diff options
| -rw-r--r-- | wqflask/wqflask/api/gen_menu.py | 231 | ||||
| -rw-r--r-- | wqflask/wqflask/api/router.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js | 3 |
3 files changed, 243 insertions, 2 deletions
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py new file mode 100644 index 00000000..a2faa463 --- /dev/null +++ b/wqflask/wqflask/api/gen_menu.py @@ -0,0 +1,231 @@ +from __future__ import print_function, division + +import sys + +from flask import g + +from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI + +import MySQLdb + +import urlparse + +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +def gen_dropdown_json(): + """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) + + return data + +def get_species(): + """Build species list""" + results = g.db.execute("""SELECT Name, MenuName + FROM Species + WHERE Species.Name != 'macaque monkey' + ORDER BY OrderId""").fetchall() + + species = [] + for result in results: + species.append([str(result[0]), str(result[1])]) + + return species + +def get_groups(species): + """Build groups list""" + groups = {} + for species_name, _species_full_name in species: + groups[species_name] = [] + results = g.db.execute("""SELECT InbredSet.Name, InbredSet.FullName + FROM InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze + WHERE Species.Name = '{}' 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.FullName""".format(species_name)).fetchall() + + for result in results: + groups[species_name].append([str(result[0]), str(result[1])]) + + 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: + if phenotypes_exist(group_name): + types[species][group_name] = [("Phenotypes", "Phenotypes")] + if genotypes_exist(group_name): + if group_name in types[species]: + types[species][group_name] += [("Genotypes", "Genotypes")] + else: + types[species][group_name] = [("Genotypes", "Genotypes")] + if group_name in types[species]: + 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] = list(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] = list(group for group in groups[species] if group[0] != group_name) + return types + +def phenotypes_exist(group_name): + results = g.db.execute("""SELECT Name + FROM PublishFreeze + WHERE PublishFreeze.Name = '{}'""".format(group_name+"Publish")).fetchone() + + if results != None: + return True + else: + return False + +def genotypes_exist(group_name): + results = g.db.execute("""SELECT Name + FROM GenoFreeze + WHERE GenoFreeze.Name = '{}'""".format(group_name+"Geno")).fetchone() + + if results != None: + return True + else: + return False + +def build_types(species, group): + """Fetches tissues + + Gets the tissues with data for this species/group + (all types except phenotype/genotype are tissues) + + """ + + query = """SELECT DISTINCT Tissue.Name + FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species + WHERE Species.Name = '{0}' AND + Species.Id = InbredSet.SpeciesId AND + InbredSet.Name = '{1}' AND + ProbeFreeze.TissueId = Tissue.Id AND + ProbeFreeze.InbredSetId = InbredSet.Id AND + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND + ProbeSetFreeze.public > 0 AND + ProbeSetFreeze.confidentiality < 1 + ORDER BY Tissue.Name""".format(species, group) + + results = [] + for result in g.db.execute(query).fetchall(): + if len(result): + these_datasets = build_datasets(species, group, result[0]) + if len(these_datasets) > 0: + results.append([str(result[0]), str(result[0])]) + + return results + +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 in type_list: + these_datasets = build_datasets(species, group, type_name[0]) + if len(these_datasets) > 0: + datasets[species][group][type_name[0]] = these_datasets + + return datasets + + +def build_datasets(species, group, type_name): + """Gets dataset names from database""" + dataset_text = dataset_value = None + datasets = [] + if type_name == "Phenotypes": + results = g.db.execute("""SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, PublishFreeze.FullName + FROM InfoFiles, PublishFreeze, InbredSet + WHERE InbredSet.Name = '{}' AND + PublishFreeze.InbredSetId = InbredSet.Id AND + InfoFiles.InfoPageName = PublishFreeze.Name + ORDER BY PublishFreeze.CreateTime ASC""".format(group)).fetchall() + + if len(results) > 0: + for result in results: + 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 + dataset_text = "%s Phenotypes" % group + datasets.append([dataset_id, dataset_value, dataset_text]) + + elif type_name == "Genotypes": + results = g.db.execute("""SELECT InfoFiles.GN_AccesionId + FROM InfoFiles, GenoFreeze, InbredSet + WHERE InbredSet.Name = '{}' AND + GenoFreeze.InbredSetId = InbredSet.Id AND + InfoFiles.InfoPageName = GenoFreeze.ShortName AND + GenoFreeze.public > 0 AND + GenoFreeze.confidentiality < 1 + ORDER BY GenoFreeze.CreateTime DESC""".format(group)).fetchone() + + if results != None: + dataset_id = str(results[0]) + else: + dataset_id = "None" + dataset_value = "%sGeno" % group + dataset_text = "%s Genotypes" % group + datasets.append([dataset_id, dataset_value, dataset_text]) + + else: # for mRNA expression/ProbeSet + results = g.db.execute("""SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName + FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species + WHERE Species.Name = '{0}' AND + Species.Id = InbredSet.SpeciesId AND + InbredSet.Name = '{1}' AND + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '{2}' AND + ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id AND + ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0 + ORDER BY ProbeSetFreeze.CreateTime DESC""".format(species, group, type_name)).fetchall() + + datasets = [] + for dataset_info in results: + this_dataset_info = [] + for info in dataset_info: + this_dataset_info.append(str(info)) + datasets.append(this_dataset_info) + + return datasets \ No newline at end of file diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 1a948b1a..8ec93e48 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -11,7 +11,7 @@ from flask import g, Response, request, make_response, render_template, send_fro import sqlalchemy from wqflask import app -from wqflask.api import correlation, mapping +from wqflask.api import correlation, mapping, gen_menu from utility.tools import flat_files @@ -746,6 +746,15 @@ def get_genotypes(group_name, file_format="csv"): return output +@app.route("/api/v_{}/gen_dropdown".format(version), methods=("GET",)) +def gen_dropdown_menu(): + results = gen_menu.gen_dropdown_json() + + if len(results) > 0: + return flask.jsonify(results) + else: + return return_error(code=500, source=request.url_rule.rule, title="Some error occurred", details="") + def return_error(code, source, title, details): json_ob = {"errors": [ { diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js index 9bca1517..b80539bd 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -6,10 +6,11 @@ process_json = function(data) { return apply_default(); } }; -$.ajax('/static/new/javascript/dataset_menu_structure.json', { +$.ajax('/api/v_pre1/gen_dropdown', { dataType: 'json', success: process_json }); + populate_species = function() { var species_list; species_list = this.jdata.species; |