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-rw-r--r--wqflask/tests/unit/wqflask/api/test_gen_menu.py408
-rw-r--r--wqflask/utility/startup_config.py26
-rw-r--r--wqflask/wqflask/__init__.py21
-rw-r--r--wqflask/wqflask/api/gen_menu.py251
-rw-r--r--wqflask/wqflask/api/router.py8
-rw-r--r--wqflask/wqflask/gsearch.py115
-rw-r--r--wqflask/wqflask/templates/gsearch_gene.html15
-rw-r--r--wqflask/wqflask/templates/gsearch_pheno.html15
-rw-r--r--wqflask/wqflask/views.py13
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': '&nbsp;',
'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': '&nbsp;',
'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():
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 23:07:21 +0000