU_POS is not defined", then you've made syntax - // error in menu_tpl.js file or that file isn't linked properly. - - // also take a look at stylesheets loaded in header in order to set styles - //--> -</script> -</BODY> -</HTML> -""" diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index bf87e879..5525472e 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -3,14 +3,17 @@ from __future__ import absolute_import, division, print_function import string import resource import codecs +import requests -from htmlgen import HTMLgen2 as HT +import redis +Redis = redis.StrictRedis() from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData from base.data_set import create_dataset from db import webqtlDatabaseFunction from utility import webqtlUtil +from utility import hmac from wqflask import app @@ -18,17 +21,11 @@ import simplejson as json from MySQLdb import escape_string as escape from pprint import pformat as pf -from flask import Flask, g, request +from flask import Flask, g, request, url_for from utility.logger import getLogger logger = getLogger(__name__ ) -from wqflask import user_manager - -def print_mem(stage=""): - mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss - print("{}: {}".format(stage, mem/1024)) - class GeneralTrait(object): """ Trait class defines a trait in webqtl, can be either Microarray, @@ -39,13 +36,15 @@ class GeneralTrait(object): def __init__(self, get_qtl_info=False, get_sample_info=True, **kw): # xor assertion assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; + self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. if kw.get('dataset_name'): - self.dataset = create_dataset(kw.get('dataset_name')) - #print(" in GeneralTrait created dataset:", self.dataset) + if kw.get('dataset_name') == "Temp": + temp_group = self.name.split("_")[2] + self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group) + else: + self.dataset = create_dataset(kw.get('dataset_name')) else: self.dataset = kw.get('dataset') - self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. - #print("THE NAME IS:", self.name) self.cellid = kw.get('cellid') self.identification = kw.get('identification', 'un-named trait') self.haveinfo = kw.get('haveinfo', False) @@ -61,6 +60,10 @@ class GeneralTrait(object): self.num_overlap = None self.strand_probe = None self.symbol = None + self.display_name = self.name + + self.LRS_score_repr = "N/A" + self.LRS_location_repr = "N/A" if kw.get('fullname'): name2 = value.split("::") @@ -72,94 +75,11 @@ class GeneralTrait(object): # Todo: These two lines are necessary most of the time, but perhaps not all of the time # So we could add a simple if statement to short-circuit this if necessary - self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info) + if self.dataset.type != "Temp": + self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info) if get_sample_info != False: self = retrieve_sample_data(self, self.dataset) - - def get_name(self): - stringy = "" - if self.dataset and self.name: - stringy = "%s::%s" % (self.dataset, self.name) - if self.cellid: - stringy += "::" + self.cellid - else: - stringy = self.description - return stringy - - - def get_given_name(self): - """ - when user enter a trait or GN generate a trait, user want show the name - not the name that generated by GN randomly, the two follow function are - used to give the real name and the database. displayName() will show the - database also, getGivenName() just show the name. - For other trait, displayName() as same as getName(), getGivenName() as - same as self.name - - Hongqiang 11/29/07 - - """ - stringy = self.name - if self.dataset and self.name: - desc = self.dataset.get_desc() - if desc: - #desc = self.handle_pca(desc) - stringy = desc - return stringy - - - def display_name(self): - stringy = "" - if self.dataset and self.name: - desc = self.dataset.get_desc() - #desc = self.handle_pca(desc) - if desc: - #desc = self.handle_pca(desc) - #stringy = desc - #if desc.__contains__('PCA'): - # desc = desc[desc.rindex(':')+1:].strip() - #else: - # desc = desc[:desc.index('entered')].strip() - #desc = self.handle_pca(desc) - stringy = "%s::%s" % (self.dataset, desc) - else: - stringy = "%s::%s" % (self.dataset, self.name) - if self.cellid: - stringy += "::" + self.cellid - else: - stringy = self.description - - return stringy - - - #def __str__(self): - # #return "%s %s" % (self.getName(), self.group) - # return self.getName() - #__str__ = getName - #__repr__ = __str__ - - def export_data(self, samplelist, the_type="val"): - """ - export data according to samplelist - mostly used in calculating correlation - - """ - result = [] - for sample in samplelist: - if self.data.has_key(sample): - if the_type=='val': - result.append(self.data[sample].val) - elif the_type=='var': - result.append(self.data[sample].var) - elif the_type=='N': - result.append(self.data[sample].N) - else: - raise KeyError, `the_type`+' the_type is incorrect.' - else: - result.append(None) - return result - def export_informative(self, include_variance=0): """ export informative sample @@ -179,19 +99,6 @@ class GeneralTrait(object): sample_aliases.append(sample_data.name2) return samples, vals, the_vars, sample_aliases - - @property - def name_header_fmt(self): - '''Return a human-readable name for use in page header''' - if self.dataset.type == 'ProbeSet': - return self.symbol - elif self.dataset.type == 'Geno': - return self.name - elif self.dataset.type == 'Publish': - return self.post_publication_abbreviation - else: - return "unnamed" - @property def description_fmt(self): '''Return a text formated description''' @@ -200,6 +107,8 @@ class GeneralTrait(object): formatted = self.description if self.probe_target_description: formatted += "; " + self.probe_target_description + else: + formatted = "Not available" elif self.dataset.type == 'Publish': if self.confidential: formatted = self.pre_publication_description @@ -212,11 +121,36 @@ 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()) + + if human_response and mouse_response and other_response: + 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 @@ -244,60 +178,33 @@ class GeneralTrait(object): fmt += (' on the minus strand ') return fmt - -# In ProbeSet, there are maybe several annotations match one sequence -# so we need use sequence(BlatSeq) as the identification, when we update -# one annotation, we update the others who match the sequence also. -# -# Hongqiang Li, 3/3/2008 -def getSequence(trait, dataset_name): - dataset = create_dataset(dataset_name) - - if dataset.type == 'ProbeSet': - results = g.db.execute(''' - SELECT - ProbeSet.BlatSeq - FROM - ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSet.Id=ProbeSetXRef.ProbeSetId and - ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and - ProbeSet.Name = %s - ProbeSetFreeze.Name = %s - ''', trait.name, dataset.name).fetchone() - - return results[0] def retrieve_sample_data(trait, dataset, samplelist=None): if samplelist == None: samplelist = [] - results = dataset.retrieve_sample_data(trait.name) + if dataset.type == "Temp": + results = Redis.get(trait.name).split() + else: + results = dataset.retrieve_sample_data(trait.name) # Todo: is this necessary? If not remove trait.data.clear() - all_samples_ordered = dataset.group.all_samples_ordered() - if results: - for item in results: - name, value, variance, num_cases, name2 = item - if not samplelist or (samplelist and name in samplelist): - trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) - - return trait - -def convert_location_to_value(chromosome, mb): - try: - location_value = int(chromosome)*1000 + float(mb) - except ValueError: - if chromosome.upper() == 'X': - location_value = 20*1000 + float(mb) + if dataset.type == "Temp": + all_samples_ordered = dataset.group.all_samples_ordered() + for i, item in enumerate(results): + try: + trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item)) + except: + pass else: - location_value = (ord(str(chromosome).upper()[0])*1000 + - float(mb)) - - return location_value + for item in results: + name, value, variance, num_cases, name2 = item + if not samplelist or (samplelist and name in samplelist): + trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) + return trait @app.route("/trait/get_sample_data") def get_sample_data(): @@ -307,25 +214,37 @@ def get_sample_data(): trait_ob = GeneralTrait(name=trait, dataset_name=dataset) - return json.dumps([trait, {key: value.value for key, value in trait_ob.data.iteritems() }]) - - #jsonable_sample_data = {} - #for sample in trait_ob.data.iteritems(): - # jsonable_sample_data[sample] = trait_ob.data[sample].value - # - #return jsonable_sample_data + trait_dict = {} + trait_dict['name'] = trait + trait_dict['db'] = dataset + trait_dict['type'] = trait_ob.dataset.type + trait_dict['group'] = trait_ob.dataset.group.name + trait_dict['tissue'] = trait_ob.dataset.tissue + trait_dict['species'] = trait_ob.dataset.group.species + trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset) + trait_dict['description'] = trait_ob.description_display + if trait_ob.dataset.type == "ProbeSet": + trait_dict['symbol'] = trait_ob.symbol + trait_dict['location'] = trait_ob.location_repr + elif trait_ob.dataset.type == "Publish": + if trait_ob.pubmed_id: + trait_dict['pubmed_link'] = trait_ob.pubmed_link + trait_dict['pubmed_text'] = trait_ob.pubmed_text + + return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }]) -def jsonable(trait, dataset_name): +def jsonable(trait): """Return a dict suitable for using as json Actual turning into json doesn't happen here though""" - dataset = create_dataset(dataset_name) + dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name) if dataset.type == "ProbeSet": return