diff options
Diffstat (limited to 'wqflask')
49 files changed, 1022 insertions, 1000 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 44325d5b..3183363b 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -17,7 +17,10 @@ # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # # This module is used by GeneNetwork project (www.genenetwork.org) - +from dataclasses import dataclass +from dataclasses import field +from dataclasses import InitVar +from typing import Optional, Dict from db.call import fetchall, fetchone, fetch1 from utility.logger import getLogger from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL @@ -59,7 +62,8 @@ logger = getLogger(__name__) DS_NAME_MAP = {} -def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_name=None): +def create_dataset(dataset_name, dataset_type=None, + get_samplelist=True, group_name=None): if dataset_name == "Temp": dataset_type = "Temp" @@ -74,11 +78,10 @@ def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_n return dataset_class(dataset_name, get_samplelist) +@dataclass class DatasetType: - - def __init__(self, redis_instance): - """Create a dictionary of samples where the value is set to Geno, -Publish or ProbeSet. E.g. + """Create a dictionary of samples where the value is set to Geno, + Publish or ProbeSet. E.g. {'AD-cases-controls-MyersGeno': 'Geno', 'AD-cases-controls-MyersPublish': 'Publish', @@ -89,21 +92,28 @@ Publish or ProbeSet. E.g. 'All Phenotypes': 'Publish', 'B139_K_1206_M': 'ProbeSet', 'B139_K_1206_R': 'ProbeSet' ... - + } """ + redis_instance: InitVar[Redis] + datasets: Optional[Dict] = field(init=False, default_factory=dict) + data: Optional[Dict] = field(init=False) + + def __post_init__(self, redis_instance): self.redis_instance = redis_instance - self.datasets = {} - data = self.redis_instance.get("dataset_structure") + data = redis_instance.get("dataset_structure") if data: self.datasets = json.loads(data) - else: # ZS: I don't think this should ever run unless Redis is emptied + else: + # ZS: I don't think this should ever run unless Redis is + # emptied try: data = json.loads(requests.get( - GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content) - for species in data['datasets']: - for group in data['datasets'][species]: - for dataset_type in data['datasets'][species][group]: - for dataset in data['datasets'][species][group][dataset_type]: + GN2_BASE_URL + "/api/v_pre1/gen_dropdown", + timeout=5).content) + for _species in data['datasets']: + for group in data['datasets'][_species]: + for dataset_type in data['datasets'][_species][group]: + for dataset in data['datasets'][_species][group][dataset_type]: short_dataset_name = dataset[1] if dataset_type == "Phenotypes": new_type = "Publish" @@ -112,15 +122,15 @@ Publish or ProbeSet. E.g. else: new_type = "ProbeSet" self.datasets[short_dataset_name] = new_type - except: + except Exception: # Do nothing pass - - self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) + self.redis_instance.set("dataset_structure", + json.dumps(self.datasets)) + self.data = data def set_dataset_key(self, t, name): - """If name is not in the object's dataset dictionary, set it, and update - dataset_structure in Redis - + """If name is not in the object's dataset dictionary, set it, and + update dataset_structure in Redis args: t: Type of dataset structure which can be: 'mrna_expr', 'pheno', 'other_pheno', 'geno' @@ -128,19 +138,20 @@ Publish or ProbeSet. E.g. """ sql_query_mapping = { - 'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ + - """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """), - 'pheno': ("""SELECT InfoFiles.GN_AccesionId """ + - """FROM InfoFiles, PublishFreeze, InbredSet """ + - """WHERE InbredSet.Name = '{}' AND """ + - """PublishFreeze.InbredSetId = InbredSet.Id AND """ + - """InfoFiles.InfoPageName = PublishFreeze.Name"""), - 'other_pheno': ("""SELECT PublishFreeze.Name """ + - """FROM PublishFreeze, InbredSet """ + - """WHERE InbredSet.Name = '{}' AND """ + - """PublishFreeze.InbredSetId = InbredSet.Id"""), - 'geno': ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ + - """GenoFreeze.Name = "{}" """) + 'mrna_expr': ("SELECT ProbeSetFreeze.Id FROM " + "ProbeSetFreeze WHERE " + "ProbeSetFreeze.Name = \"%s\" "), + 'pheno': ("SELECT InfoFiles.GN_AccesionId " + "FROM InfoFiles, PublishFreeze, InbredSet " + "WHERE InbredSet.Name = '%s' AND " + "PublishFreeze.InbredSetId = InbredSet.Id AND " + "InfoFiles.InfoPageName = PublishFreeze.Name"), + 'other_pheno': ("SELECT PublishFreeze.Name " + "FROM PublishFreeze, InbredSet " + "WHERE InbredSet.Name = '%s' AND " + "PublishFreeze.InbredSetId = InbredSet.Id"), + 'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE " + "GenoFreeze.Name = \"%s\" ") } dataset_name_mapping = { @@ -154,22 +165,22 @@ Publish or ProbeSet. E.g. if t in ['pheno', 'other_pheno']: group_name = name.replace("Publish", "") - results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone() + results = g.db.execute(sql_query_mapping[t] % group_name).fetchone() if results: self.datasets[name] = dataset_name_mapping[t] self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) return True - return None def __call__(self, name): - if name not in self.datasets: for t in ["mrna_expr", "pheno", "other_pheno", "geno"]: - # This has side-effects, with the end result being a truth-y value + # This has side-effects, with the end result being a + # truth-y value if(self.set_dataset_key(t, name)): break - return self.datasets.get(name, None) # Return None if name has not been set + # Return None if name has not been set + return self.datasets.get(name, None) # Do the intensive work at startup one time only @@ -209,7 +220,7 @@ def create_datasets_list(): return datasets -class Markers(object): +class Markers: """Todo: Build in cacheing so it saves us reading the same file more than once""" def __init__(self, name): @@ -262,8 +273,6 @@ class Markers(object): elif isinstance(p_values, dict): filtered_markers = [] for marker in self.markers: - #logger.debug("marker[name]", marker['name']) - #logger.debug("p_values:", p_values) if marker['name'] in p_values: #logger.debug("marker {} IS in p_values".format(i)) marker['p_value'] = p_values[marker['name']] @@ -276,10 +285,6 @@ class Markers(object): marker['lrs_value'] = - \ math.log10(marker['p_value']) * 4.61 filtered_markers.append(marker) - # else: - #logger.debug("marker {} NOT in p_values".format(i)) - # self.markers.remove(marker) - #del self.markers[i] self.markers = filtered_markers @@ -306,13 +311,12 @@ class HumanMarkers(Markers): marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) - #logger.debug("markers is: ", pf(self.markers)) def add_pvalues(self, p_values): super(HumanMarkers, self).add_pvalues(p_values) -class DatasetGroup(object): +class DatasetGroup: """ Each group has multiple datasets; each species has multiple groups. @@ -520,7 +524,6 @@ def datasets(group_name, this_group=None): break if tissue_already_exists: - #logger.debug("dataset_menu:", dataset_menu[i]['datasets']) dataset_menu[i]['datasets'].append((dataset, dataset_short)) else: dataset_menu.append(dict(tissue=tissue_name, @@ -537,7 +540,7 @@ def datasets(group_name, this_group=None): return dataset_menu -class DataSet(object): +class DataSet: """ DataSet class defines a dataset in webqtl, can be either Microarray, Published phenotype, genotype, or user input dataset(temp) @@ -569,10 +572,6 @@ class DataSet(object): self.group.get_samplelist() self.species = species.TheSpecies(self) - def get_desc(self): - """Gets overridden later, at least for Temp...used by trait's get_given_name""" - return None - def get_accession_id(self): if self.type == "Publish": results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where @@ -730,9 +729,6 @@ class PhenotypeDataSet(DataSet): DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' def setup(self): - - #logger.debug("IS A PHENOTYPEDATASET") - # Fields in the database table self.search_fields = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index f1929518..1f8224af 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -11,7 +11,7 @@ from utility.db_tools import escape from utility.logger import getLogger logger = getLogger(__name__ ) -class MrnaAssayTissueData(object): +class MrnaAssayTissueData: def __init__(self, gene_symbols=None): self.gene_symbols = gene_symbols diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 2771d116..eae3325a 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -6,7 +6,7 @@ from flask import Flask, g from utility.logger import getLogger logger = getLogger(__name__ ) -class TheSpecies(object): +class TheSpecies: def __init__(self, dataset=None, species_name=None): if species_name != None: self.name = species_name @@ -15,7 +15,7 @@ class TheSpecies(object): self.dataset = dataset self.chromosomes = Chromosomes(dataset=self.dataset) -class IndChromosome(object): +class IndChromosome: def __init__(self, name, length): self.name = name self.length = length @@ -25,7 +25,7 @@ class IndChromosome(object): """Chromosome length in megabases""" return self.length / 1000000 -class Chromosomes(object): +class Chromosomes: def __init__(self, dataset=None, species=None): self.chromosomes = collections.OrderedDict() if species != None: diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index df96d46e..5574128d 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -51,7 +51,7 @@ def create_trait(**kw): return None -class GeneralTrait(object): +class GeneralTrait: """ Trait class defines a trait in webqtl, can be either Microarray, Published phenotype, genotype, or user input trait @@ -337,74 +337,10 @@ def jsonable(trait): dataset_name=dataset.shortname, location=trait.location_repr ) - else: - return dict() - - -def jsonable_table_row(trait, dataset_name, index): - """Return a list suitable for json and intended to be displayed in a table - - Actual turning into json doesn't happen here though""" - - dataset = create_dataset(dataset_name) - - if dataset.type == "ProbeSet": - if trait.mean == "": - mean = "N/A" - else: - mean = "%.3f" % round(float(trait.mean), 2) - if trait.additive == "": - additive = "N/A" - else: - additive = "%.3f" % round(float(trait.additive), 2) - 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, - trait.description_display, - trait.location_repr, - mean, - trait.LRS_score_repr, - trait.LRS_location_repr, - additive] - elif dataset.type == "Publish": - if trait.additive == "": - additive = "N/A" - else: - additive = "%.2f" % round(float(trait.additive), 2) - if trait.pubmed_id: - 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, - trait.authors, - '<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>', - trait.LRS_score_repr, - trait.LRS_location_repr, - additive] - else: - 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, - trait.authors, - trait.pubmed_text, - trait.LRS_score_repr, - trait.LRS_location_repr, - additive] - elif dataset.type == "Geno": - 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] + elif dataset.name == "Temp": + return dict(name=trait.name, + dataset="Temp", + dataset_name="Temp") else: return dict() diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index d49742f2..0853b3ac 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -22,7 +22,7 @@ from pprint import pformat as pf class EmptyConfigurations(Exception): pass -class Marker(object): +class Marker: def __init__(self): self.name = None self.chr = None @@ -30,7 +30,7 @@ class Marker(object): self.Mb = None self.genotypes = [] -class ConvertGenoFile(object): +class ConvertGenoFile: def __init__(self, input_file, output_files): self.input_file = input_file diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index 60257b28..3e4d1741 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -13,7 +13,7 @@ sys.path.append("..") import os import glob -class GenerateKinshipMatrices(object): +class GenerateKinshipMatrices: def __init__(self, group_name, geno_file, pheno_file): self.group_name = group_name self.geno_file = geno_file diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index 7e7fd241..f5f7e0e7 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -29,7 +29,7 @@ class EmptyConfigurations(Exception): pass -class Marker(object): +class Marker: def __init__(self): self.name = None self.chr = None @@ -37,7 +37,7 @@ class Marker(object): self.Mb = None self.genotypes = [] -class ConvertGenoFile(object): +class ConvertGenoFile: def __init__(self, input_file, output_file): diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py index b24ce4f1..a1046c86 100644 --- a/wqflask/maintenance/print_benchmark.py +++ b/wqflask/maintenance/print_benchmark.py @@ -5,7 +5,7 @@ import time from pprint import pformat as pf -class TheCounter(object): +class TheCounter: Counters = {} def __init__(self): diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py index 96563a16..ee5d6f06 100644 --- a/wqflask/tests/unit/base/test_data_set.py +++ b/wqflask/tests/unit/base/test_data_set.py @@ -31,14 +31,12 @@ class TestDataSetTypes(unittest.TestCase): def tearDown(self): self.app_context.pop() - @mock.patch('base.data_set.g') - def test_data_set_type(self, db_mock): + def test_data_set_type(self): """Test that DatasetType returns correctly if the Redis Instance is not empty and the name variable exists in the dictionary """ with app.app_context(): - db_mock.get = mock.Mock() redis_mock = mock.Mock() redis_mock.get.return_value = self.test_dataset self.assertEqual(DatasetType(redis_mock) @@ -89,8 +87,7 @@ class TestDataSetTypes(unittest.TestCase): '"B139_K_1206_M": "ProbeSet", ' '"B139_K_1206_R": "ProbeSet", ' '"Test": "ProbeSet"}')) - - db_mock.db.execute.assert_called_with( + db_mock.db.execute.assert_called_once_with( ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " + "WHERE ProbeSetFreeze.Name = \"Test\" ") ) diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index 204ff59a..df926884 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -2,7 +2,7 @@ from pprint import pformat as pf # Todo: Move these out of __init__ -class Bunch(object): +class Bunch: """Like a dictionary but using object notation""" def __init__(self, **kw): self.__dict__ = kw @@ -11,7 +11,7 @@ class Bunch(object): return pf(self.