Merge branch 'flask' of http://github.com/zsloan/genenetwork

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()