dict(name=trait.name, symbol=trait.symbol, dataset=dataset.name, + dataset_name = dataset.shortname, description=trait.description_display, mean=trait.mean, location=trait.location_repr, @@ -337,7 +256,9 @@ def jsonable(trait, dataset_name): if trait.pubmed_id: return dict(name=trait.name, dataset=dataset.name, + dataset_name = dataset.shortname, description=trait.description_display, + abbreviation=trait.abbreviation, authors=trait.authors, pubmed_text=trait.pubmed_text, pubmed_link=trait.pubmed_link, @@ -348,7 +269,9 @@ def jsonable(trait, dataset_name): else: return dict(name=trait.name, dataset=dataset.name, + dataset_name = dataset.shortname, description=trait.description_display, + abbreviation=trait.abbreviation, authors=trait.authors, pubmed_text=trait.pubmed_text, lrs_score=trait.LRS_score_repr, @@ -358,6 +281,7 @@ def jsonable(trait, dataset_name): elif dataset.type == "Geno": return dict(name=trait.name, dataset=dataset.name, + dataset_name = dataset.shortname, location=trait.location_repr ) else: @@ -379,7 +303,7 @@ def jsonable_table_row(trait, dataset_name, index): additive = "N/A" else: additive = "%.3f" % round(float(trait.additive), 2) - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.symbol, @@ -395,7 +319,7 @@ def jsonable_table_row(trait, dataset_name, index): else: additive = "%.2f" % round(float(trait.additive), 2) if trait.pubmed_id: - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.description_display, @@ -405,7 +329,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.LRS_location_repr, additive] else: - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.description_display, @@ -415,7 +339,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.LRS_location_repr, additive] elif dataset.type == "Geno": - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.location_repr] @@ -428,21 +352,22 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if dataset.type == 'Publish': query = """ SELECT - PublishXRef.Id, Publication.PubMed_ID, + PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID, Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, - Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, + Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean, Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, Publication.Authors, Publication.Title, Publication.Abstract, Publication.Journal, Publication.Volume, Publication.Pages, Publication.Month, Publication.Year, PublishXRef.Sequence, Phenotype.Units, PublishXRef.comments FROM - PublishXRef, Publication, Phenotype, PublishFreeze + PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet WHERE PublishXRef.Id = %s AND Phenotype.Id = PublishXRef.PhenotypeId AND Publication.Id = PublishXRef.PublicationId AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishXRef.InbredSetId = InbredSet.Id AND PublishFreeze.Id = %s """ % (trait.name, dataset.id) @@ -492,17 +417,25 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait_info = g.db.execute(query, (string.join(dataset.display_fields,','), dataset.type, trait.name)).fetchone() + if trait_info: trait.haveinfo = True #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): + # logger.debug("HOLDER:", holder) + # logger.debug("HOLDER2:", holder.decode(encoding='latin1')) + # holder = unicode(trait_info[i], "utf-8", "ignore") if isinstance(trait_info[i], basestring): - holder = unicode(trait_info[i], "utf-8", "ignore") + holder = holder.encode('latin1') setattr(trait, field, holder) if dataset.type == 'Publish': + if trait.group_code: + trait.display_name = trait.group_code + "_" + str(trait.name) + trait.confidential = 0 if trait.pre_publication_description and not trait.pubmed_id: trait.confidential = 1 @@ -513,6 +446,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): #phenotype traits, then display the pre-publication description instead #of the post-publication description if trait.confidential: + trait.abbreviation = trait.pre_publication_abbreviation trait.description_display = trait.pre_publication_description #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( @@ -522,11 +456,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): # # description = self.pre_publication_description else: + trait.abbreviation = trait.post_publication_abbreviation if description: trait.description_display = description.strip() else: trait.description_display = "" + trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") + trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") + trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") + if not trait.year.isdigit(): trait.pubmed_text = "N/A" else: @@ -535,38 +474,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if trait.pubmed_id: trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id - - trait.homologeneid = None if dataset.type == 'ProbeSet' and dataset.group: - if trait.geneid: - #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. - #XZ: So I have to test if geneid is number before execute the query. - #XZ: The geneid values in database should be cleaned up. - #try: - # float(self.geneid) - # geneidIsNumber = True - #except ValueError: - # geneidIsNumber = False - #if geneidIsNumber: - query = """ - SELECT - HomologeneId - FROM - Homologene, Species, InbredSet - WHERE - Homologene.GeneId ='%s' AND - InbredSet.Name = '%s' AND - InbredSet.SpeciesId = Species.Id AND - Species.TaxonomyId = Homologene.TaxonomyId - """ % (escape(str(trait.geneid)), escape(dataset.group.name)) - logger.sql(query) - result = g.db.execute(query).fetchone() - #else: - # result = None - - if result: - trait.homologeneid = result[0] - description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') @@ -582,47 +490,22 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): # Save it for the jinja2 template trait.description_display = description_display - #XZ: trait_location_value is used for sorting trait.location_repr = 'N/A' - trait.location_value = 1000000 - if trait.chr and trait.mb: - #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") - #This is so we can convert the location to a number used for sorting - trait_location_value = convert_location_to_value(trait.chr, trait.mb) - #try: - # trait_location_value = int(self.chr)*1000 + self.mb - #except ValueError: - # if self.chr.upper() == 'X': - # trait_location_value = 20*1000 + self.mb - # else: - # trait_location_value = (ord(str(self.chr).upper()[0])*1000 + - # self.mb) - - #ZS: Put this in function currently called "convert_location_to_value" trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb)) - trait.location_value = trait_location_value elif dataset.type == "Geno": trait.location_repr = 'N/A' - trait.location_value = 1000000 - if trait.chr and trait.mb: - #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") - #This is so we can convert the location to a number used for sorting - trait_location_value = convert_location_to_value(trait.chr, trait.mb) - - #ZS: Put this in function currently called "convert_location_to_value" trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb)) - trait.location_value = trait_location_value if get_qtl_info: #LRS and its location trait.LRS_score_repr = "N/A" - trait.LRS_score_value = 0 trait.LRS_location_repr = "N/A" - trait.LRS_location_value = 1000000 + trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = "" if dataset.type == 'ProbeSet' and not trait.cellid: + trait.mean = "" query = """ SELECT ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive @@ -653,9 +536,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" else: trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" - else: - trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.mean = trait.additive = "" - if dataset.type == 'Publish': query = """ @@ -692,19 +572,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.locus = trait.lrs = trait.additive = "" if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "": - #XZ: LRS_location_value is used for sorting - try: - LRS_location_value = int(trait.locus_chr)*1000 + float(trait.locus_mb) - except: - if trait.locus_chr.upper() == 'X': - LRS_location_value = 20*1000 + float(trait.locus_mb) - else: - LRS_location_value = ord(str(trait.locus_chr).upper()[0])*1000 + float(trait.locus_mb) - trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb)) if trait.lrs != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs - trait.LRS_score_value = LRS_score_value = trait.lrs else: raise KeyError, `trait.name`+' information is not found in the database.' diff --git a/wqflask/base/trait_collection.py b/wqflask/base/trait_collection.py deleted file mode 100644 index d388a3af..00000000 --- a/wqflask/base/trait_collection.py +++ /dev/null @@ -1,53 +0,0 @@ -class TraitCollection(object): - - def __init__(self, is_anon=False): - self.is_anon = is_anon - - - @app.route("/collections/remove", methods=('POST',)) - def remove_traits(): - if is_anon: - AnonCollection.remove_traits() - else: - UserCollection.remove_traits() - - params = request.form - print("params are:", params) - uc_id = params['uc_id'] - uc = model.UserCollection.query.get(uc_id) - traits_to_remove = params.getlist('traits[]') - print("traits_to_remove are:", traits_to_remove) - traits_to_remove = process_traits(traits_to_remove) - print("\n\n after processing, traits_to_remove:", traits_to_remove) - all_traits = uc.members_as_set() - print(" all_traits:", all_traits) - members_now = all_traits - traits_to_remove - print(" members_now:", members_now) - print("Went from {} to {} members in set.".format(len(all_traits), len(members_now))) - uc.members = json.dumps(list(members_now)) - uc.changed_timestamp = datetime.datetime.utcnow() - db_session.commit() - - # We need to return something so we'll return this...maybe in the