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Diffstat (limited to 'wqflask/maintenance/gen_select_dataset.py')
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 186 |
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 index 00000000..4c544192 --- /dev/null +++ b/wqflask/maintenance/gen_select_dataset.py @@ -0,0 +1,186 @@ +"""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() |