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-rw-r--r--wqflask/tests/unit/utility/test_type_checking.py54
-rw-r--r--wqflask/tests/unit/wqflask/api/test_correlation.py153
-rw-r--r--wqflask/tests/unit/wqflask/api/test_mapping.py108
-rw-r--r--wqflask/tests/unit/wqflask/correlation/__init__.py0
-rw-r--r--wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py20
-rw-r--r--wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py98
-rw-r--r--wqflask/tests/unit/wqflask/snp_browser/__init__.py0
-rw-r--r--wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py105
-rw-r--r--wqflask/tests/unit/wqflask/test_server_side.py31
-rw-r--r--wqflask/utility/type_checking.py24
-rw-r--r--wqflask/wqflask/correlation/correlation_functions.py28
-rw-r--r--wqflask/wqflask/search_results.py16
-rw-r--r--wqflask/wqflask/server_side.py93
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py54
-rw-r--r--wqflask/wqflask/static/new/css/snp_browser.css6
-rw-r--r--wqflask/wqflask/static/new/javascript/draw_probability_plot.js1
-rw-r--r--wqflask/wqflask/static/new/javascript/init_genome_browser.js2
-rw-r--r--wqflask/wqflask/static/new/javascript/search_results.js4
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js35
-rw-r--r--wqflask/wqflask/static/new/javascript/stats.js2
-rw-r--r--wqflask/wqflask/templates/mapping_results.html16
-rw-r--r--wqflask/wqflask/templates/search_result_page.html40
-rw-r--r--wqflask/wqflask/templates/show_trait_statistics.html16
-rw-r--r--wqflask/wqflask/templates/snp_browser.html142
-rw-r--r--wqflask/wqflask/views.py42
25 files changed, 930 insertions, 160 deletions
diff --git a/wqflask/tests/unit/utility/test_type_checking.py b/wqflask/tests/unit/utility/test_type_checking.py
new file mode 100644
index 00000000..48d110c7
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_type_checking.py
@@ -0,0 +1,54 @@
+import unittest
+from utility.type_checking import is_float
+from utility.type_checking import is_int
+from utility.type_checking import is_str
+from utility.type_checking import get_float
+from utility.type_checking import get_int
+from utility.type_checking import get_string
+
+
+class TestTypeChecking(unittest.TestCase):
+ def test_is_float(self):
+ floats = [2, 1.2, '3.1']
+ not_floats = ["String", None, [], ()]
+ for flt in floats:
+ results = is_float(flt)
+ self.assertTrue(results)
+ for nflt in not_floats:
+ results = is_float(nflt)
+ self.assertFalse(results)
+
+ def test_is_int(self):
+ int_values = [1, 1.1]
+ not_int_values = ["string", None, [], "1.1"]
+ for int_val in int_values:
+ results = is_int(int_val)
+ self.assertTrue(results)
+ for not_int in not_int_values:
+ results = is_int(not_int)
+ self.assertFalse(results)
+
+ def test_is_str(self):
+ string_values = [1, False, [], {}, "string_value"]
+ falsey_values = [None]
+ for string_val in string_values:
+ results = is_str(string_val)
+ self.assertTrue(results)
+ for non_string in falsey_values:
+ results = is_str(non_string)
+ self.assertFalse(results)
+
+ def test_get_float(self):
+ vars_object = {"min_value": "12"}
+ results = get_float(vars_object, "min_value")
+ self.assertEqual(results, 12.0)
+
+ def test_get_int(self):
+ vars_object = {"lx_value": "1"}
+ results = get_int(vars_object, "lx_value")
+ self.assertEqual(results, 1)
+
+ def test_get_string(self):
+ string_object = {"mx_value": 1}
+ results = get_string(string_object, "mx_value")
+ self.assertEqual(results, "1") \ No newline at end of file
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
new file mode 100644
index 00000000..d0264b87
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -0,0 +1,153 @@
+import unittest
+from unittest import mock
+from wqflask import app
+from collections import OrderedDict
+from wqflask.api.correlation import init_corr_params
+from wqflask.api.correlation import convert_to_mouse_gene_id
+from wqflask.api.correlation import do_literature_correlation_for_all_traits
+from wqflask.api.correlation import get_sample_r_and_p_values
+from wqflask.api.correlation import calculate_results
+
+
+class AttributeSetter:
+ def __init__(self, obj):
+ for k, v in obj.items():
+ setattr(self, k, v)
+
+
+class MockDataset(AttributeSetter):
+ def get_trait_data(self):
