aboutsummaryrefslogtreecommitdiff
path: root/wqflask/maintenance/gen_select_dataset.py
diff options
context:
space:
mode:
authorPjotr Prins2020-04-26 12:32:46 -0500
committerPjotr Prins2020-04-26 12:32:46 -0500
commit14d49450c47e8ef3b34bca9e759acd371319a854 (patch)
tree3f45b7455ec114ebdd9fdd2f2c4a92c9eb3cf756 /wqflask/maintenance/gen_select_dataset.py
parent33e2e09d00881de9b07274bc52b58587e5135cab (diff)
parent15d8e24da26cf6d42d1bdb8a9a189b9ec061d147 (diff)
downloadgenenetwork2-14d49450c47e8ef3b34bca9e759acd371319a854.tar.gz
Merge master and testingmaster
Diffstat (limited to 'wqflask/maintenance/gen_select_dataset.py')
-rw-r--r--wqflask/maintenance/gen_select_dataset.py78
1 files changed, 46 insertions, 32 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 18b2dac9..647e58a2 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -80,7 +80,8 @@ def parse_db_uri():
def get_species():
"""Build species list"""
- Cursor.execute("select Name, MenuName from Species where Species.Name != 'macaque monkey' order by OrderId")
+ #Cursor.execute("select Name, MenuName from Species where Species.Name != 'macaque monkey' order by OrderId")
+ Cursor.execute("select Name, MenuName from Species order by OrderId")
species = list(Cursor.fetchall())
return species
@@ -120,10 +121,20 @@ def get_types(groups):
else:
types[species][group_name] = [("Genotypes", "Genotypes")]
if group_name in types[species]:
- types[species][group_name] += build_types(species, group_name)
- else:
- types[species][group_name] = build_types(species, group_name)
-
+ types_list = build_types(species, group_name)
+ if len(types_list) > 0:
+ types[species][group_name] += types_list
+ else:
+ if not phenotypes_exist(group_name) and not genotypes_exist(group_name):
+ types[species].pop(group_name, None)
+ groups[species] = tuple(group for group in groups[species] if group[0] != group_name)
+ else: #ZS: This whole else statement might be unnecessary, need to check
+ types_list = build_types(species, group_name)
+ if len(types_list) > 0:
+ types[species][group_name] = types_list
+ else:
+ types[species].pop(group_name, None)
+ groups[species] = tuple(group for group in groups[species] if group[0] != group_name)
return types
@@ -187,7 +198,6 @@ def get_datasets(types):
for species, group_dict in types.iteritems():
datasets[species] = {}
for group, type_list in group_dict.iteritems():
- #print("type_list: ", type_list)
datasets[species][group] = {}
for type_name in type_list:
these_datasets = build_datasets(species, group, type_name[0])
@@ -200,26 +210,31 @@ def get_datasets(types):
def build_datasets(species, group, type_name):
"""Gets dataset names from database"""
dataset_text = dataset_value = None
+ datasets = []
if type_name == "Phenotypes":
- print("GROUP:", group)
- Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
+ Cursor.execute("""select InfoFiles.GN_AccesionId, PublishFreeze.Name, PublishFreeze.FullName from InfoFiles, PublishFreeze, InbredSet where
InbredSet.Name = '%s' and
PublishFreeze.InbredSetId = InbredSet.Id and
- InfoFiles.InfoPageName = PublishFreeze.Name and
- PublishFreeze.public > 0 and
- PublishFreeze.confidentiality < 1 order by
- PublishFreeze.CreateTime desc""" % group)
+ InfoFiles.InfoPageName = PublishFreeze.Name order by
+ PublishFreeze.CreateTime asc""" % group)
- results = Cursor.fetchone()
- if results != None:
- dataset_id = str(results[0])
+ results = Cursor.fetchall()
+ if len(results) > 0:
+ for result in results:
+ print(result)
+ dataset_id = str(result[0])
+ dataset_value = str(result[1])
+ if group == 'MDP':
+ dataset_text = "Mouse Phenome Database"
+ else:
+ #dataset_text = "%s Phenotypes" % group
+ dataset_text = str(result[2])
+ datasets.append((dataset_id, dataset_value, dataset_text))
else:
dataset_id = "None"
- dataset_value = "%sPublish" % group
- if group == 'MDP':
- dataset_text = "Mouse Phenome Database"
- else:
- dataset_text = "%s Published Phenotypes" % group
+ dataset_value = "%sPublish" % group
+ dataset_text = "%s Phenotypes" % group
+ datasets.append((dataset_id, dataset_value, dataset_text))
elif type_name == "Genotypes":
Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where
@@ -237,10 +252,9 @@ def build_datasets(species, group, type_name):
dataset_id = "None"
dataset_value = "%sGeno" % group
dataset_text = "%s Genotypes" % group
+ datasets.append((dataset_id, dataset_value, dataset_text))
- if dataset_value:
- return [(dataset_id, dataset_value, dataset_text)]
- else:
+ else: # for mRNA expression/ProbeSet
Cursor.execute("""select ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and
@@ -248,7 +262,7 @@ def build_datasets(species, group, type_name):
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '%s' and
ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and
ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0 order by
- ProbeSetFreeze.OrderList asc""" % (species, group, type_name))
+ ProbeSetFreeze.CreateTime desc""" % (species, group, type_name))
dataset_results = Cursor.fetchall()
datasets = []
@@ -258,7 +272,7 @@ def build_datasets(species, group, type_name):
this_dataset_info.append(str(info))
datasets.append(this_dataset_info)
- return datasets
+ return datasets
def main():
@@ -271,13 +285,13 @@ def main():
types = get_types(groups)
datasets = get_datasets(types)
- species.append(('All Species', 'All Species'))
- groups['All Species'] = [('All Groups', 'All Groups')]
- types['All Species'] = {}
- types['All Species']['All Groups'] = [('Phenotypes', 'Phenotypes')]
- datasets['All Species'] = {}
- datasets['All Species']['All Groups'] = {}
- datasets['All Species']['All Groups']['Phenotypes'] = [('All Phenotypes','All Phenotypes')]
+ #species.append(('All Species', 'All Species'))
+ #groups['All Species'] = [('All Groups', 'All Groups')]
+ #types['All Species'] = {}
+ #types['All Species']['All Groups'] = [('Phenotypes', 'Phenotypes')]
+ #datasets['All Species'] = {}
+ #datasets['All Species']['All Groups'] = {}
+ #datasets['All Species']['All Groups']['Phenotypes'] = [('All Phenotypes','All Phenotypes')]
data = dict(species=species,
groups=groups,