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-rw-r--r--wqflask/wqflask/api/router.py290
1 files changed, 145 insertions, 145 deletions
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 707e4e65..aab3d660 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -22,7 +22,7 @@ version = "pre1"
@app.route("/api/v_{}/".format(version))
def hello_world():
- return flask.jsonify({'hello':'world'})
+ return flask.jsonify({"hello":"world"})
@app.route("/api/v_{}/species".format(version))
def get_species_list():
@@ -31,10 +31,10 @@ def get_species_list():
species_list = []
for species in the_species:
species_dict = {
- 'Id' : species[0],
- 'Name' : species[1],
- 'FullName' : species[2],
- 'TaxonomyId' : species[3]
+ "Id" : species[0],
+ "Name" : species[1],
+ "FullName" : species[2],
+ "TaxonomyId" : species[3]
}
species_list.append(species_dict)
@@ -45,14 +45,14 @@ def get_species_list():
def get_species_info(species_name, file_format = "json"):
results = g.db.execute("""SELECT SpeciesId, Name, FullName, TaxonomyId
FROM Species
- WHERE (Name='{0}' OR FullName='{0}' OR SpeciesName='{0}');""".format(species_name))
+ WHERE (Name="{0}" OR FullName="{0}" OR SpeciesName="{0}");""".format(species_name))
the_species = results.fetchone()
species_dict = {
- 'Id' : the_species[0],
- 'Name' : the_species[1],
- 'FullName' : the_species[2],
- 'TaxonomyId' : the_species[3]
+ "Id" : the_species[0],
+ "Name" : the_species[1],
+ "FullName" : the_species[2],
+ "TaxonomyId" : the_species[3]
}
return flask.jsonify(species_dict)
@@ -61,14 +61,14 @@ def get_species_info(species_name, file_format = "json"):
@app.route("/api/v_{}/<path:species_name>/groups".format(version))
def get_groups_list(species_name=None):
if species_name:
- results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName,
- InbredSet.Name, InbredSet.FullName, InbredSet.public,
+ results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName,
+ InbredSet.Name, InbredSet.FullName, InbredSet.public,
InbredSet.MappingMethodId, InbredSet.GeneticType
FROM InbredSet, Species
WHERE InbredSet.SpeciesId = Species.Id AND
- (Species.Name = '{0}' OR
- Species.FullName='{0}' OR
- Species.SpeciesName='{0}');""".format(species_name))
+ (Species.Name = "{0}" OR
+ Species.FullName="{0}" OR
+ Species.SpeciesName="{0}");""".format(species_name))
else:
results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName,
InbredSet.Name, InbredSet.FullName, InbredSet.public,
@@ -80,14 +80,14 @@ def get_groups_list(species_name=None):
groups_list = []
for group in the_groups:
group_dict = {
- 'Id' : group[0],
- 'SpeciesId' : group[1],
- 'DisplayName' : group[2],
- 'Name' : group[3],
- 'FullName' : group[4],
- 'public' : group[5],
- 'MappingMethodId' : group[6],
- 'GeneticType' : group[7]
+ "Id" : group[0],
+ "SpeciesId" : group[1],
+ "DisplayName" : group[2],
+ "Name" : group[3],
+ "FullName" : group[4],
+ "public" : group[5],
+ "MappingMethodId" : group[6],
+ "GeneticType" : group[7]
}
groups_list.append(group_dict)
@@ -106,32 +106,32 @@ def get_group_info(group_name, species_name = None, file_format = "json"):
InbredSet.MappingMethodId, InbredSet.GeneticType
FROM InbredSet, Species
WHERE InbredSet.SpeciesId = Species.Id AND
- (InbredSet.InbredSetName = '{0}' OR
- InbredSet.Name = '{0}' OR
- InbredSet.FullName = '{0}') AND
- (Species.Name = '{1}' OR
- Species.FullName='{1}' OR
