diff options
Diffstat (limited to 'wqflask/maintenance/gen_select_dataset.py')
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 97 |
1 files changed, 57 insertions, 40 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 33813051..9224b884 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -76,17 +76,22 @@ def get_types(groups): types[species] = {} for group_name, _group_full_name in group_dict: # make group an alias to shorten the code - group = types[species][group_name] = [("Phenotypes", "Phenotypes"), - ("Genotypes", "Genotypes")] - Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from - ProbeFreeze, - ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and + types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")] + types[species][group_name] += build_types(species, group_name) + return types + + +def build_types(species, group): + 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 - InbredSet.Name = %s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %s - order by Tissue.Name""", (group_name, webqtlConfig.PUBLICTHRESH)) - group += Cursor.fetchall() - return types + order by Tissue.Name""", (species, group, webqtlConfig.PUBLICTHRESH)) + return Cursor.fetchall() def get_datasets(types): @@ -97,39 +102,44 @@ def get_datasets(types): for group, type_list in group_dict.iteritems(): datasets[species][group] = {} for type_name, type_full_name in type_list: - 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: - datasets[species][group][type_name] = [(dataset_value, dataset_text)] - else: - Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from - ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where - 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""", (type_name, - webqtlConfig.PUBLICTHRESH)) - datasets[species][group][type_name] = Cursor.fetchall() - + datasets[species][group][type_name] = build_datasets(species, group, type_name) return datasets +def build_datasets(species, group, type_name): + 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(): 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'] = {} @@ -137,18 +147,25 @@ def main(): 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""" - + + output_file = """../wqflask/static/new/javascript/dataset_menu_structure""" + with open(output_file, 'w') as fh: json.dump(data, fh, indent=" ", sort_keys=True) - + + print("\nWrote file to:", output_file) + +def test_it(): + 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()
\ No newline at end of file + main() |