future - # we can use it to check the results - return str(len(members_now)) - - def __init__(self, anon_id) - self.anon_key = anon_key - self.collection_members = Redis.smembers(self.anon_id) - print("self.collection_members is:", self.collection_members) - self.num_members = len(self.collection_members) - - - @app.route("/collections/remove", methods=('POST',)) - def remove_traits(traits_to_remove): - print("traits_to_remove:", traits_to_remove) - for trait in traits_to_remove: - Redis.srem(self.anon_id, trait) - members_now = self.collection_members - traits_to_remove - print("members_now:", members_now) - print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now))) - - # We need to return something so we'll return this...maybe in the future - # we can use it to check the results - return str(len(members_now)) diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 845a7224..d8487f01 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -44,12 +44,12 @@ class webqtlCaseData(object): def __repr__(self): str = "<webqtlCaseData> " - if self.value: + if self.value != None: str += "value=%2.3f" % self.value - if self.variance: + if self.variance != None: str += " variance=%2.3f" % self.variance if self.num_cases: - str += " ndata=%d" % self.num_cases + str += " ndata=%s" % self.num_cases if self.name: str += " name=%s" % self.name if self.name2: @@ -66,14 +66,21 @@ class webqtlCaseData(object): @property def display_value(self): - if self.value: + if self.value != None: return "%2.3f" % self.value else: return "x" @property def display_variance(self): - if self.variance: + if self.variance != None: return "%2.3f" % self.variance else: return "x" + + @property + def display_num_cases(self): + if self.num_cases != None: + return "%s" % self.num_cases + else: + return "x" diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index e5f10edf..018d5d54 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -20,45 +20,44 @@ USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4} #minimum number of informative strains KMININFORMATIVE = 5 -#maximum number of traits for interval mapping -MULTIPLEMAPPINGLIMIT = 11 - -#maximum number of traits for correlation -MAXCORR = 100 - #Daily download limit from one IP DAILYMAXIMUM = 1000 #maximum LRS value MAXLRS = 460.0 -#temporary data life span -MAXLIFE = 86400 - #MINIMUM Database public value PUBLICTHRESH = 0 -#NBCI address -NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" -UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s" -GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s" -OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s" -UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s"; -HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s" +#EXTERNAL LINK ADDRESSES PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract" -UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit" UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' -UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s" -ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s' -DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s' -UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%s" -GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit" -ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s" - -# The following paths are no longer in use! -# HTMLPATH is replaced by GENODIR -# IMGDIR is replaced by GENERATED_IMAGE_DIR +UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' +GENOMEBROWSER_URL="https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s" +NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=%s" +GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s" +OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s" +UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s" +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" +PANTHER_URL = "http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=%s" +GEMMA_URL = "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" +ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=%s" +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://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" +UNIPROT_URL = "https://www.uniprot.org/uniprot/%s" +RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&species=%s" # Temporary storage (note that this TMPDIR can be set as an # environment variable - use utility.tools.TEMPDIR when you @@ -70,8 +69,8 @@ assert_writable_dir(TMPDIR) CACHEDIR = mk_dir(TMPDIR+'/cache/') # We can no longer write into the git tree: -GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'/generated/') -GENERATED_TEXT_DIR = mk_dir(TMPDIR+'/generated_text/') +GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'generated/') +GENERATED_TEXT_DIR = mk_dir(TMPDIR+'generated_text/') # Make sure we have permissions to access these assert_writable_dir(CACHEDIR) @@ -81,6 +80,7 @@ assert_writable_dir(GENERATED_TEXT_DIR) # Flat file directories GENODIR = flat_files('genotype')+'/' assert_dir(GENODIR) +assert_dir(GENODIR+'bimbam') # for gemma # JSON genotypes are OBSOLETE JSON_GENODIR = flat_files('genotype/json')+'/' @@ -92,4 +92,3 @@ 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/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py deleted file mode 100644 index 10251756..00000000 --- a/wqflask/base/webqtlFormData.py +++ /dev/null @@ -1,352 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -#from mod_python import Cookie - -from __future__ import print_function -from pprint import pformat as pf - -import string -import os - -import reaper - -import webqtlConfig -from webqtlCaseData import webqtlCaseData -from utility import webqtlUtil - -class webqtlFormData(object): - 'Represents data from a WebQTL form page, needed to generate the next page' - - attrs = ('formID','group','genotype','samplelist','allsamplelist', 'display_variance' - 'suggestive','significance','submitID','identification', 'enablevariance', - 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') - - #XZ: Attention! All attribute values must be picklable! - - def __init__(self, - start_vars = None, - req = None, - mod_python_session=None, - FieldStorage_formdata=None): - # Todo: rework this whole thing - print("in webqtlFormData start_vars are:", pf(start_vars)) - for item in webqtlFormData.attrs: - self.__dict__[item] = None - - #ZS: This is only used in DataEditingPage.py (as far as I know) - self.varianceDispName = None - - for item in start_vars: - self.__dict__[item] = start_vars[item] - print(" Now self.dict is:", pf(self.__dict__)) - - #Todo: This can't be good below...rework - try: - self.remote_ip = req.connection.remote_ip - except: - self.remote_ip = '1.2.3.4' - - if req and req.headers_in.has_key('referer'): - self.refURL = req.headers_in['referer'] - else: - self.refURL = None - - # For now let's just comment all this out - Sam - - #self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie. - # - ##XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable. - #self.input_session_data = sessionData.sessionData( mod_python_session ) - # - ##XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data. - #self.formdata = cgiData( FieldStorage_formdata ) - # - ##get Form ID - #self.formID = self.formdata.getfirst('FormID') - # - ##get rest of the attributes - #if self.formID: - # for item in self.attrs: - # value = self.formdata.getfirst(item) - # if value != None: - # setattr(self,item,string.strip(value)) - - self.ppolar = None - self.mpolar = None - - print("[yellow] self.group is:", self.group) - if self.group: - #try: - # # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - _f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group] - #except: - # f1 = f12 = self.mpolar = self.ppolar = None - - - def set_number(stringy): - return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000 - - self.nperm = set_number(self.nperm) - self.nboot = set_number(self.nboot) - - - #if self.allsamplelist: - # self.allsamplelist = map(string.strip, string.split(self.allsamplelist)) - print("self.allsamplelist is:", self.allsamplelist) - if self.allsamplelist: - self.allsamplelist = self.allsamplelist.split() - print("now self.allsamplelist is:", self.allsamplelist) - #self.readGenotype() - #self.readData() - - if self.group == 'BXD300': - self.group = 'BXD' - - - def __getitem__(self, key): - print("in __getitem__") - return self.__dict__[key] - - def get(self, key, default=None): - if key in self.__dict__: - return self.__dict__[key] - else: - return default - - def __str__(self): - rstr = '' - for item in self.attrs: - if item != 'genotype': - rstr += '%s:%s\n' % (item,str(getattr(self,item))) - return rstr - - - def readGenotype(self): - '''read genotype from .geno file''' - if self.group == 'BXD300': - self.group = 'BXD' - - assert self.group, "self.group needs to be set" - - #genotype_1 is Dataset Object without parents and f1 - #genotype_2 is Dataset Object with parents and f1 (not for intercross) - - self.genotype_1 = reaper.Dataset() - - full_filename = locate(self.group + '.geno','genotype') - - # reaper barfs on unicode filenames, so here we ensure it's a string - full_filename = str(full_filename) - self.genotype_1.read(full_filename) - - print("Got to after read") - - try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.group] - except KeyError: - _f1 = _f12 = _mat = _pat = None - - self.genotype_2 = self.genotype_1 - if self.genotype_1.type == "group" and _mat and _pat: - self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1) - - #determine default genotype object - if self.incparentsf1 and self.genotype_1.type != "intercross": - self.genotype = self.genotype_2 - else: - self.incparentsf1 = 0 - self.genotype = self.genotype_1 - - self.samplelist = list(self.genotype.prgy) - self.f1list = [] - self.parlist = [] - - if _f1 and _f12: - self.f1list = [_f1, _f12] - if _mat and _pat: - self.parlist = [_mat, _pat] - - - def readData(self, samplelist, incf1=None): - '''read user input data or from trait data and analysis form''' - - if incf1 == None: - incf1 = [] - - if not self.genotype: - self.readGenotype() - if not samplelist: - if incf1: - samplelist = self.f1list + self.samplelist - else: - samplelist = self.samplelist - - #print("before traitfiledata self.traitfile is:", pf(self.traitfile)) - - traitfiledata = getattr(self, "traitfile", None) - traitpastedata = getattr(self, "traitpaste", None) - variancefiledata = getattr(self, "variancefile", None) - variancepastedata = getattr(self, "variancepaste", None) - Nfiledata = getattr(self, "Nfile", None) - - #### Todo: Rewrite below when we get to someone submitting their own trait ##### - - def to_float(item): - try: - return float(item) - except ValueError: - return None - - print("bottle samplelist is:", samplelist) - if traitfiledata: - tt = traitfiledata.split() - values = map(webqtlUtil.StringAsFloat, tt) - elif traitpastedata: - tt = traitpastedata.split() - values = map(webqtlUtil.StringAsFloat, tt) - else: - print("mapping formdataasfloat") - #values = map(self.FormDataAsFloat, samplelist) - values = [to_float(getattr(self, key)) for key in samplelist] - print("rocket values is:", values) - - - if len(values) < len(samplelist): - values += [None] * (len(samplelist) - len(values)) - elif len(values) > len(samplelist): - values = values[:len(samplelist)] - print("now values is:", values) - - - if variancefiledata: - tt = variancefiledata.split() - variances = map(webqtlUtil.StringAsFloat, tt) - elif variancepastedata: - tt = variancepastedata.split() - variances = map(webqtlUtil.StringAsFloat, tt) - else: - variances = map(self.FormVarianceAsFloat, samplelist) - - if len(variances) < len(samplelist): - variances += [None]*(len(samplelist) - len(variances)) - elif len(variances) > len(samplelist): - variances = variances[:len(samplelist)] - - if Nfiledata: - tt = string.split(Nfiledata) - nsamples = map(webqtlUtil.IntAsFloat, tt) - if len(nsamples) < len(samplelist): - nsamples += [None]*(len(samplelist) - len(nsamples)) - else: - nsamples = map(self.FormNAsFloat, samplelist) - - ##values, variances, nsamples is obsolete - self.allTraitData = {} - for i, _sample in enumerate(samplelist): - if values[i] != None: - self.allTraitData[_sample] = webqtlCaseData( - _sample, values[i], variances[i], nsamples[i]) - print("allTraitData is:", pf(self.allTraitData)) - - - - def informativeStrains(self, samplelist=None, include_variances = None): - '''if readData was called, use this to output informative samples (sample with values)''' - - if not samplelist: - samplelist = self.samplelist - - samples = [] - values = [] - variances = [] - - #print("self.allTraitData is:", pf(self.allTraitData)) - - for sample in samplelist: - if sample in self.allTraitData: - _val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance - if _val != None: - if include_variances: - if _var != None: - samples.append(sample) - values.append(_val) - variances.append(_var) - else: - samples.append(sample) - values.append(_val) - variances.append(None) - - return samples, values, variances, len(samples) - - - - #def FormDataAsFloat(self, key): - # - # #try: - # # return float(self.key) - # #except: - # # return None - - - def FormVarianceAsFloat(self, key): - try: - return float(self.formdata.getfirst('V' + key)) - except: - return None - - def FormNAsFloat(self, key): - try: - return int(self.formdata.getfirst('N' + key)) - except: - return None - - def Sample(self): - 'Create some dummy data for testing' - self.group = 'BXD' - self.incparentsf1 = 'on' - #self.display = 9.2 - #self.significance = 16.1 - self.readGenotype() - self.identification = 'BXD : Coat color example by Lu Lu, et al' - #self.readGenotype() - #self.genotype.ReadMM('AXBXAforQTL') - #self.samplelist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy) - #self.samplelist.sort() - self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2), - 'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2), - 'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4), - 'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2), - 'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3), - 'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3), - 'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2), - 'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4), - 'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4), - 'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1), - 'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4), - 'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4), - 'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)} |