__dict__) -class Struct(object): +class Struct: '''The recursive class for building and representing objects with. From http://stackoverflow.com/a/6573827/1175849 diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index ea5a0ab6..91ea91e8 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -6,7 +6,7 @@ from utility.tools import LOG_BENCH from utility.logger import getLogger logger = getLogger(__name__ ) -class Bench(object): +class Bench: entries = collections.OrderedDict() def __init__(self, name=None, write_output=LOG_BENCH): diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 81085ffe..0a381c9b 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,7 +1,7 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) -class genotype(object): +class genotype: """ Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure """ @@ -119,7 +119,7 @@ class genotype(object): self.chromosomes.append(chr_ob) -class Chr(object): +class Chr: def __init__(self, name, geno_ob): self.name = name self.loci = [] @@ -140,7 +140,7 @@ class Chr(object): def add_marker(self, marker_row): self.loci.append(Locus(self.geno_ob, marker_row)) -class Locus(object): +class Locus: def __init__(self, geno_ob, marker_row = None): self.chr = None self.name = None diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index 0b736176..f8e96d19 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -12,7 +12,7 @@ import simplejson as json from pprint import pformat as pf -class Marker(object): +class Marker: def __init__(self): self.name = None self.chr = None @@ -21,7 +21,7 @@ class Marker(object): self.genotypes = [] -class ConvertGenoFile(object): +class ConvertGenoFile: def __init__(self, input_file): self.mb_exists = False diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 46eeb35d..12fd6be5 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -4,20 +4,23 @@ from base.species import TheSpecies from utility import hmac -from flask import Flask, g +from flask import g import logging -logger = logging.getLogger(__name__ ) +logger = logging.getLogger(__name__) + def get_species_dataset_trait(self, start_vars): - #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" if "temp_trait" in list(start_vars.keys()): - if start_vars['temp_trait'] == "True": - self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group']) - else: - self.dataset = data_set.create_dataset(start_vars['dataset']) + if start_vars['temp_trait'] == "True": + self.dataset = data_set.create_dataset( + dataset_name="Temp", + dataset_type="Temp", + group_name=start_vars['group']) + else: + self.dataset = data_set.create_dataset(start_vars['dataset']) else: - self.dataset = data_set.create_dataset(start_vars['dataset']) + self.dataset = data_set.create_dataset(start_vars['dataset']) logger.debug("After creating dataset") self.species = TheSpecies(dataset=self.dataset) logger.debug("After creating species") @@ -27,9 +30,6 @@ def get_species_dataset_trait(self, start_vars): get_qtl_info=True) logger.debug("After creating trait") - #if read_genotype: - #self.dataset.group.read_genotype_file() - #self.genotype = self.dataset.group.genotype def get_trait_db_obs(self, trait_db_list): if isinstance(trait_db_list, str): @@ -42,28 +42,29 @@ def get_trait_db_obs(self, trait_db_list): assert hmac_string==hmac.hmac_creation(data), "Data tampering?" trait_name, dataset_name = data.split(":")[:2] if dataset_name == "Temp": - dataset_ob = data_set.create_dataset(dataset_name=dataset_name, dataset_type="Temp", group_name=trait_name.split("_")[2]) + dataset_ob = data_set.create_dataset( + dataset_name=dataset_name, dataset_type="Temp", + group_name=trait_name.split("_")[2]) else: dataset_ob = data_set.create_dataset(dataset_name) trait_ob = create_trait(dataset=dataset_ob, - name=trait_name, - cellid=None) + name=trait_name, + cellid=None) if trait_ob: self.trait_list.append((trait_ob, dataset_ob)) -def get_species_groups(): - - species_query = "SELECT SpeciesId, MenuName FROM Species" - species_ids_and_names = g.db.execute(species_query).fetchall() - - species_and_groups = [] - for species_id, species_name in species_ids_and_names: - this_species_groups = {} - this_species_groups['species'] = species_name - groups_query = "SELECT InbredSetName FROM InbredSet WHERE SpeciesId = %s" % (species_id) - groups = [group[0] for group in g.db.execute(groups_query).fetchall()] - - this_species_groups['groups'] = groups - species_and_groups.append(this_species_groups) - return species_and_groups +def get_species_groups(): + """Group each species into a group""" + _menu = {} + for species, group_name in g.db.execute( + "SELECT s.MenuName, i.InbredSetName FROM InbredSet i " + "INNER JOIN Species s ON s.SpeciesId = i.SpeciesId " + "ORDER BY i.SpeciesId ASC, i.Name ASC").fetchall(): + if _menu.get(species): + _menu = _menu[species].append(group_name) + else: + _menu[species] = [group_name] + return [{"species": key, + "groups": value} for key, value in + list(_menu.items())] diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 4144ae00..b2cbd458 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -2,7 +2,7 @@ from redis import Redis import simplejson as json -class TempData(object): +class TempData: def __init__(self, temp_uuid): self.temp_uuid = temp_uuid diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index 18afc5ad..eaddecd7 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -23,12 +23,7 @@ def get_species(): """Build species list""" results = g.db.execute( "SELECT Name, MenuName FROM Species ORDER BY OrderId").fetchall() - - species = [] - for result in results: - species.append([str(result[0]), str(result[1])]) - - return species + return [[name, menu_name] for name, menu_name in results] def get_groups(species): diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index 92de6073..5855ccf0 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -31,7 +31,7 @@ from MySQLdb import escape_string as escape from flask import Flask, g -class ComparisonBarChart(object): +class ComparisonBarChart: def __init__(self, start_vars): trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index c87776bb..d5dc26f5 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -11,7 +11,7 @@ import numpy as np import utility.logger logger = utility.logger.getLogger(__name__ ) -class CorrScatterPlot(object): +class CorrScatterPlot: """Page that displays a correlation scatterplot with a line fitted to it""" def __init__(self, params): diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index fb4dc4f4..cb341e79 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -58,7 +58,7 @@ TISSUE_METHODS = [METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK] TISSUE_MOUSE_DB = 1 -class CorrelationResults(object): +class CorrelationResults: def __init__(self, start_vars): # get trait list from db (database name) # calculate correlation with Base vector and targets diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index f77761d8..d0b4a156 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -41,7 +41,7 @@ Redis = get_redis_conn() THIRTY_DAYS = 60 * 60 * 24 * 30 -class CorrelationMatrix(object): +class CorrelationMatrix: def __init__(self, start_vars): trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 72b4f3a3..1556e370 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -39,7 +39,7 @@ r_write_table = ro.r["write.table"] # Map the write.table function r_data_frame = ro.r["data.frame"] # Map the write.table function r_as_numeric = ro.r["as.numeric"] # Map the write.table function -class CTL(object): +class CTL: def __init__(self): logger.info("Initialization of CTL") #log = r_file("/tmp/genenetwork_ctl.log", open = "wt") diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py index f420b472..25e624ef 100644 --- a/wqflask/wqflask/db_info.py +++ b/wqflask/wqflask/db_info.py @@ -10,7 +10,7 @@ from utility.logger import getLogger logger = getLogger(__name__) -class InfoPage(object): +class InfoPage: def __init__(self, start_vars): self.info = None self.gn_accession_id = None diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 00636563..364a3eed 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -17,7 +17,7 @@ from utility.logger import getLogger logger = getLogger(__name__) -class DoSearch(object): +class DoSearch: """Parent class containing parameters/functions used for all searches""" # Used to translate search phrases into classes diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 23fc3cad..207767c4 100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -5,7 +5,7 @@ from flask import g from utility.logger import getLogger logger = getLogger(__name__) -class Docs(object): +class Docs: def __init__(self, entry, start_vars={}): sql = """ diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py index efa17f05..c5c79e98 100644 --- a/wqflask/wqflask/external_tools/send_to_bnw.py +++ b/wqflask/wqflask/external_tools/send_to_bnw.py @@ -24,7 +24,7 @@ from utility import helper_functions, corr_result_helpers import utility.logger logger = utility.logger.getLogger(__name__ ) -class SendToBNW(object): +class SendToBNW: def __init__(self, start_vars): trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index 4c958a88..47e4c53a 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -29,7 +29,7 @@ from utility import helper_functions, corr_result_helpers import utility.logger logger = utility.logger.getLogger(__name__ ) -class SendToGeneWeaver(object): +class SendToGeneWeaver: def __init__(self, start_vars): trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py index 2f068792..e1e5e655 100644 --- a/wqflask/wqflask/external_tools/send_to_webgestalt.py +++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py @@ -29,7 +29,7 @@ from utility import helper_functions, corr_result_helpers import utility.logger logger = utility.logger.getLogger(__name__ ) -class SendToWebGestalt(object): +class SendToWebGestalt: def __init__(self, start_vars): trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 907f1180..9bf23d57 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -18,7 +18,7 @@ from utility.type_checking import is_float, is_int, is_str, get_float, get_int, from utility.logger import getLogger logger = getLogger(__name__) -class GSearch(object): +class GSearch: def __init__(self, kw): assert('type' in kw) diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index cca5a4fc..20e3559a 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -14,7 +14,7 @@ Redis = Redis() logger = getLogger(__name__ ) -class Heatmap(object): +class Heatmap: def __init__(self, start_vars, temp_uuid): trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 6a5fe2f6..4074f098 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -152,7 +152,7 @@ class HtmlGenWrapper: return map_ -class DisplayMappingResults(object): +class DisplayMappingResults: """Inteval Mapping Plot Page""" cMGraphInterval = 5 GRAPH_MIN_WIDTH = 900 diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 83ebcdf9..06c9300a 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -146,7 +146,12 @@ def gen_covariates_file(this_dataset, covariates, samples): for covariate in covariate_list: this_covariate_data = [] trait_name = covariate.split(":")[0] - dataset_ob = create_dataset(covariate.split(":")[1]) + dataset_name = covariate.split(":")[1] + if dataset_name == "Temp": + temp_group = trait_name.split("_")[2] + dataset_ob = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group) + else: + dataset_ob = create_dataset(covariate.split(":")[1]) trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 8f051c14..7dd0bcb6 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -45,7 +45,7 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR import utility.logger logger = utility.logger.getLogger(__name__ ) -class RunMapping(object): +class RunMapping: def __init__(self, start_vars, temp_uuid): helper_functions.get_species_dataset_trait(self, start_vars) diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index a45eaad4..93785a3a 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -27,7 +27,7 @@ from utility import helper_functions from utility import corr_result_helpers from utility.tools import GN2_BRANCH_URL -class NetworkGraph(object): +class NetworkGraph: def __init__(self, start_vars): trait_db_list = [trait.strip() diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py index 0675ec4b..861a93f2 100644 --- a/wqflask/wqflask/news.py +++ b/wqflask/wqflask/news.py @@ -1,6 +1,6 @@ from flask import g -class News(object): +class News: def __init__(self): sql = """ diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index cb01a2af..fd7c132b 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -24,7 +24,7 @@ from utility.type_checking import is_str from utility.logger import getLogger logger = getLogger(__name__ ) -class SearchResultPage(object): +class SearchResultPage: #maxReturn = 3000 def __init__(self, kw): diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py index 5f764767..48761fa0 100644 --- a/wqflask/wqflask/server_side.py +++ b/wqflask/wqflask/server_side.py @@ -2,7 +2,7 @@ -class ServerSideTable(object): +class ServerSideTable: """ This class is used to do server-side processing on the DataTables table such as paginating, sorting, diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 857e4456..f955f632 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -8,7 +8,7 @@ from pprint import pformat as pf from utility import Plot from utility import Bunch -class SampleList(object): +class SampleList: def __init__(self, dataset, sample_names, diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 6892f02b..f9c5fbe6 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -1,7 +1,5 @@ import string -import os import datetime -import pickle import uuid import requests import json as json @@ -11,75 +9,80 @@ from collections import OrderedDict import numpy as np import scipy.stats as ss -from flask import Flask, g +from flask import g from base import webqtlConfig -from base import webqtlCaseData from wqflask.show_trait.SampleList import SampleList from base.trait import create_trait from base import data_set -from db import webqtlDatabaseFunction -from utility import webqtlUtil, Plot, Bunch, helper_functions +from utility import helper_functions from utility.authentication_tools import check_owner_or_admin from utility.tools import locate_ignore_error from utility.redis_tools import get_redis_conn, get_resource_id +from utility.logger import getLogger + + Redis = get_redis_conn() ONE_YEAR = 60 * 60 * 24 * 365 -from pprint import pformat as pf - -from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) ############################################### # -# Todo: Put in security to ensure that user has permission to access confidential data sets -# And add i.p.limiting as necessary +# Todo: Put in security to ensure that user has permission to access +# confidential data sets And add i.p.limiting as necessary # ############################################## -class ShowTrait(object): +class ShowTrait: def __init__(self, kw): if 'trait_id' in kw and kw['dataset'] != "Temp": self.temp_trait = False self.trait_id = kw['trait_id'] helper_functions.get_species_dataset_trait(self, kw) self.resource_id = get_resource_id(self.dataset, self.trait_id) - self.admin_status = check_owner_or_admin(resource_id=self.resource_id) + self.admin_status = check_owner_or_admin( + resource_id=self.resource_id) elif 'group' in kw: self.temp_trait = True - self.trait_id = "Temp_"+kw['species']+ "_" + kw['group'] + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") + self.trait_id = "Temp_"+kw['species'] + "_" + kw['group'] + \ + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") self.temp_species = kw['species'] self.temp_group = kw['group'] - self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group) + self.dataset = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name=self.temp_group) - # Put values in Redis so they can be looked up later if added to a collection + # Put values in Redis so they can be looked up later if + # added to a collection Redis.set(self.trait_id, kw['trait_paste'], ex=ONE_YEAR) self.trait_vals = kw['trait_paste'].split() self.this_trait = create_trait(dataset=self.dataset, name=self.trait_id, cellid=None) - self.admin_status = check_owner_or_admin(dataset=self.dataset, trait_id=self.trait_id) + self.admin_status = check_owner_or_admin( + dataset=self.dataset, trait_id=self.trait_id) else: self.temp_trait = True self.trait_id = kw['trait_id'] self.temp_species = self.trait_id.split("_")[1] self.temp_group = self.trait_id.split("_")[2] - self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group) + self.dataset = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name=self.temp_group) self.this_trait = create_trait(dataset=self.dataset, name=self.trait_id, cellid=None) self.trait_vals = Redis.get(self.trait_id).split() - self.admin_status = check_owner_or_admin(dataset=self.dataset, trait_id=self.trait_id) + self.admin_status = check_owner_or_admin( + dataset=self.dataset, trait_id=self.trait_id) - #ZS: Get verify/rna-seq link URLs + # ZS: Get verify/rna-seq link URLs try: blatsequence = self.this_trait.blatseq if not blatsequence: - #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. + # XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. query1 = """SELECT Probe.Sequence, Probe.Name FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND @@ -96,10 +99,10 @@ class ShowTrait(object): if int(seqt[1][-1]) % 2 == 1: blatsequence += string.strip(seqt[0]) - #--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe + # --------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe blatsequence = '%3E' + self.this_trait.name + '%0A' + blatsequence + '%0A' - #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. + # XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. query2 = """SELECT Probe.Sequence, Probe.Name FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND @@ -110,24 +113,29 @@ class ShowTrait(object): seqs = g.db.execute(query2).fetchall() for seqt in seqs: - if int(seqt[1][-1]) %2 == 1: - blatsequence += '%3EProbe_' + seqt[1].strip() + '%0A' + seqt[0].strip() + '%0A' + if int(seqt[1][-1]) % 2 == 1: + blatsequence += '%3EProbe_' + \ + seqt[1].strip() + '%0A' + seqt[0].strip() + '%0A' if self.dataset.group.species == "rat": - self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn6', 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) - self.UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm10', blatsequence) + self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ( + 'mouse', 'mm10', blatsequence) + self.UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ( + 'mouse', 'mm10', blatsequence) elif self.dataset.group.species == "human": - self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg38', blatsequence) + self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ( + 'human', 'hg38', blatsequence) self.UTHSC_BLAT_URL = "" else: self.UCSC_BLAT_URL = "" self.UTHSC_BLAT_URL = "" except: - self.UCSC_BLAT_URL = "" - self.UTHSC_BLAT_URL = "" + self.UCSC_BLAT_URL = "" + self.UTHSC_BLAT_URL = "" if self.dataset.type == "ProbeSet": self.show_probes = "True" @@ -138,17 +146,13 @@ class ShowTrait(object): self.ncbi_summary = get_ncbi_summary(self.this_trait) - #Get nearest marker for composite mapping + # Get nearest marker for composite mapping if not self.temp_trait: if check_if_attr_exists(self.this_trait, 'locus_chr') and self.dataset.type != "Geno" and self.dataset.type != "Publish": - self.nearest_marker = get_nearest_marker(self.this_trait, self.dataset) - #self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0] - #self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1] + self.nearest_marker = get_nearest_marker( + self.this_trait, self.dataset) else: self.nearest_marker = "" - #self.nearest_marker1 = "" - #self.nearest_marker2 = "" - self.make_sample_lists() @@ -168,29 +172,40 @@ class ShowTrait(object): categorical_var_list = [] if not self.temp_trait: - categorical_var_list = get_categorical_variables(self.this_trait, self.sample_groups[0]) #ZS: Only using first samplelist, since I think mapping only uses those samples + # ZS: Only using first samplelist, since I think mapping only uses those samples + categorical_var_list = get_categorical_variables( + self.this_trait, self.sample_groups[0]) - #ZS: Get list of chromosomes to select for mapping + # ZS: Get list of chromosomes to select for mapping self.chr_list = [["All", -1]] for i, this_chr in enumerate(self.dataset.species.chromosomes.chromosomes): - self.chr_list.append([self.dataset.species.chromosomes.chromosomes[this_chr].name, i]) + self.chr_list.append( + [self.dataset.species.chromosomes.chromosomes[this_chr].name, i]) self.genofiles = self.dataset.group.get_genofiles() - if "QTLReaper" or "R/qtl" in dataset.group.mapping_names: #ZS: No need to grab scales from .geno file unless it's using a mapping method that reads .geno files + # ZS: No need to grab scales from .geno file unless it's using + # a mapping method that reads .geno files + if "QTLReaper" or "R/qtl" in dataset.group.mapping_names: if self.genofiles: self.scales_in_geno = get_genotype_scales(self.genofiles) else: - self.scales_in_geno = get_genotype_scales(self.dataset.group.name + ".geno") + self.scales_in_geno = get_genotype_scales( + self.dataset.group.name + ".geno") else: self.scales_in_geno = {} self.has_num_cases = has_num_cases(self.this_trait) - #ZS: Needed to know whether to display bar chart + get max sample name length in order to set table column width + # ZS: Needed to know whether to display bar chart + get max + # sample name length in order to set table column width self.num_values = 0 - self.binary = "true" #ZS: So it knows whether to display the Binary R/qtl mapping method, which doesn't work unless all values are 0 or 1 - self.negative_vals_exist = "false" #ZS: Since we don't want to show log2 transform option for situations where it doesn't make sense + # ZS: So it knows whether to display the Binary R/qtl mapping + # method, which doesn't work unless all values are 0 or 1 + self.binary = "true" + # ZS: Since we don't want to show log2 transform option for + # situations where it doesn't make sense + self.negative_vals_exist = "false" max_samplename_width = 1 for group in self.sample_groups: for sample in group.sample_list: @@ -203,7 +218,8 @@ class ShowTrait(object): if sample.value < 0: self.negative_vals_exist = "true" - #ZS: Check whether any attributes have few enough distinct values to show the "Block samples by group" option + # ZS: Check whether any attributes have few enough distinct + # values to show the "Block samples by group" option self.categorical_attr_exists = "false" for attribute in self.sample_groups[0].attributes: if len(self.sample_groups[0].attributes[attribute].distinct_values) <= 10: @@ -212,7 +228,8 @@ class ShowTrait(object): sample_column_width = max_samplename_width * 8 - self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, sample_column_width, self.has_num_cases) + self.stats_table_width, self.trait_table_width = get_table_widths( + self.sample_groups, sample_column_width, self.has_num_cases) if self.num_values >= 5000: self.maf = 0.01 @@ -243,9 +260,9 @@ class ShowTrait(object): 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['temp_trait'] = True + hddn['group'] = self.temp_group + hddn['species'] = self.temp_species hddn['use_outliers'] = False hddn['method'] = "gemma" hddn['selected_chr'] = -1 @@ -258,7 +275,6 @@ class ShowTrait(object): 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['mapping_scale'] = "physic" @@ -266,39 +282,46 @@ class ShowTrait(object): hddn['export_data'] = "" hddn['export_format'] = "excel" if len(self.scales_in_geno) < 2: - hddn['mapping_scale'] = self.scales_in_geno[list(self.scales_in_geno.keys())[0]][0][0] + hddn['mapping_scale'] = self.scales_in_geno[list( + self.scales_in_geno.keys())[0]][0][0] - # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self + # 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, - species = self.dataset.group.species, - scales_in_geno = self.scales_in_geno, - data_scale = self.dataset.data_scale, - sample_group_types = self.sample_group_types, - sample_lists = sample_lists, - se_exists = self.sample_groups[0].se_exists, - has_num_cases = self.has_num_cases, - attributes = self.sample_groups[0].attributes, - categorical_attr_exists = self.categorical_attr_exists, - categorical_vars = ",".join(categorical_var_list), - num_values = self.num_values, - qnorm_values = self.qnorm_vals, - zscore_values = self.z_scores, - sample_column_width = sample_column_width, - temp_uuid = self.temp_uuid) + 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, + species=self.dataset.group.species, + scales_in_geno=self.scales_in_geno, + data_scale=self.dataset.data_scale, + sample_group_types=self.sample_group_types, + sample_lists=sample_lists, + se_exists=self.sample_groups[0].se_exists, + has_num_cases=self.has_num_cases, + attributes=self.sample_groups[0].attributes, + categorical_attr_exists=self.categorical_attr_exists, + categorical_vars=",".join(categorical_var_list), + num_values=self.num_values, + qnorm_values=self.qnorm_vals, + zscore_values=self.z_scores, + sample_column_width=sample_column_width, + temp_uuid=self.temp_uuid) self.js_data = js_data def get_external_links(self): - #ZS: There's some weirdness here because some fields don't exist while others are empty strings - 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.homologene_link = webqtlConfig.HOMOLOGENE_ID % self.this_trait.homologeneid if check_if_attr_exists(self.this_trait, 'homologeneid') else None + # ZS: There's some weirdness here because some fields don't + # exist while others are empty strings + 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.homologene_link = webqtlConfig.HOMOLOGENE_ID % self.this_trait.homologeneid if check_if_attr_exists( + self.this_trait, 'homologeneid') else None self.genbank_link = None if check_if_attr_exists(self.this_trait, 'genbankid'): @@ -320,14 +343,16 @@ class ShowTrait(object): 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.rgd_link = webqtlConfig.RGD_URL % (self.this_trait.symbol, self.dataset.group.species.capitalize()) + self.rgd_link = webqtlConfig.RGD_URL % ( + self.this_trait.symbol, self.dataset.group.species.capitalize()) if self.dataset.group.species == "mouse": - self.genemania_link = webqtlConfig.GENEMANIA_URL % ("mus-musculus", self.this_trait.symbol) + 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) + 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 @@ -345,12 +370,16 @@ class ShowTrait(object): 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) + 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.rgd_link = webqtlConfig.RGD_URL % (self.this_trait.symbol, self.dataset.group.species.capitalize()) - self.phenogen_link = webqtlConfig.PHENOGEN_URL % (self.this_trait.symbol) - self.genemania_link = webqtlConfig.GENEMANIA_URL % ("rattus-norvegicus", self.this_trait.symbol) + self.rgd_link = webqtlConfig.RGD_URL % ( + self.this_trait.symbol, self.dataset.group.species.capitalize()) + self.phenogen_link = webqtlConfig.PHENOGEN_URL % ( + self.this_trait.symbol) + self.genemania_link = webqtlConfig.GENEMANIA_URL % ( + "rattus-norvegicus", self.this_trait.symbol) query = """SELECT kgID, chromosome, txStart, txEnd FROM GeneList_rn33 @@ -363,12 +392,15 @@ class ShowTrait(object): 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 + # Convert to bases from megabases + transcript_start = int(transcript_start*1000000) transcript_end = int(transcript_end*1000000) - self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('rn6', 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) + self.biogps_link = webqtlConfig.BIOGPS_URL % ( + self.dataset.group.species, self.this_trait.geneid) self.gemma_link = webqtlConfig.GEMMA_URL % self.this_trait.geneid if self.dataset.group.species == "human": @@ -389,47 +421,52 @@ class ShowTrait(object): if self.temp_trait == True: dataset_menu = data_set.datasets(this_group) else: - dataset_menu = data_set.datasets(this_group, self.dataset.group) + dataset_menu = data_set.datasets( + this_group, self.dataset.group) dataset_menu_selected = None if len(dataset_menu): if self.dataset: dataset_menu_selected = self.dataset.name - return_results_menu = (100, 200, 500, 1000, 2000, 5000, 10000, 15000, 20000) + return_results_menu = (100, 200, 500, 1000, + 2000, 5000, 10000, 15000, 20000) return_results_menu_selected = 500 - self.corr_tools = dict(dataset_menu = dataset_menu, - dataset_menu_selected = dataset_menu_selected, - return_results_menu = return_results_menu, - return_results_menu_selected = return_results_menu_selected,) + self.corr_tools = dict(dataset_menu=dataset_menu, + dataset_menu_selected=dataset_menu_selected, + return_results_menu=return_results_menu, + return_results_menu_selected=return_results_menu_selected,) def make_sample_lists(self): all_samples_ordered = self.dataset.group.all_samples_ordered() - + parent_f1_samples = [] if self.dataset.group.parlist and self.dataset.group.f1list: parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list primary_sample_names = list(all_samples_ordered) - if not self.temp_trait: other_sample_names = [] for sample in list(self.this_trait.data.keys()): if (self.this_trait.data[sample].name2 != self.this_trait.data[sample].name): if ((self.this_trait.data[sample].name2 in primary_sample_names) and - (self.this_trait.data[sample].name not in primary_sample_names)): - primary_sample_names.append(self.this_trait.data[sample].name) - primary_sample_names.remove(self.this_trait.data[sample].name2) + (self.this_trait.data[sample].name not in primary_sample_names)): + primary_sample_names.append( + self.this_trait.data[sample].name) + primary_sample_names.remove( + self.this_trait.data[sample].name2) all_samples_set = set(all_samples_ordered) if sample not in all_samples_set: all_samples_ordered.append(sample) other_sample_names.append(sample) - #ZS: CFW is here because the .geno file doesn't properly contain its full list of samples. This should probably be fixed. + # ZS: CFW is here because the .geno file doesn't properly + # contain its full list of samples. This should probably + # be fixed. if self.dataset.group.species == "human" or (set(primary_sample_names) == set(parent_f1_samples)) or self.dataset.group.name == "CFW": primary_sample_names += other_sample_names other_sample_names = [] @@ -439,33 +476,34 @@ class ShowTrait(object): else: primary_header = "Samples" - primary_samples = SampleList(dataset = self.dataset, - sample_names=primary_sample_names, - this_trait=self.this_trait, - sample_group_type='primary', - header=primary_header) + primary_samples = SampleList(dataset=self.dataset, + sample_names=primary_sample_names, + this_trait=self.this_trait, + sample_group_type='primary', + header=primary_header) - #if other_sample_names and self.dataset.group.species != "human" and self.dataset.group.name != "CFW": + # if other_sample_names and self.dataset.group.species != + # "human" and self.dataset.group.name != "CFW": if len(other_sample_names) > 0: - other_sample_names.sort() #Sort other samples + other_sample_names.sort() # Sort other samples if parent_f1_samples: other_sample_names = parent_f1_samples + other_sample_names other_samples = SampleList(dataset=self.dataset, - sample_names=other_sample_names, - this_trait=self.this_trait, - sample_group_type='other', - header="Other") + sample_names=other_sample_names, + this_trait=self.this_trait, + sample_group_type='other', + header="Other") self.sample_groups = (primary_samples, other_samples) else: self.sample_groups = (primary_samples,) else: - primary_samples = SampleList(dataset = self.dataset, - sample_names=primary_sample_names, - this_trait=self.trait_vals, - sample_group_type='primary', - header="%s Only" % (self.dataset.group.name)) + primary_samples = SampleList(dataset=self.dataset, + sample_names=primary_sample_names, + this_trait=self.trait_vals, + sample_group_type='primary', + header="%s Only" % (self.dataset.group.name)) self.sample_groups = (primary_samples,) self.primary_sample_names = primary_sample_names @@ -539,7 +577,8 @@ def get_z_scores(sample_groups): def get_nearest_marker(this_trait, this_db): this_chr = this_trait.locus_chr this_mb = this_trait.locus_mb - #One option is to take flanking markers, another is to take the two (or one) closest + # One option is to take flanking markers, another is to take the + # two (or one) closest query = """SELECT Geno.Name FROM Geno, GenoXRef, GenoFreeze WHERE Geno.Chr = '{}' AND @@ -552,7 +591,6 @@ def get_nearest_marker(this_trait, this_db): if result == []: return "" - #return "", "" else: return result[0][0] @@ -617,10 +655,13 @@ def check_if_attr_exists(the_trait, id_type): def get_ncbi_summary(this_trait): if check_if_attr_exists(this_trait, 'geneid'): - #ZS: Need to switch this try/except to something that checks the output later + # ZS: Need to switch this try/except to something that checks + # the output later try: - response = requests.get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=%s&retmode=json" % this_trait.geneid) - summary = json.loads(response.content)['result'][this_trait.geneid]['summary'] + response = requests.get( + "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=%s&retmode=json" % this_trait.geneid) + summary = json.loads(response.content)[ + 'result'][this_trait.geneid]['summary'] return summary except: return None @@ -636,13 +677,15 @@ def get_categorical_variables(this_trait, sample_list): attribute_vals = [] for sample_name in list(this_trait.data.keys()): if sample_list.attributes[attribute].name in this_trait.data[sample_name].extra_attributes: - attribute_vals.append(this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name]) + attribute_vals.append( + this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name]) else: attribute_vals.append("N/A") num_distinct = len(set(attribute_vals)) if num_distinct < 10: - categorical_var_list.append(sample_list.attributes[attribute].name) + categorical_var_list.append( + sample_list.attributes[attribute].name) return categorical_var_list @@ -652,7 +695,8 @@ def get_genotype_scales(genofiles): if isinstance(genofiles, list): for the_file in genofiles: file_location = the_file['location'] - geno_scales[file_location] = get_scales_from_genofile(file_location) + geno_scales[file_location] = get_scales_from_genofile( + file_location) else: geno_scales[genofiles] = get_scales_from_genofile(genofiles) @@ -661,8 +705,8 @@ def get_genotype_scales(genofiles): def get_scales_from_genofile(file_location): geno_path = locate_ignore_error(file_location, 'genotype') - - if not geno_path: #ZS: This is just to allow the code to run when + # ZS: This is just to allow the code to run when + if not geno_path: return [["physic", "Mb"]] cm_and_mb_cols_exist = True cm_column = None @@ -670,7 +714,9 @@ def get_scales_from_genofile(file_location): with open(geno_path, "r") as geno_fh: for i, line in enumerate(geno_fh): if line[0] == "#" or line[0] == "@": - if "@scale" in line: #ZS: If the scale is made explicit in the metadata, use that + # ZS: If the scale is made explicit in the metadata, + # use that + if "@scale" in line: scale = line.split(":")[1].strip() if scale == "morgan": return [["morgan", "cM"]] @@ -690,12 +736,16 @@ def get_scales_from_genofile(file_location): mb_column = 3 break - #ZS: This attempts to check whether the cM and Mb columns are 'real', since some .geno files have one column be a copy of the other column, or have one column that is all 0s + # ZS: This attempts to check whether the cM and Mb columns are + # 'real', since some .geno files have one column be a copy of + # the other column, or have one column that is all 0s cm_all_zero = True mb_all_zero = True cm_mb_all_equal = True for i, line in enumerate(geno_fh): - if first_marker_line <= i < first_marker_line + 10: #ZS: I'm assuming there won't be more than 10 markers where the position is listed as 0 + # ZS: I'm assuming there won't be more than 10 markers + # where the position is listed as 0 + if first_marker_line <= i < first_marker_line + 10: if cm_column: cm_val = line.split("\t")[cm_column].strip() if cm_val != "0": @@ -711,8 +761,8 @@ def get_scales_from_genofile(file_location): if i > first_marker_line + 10: break - - #ZS: This assumes that both won't be all zero, since if that's the case mapping shouldn't be an option to begin with + # ZS: This assumes that both won't be all zero, since if that's + # the case mapping shouldn't be an option to begin with if mb_all_zero: return [["morgan", "cM"]] elif cm_mb_all_equal: diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index a52399a2..8658abf8 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -9,7 +9,7 @@ logger = getLogger(__name__) from base import species from base import webqtlConfig -class SnpBrowser(object): +class SnpBrowser: def __init__(self, start_vars): self.strain_lists = get_browser_sample_lists() diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js new file mode 100644 index 00000000..1d4a94d9 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js @@ -0,0 +1,253 @@ +var apply_default, check_search_term, dataset_info, group_info, make_default, open_window, populate_dataset, populate_group, populate_species, populate_type, process_json, redo_dropdown; +process_json = function(data) { + window.jdata = data; + populate_species(); + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return apply_default(); + } +}; + +$.ajax('/api/v_pre1/gen_dropdown', { + dataType: 'json', + success: process_json +}); + +populate_species = function() { + var species_list; + species_list = this.jdata.species; + redo_dropdown($('#species'), species_list); + return populate_group(); +}; +window.populate_species = populate_species; +populate_group = function() { + var group_list, species; + console.log("in populate group"); + species = $('#species').val(); + group_list = this.jdata.groups[species]; + for (_i = 0, _len = group_list.length; _i < (_len - 1); _i++) { + if (group_list[_i][0] == "BXD300"){ + group_list.splice(_i, 1) + } + } + redo_dropdown($('#group'), group_list); + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return populate_type(); + } +}; +window.populate_group = populate_group; +populate_type = function() { + var group, species, type_list; + console.log("in populate type"); + species = $('#species').val(); + group = $('#group').val(); + type_list = this.jdata.types[species][group]; + redo_dropdown($('#type'), type_list); + return populate_dataset(); +}; +window.populate_type = populate_type; +populate_dataset = function() { + var dataset_list, group, species, type; + console.log("in populate dataset"); + species = $('#species').val(); + group = $('#group').val(); + type = $('#type').val(); + console.log("sgt:", species, group, type); + dataset_list = this.jdata.datasets[species][group][type]; + console.log("pop_dataset:", dataset_list); + return redo_dropdown($('#dataset'), dataset_list); +}; +window.populate_dataset = populate_dataset; +redo_dropdown = function(dropdown, items) { + var item, _i, _len, _results; + console.log("in redo:", dropdown, items); + dropdown.empty(); + _results = []; + + if (dropdown.attr('id') == "group"){ + group_family_list = []; + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + group_family = item[2].toString().split(":")[1] + group_family_list.push([item[0], item[1], group_family]) + } + + current_family = "" + this_opt_group = null + for (_i = 0, _len = group_family_list.length; _i < _len; _i++) { + item = group_family_list[_i]; + if (item[2] != "None" && current_family == ""){ + current_family = item[2] + this_opt_group = $("<optgroup label=\"" + item[2] + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + } else if (current_family != "" && item[2] == current_family){ + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == group_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] != current_family && item[2] != "None"){ + current_family = item[2] + _results.push(dropdown.append(this_opt_group)) + this_opt_group = $("<optgroup label=\"" + current_family + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == group_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && this_opt_group != null && item[2] == "None"){ + _results.push(dropdown.append(this_opt_group)) + current_family = "" + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } else { + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } else if (dropdown.attr('id') == "type"){ + type_family_list = []; + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + type_family_list.push([item[0], item[1], item[2]]) + } + + current_family = "" + this_opt_group = null + for (_i = 0, _len = type_family_list.length; _i < _len; _i++) { + item = type_family_list[_i]; + if (item[2] != "None" && current_family == ""){ + current_family = item[2] + this_opt_group = $("<optgroup label=\"" + item[2] + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == type_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] == current_family){ + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == type_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] != current_family && item[2] != "None"){ + current_family = item[2] + _results.push(dropdown.append(this_opt_group)) + this_opt_group = $("<optgroup label=\"" + current_family + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == type_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else { + _results.push(dropdown.append(this_opt_group)) + current_family = "" + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } else { + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + if (item.length > 2){ + _results.push(dropdown.append($("<option data-id=\""+item[0]+"\" />").val(item[1]).text(item[2]))); + } else { + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } + + return _results; +}; +$('#species').change((function(_this) { + return function() { + return populate_group(); + }; +})(this)); +$('#group').change((function(_this) { + return function() { + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return populate_type(); + } + else { + return false + } + }; +})(this)); +$('#type').change((function(_this) { + return function() { + return populate_dataset(); + }; +})(this)); +open_window = function(url, name) { + var options; + options = "menubar=yes,toolbar=yes,titlebar=yes,location=yes,resizable=yes,status=yes,scrollbars=yes,directories=yes,width=900"; + return open(url, name, options).focus(); +}; +group_info = function() { + var group, species, url; + species = $('#species').val(); + group = $('#group').val(); + url = "http://gn1.genenetwork.org/" + species + "Cross.html#" + group; + return open_window(url, "Group Info"); +}; +$('#group_info').click(group_info); +dataset_info = function() { + var dataset, url; + accession_id = $('#dataset option:selected').data("id"); + name = $('#dataset option:selected').val(); + if (accession_id != "None") { + url = "http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + accession_id + "&InfoPageName=" + name; + } else { + url = "http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + name; + } + return open_window(url, "Dataset Info"); +}; +$('#dataset_info').click(dataset_info); +make_default = function() { + var holder, item, jholder, _i, _len, _ref; + alert("The current settings are now your default.") + holder = {}; + _ref = ['species', 'group', 'type', 'dataset']; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + item = _ref[_i]; + holder[item] = $("#" + item).val(); + } + jholder = JSON.stringify(holder); + return $.cookie('search_defaults', jholder, { + expires: 365 + }); +}; +apply_default = function() { + var defaults, item, populate_function, _i, _len, _ref, _results; + defaults = $.cookie('search_defaults'); + if (defaults) { + defaults = $.parseJSON(defaults); + } else { + defaults = { + species: "mouse", + group: "BXD", + type: "Hippocampus mRNA", + dataset: "HC_M2_0606_P" + }; + } + + _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]]; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + item = _ref[_i]; + $("#" + item[0]).val(defaults[item[0]]); + if (item[1]) { + populate_function = "populate_" + item[1]; + console.log("Calling:", populate_function); + _results.push(window[populate_function]()); + } else { + _results.push(void 0); + } + } + return _results; +}; +check_search_term = function() { + var or_search_term, and_search_term; + or_search_term = $('#or_search').val(); + and_search_term = $('#and_search').val(); + console.log("or_search_term:", or_search_term); + console.log("and_search_term:", and_search_term); + if (or_search_term === "" && and_search_term === "") { + alert("Please enter one or more search terms or search equations."); + return false; + } +}; +$("#make_default").click(make_default); +$("#btsearch").click(check_search_term); diff --git a/wqflask/wqflask/templates/edit_trait.html b/wqflask/wqflask/templates/edit_trait.html new file mode 100644 index 00000000..b9a31fc6 --- /dev/null +++ b/wqflask/wqflask/templates/edit_trait.html @@ -0,0 +1,86 @@ +{% extends "base.html" %} +{% block title %}Trait Submission{% endblock %} +{% block content %} +<!-- Start of body --> + <form method="post" action="/show_temp_trait"> + <div class="container-fluid"> + + {{ flash_me() }} + + <div class="row" style="width: 1400px !important;"> + <div class="col-xs-3"> + <section id="description"> + <div> + <h2 style="color: #5a5a5a;">Introduction</h2> + <hr> + <p>The trait values that you enter are statistically compared with verified genotypes collected at a set of microsatellite markers in each RI set. The markers are drawn from a set of over 750, but for each set redundant markers have been removed, preferentially retaining those that are most informative.</p> + <p>These error-checked RI mapping data match theoretical expectations for RI strain sets. The cumulative adjusted length of the RI maps are approximately 1400 cM, a value that matches those of both MIT maps and Chromosome Committee Report maps. See our <a target="_blank" href="http://www.nervenet.org/papers/BXN.html">full description</a> of the genetic data collected as part of the WebQTL project.</p> + </div> + </section> + <br> + <section id="description"> + <div> + <h2 style="color: #5a5a5a;">About Your Data</h2> + <hr> + <p>You can open a separate window giving the number of strains for each data set and sample data.