diff options
| -rw-r--r-- | wqflask/tests/unit/wqflask/api/test_gen_menu.py | 408 | ||||
| -rw-r--r-- | wqflask/utility/startup_config.py | 26 | ||||
| -rw-r--r-- | wqflask/wqflask/__init__.py | 21 | ||||
| -rw-r--r-- | wqflask/wqflask/api/gen_menu.py | 251 | ||||
| -rw-r--r-- | wqflask/wqflask/api/router.py | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/gsearch.py | 115 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gsearch_gene.html | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gsearch_pheno.html | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 13 |
9 files changed, 500 insertions, 372 deletions
diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py index fd0fe52e..743b3bde 100644 --- a/wqflask/tests/unit/wqflask/api/test_gen_menu.py +++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py @@ -2,7 +2,6 @@ import unittest from unittest import mock -from wqflask import app from wqflask.api.gen_menu import gen_dropdown_json from wqflask.api.gen_menu import get_species from wqflask.api.gen_menu import get_groups @@ -18,8 +17,6 @@ class TestGenMenu(unittest.TestCase): """Tests for the gen_menu module""" def setUp(self): - self.app_context = app.app_context() - self.app_context.push() self.test_group = { 'mouse': [ ['H_T1', @@ -70,212 +67,239 @@ class TestGenMenu(unittest.TestCase): } } - def tearDown(self): - self.app_context.pop() - - @mock.patch('wqflask.api.gen_menu.g') - def test_get_species(self, db_mock): + def test_get_species(self): """Test that assertion is raised when dataset and dataset_name are defined""" - db_mock.db.execute.return_value.fetchall.return_value = ( - ('human', 'Human'), - ('mouse', 'Mouse')) - self.assertEqual(get_species(), - [['human', 'Human'], ['mouse', 'Mouse']]) - db_mock.db.execute.assert_called_once_with( - "SELECT Name, MenuName FROM Species ORDER BY OrderId" - ) - - @mock.patch('wqflask.api.gen_menu.g') - def test_get_groups(self, db_mock): - """Test that species groups are grouped correctly""" - db_mock.db.execute.return_value.fetchall.side_effect = [ - # Mouse - (('BXD', 'BXD', None), - ('HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)', - 'Test')), - # Human - (('H_T1', "H_T", "DescriptionA"), - ('H_T2', "H_T'", None)) - ] - - self.assertEqual(get_groups([["human", "Human"], ["mouse", "Mouse"]]), - self.test_group) - - for name in ["mouse", "human"]: - db_mock.db.execute.assert_any_call( - ("SELECT InbredSet.Name, InbredSet.FullName, " + - "IFNULL(InbredSet.Family, 'None') " - + "FROM InbredSet, Species WHERE Species.Name " - + "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by " - + "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " - + "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " - + "InbredSet.FullName) ASC, InbredSet.FullName ASC, " - + "InbredSet.MenuOrderId ASC").format(name) + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchall.return_value = ( + ('human', 'Human'), + ('mouse', 'Mouse')) + self.assertEqual(get_species(db_mock), + [['human', 'Human'], ['mouse', 'Mouse']]) + cursor.execute.assert_called_once_with( + "SELECT Name, MenuName FROM Species ORDER BY OrderId" ) - @mock.patch('wqflask.api.gen_menu.g') - def test_phenotypes_exist_called_with_correct_query(self, db_mock): + def test_get_groups(self): + """Test that species groups are grouped correctly""" + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchall.side_effect = [ + # Mouse + (('BXD', 'BXD', None), + ('HLC', ('Liver: Normal Gene Expression ' + 'with Genotypes (Merck)'), + 'Test')), + # Human + (('H_T1', "H_T", "DescriptionA"), + ('H_T2', "H_T'", None)) + ] + self.assertEqual(get_groups([["human", "Human"], + ["mouse", "Mouse"]], + db_mock), + self.test_group) + + for name in ["mouse", "human"]: + cursor.execute.assert_any_call( + ("SELECT InbredSet.Name, InbredSet.FullName, " + "IFNULL(InbredSet.Family, 'None') " + "FROM InbredSet, Species WHERE Species.Name " + "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by " + "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " + "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " + "InbredSet.FullName) ASC, InbredSet.FullName ASC, " + "InbredSet.MenuOrderId ASC").format(name) + ) + + def test_phenotypes_exist_called_with_correct_query(self): """Test that phenotypes_exist is called with the correct query""" - db_mock.db.execute.return_value.fetchone.return_value = None - phenotypes_exist("test") - db_mock.db.execute.assert_called_with( - "SELECT Name FROM PublishFreeze " - "WHERE PublishFreeze.Name = 'testPublish'" - ) - - @mock.patch('wqflask.api.gen_menu.g') - def test_phenotypes_exist_with_falsy_values(self, db_mock): + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = None + phenotypes_exist("test", db_mock) + cursor.execute.assert_called_with( + "SELECT Name FROM PublishFreeze " + "WHERE PublishFreeze.Name = 'testPublish'" + ) + + def test_phenotypes_exist_with_falsy_values(self): """Test