- Species.SpeciesName='{1}');""".format(group_name, species_name))
+ (InbredSet.InbredSetName = "{0}" OR
+ InbredSet.Name = "{0}" OR
+ InbredSet.FullName = "{0}") AND
+ (Species.Name = "{1}" OR
+ Species.FullName="{1}" OR
+ Species.SpeciesName="{1}");""".format(group_name, species_name))
else:
results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName,
InbredSet.Name, InbredSet.FullName, InbredSet.public,
InbredSet.MappingMethodId, InbredSet.GeneticType
FROM InbredSet
- WHERE (InbredSet.InbredSetName = '{0}' OR
- InbredSet.Name = '{0}' OR
- InbredSet.FullName = '{0}');""".format(group_name))
+ WHERE (InbredSet.InbredSetName = "{0}" OR
+ InbredSet.Name = "{0}" OR
+ InbredSet.FullName = "{0}");""".format(group_name))
group = results.fetchone()
if group:
group_dict = {
- 'Id' : group[0],
- 'SpeciesId' : group[1],
- 'DisplayName' : group[2],
- 'Name' : group[3],
- 'FullName' : group[4],
- 'public' : group[5],
- 'MappingMethodId' : group[6],
- 'GeneticType' : group[7]
+ "Id" : group[0],
+ "SpeciesId" : group[1],
+ "DisplayName" : group[2],
+ "Name" : group[3],
+ "FullName" : group[4],
+ "public" : group[5],
+ "MappingMethodId" : group[6],
+ "GeneticType" : group[7]
}
return flask.jsonify(group_dict)
@@ -150,9 +150,9 @@ def get_datasets_for_group(group_name, species_name=None):
FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Species
WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
ProbeFreeze.InbredSetId = InbredSet.Id AND
- (InbredSet.Name = '{0}' OR InbredSet.InbredSetName = '{0}' OR InbredSet.FullName = '{0}') AND
+ (InbredSet.Name = "{0}" OR InbredSet.InbredSetName = "{0}" OR InbredSet.FullName = "{0}") AND
InbredSet.SpeciesId = Species.Id AND
- (Species.SpeciesName = '{1}' OR Species.MenuName = '{1}' OR Species.FullName = '{1}');
+ (Species.SpeciesName = "{1}" OR Species.MenuName = "{1}" OR Species.FullName = "{1}");
""".format(group_name, species_name))
else:
results = g.db.execute("""
@@ -163,7 +163,7 @@ def get_datasets_for_group(group_name, species_name=None):
FROM ProbeSetFreeze, ProbeFreeze, InbredSet
WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
ProbeFreeze.InbredSetId = InbredSet.Id AND
- (InbredSet.Name = '{0}' OR InbredSet.InbredSetName = '{0}' OR InbredSet.FullName = '{0}');
+ (InbredSet.Name = "{0}" OR InbredSet.InbredSetName = "{0}" OR InbredSet.FullName = "{0}");
""".format(group_name))
the_datasets = results.fetchall()
@@ -172,17 +172,17 @@ def get_datasets_for_group(group_name, species_name=None):
datasets_list = []
for dataset in the_datasets:
dataset_dict = {
- 'Id' : dataset[0],
- 'ProbeFreezeId' : dataset[1],
- 'AvgID' : dataset[2],
- 'Short_Abbreviation' : dataset[3],
- 'Long_Abbreviation' : dataset[4],
- 'FullName' : dataset[5],
- 'ShortName' : dataset[6],
- 'CreateTime' : dataset[7],
- 'public' : dataset[8],
- 'confidentiality' : dataset[9],
- 'DataScale' : dataset[10]
+ "Id" : dataset[0],
+ "ProbeFreezeId" : dataset[1],
+ "AvgID" : dataset[2],
+ "Short_Abbreviation" : dataset[3],
+ "Long_Abbreviation" : dataset[4],
+ "FullName" : dataset[5],
+ "ShortName" : dataset[6],
+ "CreateTime" : dataset[7],
+ "public" : dataset[8],
+ "confidentiality" : dataset[9],
+ "DataScale" : dataset[10]
}
datasets_list.append(dataset_dict)
@@ -197,7 +197,7 @@ def get_datasets_for_group(group_name, species_name=None):
def get_dataset_info(dataset_name, group_name = None, file_format="json"):