</p> + <p>None of your submitted data is copied or stored by this system except during the actual processing of your submission. By the time the reply page displays in your browser, your submission has been cleared from this system.</p> + </div> + </section> + </div> + <div style="padding-left:20px" class="col-xs-6" style="width: 600px !important;"> + <section id="submission_form"> + <div class="form-group"> + <h2 style="color: #5a5a5a;">Edit Trait Form</h2> + <hr> + <div style="margin-bottom: 150px;" class="form-horizontal"> + <h3>Choose Dataset to Edit:</h3> + <br> + <div class="col-xs-10"> + <!-- Species --> + <div class="form-group"> + <label for="species" class="col-xs-2 control-label">Species: </label> + <div class="col-xs-4 controls"> + <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select> + </div> + </div> + <!-- Group --> + <div class="form-group"> + <label for="group" class="col-xs-2 control-label">Group: </label> + <div class="col-xs-4 controls"> + <select name="group" id="group" class="form-control span3" style="width: 280px !important;"></select> + </div> + </div> + <!-- Type --> + <div class="form-group"> + <label for="group" class="col-xs-2 control-label">Type: </label> + <div class="col-xs-4 controls"> + <select name="type" id="type" class="form-control span3" style="width: 280px !important;"></select> + </div> + </div> + <!-- Dataset --> + <div class="form-group"> + <label for="group" class="col-xs-2 control-label">DataSet: </label> + <div class="col-xs-4 controls"> + <select name="dataset" id="dataset" class="form-control span3" style="width: 280px !important;"></select> + </div> + </div> + </div> + <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;"> + <input type="submit" style="width: 110px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2" value="Submit Trait"> + <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2" value="Reset"> + </div> + </div> + </section> + </div> + </div> + </div> + </form> + +{%endblock%} + + {% block js %} + <script src="/static/new/javascript/dataset_select_menu_edit_trait.js"></script> + <script> + gn_server_url = "{{ gn_server_url }}"; + </script> +{% endblock %} diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 31846f87..942776e7 100644..100755 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -1,88 +1,77 @@ {% extends "base.html" %} {% block title %}GeneNetwork{% endblock %} +{% block css %} +<style TYPE="text/css"> + p.interact { display: none; } +</style> +{% endblock %} {% block content %} <!-- Start of body --> - -<!-- - <header class="jumbotron subhead" id="overview"> - <div class="container"> - <h1>GeneNetwork</h1> - <p class="lead">Open source bioinformatics for systems genetics</p> - </div> - </header> ---> - - <div class="container-fluid"> + <div class="container-fluid" style="min-width: 1210px;"> {{ flash_me() }} - <div class="row" style="width: 1400px !important;"> + <div class="row" style="width: 100%;"> - <div class="col-xs-5"> + <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;"> <section id="search"> - <div class="page-header"> + <div> <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"> <div class="form-group"> <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label> - <div class="col-xs-10 controls input-append" style="padding-right: 0px;"> - <div class="col-xs-8"> - <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select> - </div> - <div class="col-xs-4"> - <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button> + <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;"><option>Loading...</option></select> </div> </div> </div> <div class="form-group"> <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label> - <div class="col-xs-10 controls input-append"> - <div class="col-xs-8"> - <select name="group" id="group" class="form-control span3" style="width: 280px !important;"></select> + <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> + <div class="col-9"> + <select name="group" id="group" 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;"> + <button type="button" id="group_info" class="btn btn-primary form-control" style="width: 50px !important;">Info</button> + </div> </div> </div> <div class="form-group"> <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label> - <div class="col-xs-10 controls"> - <div class="col-xs-8"> - <select name="type" id="type" class="form-control span3" style="width: 280px !important;"></select> + <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> + <div class="col-9"> + <select name="type" id="type" class="form-control" style="width: 340px !important;"><option>Loading...</option></select> + </div> + <div class="col-3" style="margin-left: 10px;"> + <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 50px !important;">Info</button> </div> </div> </div> <div class="form-group"> <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label> - <div class="col-xs-10 controls input-append"> - <div class="col-xs-10"> - <select name="dataset" id="dataset" class="form-control span5" style="width: 340px !important;"></select> + <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;"> + <div class="col-9"> + <select name="dataset" id="dataset" class="form-control" style="max-width: 550px; width: 450px !important;"><option>Loading...</option></select> <i class="icon-question-sign"></i> </div> - <div class="col-xs-2"> - <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button> - </div> </div> </div> - - <!-- USER HELP --> - <!--<p>Databases marked with <b>**</b>--> - <!-- suffix are not public yet.<br>--> - <!-- Access requires <a href="/account.html" target=--> - <!-- "_blank" class="fs14">user login</a>.</p>--> <!-- GET ANY SEARCH --> <div class="form-group"> <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label> - <div class="col-xs-10 controls"> - <div class="col-xs-8"> - <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea> + <div class="col-xs-10 controls" style="padding-left: 20px;"> + <div class="col-8"> + <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea> </div> </div> </div> @@ -90,8 +79,8 @@ <!-- GET ANY HELP --> <div class="form-group"> <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label> - <div class="col-xs-10 controls"> - <div class="col-xs-12 controls"> + <div class="col-xs-10 controls" style="padding-left: 20px;"> + <div class="col-12 controls"> Enter terms, genes, ID numbers in the <b>Search</b> field.<br> Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br> Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>. @@ -101,29 +90,30 @@ <div class="form-group"> <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label> - <div class="col-xs-10 controls"> - <div class="col-xs-8"> - <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea> + <div class="col-xs-10 controls" style="padding-left: 20px;"> + <div class="col-8"> + <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea> </div> </div> </div> <div class="form-group"> <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label> - <div class="col-xs-10 controls"> - <div class="col-xs-2 controls" style="width: 100px !important;"> + <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;"> + <div class="col-2 controls"> <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search"> </div> + <div class="col-2 controls" style="padding-left: 20px;"> + <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button> + </div> </div> </div> <!-- SEARCH, MAKE DEFAULT --> - <div class="form-group"> </div> <input type="hidden" name="FormID" value="searchResult" class="form-control"> - <!--!<input type="hidden" name="RISet" value="BXD">--> </div> </fieldset> </form> @@ -133,33 +123,43 @@ <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="{{ url_for('glossary_blueprint.glossary') }}#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. You can also add a fourth term specifying which chromosome you want the transLRS to be on + (for example transLRS=(15 1000 5 7) would find all trans eQTLs with peak LRS on chromosome 7 that is also a trans eQTL with exclusionary zone of 5Mb).</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> - <li><b>WIKI=nicotine</b> searches <a href="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki"> + <li><b>WIKI=nicotine</b> searches <a href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki"> GeneWiki</a> for genes that you or other users have annotated with the word <i>nicotine</i>.</li> <li><b>GO:0045202</b> searches for synapse-associated genes listed in the - <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="{{ url_for('glossary_blueprint.glossary') }}#E"> - cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores - between 9 and 999.</li> + <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202"> + Gene Ontology</a>.</li> <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b> finds diabetes-associated transcripts with peak <a href="{{ url_for('glossary_blueprint.glossary') }}#E"> @@ -168,99 +168,57 @@ </ul> </section> </div> - <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;"> - <!-- - <section id="tour-info"> - <div class="page-header"> - <h1>Tour and more info</h1> - </div> - - <h3>Thirty minute tour</h3> - <p> - Take the 30 minute - GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" class="fs14">tour</a> that includes screen shots and - typical steps in the analysis. - </p> - - <h3>Even more info</h3> - <p> - For information about - resources and methods, select the Info buttons next to the Group - and Database fields above. - </p> - - <p>The <a href="/conditionsofUse.html">conditions</a> - and <a href="/statusandContact.html">contact - </a> pages have information on the status of data sets - and advice on their use and citation.</p> + <div class="col-xs-4" style="width: 600px !important;"> + <section id="affiliates"> + <div class="page-header"> + <h1>Affiliates</h1> + <ul> + <li><b><a href="http://gn1.genenetwork.org">GeneNetwork 1</a> at UTHSC</b></li> + <li><span class="broken_link" href="http://ucscbrowser.genenetwork.org/">Genome Browser</span> at UTHSC</li> + <li><a href="https://systems-genetics.org/">Systems Genetics</a> at EPFL</li> + <li><a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a> at UTHSC</li> + <li><a href="https://www.geneweaver.org/">GeneWeaver</a></li> + <li><a href="https://phenogen.org/">PhenoGen</a> at University of Colorado</li> + <li><a href="http://www.webgestalt.org/">WebGestalt</a> at Baylor</li> + </ul> + </div> </section> - --> - + <section id="news-section"> + <div class="page-header"> + <h1>News</h1> + <div id="tweets" style="height: 300px; overflow: scroll; overflow-x: hidden;"></div> + <div align="right"> + <a href="https://twitter.com/GeneNetwork2">more news items...</a> + </div> + </div> + </section> <section id="websites"> <div class="page-header"> - <h1>Affiliates and mirrors</h1> + <h1>Github</h1> + <ul> + <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li> + <li><a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a></li> + <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li> + </ul> </div> - <h3>Websites affiliated with GeneNetwork</h3> - <ul> - <li><span class="broken_link" href="http://ucscbrowser.genenetwork.org/">Genome Browser</span> at UTHSC</li> - - <li><a href="http://galaxy.genenetwork.org/">Galaxy</a> at - UTHSC</li> - - <li>GeneNetwork 1 at <span class="broken_link" href="http://ec2.genenetwork.org/">Amazon - Cloud (EC2)</span></li> - - <li>GeneNetwork 1 Source Code at <a href="http://sourceforge.net/projects/genenetwork/">SourceForge</a></li> - - <li>GeneNetwork 2 Source Code at <a href="https://github.com/genenetwork/genenetwork2">GitHub</a></li> - </ul> - <h3>GN1 Mirror and development sites</h3> - - <ul> - <li><a href="http://gn1.genenetwork.org/">Main GN1 site at UTHSC</a> (main site)</li> - <li><span class="broken_link" href="http://genenetwork.helmholtz-hzi.de/">Germany at the HZI</span></li> - <li><a href="http://genenetwork.org/">Memphis at the U of M</a></li> - </ul> - </section> - - <!--<section id="getting-started"> + </section> + <section id="websites"> <div class="page-header"> - <h1>Getting started</h1> + <h1>Links</h1> </div> - - <ol style="font-size:12px;font-family:verdana;color:black"> - <li>Select <b>Species</b> (or All)</li> - - <li>Select <b>Group</b> (a specific sample)</li> - - <li>Select <b>Type</b> of data: - + <h3>GeneNetwork v2:</h3> + <ul> + <li><a href="http://genenetwork.org/">Main website</a> at UTHSC</li> + </ul> + <h3>GeneNetwork v1:</h3> <ul> - <li>Phenotype (traits)</li> - - <li>Genotype (markers)</li> - - <li>Expression (mRNAs)</li> + <li><a href="http://gn1.genenetwork.org/">Main website</a> at UTHSC</li> + <li><span class="broken_link" href="http://artemis.uthsc.edu/">Time Machine</span>: Full GN versions from 2009 to 2016 (mm9)</li> + Cloud (EC2)</a></li> </ul> - </li> - - <li>Select a <b>Dataset</b></li> - - <li>Enter terms in the search field: words, - genes, ID numbers, probes, advanced search commands</li> - - <li>Click the <b>Search</b> button</li> - - <li>Optional: Use the <b>Make Default</b> button to save your preferences</li> - </ol> - - <h3>User Guide</h3> - <h5>Read the - <a href="http://www.genenetwork.org/index4.html"> - user guide</a>.</h5> - - </section>--> + <script type="text/javascript" src="//rf.revolvermaps.com/0/0/8.js?i=526mdlpknyd&m=0&c=ff0000&cr1=ffffff&f=arial&l=33" async="async"></script> + </section> </div> </div> </div> @@ -268,11 +226,7 @@ {%endblock%} {% block js %} - - <script> - gn_server_url = "{{ gn_server_url }}"; - </script> - <script src="/static/new/javascript/dataset_select_menu.js"></script> + <script src="/static/new/javascript/dataset_select_menu_orig.js"></script> <script> function pressed(e) { @@ -288,4 +242,21 @@ } </script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='javascript-twitter-post-fetcher/js/twitterFetcher_min.js') }}"></script> + + <script type="text/javascript"> + var configProfile = { + "profile": {"screenName": 'GeneNetwork2'}, + "domId": 'tweets', + "maxTweets": 5, + "enableLinks": true, + "showUser": false, + "showTime": true, + "showImages": true, + "lang": 'en' + }; + twitterFetcher.fetch(configProfile); + </script> + + {% endblock %} diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html deleted file mode 100755 index 7f82b35c..00000000 --- a/wqflask/wqflask/templates/index_page_orig.html +++ /dev/null @@ -1,349 +0,0 @@ -{% extends "base.html" %} -{% block title %}GeneNetwork{% endblock %} -{% block css %} -<style TYPE="text/css"> - p.interact { display: none; } -</style> -{% endblock %} -{% block content %} -<!-- Start of body --> - -<!-- - <header class="jumbotron subhead" id="overview"> - <div class="container"> - <h1>GeneNetwork</h1> - <p class="lead">Open source bioinformatics for systems genetics</p> - </div> - </header> ---> - - <div class="container-fluid" style="min-width: 1210px;"> - - {{ flash_me() }} - - <div class="row" style="width: 100%;"> - - <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;"> - <section id="search"> - <div> - <h1>Select and search</h1> - </div> - <form method="get" action="/search" target="_blank" name="SEARCHFORM"> - <fieldset> - <div style="padding: 20px" class="form-horizontal"> - - <div class="form-group"> - <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;"><option>Loading...