that phenotype check returns correctly when given a None value""" - for x in [None, False, (), [], ""]: - db_mock.db.execute.return_value.fetchone.return_value = x - self.assertFalse(phenotypes_exist("test")) - - @mock.patch('wqflask.api.gen_menu.g') - def test_phenotypes_exist_with_truthy_value(self, db_mock): - """Test that phenotype check returns correctly when given Truthy """ - for x in ["x", ("result"), ["result"], [1]]: - db_mock.db.execute.return_value.fetchone.return_value = (x) - self.assertTrue(phenotypes_exist("test")) - - @mock.patch('wqflask.api.gen_menu.g') - def test_genotypes_exist_called_with_correct_query(self, db_mock): + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + for x in [None, False, (), [], ""]: + cursor.fetchone.return_value = x + self.assertFalse(phenotypes_exist("test", db_mock)) + + def test_phenotypes_exist_with_truthy_value(self): + """Test that phenotype check returns correctly when given Truthy""" + db_mock = mock.MagicMock() + with db_mock.cursor() as conn: + with conn.cursor() as cursor: + for x in ["x", ("result"), ["result"], [1]]: + cursor.fetchone.return_value = (x) + self.assertTrue(phenotypes_exist("test", db_mock)) + + def test_genotypes_exist_called_with_correct_query(self): """Test that genotypes_exist is called with the correct query""" - db_mock.db.execute.return_value.fetchone.return_value = None - genotypes_exist("test") - db_mock.db.execute.assert_called_with( - "SELECT Name FROM GenoFreeze WHERE GenoFreeze.Name = 'testGeno'" - ) - - @mock.patch('wqflask.api.gen_menu.g') - def test_genotypes_exist_with_falsy_values(self, db_mock): - """Test that genotype check returns correctly when given - a None value""" - for x in [None, False, (), [], ""]: - db_mock.db.execute.return_value.fetchone.return_value = x - self.assertFalse(genotypes_exist("test")) + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = None + genotypes_exist("test", db_mock) + cursor.execute.assert_called_with( + "SELECT Name FROM GenoFreeze WHERE " + "GenoFreeze.Name = 'testGeno'" + ) + + def test_genotypes_exist_with_falsy_values(self): + """Test that genotype check returns correctly when given a None value + + """ + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + for x in [None, False, (), [], ""]: + cursor.fetchone.return_value = x + self.assertFalse(genotypes_exist("test", db_mock)) - @mock.patch('wqflask.api.gen_menu.g') - def test_genotypes_exist_with_truthy_value(self, db_mock): + def test_genotypes_exist_with_truthy_value(self): """Test that genotype check returns correctly when given Truthy """ - for x in ["x", ("result"), ["result"], [1]]: - db_mock.db.execute.return_value.fetchone.return_value = (x) - self.assertTrue(phenotypes_exist("test")) + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + for x in ["x", ("result"), ["result"], [1]]: + cursor.fetchone.return_value = (x) + self.assertTrue(phenotypes_exist("test", db_mock)) - @mock.patch('wqflask.api.gen_menu.g') - def test_build_datasets_with_type_phenotypes(self, db_mock): + def test_build_datasets_with_type_phenotypes(self): """Test that correct dataset is returned for a phenotype type""" - db_mock.db.execute.return_value.fetchall.return_value = ( - (602, "BXDPublish", "BXD Published Phenotypes"), - ) - self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"), - [['602', "BXDPublish", "BXD Published Phenotypes"]]) - db_mock.db.execute.assert_called_with( - "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " - + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " - + "InbredSet WHERE InbredSet.Name = 'BXD' AND " - + "PublishFreeze.InbredSetId = InbredSet.Id AND " - + "InfoFiles.InfoPageName = PublishFreeze.Name " - + "ORDER BY PublishFreeze.CreateTime ASC" - ) - self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"), - [['602', "BXDPublish", "Mouse Phenome Database"]]) - - db_mock.db.execute.return_value.fetchall.return_value = () - db_mock.db.execute.return_value.fetchone.return_value = ( - "BXDPublish", "Mouse Phenome Database" - ) - self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"), - [["None", "BXDPublish", "Mouse Phenome Database"]]) - - @mock.patch('wqflask.api.gen_menu.g') - def test_build_datasets_with_type_phenotypes_and_no_results(self, db_mock): + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchall.return_value = ( + (602, "BXDPublish", "BXD Published Phenotypes"), + ) + self.assertEqual(build_datasets("Mouse", "BXD", + "Phenotypes", db_mock), + [['602', "BXDPublish", + "BXD Published Phenotypes"]]) + cursor.execute.assert_called_with( + "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " + + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " + + "InbredSet WHERE InbredSet.Name = 'BXD' AND " + + "PublishFreeze.InbredSetId = InbredSet.Id AND " + + "InfoFiles.InfoPageName = PublishFreeze.Name " + + "ORDER BY PublishFreeze.CreateTime