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authorZachary Sloan2013-01-11 23:59:41 +0000
committerZachary Sloan2013-01-11 23:59:41 +0000
commit2b2970d167c5b555e0e0ad0b34b72f817c1fac91 (patch)
tree36fa8c708138fff03593e0f50cc933bcb62b5592 /wqflask/maintenance
parent1db9237a05fd27c80dc963db9916072594156198 (diff)
parentd39b691994a395c45fa242de6d64d12a5470af10 (diff)
downloadgenenetwork2-2b2970d167c5b555e0e0ad0b34b72f817c1fac91.tar.gz
Merge branch 'flask' of http://github.com/zsloan/genenetwork
Diffstat (limited to 'wqflask/maintenance')
-rw-r--r--wqflask/maintenance/gen_select_dataset.py186
1 files changed, 186 insertions, 0 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
new file mode 100644
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+++ b/wqflask/maintenance/gen_select_dataset.py
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+"""Script that generates the data for the main dropdown menus on the home page
+
+Writes out data as /static/new/javascript/dataset_menu_structure.json
+It needs to be run manually when database has been changed.
+
+"""
+
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams
+# at rwilliams@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+
+from __future__ import print_function, division
+
+import sys
+
+sys.path.insert(0, "..")
+
+import MySQLdb
+
+import simplejson as json
+
+from pprint import pformat as pf
+
+from base import webqtlConfig
+
+
+# build MySql database connection
+Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,
+ host=webqtlConfig.MYSQL_SERVER,
+ user=webqtlConfig.DB_USER,
+ passwd=webqtlConfig.DB_PASSWD)
+Cursor = Con.cursor()
+
+
+def get_species():
+ """Build species list"""
+ Cursor.execute("select Name, MenuName from Species order by OrderId")
+ species = list(Cursor.fetchall())
+ return species
+
+
+def get_groups(species):
+ """Build groups list"""
+ groups = {}
+ for species_name, _species_full_name in species:
+ Cursor.execute("""select InbredSet.Name, InbredSet.FullName from InbredSet,
+ 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)
+ group by InbredSet.Name
+ order by InbredSet.Name""", (species_name))
+ groups[species_name] = list(Cursor.fetchall())
+ return groups
+
+
+def get_types(groups):
+ """Build types list"""
+ types = {}
+ for species, group_dict in groups.iteritems():
+ types[species] = {}
+ for group_name, _group_full_name in group_dict:
+ # make group an alias to shorten the code
+ types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")]
+ types[species][group_name] += build_types(species, group_name)
+ return types
+
+
+def build_types(species, group):
+ """Fetches tissues
+
+ Gets the tissues with data for this species/group
+ (all types except phenotype/genotype are tissues)
+
+ """
+ Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
+ from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
+ where Species.Name = %s and Species.Id = InbredSet.SpeciesId and
+ InbredSet.Name = %s and
+ ProbeFreeze.TissueId = Tissue.Id and
+ ProbeFreeze.InbredSetId = InbredSet.Id and
+ ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
+ ProbeSetFreeze.public > %s
+ order by Tissue.Name""", (species, group, webqtlConfig.PUBLICTHRESH))
+ return Cursor.fetchall()
+
+
+def get_datasets(types):
+ """Build datasets list"""
+ datasets = {}
+ for species, group_dict in types.iteritems():
+ datasets[species] = {}
+ for group, type_list in group_dict.iteritems():
+ datasets[species][group] = {}
+ for type_name, _type_full_name in type_list:
+ datasets[species][group][type_name] = build_datasets(species, group, type_name)
+ return datasets
+
+
+def build_datasets(species, group, type_name):
+ """Gets dataset names from database"""
+ dataset_text = dataset_value = None
+ if type_name == "Phenotypes":
+ dataset_value = "%sPublish" % group
+ if group == 'MDP':
+ dataset_text = "Mouse Phenome Database"
+ else:
+ dataset_text = "%s Published Phenotypes" % group
+
+ elif type_name == "Genotypes":
+ dataset_value = "%sGeno" % group
+ dataset_text = "%s Genotypes" % group
+
+ if dataset_value:
+ return [(dataset_value, dataset_text)]
+ else:
+ Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
+ 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 > %s order by
+ ProbeSetFreeze.CreateTime desc""", (
+ species, group, type_name, webqtlConfig.PUBLICTHRESH))
+ return Cursor.fetchall()
+
+
+def main():
+ """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
+ species = get_species()
+ groups = get_groups(species)
+ 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')]
+
+ data = dict(species=species,
+ groups=groups,
+ types=types,
+ datasets=datasets,
+ )
+
+ output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json"""
+
+ with open(output_file, 'w') as fh:
+ json.dump(data, fh, indent=" ", sort_keys=True)
+
+ print("\nWrote file to:", output_file)
+
+
+def _test_it():
+ """Used for internal testing only"""
+ types = build_types("Mouse", "BXD")
+ print("build_types:", pf(types))
+ datasets = build_datasets("Mouse", "BXD", "Hippocampus")
+ print("build_datasets:", pf(datasets))
+
+if __name__ == '__main__':
+ main()