</option></select> - </div> - </div> - </div> - - <div class="form-group"> - <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label> - <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> - <div class="col-9"> - <select name="group" id="group" 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;"> - <button type="button" id="group_info" class="btn btn-primary form-control" style="width: 50px !important;">Info</button> - </div> - </div> - </div> - - <div class="form-group"> - <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label> - <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> - <div class="col-9"> - <select name="type" id="type" class="form-control" style="width: 340px !important;"><option>Loading...</option></select> - </div> - <div class="col-3" style="margin-left: 10px;"> - <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 50px !important;">Info</button> - </div> - </div> - </div> - - <div class="form-group"> - <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label> - <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;"> - <div class="col-9"> - <select name="dataset" id="dataset" class="form-control" style="max-width: 550px; width: 450px !important;"><option>Loading...</option></select> - <i class="icon-question-sign"></i> - </div> - </div> - </div> - - <!-- USER HELP --> - <!--<p >Databases marked with <b>**</b>--> - <!-- suffix are not public yet.<br>--> - <!-- Access requires <a href="/account.html" target=--> - <!-- "_blank" class="fs14">user login</a>.</p>--> - <!-- GET ANY SEARCH --> - - <div class="form-group"> - <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label> - <div class="col-xs-10 controls" style="padding-left: 20px;"> - <div class="col-8"> - <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea> - </div> - </div> - </div> - - <!-- GET ANY HELP --> - <div class="form-group"> - <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label> - <div class="col-xs-10 controls" style="padding-left: 20px;"> - <div class="col-12 controls"> - Enter terms, genes, ID numbers in the <b>Search</b> field.<br> - Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br> - Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>. - </div> - </div> - </div> - - <div class="form-group"> - <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label> - <div class="col-xs-10 controls" style="padding-left: 20px;"> - <div class="col-8"> - <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea> - </div> - </div> - </div> - - <div class="form-group"> - <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label> - <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;"> - <div class="col-2 controls"> - <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search"> - </div> - <div class="col-2 controls" style="padding-left: 20px;"> - <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button> - </div> - </div> - </div> - - <!-- SEARCH, MAKE DEFAULT --> - - <div class="form-group"> - </div> - - <input type="hidden" name="FormID" value="searchResult" class="form-control"> - <!--!<input type="hidden" name="RISet" value="BXD">--> - </div> - </fieldset> - </form> - </section> - <section id="advanced"> - <div class="page-header"> - <h2>Advanced commands</h2> - </div> - - <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)</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. You can also add a fourth term specifying which chromosome you want the transLRS to be on - (for example transLRS=(15 1000 5 7) would find all trans eQTLs with peak LRS on chromosome 7 that is also a trans eQTL with exclusionary zone of 5Mb).</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> - - <li><b>WIKI=nicotine</b> searches <a href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki"> - GeneWiki</a> for genes that you or other users have annotated - with the word <i>nicotine</i>.</li> - - <li><b>GO:0045202</b> searches for synapse-associated genes listed in the - <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202"> - Gene Ontology</a>.</li> - - <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b> - finds diabetes-associated transcripts with peak <a href="{{ url_for('glossary_blueprint.glossary') }}#E"> - trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS - scores between 9 and 999.</li> - </ul> - </section> - </div> - - <div class="col-xs-4" style="width: 600px !important;"> - <section id="affiliates"> - <div class="page-header"> - <h1>Affiliates</h1> - <ul> - <li><b><a href="http://gn1.genenetwork.org">GeneNetwork 1</a> at UTHSC</b></li> - <li><span class="broken_link" href="http://ucscbrowser.genenetwork.org/">Genome Browser</span> at UTHSC</li> - <li><a href="https://systems-genetics.org/">Systems Genetics</a> at EPFL</li> - <li><a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a> at UTHSC</li> - <li><a href="https://www.geneweaver.org/">GeneWeaver</a></li> - <li><a href="https://phenogen.org/">PhenoGen</a> at University of Colorado</li> - <li><a href="http://www.webgestalt.org/">WebGestalt</a> at Baylor</li> - </ul> - </div> - </section> - <section id="news-section"> - <div class="page-header"> - <h1>News</h1> - <div id="tweets" style="height: 300px; overflow: scroll; overflow-x: hidden;"></div> - <div align="right"> - <a href="https://twitter.com/GeneNetwork2">more news items...</a> - </div> - </div> - </section> - <section id="websites"> - <div class="page-header"> - <h1>Github</h1> - <ul> - <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source 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> - <!-- - <section id="tour-info"> - <div class="page-header"> - <h1>Tour and more info</h1> - </div> - - <h3>Thirty minute tour</h3> - <p> - Take the 30 minute - GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" class="fs14">tour</a> that includes screen shots and - typical steps in the analysis. - </p> - - <h3>Even more info</h3> - <p> - For information about - resources and methods, select the Info buttons next to the Group - and Database fields above. - </p> - - <p>The <a href="/conditionsofUse.html">conditions</a> - and <a href="/statusandContact.html">contact - </a> pages have information on the status of data sets - and advice on their use and citation.</p> - - </section> - - </section> - --> - <section id="websites"> - <div class="page-header"> - <h1>Links</h1> - </div> - <h3>GeneNetwork v2:</h3> - <ul> - <li><a href="http://genenetwork.org/">Main website</a> at UTHSC</li> - <!--<li><a href="http://test-genenetwork.org/">Testing website</a> at UTHSC</li>--> - </ul> - <h3>GeneNetwork v1:</h3> - <ul> - <li><a href="http://gn1.genenetwork.org/">Main website</a> at UTHSC</li> - <li><span class="broken_link" href="http://artemis.uthsc.edu/">Time Machine</span>: Full GN versions from 2009 to 2016 (mm9)</li> - Cloud (EC2)</a></li> - </ul> - <script type="text/javascript" src="//rf.revolvermaps.com/0/0/8.js?i=526mdlpknyd&m=0&c=ff0000&cr1=ffffff&f=arial&l=33" async="async"></script> - </section> - - <!--<section id="getting-started"> - <div class="page-header"> - <h1>Getting started</h1> - </div> - - <ol style="font-size:12px;font-family:verdana;color:black"> - <li>Select <b>Species</b> (or All)</li> - - <li>Select <b>Group</b> (a specific sample)</li> - - <li>Select <b>Type</b> of data: - - <ul> - <li>Phenotype (traits)</li> - - <li>Genotype (markers)</li> - - <li>Expression (mRNAs)</li> - </ul> - </li> - - <li>Select a <b>Dataset</b></li> - - <li>Enter terms in the search field: words, - genes, probes, advanced search commands</li> - - <li>Click the <b>Search</b> button</li> - - <li>Optional: Use the <b>Make Default</b> button to save your preferences</li> - </ol> - - <h3>User Guide</h3> - <h5>Read the - <a href="http://gn1.genenetwork.org/index4.html"> - user guide</a>.</h5> - - </section>--> - </div> - </div> - </div> - -{%endblock%} - -{% block js %} - <script src="/static/new/javascript/dataset_select_menu_orig.js"></script> - - <script> - function pressed(e) { - // Has the enter key been pressed? - if ( (window.event ? event.keyCode : e.which) == 13) { - e.preventDefault(); - // If enter key has been pressed and the search fields are non-empty - // manually submit the <form> - if( event.target.value.trim() != "" ) { - document.forms[1].submit(); - } - } - } - </script> - - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='javascript-twitter-post-fetcher/js/twitterFetcher_min.js') }}"></script> - - <script type="text/javascript"> - var configProfile = { - "profile": {"screenName": 'GeneNetwork2'}, - "domId": 'tweets', - "maxTweets": 5, - "enableLinks": true, - "showUser": false, - "showTime": true, - "showImages": true, - "lang": 'en' - }; - twitterFetcher.fetch(configProfile); - </script> - - -{% endblock %} diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html index 68b06f55..3572b0a9 100644 --- a/wqflask/wqflask/templates/submit_trait.html +++ b/wqflask/wqflask/templates/submit_trait.html @@ -14,7 +14,7 @@ <h2 style="color: #5a5a5a;">Introduction</h2> <hr> <p>The trait values that you enter are statistically compared with verified genotypes collected at a set of microsatellite markers in each RI set. The markers are drawn from a set of over 750, but for each set redundant markers have been removed, preferentially retaining those that are most informative.</p> - <p>These error-checked RI mapping data match theoretical expectations for RI strain sets. The cumulative adjusted length of the RI maps are approximately 1400 cM, a value that matches those of both MIT maps and Chromosome Committee Report maps. See our full description of the genetic data collected as part of the WebQTL project.</p> + <p>These error-checked RI mapping data match theoretical expectations for RI strain sets. The cumulative adjusted length of the RI maps are approximately 1400 cM, a value that matches those of both MIT maps and Chromosome Committee Report maps. See our <a target="_blank" href="http://www.nervenet.org/papers/BXN.html">full description</a> of the genetic data collected as part of the WebQTL project.</p> </div> </section> <br> @@ -53,7 +53,7 @@ </div> </div> </div> - <div style="padding-bottom: 50px;" class="form-horizontal"> + <div style="padding-bottom: 50px; margin-bottom:400px" class="form-horizontal"> <h3>2. Enter Trait Data:</h3> <h4 style="color:red;">File uploading isn't enabled yet, but is coming soon.</h4> <br> @@ -61,18 +61,6 @@ <img src="/static/new/images/step2.gif"> </div> <div class="col-xs-10"> - <!-- - <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 - 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;"> - </div> - --> <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. @@ -89,6 +77,24 @@ <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2" value="Reset"> </div> </div> + <div style="padding-bottom: 50px;" class="form-horizontal"> + <h3>3. Enable Use of Trait Variance:</h3> + <div class="col-xs-2" style=""display: flex; align-items: center;"> + <img src="/static/new/images/step3.gif"> + </div> + <div class="col-xs-10"> + <div class="form-group" style="padding-left: 15px;"> + <p> + <b>Name Your Trait:</b> <span style="color:red;">(optional)</span> + </p> + <textarea name="trait_name" rows="1" cols="30"></textarea> + </div> + </div> + <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;"> + <input type="submit" style="width: 110px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2" value="Submit Trait"> + <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2" value="Reset"> + </div> + </div> </section> </div> </div> diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py index 672f95b1..22a46ef2 100644 --- a/wqflask/wqflask/update_search_results.py +++ b/wqflask/wqflask/update_search_results.py @@ -10,7 +10,7 @@ from utility.benchmark import Bench from utility.logger import getLogger logger = getLogger(__name__) -class GSearch(object): +class GSearch: def __init__(self, kw): self.type = kw['type'] diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 7b25b68e..fcec3b67 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -58,7 +58,7 @@ def timestamp(): return datetime.datetime.utcnow().isoformat() -class AnonUser(object): +class AnonUser: """Anonymous user handling""" cookie_name = 'anon_user_v1' @@ -158,7 +158,7 @@ def create_signed_cookie(): logger.debug("uuid_signed:", uuid_signed) return the_uuid, uuid_signed -class UserSession(object): +class UserSession: """Logged in user handling""" cookie_name = 'session_id_v1' @@ -353,12 +353,12 @@ def set_cookie(response): response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie) return response -class UsersManager(object): +class UsersManager: def __init__(self): self.users = model.User.query.all() logger.debug("Users are:", self.users) -class UserManager(object): +class UserManager: def __init__(self, kw): self.user_id = kw['user_id'] logger.debug("In UserManager locals are:", pf(locals())) @@ -377,7 +377,7 @@ class UserManager(object): #logger.debug(" ---> self.datasets:", self.datasets) -class RegisterUser(object): +class RegisterUser: def __init__(self, kw): self.thank_you_mode = False self.errors = [] @@ -454,7 +454,7 @@ def set_password(password, user): ) -class VerificationEmail(object): +class VerificationEmail: template_name = "email/verification.txt" key_prefix = "verification_code" subject = "GeneNetwork email verification" @@ -511,7 +511,7 @@ class ForgotPasswordEmail(VerificationEmail): send_email(toaddr, msg.as_string()) -class Password(object): +class Password: def __init__(self, unencrypted_password, salt, iterations, keylength, hashfunc): hashfunc = getattr(hashlib, hashfunc) logger.debug("hashfunc is:", hashfunc) @@ -589,7 +589,7 @@ def password_reset_step2(): return response -class DecodeUser(object): +class DecodeUser: def __init__(self, code_prefix): verify_url_hmac(request.url) @@ -695,7 +695,7 @@ def get_github_user_details(access_token): result = requests.get(GITHUB_API_URL, params={"access_token":access_token}) return result.json() -class LoginUser(object): +class LoginUser: remember_time = 60 * 60 * 24 * 30 # One month in seconds def __init__(self): @@ -1039,12 +1039,12 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"): server.quit() logger.info("Successfully sent email to "+toaddr) -class GroupsManager(object): +class GroupsManager: def __init__(self, kw): self.datasets = create_datasets_list() -class RolesManager(object): +class RolesManager: def __init__(self): self.roles = model.Role.query.all() logger.debug("Roles are:", self.roles) diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index c5a577df..cc0ac744 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -63,7 +63,7 @@ def manage_user(): return render_template("admin/manage_user.html", user_details = user_details) -class UserSession(object): +class UserSession: """Logged in user handling""" user_cookie_name = 'session_id_v2' diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 2c0ba586..81ccaf7d 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -1,20 +1,17 @@ """Main routing table for GN2""" -import traceback # for error page +import traceback # for error page import os # for error gifs import random # for random error gif import datetime # for errors -import time # for errors