ASC" + ) + self.assertEqual(build_datasets("Mouse", "MDP", + "Phenotypes", db_mock), + [['602', "BXDPublish", + "Mouse Phenome Database"]]) + + cursor.fetchall.return_value = () + cursor.fetchone.return_value = ( + "BXDPublish", "Mouse Phenome Database" + ) + self.assertEqual(build_datasets("Mouse", "MDP", + "Phenotypes", db_mock), + [["None", "BXDPublish", + "Mouse Phenome Database"]]) + + def test_build_datasets_with_type_phenotypes_and_no_results(self): """Test that correct dataset is returned for a phenotype type with no results """ - db_mock.db.execute.return_value.fetchall.return_value = None - db_mock.db.execute.return_value.fetchone.return_value = (121, - "text value") - self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"), - [["None", "121", "text value"]]) - db_mock.db.execute.assert_called_with( - "SELECT PublishFreeze.Name, PublishFreeze.FullName " - "FROM PublishFreeze, InbredSet " - "WHERE InbredSet.Name = 'BXD' AND " - "PublishFreeze.InbredSetId = InbredSet.Id " - "ORDER BY PublishFreeze.CreateTime ASC" - ) - - @mock.patch('wqflask.api.gen_menu.g') - def test_build_datasets_with_type_genotypes(self, db_mock): + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchall.return_value = None + cursor.fetchone.return_value = (121, + "text value") + self.assertEqual(build_datasets("Mouse", "BXD", + "Phenotypes", db_mock), + [["None", "121", + "text value"]]) + cursor.execute.assert_called_with( + "SELECT PublishFreeze.Name, PublishFreeze.FullName " + "FROM PublishFreeze, InbredSet " + "WHERE InbredSet.Name = 'BXD' AND " + "PublishFreeze.InbredSetId = InbredSet.Id " + "ORDER BY PublishFreeze.CreateTime ASC" + ) + + def test_build_datasets_with_type_genotypes(self): """Test that correct dataset is returned for a phenotype type""" - db_mock.db.execute.return_value.fetchone.return_value = ( - 635, "HLCPublish", "HLC Published Genotypes" - ) - - self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"), - [["635", "HLCGeno", "HLC Genotypes"]]) - db_mock.db.execute.assert_called_with( - "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, " - "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND " - "GenoFreeze.InbredSetId = InbredSet.Id AND " - "InfoFiles.InfoPageName = GenoFreeze.ShortName " - + "ORDER BY GenoFreeze.CreateTime DESC" - ) - db_mock.db.execute.return_value.fetchone.return_value = () - self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"), - [["None", "HLCGeno", "HLC Genotypes"]]) - - @mock.patch('wqflask.api.gen_menu.g') - def test_build_datasets_with_type_mrna(self, db_mock): + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = ( + 635, "HLCPublish", "HLC Published Genotypes" + ) + self.assertEqual(build_datasets("Mouse", "HLC", + "Genotypes", db_mock), + [["635", "HLCGeno", "HLC Genotypes"]]) + cursor.execute.assert_called_with( + "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, " + "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND " + "GenoFreeze.InbredSetId = InbredSet.Id AND " + "InfoFiles.InfoPageName = GenoFreeze.ShortName " + "ORDER BY GenoFreeze.CreateTime DESC" + ) + cursor.fetchone.return_value = () + self.assertEqual(build_datasets("Mouse", "HLC", + "Genotypes", db_mock), + [["None", "HLCGeno", "HLC Genotypes"]]) + + def test_build_datasets_with_type_mrna(self): """Test that correct dataset is returned for a mRNA expression/ Probeset""" - db_mock.db.execute.return_value.fetchall.return_value = ( - (112, "HC_M2_0606_P", - "Hippocampus Consortium M430v2 (Jun06) PDNN"), ) - self.assertEqual(build_datasets("Mouse", "HLC", "mRNA"), [[ - "112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN" - ]]) - db_mock.db.execute.assert_called_once_with( - "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " - + "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " - + "ProbeFreeze, InbredSet, Tissue, Species WHERE " - + "Species.Name = 'Mouse' AND Species.Id = " - + "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " - + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND " - + "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " - + "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND " - + "ProbeSetFreeze.public > 0 " - + "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC") + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchall.return_value = ( + (112, "HC_M2_0606_P", + "Hippocampus Consortium M430v2 (Jun06) PDNN"), ) + self.assertEqual(build_datasets("Mouse", + "HLC", "mRNA", db_mock), + [["112", 'HC_M2_0606_P', + "Hippocampus Consortium M430v2 (Jun06) PDNN" + ]]) + cursor.execute.assert_called_once_with( + "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " + "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " + "ProbeFreeze, InbredSet, Tissue, Species WHERE " + "Species.Name = 'Mouse' AND Species.Id = " + "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND " + "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " + "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND " + "ProbeSetFreeze.public > 0 " + "ORDER BY -ProbeSetFreeze.OrderList DESC, " + "ProbeSetFreeze.CreateTime DESC") @mock.patch('wqflask.api.gen_menu.build_datasets') - @mock.patch('wqflask.api.gen_menu.g') - def test_build_types(self, db_mock, datasets_mock): + def test_build_types(self, datasets_mock): """Test that correct tissue metadata is returned""" + db_mock = mock.MagicMock() datasets_mock.return_value = [ ["112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN"] ] - db_mock.db.execute.return_value.fetchall.return_value = ( - ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue') - ) - self.assertEqual(build_types('mouse', 'random group'), - [['M', 'M', 'Molecular Traits'], - ['H', 'H', 'Molecular Traits'], - ['R', 'R', 'Molecular Traits']]) - db_mock.db.execute.assert_called_once_with( - "SELECT DISTINCT Tissue.Name " - + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " - + "Tissue, Species WHERE Species.Name = 'mouse' " - + "AND Species.Id = InbredSet.SpeciesId AND " - + "InbredSet.Name = 'random group' AND " - + "ProbeFreeze.TissueId = Tissue.Id AND " - + "ProbeFreeze.InbredSetId = InbredSet.Id AND " - + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " - + "ORDER BY Tissue.Name" - ) + with db_mock.cursor() as cursor: + cursor.fetchall.return_value = ( + ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue') + ) + self.assertEqual(build_types('mouse', 'random group', db_mock), + [['M', 'M', 'Molecular Traits'], + ['H', 'H', 'Molecular Traits'], + ['R', 'R', 'Molecular Traits']]) + cursor.execute.assert_called_once_with( + "SELECT DISTINCT Tissue.Name " + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " + "Tissue, Species WHERE Species.Name = 'mouse' " + "AND Species.Id = InbredSet.SpeciesId AND " + "InbredSet.Name = 'random group' AND " + "ProbeFreeze.TissueId = Tissue.Id AND " + "ProbeFreeze.InbredSetId = InbredSet.Id AND " + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " + "ORDER BY Tissue.Name" + ) @mock.patch('wqflask.api.gen_menu.build_types') @mock.patch('wqflask.api.gen_menu.genotypes_exist') @@ -297,7 +321,9 @@ class TestGenMenu(unittest.TestCase): build_types_mock.return_value = [ ['M', 'M', 'Molecular Trait Datasets'] ] - self.assertEqual(get_types(self.test_group), expected_result) + self.assertEqual(get_types(self.test_group, + mock.MagicMock()), + expected_result) @mock.patch('wqflask.api.gen_menu.build_types') @mock.patch('wqflask.api.gen_menu.genotypes_exist') @@ -315,10 +341,8 @@ class TestGenMenu(unittest.TestCase): genotypes_exist_mock.return_value = False build_types_mock.return_value = [] - self.assertEqual(get_types(self.test_group), { - 'mouse': {}, - 'human': {} - }) + self.assertEqual(get_types(self.test_group, mock.MagicMock()), + {'mouse': {}, 'human': {}}) @mock.patch('wqflask.api.gen_menu.build_types') @mock.patch('wqflask.api.gen_menu.genotypes_exist') @@ -345,7 +369,7 @@ class TestGenMenu(unittest.TestCase): 'human': { 'HLC': [['M', 'M', 'Molecular Trait Datasets']], 'BXD': [['M', 'M', 'Molecular Trait Datasets']]}} - self.assertEqual(get_types(self.test_group), + self.assertEqual(get_types(self.test_group, mock.MagicMock()), expected_result) @mock.patch('wqflask.api.gen_menu.build_datasets') @@ -367,7 +391,7 @@ class TestGenMenu(unittest.TestCase): 'BXD': {'Genotypes': 'Test', 'M': 'Test', 'Phenotypes': 'Test'}}} - self.assertEqual(get_datasets(self.test_type), + self.assertEqual(get_datasets(self.test_type, mock.MagicMock()), expected_result) @mock.patch('wqflask.api.gen_menu.build_datasets') @@ -381,7 +405,7 @@ class TestGenMenu(unittest.TestCase): 'H_T1': {}}, 'human': {'HLC': {}, 'BXD': {}}} - self.assertEqual(get_datasets(self.test_type), + self.assertEqual(get_datasets(self.test_type, mock.MagicMock()), expected_result) @mock.patch('wqflask.api.gen_menu.get_datasets') @@ -411,4 +435,4 @@ class TestGenMenu(unittest.TestCase): 'groups': ['groupA', 'groupB', 'groupC', 'groupD'], 'species': ['speciesA', 'speciesB', 'speciesC', 'speciesD']} - self.assertEqual(gen_dropdown_json(), expected_result) + self.assertEqual(gen_dropdown_json(mock.MagicMock()), expected_result) diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index 6ef759e0..56d0af6f 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -1,9 +1,12 @@ from wqflask import app -from utility.tools import WEBSERVER_MODE, show_settings, get_setting_int, get_setting, get_setting_bool -import utility.logger -logger = utility.logger.getLogger(__name__) +from utility.tools import WEBSERVER_MODE +from utility.tools import show_settings +from utility.tools import get_setting_int +from utility.tools import get_setting +from utility.tools import get_setting_bool + BLUE = '\033[94m' GREEN = '\033[92m' @@ -16,27 +19,22 @@ def app_config(): if not app.config.get('SECRET_KEY'): import os app.config['SECRET_KEY'] = str(os.urandom(24)) - mode = WEBSERVER_MODE