diff options
Diffstat (limited to 'wqflask/maintenance/gen_select_dataset.py')
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 99 |
1 files changed, 55 insertions, 44 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index e5726656..647e58a2 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -57,16 +57,13 @@ import urlparse from pprint import pformat as pf -#Engine = sa.create_engine(zach_settings.SQLALCHEMY_DATABASE_URI) +#Engine = sa.create_engine(zach_settings.SQL_URI) # build MySql database connection #conn = Engine.connect() -print('WARNING: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!') - - -def parse_db_uri(db_uri): +def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" parsed_uri = urlparse.urlparse(SQL_URI) @@ -81,10 +78,10 @@ def parse_db_uri(db_uri): return db_conn_info - 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 @@ -96,13 +93,14 @@ def get_groups(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 + and InbredSet.SpeciesId = Species.Id 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()) + order by InbredSet.FullName""" % species_name) + results = Cursor.fetchall() + groups[species_name] = list(results) return groups @@ -123,10 +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 @@ -190,7 +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]) @@ -203,26 +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) - - results = Cursor.fetchone() - if results != None: - dataset_id = str(results[0]) + InfoFiles.InfoPageName = PublishFreeze.Name order by + PublishFreeze.CreateTime asc""" % group) + + 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 @@ -240,10 +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 @@ -261,26 +272,26 @@ def build_datasets(species, group, type_name): this_dataset_info.append(str(info)) datasets.append(this_dataset_info) - return datasets + return datasets def main(): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" - parse_db_uri(SQL_URI) + parse_db_uri() 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')] + #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, @@ -306,6 +317,6 @@ def _test_it(): #print("build_datasets:", pf(datasets)) if __name__ == '__main__': - Conn = MySQLdb.Connect(**parse_db_uri(SQL_URI)) + Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - main() + main()
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