#ZS: First get ProbeSet (mRNA expression) datasets and then get Phenotype datasets
- datasets_list = [] #ZS: I figure I might as well return a list if there are multiple matches, though I don't know if this will actually happen in practice
+ datasets_list = [] #ZS: I figure I might as well return a list if there are multiple matches, though I don"t know if this will actually happen in practice
probeset_query = """
SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName,
@@ -212,12 +212,12 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"):
"""
if dataset_name.isdigit():
where_statement += """
- ProbeSetFreeze.Id = '{}'
+ ProbeSetFreeze.Id = "{}"
""".format(dataset_name)
else:
where_statement += """
- (ProbeSetFreeze.Name = '{0}' OR ProbeSetFreeze.Name2 = '{0}' OR
- ProbeSetFreeze.FullName = '{0}' OR ProbeSetFreeze.ShortName = '{0}')
+ (ProbeSetFreeze.Name = "{0}" OR ProbeSetFreeze.Name2 = "{0}" OR
+ ProbeSetFreeze.FullName = "{0}" OR ProbeSetFreeze.ShortName = "{0}")
""".format(dataset_name)
probeset_query += where_statement
@@ -226,16 +226,16 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"):
if dataset:
dataset_dict = {
- 'dataset_type' : "mRNA expression",
- 'id' : dataset[0],
- 'name' : dataset[1],
- 'full_name' : dataset[2],
- 'short_name' : dataset[3],
- 'data_scale' : dataset[4],
- 'tissue_id' : dataset[5],
- 'tissue' : dataset[6],
- 'public' : dataset[7],
- 'confidential' : dataset[8]
+ "dataset_type" : "mRNA expression",
+ "id" : dataset[0],
+ "name" : dataset[1],
+ "full_name" : dataset[2],
+ "short_name" : dataset[3],
+ "data_scale" : dataset[4],
+ "tissue_id" : dataset[5],
+ "tissue" : dataset[6],
+ "public" : dataset[7],
+ "confidential" : dataset[8]
}
datasets_list.append(dataset_dict)
@@ -249,7 +249,7 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"):
WHERE PublishXRef.InbredSetId = InbredSet.Id AND
PublishXRef.PhenotypeId = Phenotype.Id AND
PublishXRef.PublicationId = Publication.Id AND
- InbredSet.Name = '{0}' AND PublishXRef.Id = '{1}'
+ InbredSet.Name = "{0}" AND PublishXRef.Id = "{1}"
""".format(group_name, dataset_name)
logger.debug("QUERY:", pheno_query)
@@ -260,25 +260,25 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"):
if dataset:
if dataset[5]:
dataset_dict = {
- 'dataset_type' : "phenotype",
- 'id' : dataset[0],
- 'name' : dataset[1],
- 'description' : dataset[2],
- 'pubmed_id' : dataset[5],
- 'title' : dataset[6],
- 'year' : dataset[7]
+ "dataset_type" : "phenotype",
+ "id" : dataset[0],
+ "name" : dataset[1],
+ "description" : dataset[2],
+ "pubmed_id" : dataset[5],
+ "title" : dataset[6],
+ "year" : dataset[7]
}
elif dataset[4]:
dataset_dict = {
- 'dataset_type' : "phenotype",
- 'id' : dataset[0],
- 'name' : dataset[3],
- 'description' : dataset[4]
+ "dataset_type" : "phenotype",
+ "id" : dataset[0],
+ "name" : dataset[3],
+ "description" : dataset[4]
}
else:
dataset_dict = {
- 'dataset_type' : "phenotype",
- 'id' : dataset[0]
+ "dataset_type" : "phenotype",
+ "id" : dataset[0]
}
datasets_list.append(dataset_dict)
@@ -290,11 +290,11 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=('GET',))
-@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=('GET',))
+@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=("GET",))
+@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=("GET",))
def fetch_traits(dataset_name, file_format = "json"):
trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name)
- if ('ids_only' in request.args) and (len(trait_ids) > 0):
+ if ("ids_only" in request.args) and (len(trait_ids) > 0):
if file_format == "json":
filename = dataset_name + "_trait_ids.json"
return flask.jsonify(trait_ids)
@@ -308,7 +308,7 @@ def fetch_traits(dataset_name, file_format = "json"):
output.headers["Content-Disposition"] = "attachment; filename=" + filename
output.headers["Content-type"] = "text/csv"
return output
- elif ('names_only' in request.args) and (len(trait_ids) > 0):
+ elif ("names_only" in request.args) and (len(trait_ids) > 0):
if file_format == "json":
filename = dataset_name + "_trait_names.json"
return flask.jsonify(trait_names)
@@ -332,7 +332,7 @@ def fetch_traits(dataset_name, file_format = "json"):
FROM
ProbeSet, ProbeSetXRef
WHERE
- ProbeSetXRef.ProbeSetFreezeId = '{0}' AND
+ ProbeSetXRef.ProbeSetFreezeId = "{0}" AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id
ORDER BY
ProbeSet.Id
@@ -346,7 +346,7 @@ def fetch_traits(dataset_name, file_format = "json"):
FROM
Geno, GenoXRef
WHERE
- GenoXRef.GenoFreezeId = '{0}' AND
+ GenoXRef.GenoFreezeId = "{0}" AND
GenoXRef.GenoId = Geno.Id
ORDER BY
Geno.Id
@@ -422,8 +422,8 @@ def all_sample_data(dataset_name, file_format = "csv"):
LEFT JOIN ProbeSetSE ON
(ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
WHERE
- ProbeSetXRef.ProbeSetFreezeId = '{0}' AND
- ProbeSetXRef.ProbeSetId = '{1}' AND
+ ProbeSetXRef.ProbeSetFreezeId = "{0}" AND
+ ProbeSetXRef.ProbeSetId = "{1}" AND
ProbeSetXRef.DataId = ProbeSetData.Id AND
ProbeSetData.StrainId = Strain.Id
ORDER BY
@@ -438,8 +438,8 @@ def all_sample_data(dataset_name, file_format = "csv"):
LEFT JOIN GenoSE ON
(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
WHERE
- GenoXRef.GenoFreezeId = '{0}' AND
- GenoXRef.GenoId = '{1}' AND
+ GenoXRef.GenoFreezeId = "{0}" AND
+ GenoXRef.GenoId = "{1}" AND
GenoXRef.DataId = GenoData.Id AND
GenoData.StrainId = Strain.Id
ORDER BY
@@ -457,8 +457,8 @@ def all_sample_data(dataset_name, file_format = "csv"):
(NStrain.DataId = PublishData.Id AND
NStrain.StrainId = PublishData.StrainId)
WHERE
- PublishXRef.InbredSetId = '{0}' AND
- PublishXRef.PhenotypeId = '{1}' AND
+ PublishXRef.InbredSetId = "{0}" AND
+ PublishXRef.PhenotypeId = "{1}" AND
PublishData.Id = PublishXRef.DataId AND
PublishData.StrainId = Strain.Id
ORDER BY
@@ -511,9 +511,9 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
LEFT JOIN ProbeSetSE ON
(ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
WHERE
- ProbeSet.Name = '{0}' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSet.Name = "{0}" AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- ProbeSetFreeze.Name = '{1}' AND
+ ProbeSetFreeze.Name = "{1}" AND
ProbeSetXRef.DataId = ProbeSetData.Id AND
ProbeSetData.StrainId = Strain.Id
ORDER BY
@@ -527,13 +527,13 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
sample_list = []
for sample in sample_data:
sample_dict = {
- 'sample_name' : sample[0],
- 'sample_name_2' : sample[1],
- 'value' : sample[2],
- 'data_id' : sample[3],
+ "sample_name" : sample[0],
+ "sample_name_2" : sample[1],
+ "value" : sample[2],
+ "data_id" : sample[3],
}
if sample[4]:
- sample_dict['se'] = sample[4]
+ sample_dict["se"] = sample[4]
sample_list.append(sample_dict)
return flask.jsonify(sample_list)
@@ -559,9 +559,9 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