if mode == "DEV" or mode == "DEBUG": app.config['TEMPLATES_AUTO_RELOAD'] = True - # if mode == "DEBUG": - # app.config['EXPLAIN_TEMPLATE_LOADING'] = True <--- use overriding app param instead + print("==========================================") + show_settings() port = get_setting_int("SERVER_PORT") if get_setting_bool("USE_GN_SERVER"): - print( - ("GN2 API server URL is [" + BLUE + get_setting("GN_SERVER_URL") + ENDC + "]")) + print(f"GN2 API server URL is [{BLUE}GN_SERVER_URL{ENDC}]") import requests page = requests.get(get_setting("GN_SERVER_URL")) if page.status_code != 200: raise Exception("API server not found!") - - # import utility.elasticsearch_tools as es - # es.test_elasticsearch_connection() - - print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % - (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL")))) + print(f"GN2 is running. Visit {BLUE}" + f"[http://localhost:{str(port)}/{ENDC}]" + f"({get_setting('WEBSERVER_URL')})") diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index bf5e094b..2e94dd01 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -5,6 +5,8 @@ import jinja2 from flask import g from flask import Flask +from typing import Tuple +from urllib.parse import urlparse from utility import formatting from wqflask.markdown_routes import glossary_blueprint from wqflask.markdown_routes import references_blueprint @@ -16,9 +18,28 @@ from wqflask.markdown_routes import blogs_blueprint app = Flask(__name__) + +# Helper function for getting the SQL objects +def parse_db_url(sql_uri: str) -> Tuple: + """Parse SQL_URI env variable from an sql URI + e.g. 'mysql://user:pass@host_name/db_name' + + """ + parsed_db = urlparse(sql_uri) + return (parsed_db.hostname, parsed_db.username, + parsed_db.password, parsed_db.path[1:]) + + # See http://flask.pocoo.org/docs/config/#configuring-from-files # Note no longer use the badly named WQFLASK_OVERRIDES (nyi) app.config.from_envvar('GN2_SETTINGS') + +DB_HOST, DB_USER, DB_PASS, DB_NAME = parse_db_url(app.config.get('SQL_URI')) +app.config["DB_HOST"] = DB_HOST +app.config["DB_USER"] = DB_USER +app.config["DB_PASS"] = DB_PASS +app.config["DB_NAME"] = DB_NAME + app.jinja_env.globals.update( undefined=jinja2.StrictUndefined, numify=formatting.numify) diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index 7f4ec1bc..0c1120ab 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -1,15 +1,12 @@ -from flask import g - - -def gen_dropdown_json(): +def gen_dropdown_json(conn): """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 = get_species(conn) + groups = get_groups(species, conn) + types = get_types(groups, conn) + datasets = get_datasets(types, conn) data = dict(species=species, groups=groups, @@ -19,48 +16,50 @@ def gen_dropdown_json(): return data -def get_species(): +def get_species(conn): """Build species list""" - results = g.db.execute( - "SELECT Name, MenuName FROM Species ORDER BY OrderId").fetchall() - return [[name, menu_name] for name, menu_name in results] + with conn.cursor() as cursor: + cursor.execute("SELECT Name, MenuName FROM Species " + "ORDER BY OrderId") + results = cursor.fetchall() + return [[name, menu_name] for name, menu_name in results] -def get_groups(species): +def get_groups(species, conn): """Build groups list""" groups = {} - for species_name, _species_full_name in species: - groups[species_name] = [] - - results = g.db.execute( - ("SELECT InbredSet.Name, InbredSet.FullName, " - "IFNULL(InbredSet.Family, 'None') " - "FROM InbredSet, Species WHERE Species.Name = '{}' " - "AND InbredSet.SpeciesId = Species.Id GROUP by InbredSet.Name " - "ORDER BY IFNULL(InbredSet.FamilyOrder, InbredSet.FullName) " - "ASC, IFNULL(InbredSet.Family, InbredSet.FullName) ASC, " - "InbredSet.FullName ASC, InbredSet.MenuOrderId ASC") - .format(species_name)).fetchall() - - for result in results: - family_name = "Family:" + str(result[2]) - groups[species_name].append( - [str(result[0]), str(result[1]), family_name]) - + with conn.cursor() as cursor: + for species_name, _species_full_name in species: + groups[species_name] = [] + cursor.execute( + ("SELECT InbredSet.Name, InbredSet.FullName, " + "IFNULL(InbredSet.Family, 'None') " + "FROM InbredSet, Species WHERE Species.Name = '{}' " + "AND InbredSet.SpeciesId = Species.Id GROUP by " + "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " + "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " + "InbredSet.FullName) ASC, InbredSet.FullName ASC, " + "InbredSet.MenuOrderId ASC") + .format(species_name)) + results = cursor.fetchall() + for result in results: + family_name = "Family:" + str(result[2]) + groups[species_name].append( + [str(result[0]), str(result[1]), family_name]) return groups -def get_types(groups): +def get_types(groups, conn): """Build types list""" types = {} for species, group_dict in list(groups.items()): types[species] = {} for group_name, _group_full_name, _family_name