+ return None
+
+ def retrieve_genes(self, id=None):
+ return {
+ "TT-1": "GH-1",
+ "TT-2": "GH-2",
+ "TT-3": "GH-3"
+
+ }
+
+
+class TestCorrelations(unittest.TestCase):
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ def test_init_corr_params(self):
+ start_vars = {
+ "return_count": "3",
+ "type": "T1",
+ "method": "spearman"
+ }
+
+ corr_params_results = init_corr_params(start_vars=start_vars)
+ expected_results = {
+ "return_count": 3,
+ "type": "T1",
+ "method": "spearman"
+ }
+
+ self.assertEqual(corr_params_results, expected_results)
+
+ @mock.patch("wqflask.api.correlation.g")
+ def test_convert_to_mouse_gene_id(self, mock_db):
+
+ results = convert_to_mouse_gene_id(species="Other", gene_id="")
+ self.assertEqual(results, None)
+
+ rat_species_results = convert_to_mouse_gene_id(
+ species="rat", gene_id="GH1")
+
+ mock_db.db.execute.return_value.fetchone.side_effect = [
+ AttributeSetter({"mouse": "MG-1"}), AttributeSetter({"mouse": "MG-2"})]
+
+ self.assertEqual(convert_to_mouse_gene_id(
+ species="mouse", gene_id="MG-4"), "MG-4")
+ self.assertEqual(convert_to_mouse_gene_id(
+ species="rat", gene_id="R1"), "MG-1")
+ self.assertEqual(convert_to_mouse_gene_id(
+ species="human", gene_id="H1"), "MG-2")
+
+ @mock.patch("wqflask.api.correlation.g")
+ @mock.patch("wqflask.api.correlation.convert_to_mouse_gene_id")
+ def test_do_literature_correlation_for_all_traits(self, mock_convert_to_mouse_geneid, mock_db):
+ mock_convert_to_mouse_geneid.side_effect = [
+ "MG-1", "MG-2;", "MG-3", "MG-4"]
+
+ trait_geneid_dict = {
+ "TT-1": "GH-1",
+ "TT-2": "GH-2",
+ "TT-3": "GH-3"
+
+ }
+ mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter(
+ {"value": "V1"}), AttributeSetter({"value": "V2"}), AttributeSetter({"value": "V3"})]
+
+ this_trait = AttributeSetter({"geneid": "GH-1"})
+
+ target_dataset = AttributeSetter(
+ {"group": AttributeSetter({"species": "rat"})})
+ results = do_literature_correlation_for_all_traits(
+ this_trait=this_trait, target_dataset=target_dataset, trait_geneid_dict=trait_geneid_dict, corr_params={})
+
+ expected_results = {'TT-1': ['GH-1', 0],
+ 'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']}
+ self.assertEqual(results, expected_results)
+
+ @mock.patch("wqflask.api.correlation.corr_result_helpers.normalize_values")
+ def test_get_sample_r_and_p_values(self, mock_normalize):
+
+ group = AttributeSetter(
+ {"samplelist": ["S1", "S2", "S3", "S4", "S5", "S6", "S7"]})
+ target_dataset = AttributeSetter({"group": group})
+
+ target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6]
+ trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
+ "S3": AttributeSetter(
+ {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
+ "S6": AttributeSetter({"value": 5.0})}
+ this_trait = AttributeSetter({"data": trait_data})
+ mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
+ [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6)
+ mock_normalize.side_effect = [([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
+ [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6),
+ ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
+ [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6),
+ ([2.3, 1.1, 1.4], [3.4, 6.2, 4.1], 3)]
+
+ results_pearsonr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+ }, target_vals=target_vals, target_dataset=target_dataset, type="pearson")
+ results_spearmanr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+ }, target_vals=target_vals, target_dataset=target_dataset, type="spearman")
+ results_num_overlap = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+ }, target_vals=target_vals, target_dataset=target_dataset, type="pearson")
+ expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6]
+ expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6]
+ for i, val in enumerate(expected_pearsonr):
+ self.assertAlmostEqual(val, results_pearsonr[i],4)
+ for i, val in enumerate(expected_spearmanr):
+ self.assertAlmostEqual(val, results_spearmanr[i],4)
+ self.assertEqual(results_num_overlap, None)
+
+ @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
+ def test_calculate_results(self, literature_correlation):
+
+ literature_correlation.return_value = {