NStrain.StrainId = PublishData.StrainId)
WHERE
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
- PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = '{1}' AND
- (PublishFreeze.Id = '{0}' OR PublishFreeze.Name = '{0}' OR
- PublishFreeze.ShortName = '{0}' OR PublishXRef.InbredSetId = '{0}') AND
+ PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = "{1}" AND
+ (PublishFreeze.Id = "{0}" OR PublishFreeze.Name = "{0}" OR
+ PublishFreeze.ShortName = "{0}" OR PublishXRef.InbredSetId = "{0}") AND
PublishData.StrainId = Strain.Id
ORDER BY
Strain.Name
@@ -574,15 +574,15 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
sample_list = []
for sample in sample_data:
sample_dict = {
- 'sample_name' : sample[0],
- 'sample_name_2' : sample[1],
- 'value' : sample[2],
- 'data_id' : sample[3]
+ "sample_name" : sample[0],
+ "sample_name_2" : sample[1],
+ "value" : sample[2],
+ "data_id" : sample[3]
}
if sample[4]:
- sample_dict['se'] = sample[4]
+ sample_dict["se"] = sample[4]
if sample[5]:
- sample_dict['n_cases'] = sample[5]
+ sample_dict["n_cases"] = sample[5]
sample_list.append(sample_dict)
return flask.jsonify(sample_list)
@@ -596,15 +596,15 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
def get_trait_info(dataset_name, trait_name, file_format = "json"):
probeset_query = """
SELECT
- ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias,
+ ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias,
ProbeSetXRef.mean, ProbeSetXRef.se, ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive
FROM
ProbeSet, ProbeSetXRef, ProbeSetFreeze
WHERE
- ProbeSet.Name = '{0}' AND
+ ProbeSet.Name = "{0}" AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- ProbeSetFreeze.Name = '{1}'
+ ProbeSetFreeze.Name = "{1}"
""".format(trait_name, dataset_name)
probeset_results = g.db.execute(probeset_query)
@@ -612,19 +612,19 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"):
trait_info = probeset_results.fetchone()
if trait_info:
trait_dict = {
- 'id' : trait_info[0],
- 'name' : trait_info[1],
- 'symbol' : trait_info[2],
- 'description' : trait_info[3],
- 'chr' : trait_info[4],
- 'mb' : trait_info[5],
- 'alias' :trait_info[6],
- 'mean' : trait_info[7],
- 'se' : trait_info[8],
- 'locus' : trait_info[9],
- 'lrs' : trait_info[10],
- 'p_value' : trait_info[11],
- 'additive' : trait_info[12]
+ "id" : trait_info[0],
+ "name" : trait_info[1],
+ "symbol" : trait_info[2],
+ "description" : trait_info[3],
+ "chr" : trait_info[4],
+ "mb" : trait_info[5],
+ "alias" :trait_info[6],
+ "mean" : trait_info[7],
+ "se" : trait_info[8],
+ "locus" : trait_info[9],
+ "lrs" : trait_info[10],
+ "p_value" : trait_info[11],
+ "additive" : trait_info[12]
}
return flask.jsonify(trait_dict)
@@ -639,8 +639,8 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"):
FROM
PublishXRef
WHERE
- PublishXRef.Id = '{0}' AND
- PublishXRef.InbredSetId = '{1}'
+ PublishXRef.Id = "{0}" AND
+ PublishXRef.InbredSetId = "{1}"
""".format(trait_name, group_id)
pheno_results = g.db.execute(pheno_query)
@@ -648,17 +648,17 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"):
trait_info = pheno_results.fetchone()
if trait_info:
trait_dict = {
- 'id' : trait_info[0],
- 'locus' : trait_info[1],
- 'lrs' : trait_info[2],
- 'additive' : trait_info[3]
+ "id" : trait_info[0],
+ "locus" : trait_info[1],
+ "lrs" : trait_info[2],
+ "additive" : trait_info[3]
}
return flask.jsonify(trait_dict)