in group_dict: - if phenotypes_exist(group_name): + if phenotypes_exist(group_name, conn): types[species][group_name] = [ ("Phenotypes", "Traits and Cofactors", "Phenotypes")] - if genotypes_exist(group_name): + if genotypes_exist(group_name, conn): if group_name in types[species]: types[species][group_name] += [ ("Genotypes", "DNA Markers and SNPs", "Genotypes")] @@ -68,11 +67,11 @@ def get_types(groups): types[species][group_name] = [ ("Genotypes", "DNA Markers and SNPs", "Genotypes")] if group_name in types[species]: - types_list = build_types(species, group_name) + types_list = build_types(species, group_name, conn) if len(types_list) > 0: types[species][group_name] += types_list else: - types_list = build_types(species, group_name) + types_list = build_types(species, group_name, conn) if len(types_list) > 0: types[species][group_name] = types_list else: @@ -83,22 +82,28 @@ def get_types(groups): return types -def phenotypes_exist(group_name): - results = g.db.execute( - ("SELECT Name FROM PublishFreeze " - "WHERE PublishFreeze.Name = " - "'{}'").format(group_name + "Publish")).fetchone() +def phenotypes_exist(group_name, conn): + results = [] + with conn.cursor() as cursor: + cursor.execute( + ("SELECT Name FROM PublishFreeze " + "WHERE PublishFreeze.Name = " + "'{}'").format(group_name + "Publish")) + results = cursor.fetchone() return bool(results) -def genotypes_exist(group_name): - results = g.db.execute( - ("SELECT Name FROM GenoFreeze " + - "WHERE GenoFreeze.Name = '{}'").format(group_name + "Geno")).fetchone() - return bool(results) +def genotypes_exist(group_name, conn): + with conn.cursor() as cursor: + cursor.execute( + ("SELECT Name FROM GenoFreeze " + + "WHERE GenoFreeze.Name = '{}'").format( + group_name + "Geno")) + results = cursor.fetchone() + return bool(results) -def build_types(species, group): +def build_types(species, group, conn): """Fetches tissues Gets the tissues with data for this species/group @@ -116,17 +121,19 @@ def build_types(species, group): "ORDER BY Tissue.Name").format(species, group) results = [] - for result in g.db.execute(query).fetchall(): - if bool(result): - these_datasets = build_datasets(species, group, result[0]) - if len(these_datasets) > 0: - results.append([str(result[0]), str(result[0]), - "Molecular Traits"]) - + with conn.cursor() as cursor: + cursor.execute(query) + for result in cursor.fetchall(): + if bool(result): + these_datasets = build_datasets(species, + group, result[0], conn) + if len(these_datasets) > 0: + results.append([str(result[0]), str(result[0]), + "Molecular Traits"]) return results -def get_datasets(types): +def get_datasets(types, conn): """Build datasets list""" datasets = {} for species, group_dict in list(types.items()): @@ -134,83 +141,89 @@ def get_datasets(types): for group, type_list in list(group_dict.items()): datasets[species][group] = {} for type_name in type_list: - these_datasets = build_datasets(species, group, type_name[0]) + these_datasets = build_datasets(species, group, + type_name[0], conn) if bool(these_datasets): datasets[species][group][type_name[0]] = these_datasets return datasets -def build_datasets(species, group, type_name): +def build_datasets(species, group, type_name, conn): """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 bool(results): - for result in results: - dataset_id = str(result[0]) - dataset_value = str(result[1]) - dataset_text = str(result[2]) - if group == 'MDP': - dataset_text = "Mouse Phenome Database" - + with conn.cursor() as cursor: + if type_name == "Phenotypes": + cursor.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)) + results = cursor.fetchall() + if bool(results): + for result in results: + dataset_id = str(result[0]) + dataset_value = str(result[1]) + dataset_text = str(result[2]) + if group == 'MDP': + dataset_text = "Mouse Phenome Database" + + datasets.append([dataset_id, dataset_value, dataset_text]) + else: + cursor.execute( + ("SELECT PublishFreeze.Name, PublishFreeze.FullName " + "FROM PublishFreeze, InbredSet " + "WHERE InbredSet.Name = '{}' AND " + "PublishFreeze.InbredSetId = InbredSet.Id " + "ORDER BY PublishFreeze.CreateTime ASC") + .format(group)) + result = cursor.fetchone() + dataset_id = "None" + dataset_value = str(result[0]) + dataset_text = str(result[1]) datasets.append([dataset_id, dataset_value, dataset_text]) - else: - result = g.db.execute( - ("SELECT PublishFreeze.Name, PublishFreeze.FullName " - "FROM PublishFreeze, InbredSet " - "WHERE InbredSet.Name = '{}' AND " - "PublishFreeze.InbredSetId = InbredSet.Id " - "ORDER BY PublishFreeze.CreateTime ASC") - .format(group)).fetchone() + elif type_name == "Genotypes": + cursor.execute( + ("SELECT InfoFiles.GN_AccesionId " + "FROM InfoFiles, GenoFreeze, InbredSet " + "WHERE InbredSet.Name = '{}' AND " + "GenoFreeze.InbredSetId = InbredSet.Id AND " + "InfoFiles.InfoPageName = GenoFreeze.ShortName " + "ORDER BY GenoFreeze.CreateTime " + "DESC").format(group)) + results = cursor.fetchone() dataset_id = "None" - dataset_value = str(result[0]) - dataset_text = str(result[1]) + if bool(results): + dataset_id = str(results[0]) + + dataset_value = "%sGeno" % group + dataset_text = "%s Genotypes" % 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 " - "ORDER BY GenoFreeze.CreateTime DESC").format(group)).fetchone() - - dataset_id = "None" - if bool(results): - dataset_id = str(results[0]) - - 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.public > 0 " - "ORDER BY -ProbeSetFreeze.OrderList DESC, 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) + else: # for mRNA expression/ProbeSet + cursor.