import sys import csv import simplejson as json -import yaml import xlsxwriter import io # Todo: Use cStringIO? from zipfile import ZipFile, ZIP_DEFLATED -import gc import numpy as np import pickle as pickle import uuid @@ -24,23 +21,26 @@ import base64 import array import sqlalchemy from wqflask import app -from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file +from flask import g +from flask import Response +from flask import request +from flask import make_response +from flask import render_template +from flask import send_from_directory +from flask import redirect +from flask import url_for +from flask import send_file -from wqflask import group_manager -from wqflask import resource_manager from wqflask import search_results -from wqflask import export_traits -from wqflask import gsearch -from wqflask import update_search_results -from wqflask import docs -from wqflask import news from wqflask import server_side from wqflask.submit_bnw import get_bnw_input -from base.data_set import create_dataset, DataSet # Used by YAML in marker_regression +from base.data_set import create_dataset # Used by YAML in marker_regression from wqflask.show_trait import show_trait from wqflask.show_trait import export_trait_data from wqflask.heatmap import heatmap -from wqflask.external_tools import send_to_bnw, send_to_webgestalt, send_to_geneweaver +from wqflask.external_tools import send_to_bnw +from wqflask.external_tools import send_to_webgestalt +from wqflask.external_tools import send_to_geneweaver from wqflask.comparison_bar_chart import comparison_bar_chart from wqflask.marker_regression import run_mapping from wqflask.marker_regression import display_mapping_results @@ -59,24 +59,31 @@ from wqflask.docs import Docs, update_text from wqflask.db_info import InfoPage from utility import temp_data -from utility.tools import SQL_URI, TEMPDIR, USE_REDIS, USE_GN_SERVER, GN_SERVER_URL, GN_VERSION, JS_TWITTER_POST_FETCHER_PATH, JS_GUIX_PATH, CSS_PATH +from utility.tools import SQL_URI +from utility.tools import TEMPDIR +from utility.tools import USE_REDIS +from utility.tools import GN_SERVER_URL +from utility.tools import GN_VERSION +from utility.tools import JS_TWITTER_POST_FETCHER_PATH +from utility.tools import JS_GUIX_PATH from utility.helper_functions import get_species_groups from utility.authentication_tools import check_resource_availability from utility.redis_tools import get_redis_conn -Redis = get_redis_conn() + from base.webqtlConfig import GENERATED_IMAGE_DIR, DEFAULT_PRIVILEGES from utility.benchmark import Bench from pprint import pformat as pf -from wqflask import collect from wqflask.database import db_session -import werkzeug import utility.logger -logger = utility.logger.getLogger(__name__ ) + +Redis = get_redis_conn() + +logger = utility.logger.getLogger(__name__) @app.before_request @@ -84,13 +91,14 @@ def connect_db(): logger.info("@app.before_request connect_db") db = getattr(g, '_database', None) if db is None: - g.db = g._database = sqlalchemy.create_engine(SQL_URI, encoding="latin1") + g.db = g._database = sqlalchemy.create_engine( + SQL_URI, encoding="latin1") logger.debug(g.db) + @app.before_request def check_access_permissions(): logger.debug("@app.before_request check_access_permissions") - available = True if 'dataset' in request.args: permissions = DEFAULT_PRIVILEGES if request.args['dataset'] != "Temp": @@ -99,7 +107,8 @@ def check_access_permissions(): if dataset.type == "Temp": permissions = DEFAULT_PRIVILEGES elif 'trait_id' in request.args: - permissions = check_resource_availability(dataset, request.args['trait_id']) + permissions = check_resource_availability( + dataset, request.args['trait_id']) elif dataset.type != "Publish": permissions = check_resource_availability(dataset) @@ -110,6 +119,7 @@ def check_access_permissions(): if permissions['data'] == 'no-access': return redirect(url_for("no_access_page")) + @app.teardown_appcontext def shutdown_session(exception=None): db = getattr(g, '_database', None) @@ -118,6 +128,7 @@ def shutdown_session(exception=None): db_session.remove() g.db = None + @app.errorhandler(Exception) def handle_bad_request(e): err_msg = str(e) @@ -128,25 +139,30 @@ def handle_bad_request(e): logger.error(traceback.format_exc()) now = datetime.datetime.utcnow() time_str = now.strftime('%l:%M%p UTC %b %d, %Y') - formatted_lines = [request.url + " ("+time_str+")"]+traceback.format_exc().splitlines() + formatted_lines = [request.url + + " ("+time_str+")"]+traceback.format_exc().splitlines() # Handle random animations # Use a cookie to have one animation on refresh animation = request.cookies.get(err_msg[:32]) if not animation: - list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ] + list = [fn for fn in os.listdir( + "./wqflask/static/gif/error") if fn.endswith(".gif")] animation = random.choice(list) - resp = make_response(render_template("error.html", message=err_msg, stack=formatted_lines, error_image=animation, version=GN_VERSION)) + resp = make_response(render_template("error.html", message=err_msg, + stack=formatted_lines, error_image=animation, version=GN_VERSION)) # logger.error("Set cookie %s with %s" % (err_msg, animation)) resp.set_cookie(err_msg[:32], animation) return resp + @app.route("/authentication_needed") def no_access_page(): return render_template("new_security/not_authenticated.html") + @app.route("/") def index_page(): logger.info("Sending index_page") @@ -156,13 +172,7 @@ def index_page(): import_collections = params['import_collections'] if import_collections == "true": g.user_session.import_traits_to_user(params['anon_id']) - #if USE_GN_SERVER: - # # The menu is generated using GN_SERVER - # return render_template("index_page.html", gn_server_url = GN_SERVER_URL, version=GN_VERSION) - #else: - - # Old style static menu (OBSOLETE) - return render_template("index_page_orig.html", version=GN_VERSION) + return render_template("index_page.html", version=GN_VERSION) @app.route("/tmp/<img_path>") @@ -177,7 +187,7 @@ def tmp_page(img_path): imgB64 = base64.b64encode(imgdata) bytesarray = array.array('B', imgB64) return render_template("show_image.html", - img_base64 = bytesarray ) + img_base64=bytesarray) @app.route("/js/<path:filename>") @@ -189,6 +199,7 @@ def js(filename): name = name.replace('js_alt/', '') return send_from_directory(js_path, name) + @app.route("/css/<path:filename>") def css(filename): js_path = JS_GUIX_PATH @@ -198,10 +209,12 @@ def css(filename): name = name.replace('js_alt/', '') return send_from_directory(js_path, name) + @app.route("/twitter/<path:filename>") def twitter(filename): return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename) + @app.route("/search", methods=('GET',)) def search_page(): logger.info("in search_page") @@ -209,7 +222,8 @@ def search_page(): result = None if USE_REDIS: with Bench("Trying Redis cache"): - key = "search_results:v1:" + json.dumps(request.args, sort_keys=True) + key = "search_results:v1:" + \ + json.dumps(request.args, sort_keys=True) logger.debug("key is:", pf(key)) result = Redis.get(key) if result: @@ -232,6 +246,7 @@ def search_page(): else: return render_template("search_error.html") + @app.route("/search_table", methods=('GET',)) def search_page_table(): logger.info("in search_page table") @@ -242,7 +257,7 @@ def search_page_table(): logger.info(type(the_search.trait_list)) logger.info(the_search.trait_list) - + current_page = server_side.ServerSideTable( len(the_search.trait_list), the_search.trait_list, @@ -252,6 +267,7 @@ def search_page_table(): return flask.jsonify(current_page) + @app.route("/gsearch", methods=('GET',)) def gsearchact(): logger.info(request.url) @@ -262,17 +278,14 @@ def gsearchact(): elif type == "phenotype": return render_template("gsearch_pheno.html", **result) + @app.route("/gsearch_updating", methods=('POST',)) def gsearch_updating(): logger.info("REQUEST ARGS:", request.values) logger.info(request.url) result = UpdateGSearch(request.args).__dict__ return result['results'] - # type = request.args['type'] - # if type == "gene": - # return render_template("gsearch_gene_updating.html", **result) - # elif type == "phenotype": - # return render_template("gsearch_pheno.html", **result) + @app.route("/docedit") def docedit(): @@ -292,41 +305,59 @@ def generated_file(filename): logger.info(request.url) return send_from_directory(GENERATED_IMAGE_DIR, filename) + @app.route("/help") def help(): logger.info(request.url) doc = Docs("help", request.args) return render_template("docs.html", **doc.__dict__) + @app.route("/wgcna_setup", methods=('POST',)) def wcgna_setup(): - logger.info("In wgcna, request.form is:", request.form) # We are going to get additional user input for the analysis + # We are going to get additional user input for the analysis + logger.info("In wgcna, request.form is:", request.form) logger.info(request.url) - return render_template("wgcna_setup.html", **request.form) # Display them using the template + # Display them using the template + return render_template("wgcna_setup.html", **request.form) + @app.route("/wgcna_results", methods=('POST',)) def wcgna_results(): logger.info("In wgcna, request.form is:", request.form) logger.info(request.url) - wgcna = wgcna_analysis.WGCNA() # Start R, load the package and pointers and create the analysis - wgcnaA = wgcna.run_analysis(request.form) # Start the analysis, a wgcnaA object should be a separate long running thread - result = wgcna.process_results(wgcnaA) # After the analysis is finished store the result - return render_template("wgcna_results.html", **result) # Display them using the template + # Start R, load the package and pointers and create the analysis + wgcna = wgcna_analysis.WGCNA() + # Start the analysis, a wgcnaA object should be a separate long running thread + wgcnaA = wgcna.run_analysis(request.form) + # After the analysis is finished store the result + result = wgcna.process_results(wgcnaA) + # Display them using the template + return render_template("wgcna_results.html", **result) + @app.route("/ctl_setup", methods=('POST',)) def ctl_setup(): - logger.info("In ctl, request.form is:", request.form) # We are going to get additional user input for the analysis + # We are going to get additional user input for the analysis + logger.info("In ctl, request.form is:", request.form) logger.info(request.url) - return render_template("ctl_setup.html", **request.form) # Display them using the template + # Display them using the template + return render_template("ctl_setup.html", **request.form) + @app.route("/ctl_results", methods=('POST',)) def ctl_results(): logger.info("In ctl, request.form is:", request.form) logger.info(request.url) - ctl = ctl_analysis.CTL() # Start R, load the package and pointers and create the analysis - ctlA = ctl.run_analysis(request.form) # Start the analysis, a ctlA object should be a separate long running thread - result = ctl.process_results(ctlA) # After the analysis is finished store the result - return render_template("ctl_results.html", **result) # Display them using the template + # Start R, load the package and pointers and create the analysis + ctl = ctl_analysis.CTL() + # Start the analysis, a ctlA object should be a separate long running thread + ctlA = ctl.run_analysis(request.form) + # After the analysis is finished store the result + result = ctl.process_results(ctlA) + # Display them using the template + return render_template("ctl_results.html", **result) + @app.route("/news") def news(): @@ -340,40 +371,50 @@ def intro(): return render_template("docs.html", **doc.__dict__) - @app.route("/tutorials") def tutorials(): - #doc = Docs("links", request.args) - #return render_template("docs.html", **doc.__dict__) return render_template("tutorials.html") + @app.route("/credits") def credits(): - #doc = Docs("links", request.args) - #return render_template("docs.html", **doc.__dict__) return render_template("credits.html") + @app.route("/update_text", methods=('POST',)) def update_page(): update_text(request.form) doc = Docs(request.form['entry_type'], request.form) return render_template("docs.html", **doc.__dict__) + @app.route("/submit_trait") def submit_trait_form(): logger.info(request.url) species_and_groups = get_species_groups() - return render_template("submit_trait.html", **{'species_and_groups' : species_and_groups, 'gn_server_url' : GN_SERVER_URL, 'version' : GN_VERSION}) + return render_template( + "submit_trait.html", + species_and_groups=species_and_groups, + gn_server_url=GN_SERVER_URL, + version=GN_VERSION) + + +@app.route("/edit_trait_form") +def edit_trait_page(): + species_and_groups = get_species_groups() + return render_template( + "edit_trait.html", + species_and_groups=species_and_groups, + gn_server_url=GN_SERVER_URL, + version=GN_VERSION) + @app.route("/create_temp_trait", methods=('POST',)) def create_temp_trait(): logger.info(request.url) - - #template_vars = submit_trait.SubmitTrait(request.form) - doc = Docs("links") return render_template("links.html", **doc.__dict__) - #return render_template("show_trait.html", **template_vars.