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@app.route("/api/v_{}/correlation".format(version), methods=('GET',))
+@app.route("/api/v_{}/correlation".format(version), methods=("GET",))
def get_corr_results():
results = correlation.do_correlation(request.args)
@@ -667,12 +667,12 @@ def get_corr_results():
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@app.route("/api/v_{}/mapping".format(version), methods=('GET',))
+@app.route("/api/v_{}/mapping".format(version), methods=("GET",))
def get_mapping_results():
results = mapping.do_mapping_for_api(request.args)
if len(results) > 0:
- filename = "mapping_" + datetime.datetime.utcnow().strftime('%b_%d_%Y_%I:%M%p') + ".csv"
+ filename = "mapping_" + datetime.datetime.utcnow().strftime("%b_%d_%Y_%I:%M%p") + ".csv"
si = StringIO.StringIO()
csv_writer = csv.writer(si)
@@ -692,28 +692,28 @@ def get_genotypes(group_name, file_format="csv"):
if file_format == "csv" or file_format == "geno":
filename = group_name + ".geno"
- if os.path.isfile('{0}/{1}.geno'.format(flat_files('genotype'), group_name)):
+ if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)):
output_lines = []
- with open('{0}/{1}.geno'.format(flat_files('genotype'), group_name)) as genofile:
+ with open("{0}/{1}.geno".format(flat_files("genotype"), group_name)) as genofile:
for line in genofile:
if line[0] == "#" or line[0] == "@":
output_lines.append([line.strip()])
else:
output_lines.append(line.split())
- csv_writer = csv.writer(si, delimiter = '\t', escapechar = "\\", quoting = csv.QUOTE_NONE)
+ csv_writer = csv.writer(si, delimiter = "\t", escapechar = "\\", quoting = csv.QUOTE_NONE)
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
else:
filename = group_name + ".bimbam"
- if os.path.isfile('{0}/{1}.geno'.format(flat_files('genotype'), group_name)):
+ if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)):
output_lines = []
- with open('{0}/{1}_geno.txt'.format(flat_files('genotype/bimbam'), group_name)) as genofile:
+ with open("{0}/{1}_geno.txt".format(flat_files("genotype/bimbam"), group_name)) as genofile:
for line in genofile:
output_lines.append([line.strip() for line in line.split(",")])
- csv_writer = csv.writer(si, delimiter = ',')
+ csv_writer = csv.writer(si, delimiter = ",")
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
@@ -747,7 +747,7 @@ def get_dataset_trait_ids(dataset_name):
WHERE
Geno.Id = GenoXRef.GenoId AND
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
- GenoFreeze.Name = '{0}'
+ GenoFreeze.Name = "{0}"
""".format(dataset_name)
results = g.db.execute(query).fetchall()
@@ -768,7 +768,7 @@ def get_dataset_trait_ids(dataset_name):
FROM
PublishXRef
WHERE
- PublishXRef.InbredSetId = '{0}'
+ PublishXRef.InbredSetId = "{0}"
""".format(dataset_id)
results = g.db.execute(query).fetchall()
@@ -787,7 +787,7 @@ def get_dataset_trait_ids(dataset_name):
WHERE
ProbeSet.Id = ProbeSetXRef.ProbeSetId AND
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- ProbeSetFreeze.Name = '{0}'
+ ProbeSetFreeze.Name = "{0}"
""".format(dataset_name)
results = g.db.execute(query).fetchall()
@@ -857,7 +857,7 @@ def get_group_id(group_name):
query = """
SELECT InbredSet.Id
FROM InbredSet
- WHERE InbredSet.Name = '{}'
+ WHERE InbredSet.Name = "{}"
""".format(group_name)
group_id = g.db.execute(query).fetchone()
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 15:05:12 +0000