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.public > 0 " + "ORDER BY -ProbeSetFreeze.OrderList DESC, " + "ProbeSetFreeze.CreateTime " + "DESC").format(species, group, type_name)) + results = cursor.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 diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index aec74c9e..a739e5a9 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -6,11 +6,13 @@ import csv import json import datetime import requests +import MySQLdb from zipfile import ZipFile, ZIP_DEFLATED import flask +from flask import current_app from flask import g from flask import request from flask import make_response @@ -845,7 +847,11 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): @app.route("/api/v_{}/gen_dropdown".format(version), methods=("GET",)) def gen_dropdown_menu(): - results = gen_menu.gen_dropdown_json() + conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), + user=current_app.config.get("DB_USER"), + passwd=current_app.config.get("DB_PASS"), + host=current_app.config.get("DB_HOST")) + results = gen_menu.gen_dropdown_json(conn) if len(results) > 0: return flask.jsonify(results) diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index fb8bdc55..8f66f7e9 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -121,16 +121,14 @@ class GSearch: continue max_lrs_text = "N/A" - if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None: - max_lrs_text = "Chr" + \ - str(this_trait['locus_chr']) + \ - ": " + str(this_trait['locus_mb']) + if this_trait['locus_chr'] and this_trait['locus_mb']: + max_lrs_text = f"Chr{str(this_trait['locus_chr'])}: {str(this_trait['locus_mb'])}" this_trait['max_lrs_text'] = max_lrs_text trait_list.append(this_trait) self.trait_count = len(trait_list) - self.trait_list = json.dumps(trait_list) + self.trait_list = trait_list self.header_fields = ['Index', 'Record', @@ -146,6 +144,22 @@ class GSearch: 'Max LRS Location', 'Additive Effect'] + self.header_data_names = [ + 'index', + 'name', + 'species', + 'group', + 'tissue', + 'dataset_fullname', + 'symbol', + 'description', + 'location_repr', + 'mean', + 'LRS_score_repr', + 'max_lrs_text', + 'additive', + ] + elif self.type == "phenotype": search_term = self.terms group_clause = "" @@ -169,24 +183,23 @@ class GSearch: PublishXRef.`LRS`, PublishXRef.`additive`, InbredSet.`InbredSetCode`, - PublishXRef.`mean` - FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication - WHERE PublishXRef.`InbredSetId`=InbredSet.`Id` - AND PublishFreeze.`InbredSetId`=InbredSet.`Id` - AND InbredSet.`SpeciesId`=Species.`Id` + PublishXRef.`mean`, + PublishFreeze.Id, + Geno.Chr as geno_chr, + Geno.Mb as geno_mb + FROM Species + INNER JOIN InbredSet ON InbredSet.`SpeciesId`=Species.`Id` + INNER JOIN PublishFreeze ON PublishFreeze.`InbredSetId`=InbredSet.`Id` + INNER JOIN PublishXRef ON PublishXRef.`InbredSetId`=InbredSet.`Id` + INNER JOIN Phenotype ON PublishXRef.`PhenotypeId`=Phenotype.`Id` + INNER JOIN Publication ON PublishXRef.`PublicationId`=Publication.`Id` + LEFT JOIN Geno ON PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id + WHERE + ( + (MATCH (Phenotype.Post_publication_description, Phenotype.Pre_publication_description, Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code) AGAINST ('{1}' IN BOOLEAN MODE) ) + OR (MATCH (Publication.Abstract, Publication.Title, Publication.Authors) AGAINST ('{1}' IN BOOLEAN MODE) ) + ) {0} - AND PublishXRef.`PhenotypeId`=Phenotype.`Id` - AND PublishXRef.`PublicationId`=Publication.