__dict__) + @app.route('/export_trait_excel', methods=('POST',)) def export_trait_excel(): @@ -381,9 +422,11 @@ def export_trait_excel(): logger.info("In export_trait_excel") logger.info("request.form:", request.form) logger.info(request.url) - trait_name, sample_data = export_trait_data.export_sample_table(request.form) + trait_name, sample_data = export_trait_data.export_sample_table( + request.form) - logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) + logger.info("sample_data - type: %s -- size: %s" % + (type(sample_data), len(sample_data))) buff = io.BytesIO() workbook = xlsxwriter.Workbook(buff, {'in_memory': True}) @@ -397,7 +440,8 @@ def export_trait_excel(): return Response(excel_data, mimetype='application/vnd.ms-excel', - headers={"Content-Disposition":"attachment;filename="+ trait_name + ".xlsx"}) + headers={"Content-Disposition": "attachment;filename=" + trait_name + ".xlsx"}) + @app.route('/export_trait_csv', methods=('POST',)) def export_trait_csv(): @@ -405,9 +449,11 @@ def export_trait_csv(): logger.info("In export_trait_csv") logger.info("request.form:", request.form) logger.info(request.url) - trait_name, sample_data = export_trait_data.export_sample_table(request.form) + trait_name, sample_data = export_trait_data.export_sample_table( + request.form) - logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) + logger.info("sample_data - type: %s -- size: %s" % + (type(sample_data), len(sample_data))) buff = io.StringIO() writer = csv.writer(buff) @@ -418,7 +464,8 @@ def export_trait_csv(): return Response(csv_data, mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename="+ trait_name + ".csv"}) + headers={"Content-Disposition": "attachment;filename=" + trait_name + ".csv"}) + @app.route('/export_traits_csv', methods=('POST',)) def export_traits_csv(): @@ -443,7 +490,8 @@ def export_traits_csv(): else: return Response(file_list[0][1], mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=" + file_list[0][0]}) + headers={"Content-Disposition": "attachment;filename=" + file_list[0][0]}) + @app.route('/export_perm_data', methods=('POST',)) def export_perm_data(): @@ -454,7 +502,8 @@ def export_perm_data(): now = datetime.datetime.now() time_str = now.strftime('%H:%M_%d%B%Y') - file_name = "Permutation_" + perm_info['num_perm'] + "_" + perm_info['trait_name'] + "_" + time_str + file_name = "Permutation_" + \ + perm_info['num_perm'] + "_" + perm_info['trait_name'] + "_" + time_str the_rows = [ ["#Permutation Test"], @@ -468,10 +517,14 @@ def export_perm_data(): ["#N_genotypes: " + str(perm_info['n_genotypes'])], ["#Genotype_file: " + perm_info['genofile']], ["#Units_linkage: " + perm_info['units_linkage']], - ["#Permutation_stratified_by: " + ", ".join([ str(cofactor) for cofactor in perm_info['strat_cofactors']])], - ["#RESULTS_1: Suggestive LRS(p=0.63) = " + str(np.percentile(np.array(perm_info['perm_data']), 67))], - ["#RESULTS_2: Significant LRS(p=0.05) = " + str(np.percentile(np.array(perm_info['perm_data']), 95))], - ["#RESULTS_3: Highly Significant LRS(p=0.01) = " + str(np.percentile(np.array(perm_info['perm_data']), 99))], + ["#Permutation_stratified_by: " + + ", ".join([str(cofactor) for cofactor in perm_info['strat_cofactors']])], + ["#RESULTS_1: Suggestive LRS(p=0.63) = " + + str(np.percentile(np.array(perm_info['perm_data']), 67))], + ["#RESULTS_2: Significant LRS(p=0.05) = " + str( + np.percentile(np.array(perm_info['perm_data']), 95))], + ["#RESULTS_3: Highly Significant LRS(p=0.01) = " + str( + np.percentile(np.array(perm_info['perm_data']), 99))], ["#Comment: Results sorted from low to high peak linkage"] ] @@ -485,38 +538,29 @@ def export_perm_data(): return Response(csv_data, mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"}) + headers={"Content-Disposition": "attachment;filename=" + file_name + ".csv"}) + @app.route("/show_temp_trait", methods=('POST',)) def show_temp_trait_page(): logger.info(request.url) template_vars = show_trait.ShowTrait(request.form) - #logger.info("js_data before dump:", template_vars.js_data) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") - # Sorting the keys messes up the ordered dictionary, so don't do that - #sort_keys=True) - - #logger.info("js_data after dump:", template_vars.js_data) - #logger.info("show_trait template_vars:", pf(template_vars.__dict__)) return render_template("show_trait.html", **template_vars.__dict__) + @app.route("/show_trait") def show_trait_page(): logger.info(request.url) template_vars = show_trait.ShowTrait(request.args) - #logger.info("js_data before dump:", template_vars.js_data) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") - # Sorting the keys messes up the ordered dictionary, so don't do that - #sort_keys=True) - - #logger.info("js_data after dump:", template_vars.js_data) - #logger.info("show_trait template_vars:", pf(template_vars.__dict__)) return render_template("show_trait.html", **template_vars.__dict__) + @app.route("/heatmap", methods=('POST',)) def heatmap_page(): logger.info("In heatmap, request.form is:", pf(request.form)) @@ -528,7 +572,8 @@ def heatmap_page(): traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] if traits[0] != "": version = "v5" - key = "heatmap:{}:".format(version) + json.dumps(start_vars, sort_keys=True) + key = "heatmap:{}:".format( + version) + json.dumps(start_vars, sort_keys=True) logger.info("key is:", pf(key)) with Bench("Loading cache"): result = Redis.get(key) @@ -549,7 +594,8 @@ def heatmap_page(): result = template_vars.__dict__ for item in list(template_vars.__dict__.keys()): - logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) + logger.info( + " ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) logger.info("pickled result length:", len(pickled_result)) @@ -560,10 +606,12 @@ def heatmap_page(): rendered_template = render_template("heatmap.html", **result) else: - rendered_template = render_template("empty_collection.html", **{'tool':'Heatmap'}) + rendered_template = render_template( + "empty_collection.html", **{'tool': 'Heatmap'}) return rendered_template + @app.route("/bnw_page", methods=('POST',)) def bnw_page(): logger.info("In run BNW, request.form is:", pf(request.form)) @@ -578,10 +626,12 @@ def bnw_page(): result = template_vars.__dict__ rendered_template = render_template("bnw_page.html", **result) else: - rendered_template = render_template("empty_collection.html", **{'tool':'BNW'}) + rendered_template = render_template( + "empty_collection.html", **{'tool': 'BNW'}) return rendered_template + @app.route("/webgestalt_page", methods=('POST',)) def webgestalt_page(): logger.info("In run WebGestalt, request.form is:", pf(request.form)) @@ -596,10 +646,12 @@ def webgestalt_page(): result = template_vars.__dict__ rendered_template = render_template("webgestalt_page.html", **result) else: - rendered_template = render_template("empty_collection.html", **{'tool':'WebGestalt'}) + rendered_template = render_template( + "empty_collection.html", **{'tool': 'WebGestalt'}) return rendered_template + @app.route("/geneweaver_page", methods=('POST',)) def geneweaver_page(): logger.info("In run WebGestalt, request.form is:", pf(request.form)) @@ -614,10 +666,12 @@ def geneweaver_page(): result = template_vars.__dict__ rendered_template = render_template("geneweaver_page.html", **result) else: - rendered_template = render_template("empty_collection.html", **{'tool':'GeneWeaver'}) + rendered_template = render_template( + "empty_collection.html", **{'tool': 'GeneWeaver'}) return rendered_template + @app.route("/comparison_bar_chart", methods=('POST',)) def comp_bar_chart_page(): logger.info("In comp bar chart, request.form is:", pf(request.form)) @@ -629,26 +683,30 @@ def comp_bar_chart_page(): if traits[0] != "": template_vars = comparison_bar_chart.ComparisonBarChart(request.form) template_vars.js_data = json.dumps(template_vars.js_data, - default=json_default_handler, - indent=" ") + default=json_default_handler, + indent=" ") result = template_vars.__dict__ - rendered_template = render_template("comparison_bar_chart.html", **result) + rendered_template = render_template( + "comparison_bar_chart.html", **result) else: - rendered_template = render_template("empty_collection.html", **{'tool':'Comparison Bar Chart'}) + rendered_template = render_template( + "empty_collection.html", **{'tool': 'Comparison Bar Chart'}) return rendered_template + @app.route("/mapping_results_container") def mapping_results_container_page(): return render_template("mapping_results_container.html") + @app.route("/loading", methods=('POST',)) def loading_page(): logger.info(request.url) initial_start_vars = request.form start_vars_container = {} - n_samples = 0 #ZS: So it can be displayed on loading page + n_samples = 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 = {} @@ -661,16 +719,17 @@ def loading_page(): else: sample_vals_dict = json.loads(start_vars['sample_vals']) if 'group' in start_vars: - dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group']) + dataset = create_dataset( + start_vars['dataset'], group_name=start_vars['group']) else: dataset = create_dataset(start_vars['dataset']) - genofile_samplelist = [] samples = start_vars['primary_samples'].split(",") if 'genofile' in start_vars: if start_vars['genofile'] != "": genofile_string = start_vars['genofile'] dataset.group.genofile = genofile_string.split(":")[0] - genofile_samples = run_mapping.get_genofile_samplelist(dataset) + genofile_samples = run_mapping.get_genofile_samplelist( + dataset) if len(genofile_samples) > 1: samples = genofile_samples @@ -690,6 +749,7 @@ def loading_page(): return rendered_template + @app.route("/run_mapping", methods=('POST',)) def mapping_results_page(): initial_start_vars = request.form @@ -760,9 +820,10 @@ def mapping_results_page(): start_vars[key] = value version = "v3" - key = "mapping_results:{}:".format(version) + json.dumps(start_vars, sort_keys=True) + key = "mapping_results:{}:".format( + version) + json.dumps(start_vars, sort_keys=True) with Bench("Loading cache"): - result = None # Just for testing + result = None # Just for testing #result = Redis.get(key) #logger.info("************************ Starting result *****************") @@ -782,12 +843,12 @@ def mapping_results_page(): rendered_template = render_template("mapping_error.html") return rendered_template except: - rendered_template = render_template("mapping_error.html") - return rendered_template + rendered_template = render_template("mapping_error.html") + return rendered_template template_vars.js_data = json.dumps(template_vars.js_data, - default=json_default_handler, - indent=" ") + default=json_default_handler, + indent=" ") result = template_vars.__dict__ @@ -802,18 +863,20 @@ def mapping_results_page(): imgB64 = base64.b64encode(imgdata) bytesarray = array.array('B', imgB64) result['pair_scan_array'] = bytesarray - rendered_template = render_template("pair_scan_results.html", **result) + rendered_template = render_template( + "pair_scan_results.html", **result) else: - gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__ + gn1_template_vars = display_mapping_results.DisplayMappingResults( + result).__dict__ 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) + rendered_template = render_template( + "mapping_results.html", **gn1_template_vars) return rendered_template -@app.route("/export_mapping_results", methods = ('POST',)) + +@app.route("/export_mapping_results", methods=('POST',)) def export_mapping_results(): logger.info("request.form:", request.form) logger.info(request.url) @@ -821,32 +884,35 @@ def export_mapping_results(): results_csv = open(file_path, "r").read() response = Response(results_csv, mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=mapping_results.csv"}) + headers={"Content-Disposition": "attachment;filename=mapping_results.csv"}) return response -@app.route("/export_corr_matrix", methods = ('POST',)) + +@app.route("/export_corr_matrix", methods=('POST',)) def export_corr_matrix(): file_path = request.form.get("export_filepath") file_name = request.form.get("export_filename") results_csv = open(file_path, "r").read() response = Response(results_csv, mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"}) + headers={"Content-Disposition": "attachment;filename=" + file_name + ".csv"}) return response -@app.route("/export", methods = ('POST',)) + +@app.route("/export", methods=('POST',)) def export(): logger.info("request.form:", request.form) logger.info(request.url) svg_xml = request.form.get("data", "Invalid data") filename = request.form.get("filename", "manhattan_plot_snp") response = Response(svg_xml, mimetype="image/svg+xml") - response.headers["Content-Disposition"] = "attachment; filename=%s"%filename + response.headers["Content-Disposition"] = "attachment; filename=%s" % filename return response -@app.route("/export_pdf", methods = ('POST',)) + +@app.route("/export_pdf", methods=('POST',)) def export_pdf(): import cairosvg logger.info("request.form:", request.form) @@ -854,12 +920,12 @@ def export_pdf(): svg_xml = request.form.get("data", "Invalid data") logger.info("svg_xml:", svg_xml) filename = request.form.get("filename", "interval_map_pdf") - filepath = GENERATED_IMAGE_DIR+filename pdf_file = cairosvg.svg2pdf(bytestring=svg_xml) response = Response(pdf_file, mimetype="application/pdf") - response.headers["Content-Disposition"] = "attachment; filename=%s"%filename + response.headers["Content-Disposition"] = "attachment; filename=%s" % filename return response + @app.route("/network_graph", methods=('POST',)) def network_graph_page(): logger.info("In network_graph, request.form is:", pf(request.form)) @@ -874,7 +940,8 @@ def network_graph_page(): return render_template("network_graph.html", **template_vars.__dict__) else: - return render_template("empty_collection.html", **{'tool':'Network Graph'}) + return render_template("empty_collection.html", **{'tool': 'Network Graph'}) + @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): @@ -883,6 +950,7 @@ def corr_compute_page(): template_vars = show_corr_results.CorrelationResults(request.form) return render_template("correlation_page.html", **template_vars.__dict__) + @app.route("/corr_matrix", methods=('POST',)) def corr_matrix_page(): logger.info("In corr_matrix, request.form is:", pf(request.form)) @@ -898,7 +966,8 @@ def corr_matrix_page(): return render_template("correlation_matrix.html", **template_vars.__dict__) else: - return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) + return render_template("empty_collection.html", **{'tool': 'Correlation Matrix'}) + @app.route("/corr_scatter_plot") def corr_scatter_plot_page(): @@ -909,6 +978,7 @@ def corr_scatter_plot_page(): indent=" ") return render_template("corr_scatterplot.html", **template_vars.__dict__) + @app.route("/snp_browser", methods=('GET',)) def snp_browser_page(): logger.info(request.url) @@ -916,12 +986,14 @@ def snp_browser_page(): return render_template("snp_browser.html", **template_vars.__dict__) + @app.route("/db_info", methods=('GET',)) def db_info_page(): template_vars = InfoPage(request.args) return render_template("info_page.html", **template_vars.__dict__) + @app.route("/snp_browser_table", methods=('GET',)) def snp_browser_table(): logger.info(request.url) @@ -935,31 +1007,36 @@ def snp_browser_table(): return flask.jsonify(current_page) + @app.route("/tutorial/WebQTLTour", methods=('GET',)) def tutorial_page(): - #ZS: Currently just links to GN1 + # ZS: Currently just links to GN1 logger.info(request.url) return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/") + @app.route("/tutorial/security", methods=('GET',)) def security_tutorial_page(): - #ZS: Currently just links to GN1 + # ZS: Currently just links to GN1 logger.info(request.url) return render_template("admin/security_help.html") + @app.route("/submit_bnw", methods=('POST',)) def submit_bnw(): logger.info(request.url) - template_vars = get_bnw_input(request.form) - return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) + return render_template("empty_collection.html", **{'tool': 'Correlation Matrix'}) # Take this out or secure it before putting into production + + @app.route("/get_temp_data") def get_temp_data(): logger.info(request.url) 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""" @@ -973,8 +1050,9 @@ def browser_inputs(): ########################################################################## + def json_default_handler(obj): - '''Based on http://stackoverflow.com/a/2680060/1175849''' + """Based on http://stackoverflow.com/a/2680060/1175849""" # Handle datestamps if hasattr(obj, 'isoformat'): return obj.isoformat() @@ -984,9 +1062,6 @@ def json_default_handler(obj): # Handle custom objects if hasattr(obj, '__dict__'): return obj.__dict__ - #elif type(obj) == "Dataset": - # logger.info("Not going to serialize Dataset") - # return None else: raise TypeError('Object of type %s with value of %s is not JSON serializable' % ( type(obj), repr(obj))) diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index 6bf75216..21516b30 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -42,7 +42,7 @@ r_png = ro.r["png"] # Map the png function for plotting r_dev_off = ro.r["dev.off"] # Map the dev.off function -class WGCNA(object): +class WGCNA: def __init__(self): # To log output from stdout/stderr to a file add `r_sink(log)` print("Initialization of WGCNA") |