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authorzsloan2016-02-18 17:14:26 +0000
committerzsloan2016-02-18 17:14:26 +0000
commit6d8503e53b48ba2e398ff7950d2a722ffc2b6026 (patch)
tree0805a4a77b464a2575519cdda466522b0f9ab14b /wqflask/maintenance/gen_select_dataset.py
parent7f5536635ac20f7c670e4dc8e650f27d47503d78 (diff)
downloadgenenetwork2-6d8503e53b48ba2e398ff7950d2a722ffc2b6026.tar.gz
Edited gen_select_dataset to remove confidential datasets
Also hard-coded the removal of Macaque Monkey since I couldn't think of a good way to retroactively check if every dataset in a species is confidential
Diffstat (limited to 'wqflask/maintenance/gen_select_dataset.py')
-rwxr-xr-xwqflask/maintenance/gen_select_dataset.py27
1 files changed, 17 insertions, 10 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index ea0d4a56..e080050e 100755
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -76,7 +76,7 @@ def parse_db_uri(db_uri):
def get_species():
"""Build species list"""
- Cursor.execute("select Name, MenuName from Species order by OrderId")
+ Cursor.execute("select Name, MenuName from Species where Species.Name != 'macaque monkey' order by OrderId")
species = list(Cursor.fetchall())
return species
@@ -90,8 +90,8 @@ def get_groups(species):
ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = %s
and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and
(PublishFreeze.InbredSetId = InbredSet.Id
- or GenoFreeze.InbredSetId = InbredSet.Id
- or ProbeFreeze.InbredSetId = InbredSet.Id)
+ or GenoFreeze.InbredSetId = InbredSet.Id
+ or ProbeFreeze.InbredSetId = InbredSet.Id)
group by InbredSet.Name
order by InbredSet.Name""", (species_name))
groups[species_name] = list(Cursor.fetchall())
@@ -169,7 +169,9 @@ def build_types(species, group):
results = []
for result in Cursor.fetchall():
if len(result):
- results.append((result[0], result[0]))
+ these_datasets = build_datasets(species, group, result[0])
+ if len(these_datasets) > 0:
+ results.append((result[0], result[0]))
return results
@@ -182,7 +184,10 @@ def get_datasets(types):
#print("type_list: ", type_list)
datasets[species][group] = {}
for type_name in type_list:
- datasets[species][group][type_name[0]] = build_datasets(species, group, type_name[0])
+ these_datasets = build_datasets(species, group, type_name[0])
+ if len(these_datasets) > 0:
+ datasets[species][group][type_name[0]] = these_datasets
+
return datasets
@@ -195,7 +200,8 @@ def build_datasets(species, group, type_name):
InbredSet.Name = %s and
PublishFreeze.InbredSetId = InbredSet.Id and
InfoFiles.InfoPageName = PublishFreeze.Name and
- PublishFreeze.public > 0 order by
+ PublishFreeze.public > 0 and
+ PublishFreeze.confidentiality < 1 order by
PublishFreeze.CreateTime desc""", (group))
results = Cursor.fetchone()
@@ -214,7 +220,8 @@ def build_datasets(species, group, type_name):
InbredSet.Name = %s and
GenoFreeze.InbredSetId = InbredSet.Id and
InfoFiles.InfoPageName = GenoFreeze.ShortName and
- GenoFreeze.public > 0 order by
+ GenoFreeze.public > 0 and
+ GenoFreeze.confidentiality < 1 order by
GenoFreeze.CreateTime desc""", (group))
results = Cursor.fetchone()
@@ -232,9 +239,9 @@ def build_datasets(species, group, type_name):
ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
Species.Name = %s and Species.Id = InbredSet.SpeciesId and
InbredSet.Name = %s and
- ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s
- and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId =
- InbredSet.Id and ProbeSetFreeze.public > 0 order by
+ 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.CreateTime desc""", (species, group, type_name))
dataset_results = Cursor.fetchall()