`Id` - AND (Phenotype.Post_publication_description REGEXP "[[:<:]]{1}[[:>:]]" - OR Phenotype.Pre_publication_description REGEXP "[[:<:]]{1}[[:>:]]" - OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]{1}[[:>:]]" - OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]{1}[[:>:]]" - OR Phenotype.Lab_code REGEXP "[[:<:]]{1}[[:>:]]" - OR Publication.PubMed_ID REGEXP "[[:<:]]{1}[[:>:]]" - OR Publication.Abstract REGEXP "[[:<:]]{1}[[:>:]]" - OR Publication.Title REGEXP "[[:<:]]{1}[[:>:]]" - OR Publication.Authors REGEXP "[[:<:]]{1}[[:>:]]" - OR PublishXRef.Id REGEXP "[[:<:]]{1}[[:>:]]") ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id` LIMIT 6000 """.format(group_clause, search_term) @@ -221,6 +234,9 @@ class GSearch: this_trait['mean'] = f"{line[13]:.3f}" else: this_trait['mean'] = "N/A" + this_trait['dataset_id'] = line[14] + this_trait['locus_chr'] = line[15] + this_trait['locus_mb'] = line[16] this_trait['authors'] = line[7] this_trait['year'] = line[8] if this_trait['year'].isdigit(): @@ -241,32 +257,51 @@ class GSearch: if line[11] != "" and line[11] != None: this_trait['additive'] = '%.3f' % line[11] + dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="Publish", species=this_trait["species"]) + permissions = check_resource_availability(dataset_ob, this_trait['name']) + if type(permissions['data']) is list: + if "view" not in permissions['data']: + continue + else: + if permissions['data'] == 'no-access': + continue + this_trait['max_lrs_text'] = "N/A" - trait_ob = create_trait( - dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) - if not trait_ob: - continue if this_trait['dataset'] == this_trait['group'] + "Publish": try: - if trait_ob.locus_chr != "" and trait_ob.locus_mb != "": - this_trait['max_lrs_text'] = "Chr" + \ - str(trait_ob.locus_chr) + \ - ": " + str(trait_ob.locus_mb) + if this_trait['locus_chr'] and this_trait['locus_mb']: + this_trait['max_lrs_text'] = f"Chr{str(this_trait['locus_chr'])}: {str(this_trait['locus_mb'])}" except: this_trait['max_lrs_text'] = "N/A" trait_list.append(this_trait) self.trait_count = len(trait_list) - self.trait_list = json.dumps(trait_list) + self.trait_list = trait_list self.header_fields = ['Index', - 'Species', - 'Group', - 'Record', - 'Description', - 'Authors', - 'Year', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] + 'Species', + 'Group', + 'Record', + 'Description', + 'Authors', + 'Year', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] + + self.header_data_names = [ + 'index', + 'name', + 'species', + 'group', + 'tissue', + 'dataset_fullname', + 'symbol', + 'description', + 'location_repr', + 'mean', + 'LRS_score_repr', + 'max_lrs_text', + 'additive', + ] diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 6fd0abe8..48953d98 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -55,7 +55,15 @@ <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script type='text/javascript'> - var the_rows = {{ trait_list|safe }}; + var getParams = function(url) { + let parser = document.createElement('a'); + parser.href = url; + let params = parser.search.substring(1); + if(params.length > 0) { + return ('?'+params); + } + return params; + }; </script> <script type="text/javascript" charset="utf-8"> @@ -142,7 +150,6 @@ $('td', row).eq(12).attr('data-export', $('td', row).eq(12).text()); $('td', row).eq(13).attr('data-export', $('td', row).eq(13).text()); }, - 'data': the_rows, 'columns': [ { 'data': null, @@ -237,11 +244,13 @@ 'order': [[1, "asc" ]], 'sDom': "pitirp", 'autoWidth': true, - 'iDisplayLength': 500, 'deferRender': false, 'paging': true, 'orderClasses': true, 'processing': true, + 'iDisplayLength': 100, + 'bServerSide': true, + 'sAjaxSource': '/gsearch_table'+getParams(window.location.href), 'language': { 'loadingRecords': ' ', 'processing': 'Loading...' diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index 987b51a7..af9740ae 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -55,7 +55,15 @@ <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script type='text/javascript'> - var the_rows = {{ trait_list|safe }}; + var getParams = function(url) { + let parser = document.createElement('a'); + parser.href = url; + let params = parser.search.substring(1); + if(params.length > 0) { + return ('?'+params); + } + return params; + }; </script> <script type="text/javascript" charset="utf-8"> @@ -130,7 +138,6 @@ $('td', row).eq(9).attr('data-export', $('td', row).eq(9).text()); $('td', row).eq(10).attr('data-export', $('td', row).eq(10).text()); }, - 'data': the_rows, 'columns': [ { 'data': null, @@ -241,10 +248,12 @@ 'sDom': "pitirp", 'autoWidth': false, 'deferRender': false, - 'iDisplayLength': 500, 'paging': true, 'orderClasses': true, 'processing': true, + 'iDisplayLength': 100, + 'bServerSide': true, + 'sAjaxSource': '/gsearch_table'+getParams(window.location.href), 'language': { 'loadingRecords': ' ', 'processing': 'Loading...' diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 276d3019..d2ede70f 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -279,6 +279,19 @@ def gsearchact(): elif type == "phenotype": return render_template("gsearch_pheno.html", **result) +@app.route("/gsearch_table", methods=('GET',)) +def gsearchtable(): + logger.info(request.url) + + gsearch_table_data = GSearch(request.args) + current_page = server_side.ServerSideTable( + gsearch_table_data.trait_count, + gsearch_table_data.trait_list, + gsearch_table_data.header_data_names, + request.args, + ).get_page() + + return flask.jsonify(current_page) @app.route("/gsearch_updating", methods=('POST',)) def gsearch_updating(): |