+ 'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1]}
+
+ this_dataset = MockDataset(
+ {"group": AttributeSetter({"species": "rat"})})
+ target_dataset = MockDataset(
+ {"group": AttributeSetter({"species": "rat"})})
+ this_trait = AttributeSetter({"geneid": "GH-1"})
+ corr_params = {"type": "literature"}
+ sorted_results = calculate_results(
+ this_trait=this_trait, this_dataset=this_dataset, target_dataset=target_dataset, corr_params=corr_params)
+ expected_results = {'TT-2': ['GH-2', 3],
+ 'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]}
+
+ self.assertTrue(isinstance(sorted_results, OrderedDict))
+ self.assertEqual(dict(sorted_results), expected_results)
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py
new file mode 100644
index 00000000..b094294a
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/api/test_mapping.py
@@ -0,0 +1,108 @@
+import unittest
+from unittest import mock
+from wqflask.api.mapping import initialize_parameters
+from wqflask.api.mapping import do_mapping_for_api
+
+
+class AttributeSetter:
+ def __init__(self, obj):
+ for key, value in obj.items():
+ setattr(self, key, value)
+
+
+class MockGroup(AttributeSetter):
+ def get_marker(self):
+ self.markers = []
+
+
+class TestMapping(unittest.TestCase):
+
+ def test_initialize_parameters(self):
+ expected_results = {
+ "format": "json",
+ "limit_to": False,
+ "mapping_method": "gemma",
+ "maf": 0.01,
+ "use_loco": True,
+ "num_perm": 0,
+ "perm_check": False
+ }
+
+ results = initialize_parameters(
+ start_vars={}, dataset={}, this_trait={})
+ self.assertEqual(results, expected_results)
+
+ start_vars = {
+ "format": "F1",
+ "limit_to": "1",
+ "mapping_method": "rqtl",
+ "control_marker": True,
+ "pair_scan": "true",
+ "interval_mapping": "true",
+ "use_loco": "true",
+ "num_perm": "14"
+
+ }
+
+ results_2 = initialize_parameters(
+ start_vars=start_vars, dataset={}, this_trait={})
+ expected_results = {
+ "format": "F1",
+ "limit_to": 1,
+ "mapping_method": "gemma",
+ "maf": 0.01,
+ "use_loco": True,
+ "num_perm": 14,
+ "perm_check": "ON"
+ }
+
+ self.assertEqual(results_2, expected_results)
+
+ @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno")
+ @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma")
+ @mock.patch("wqflask.api.mapping.initialize_parameters")
+ @mock.patch("wqflask.api.mapping.retrieve_sample_data")
+ @mock.patch("wqflask.api.mapping.create_trait")
+ @mock.patch("wqflask.api.mapping.data_set.create_dataset")
+ def test_do_mapping_for_api(self, mock_create_dataset, mock_trait, mock_retrieve_sample, mock_param, run_gemma, run_rqtl_geno):
+ start_vars = {
+ "db": "Temp",
+ "trait_id": "dewf3232rff2",
+ "format": "F1",
+ "mapping_method": "gemma",
+ "use_loco": True
+
+ }
+ sampleList = ["S1", "S2", "S3", "S4"]
+ samplelist = ["S1", "S2", "S4"]
+ dataset = AttributeSetter({"group": samplelist})
+ this_trait = AttributeSetter({})
+ trait_data = AttributeSetter({
+ "data": {
+ "item1": AttributeSetter({"name": "S1", "value": "S1_value"}),
+ "item2": AttributeSetter({"name": "S2", "value": "S2_value"}),
+ "item3": AttributeSetter({"name": "S3", "value": "S3_value"}),
+
+ }
+ })
+ trait = AttributeSetter({
+ "data": trait_data
+ })
+
+ dataset.return_value = dataset
+ mock_trait.return_value = this_trait
+
+ mock_retrieve_sample.return_value = trait
+ mock_param.return_value = {
+ "format": "F1",
+ "limit_to": False,
+ "mapping_method": "gemma",
+ "maf": 0.01,
+ "use_loco": "True",
+ "num_perm": 14,
+ "perm_check": "ON"
+ }
+
+ run_gemma.return_value = ["results"]
+ results = do_mapping_for_api(start_vars=start_vars)
+ self.assertEqual(results, ("results", None))
diff --git a/wqflask/tests/unit/wqflask/correlation/__init__.py b/wqflask/tests/unit/wqflask/correlation/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/__init__.py
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
new file mode 100644
index 00000000..44d2e0fc
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -0,0 +1,20 @@
+import unittest
+from unittest import mock
+from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values
+from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss
+
+
+class TestCorrelationFunctions(unittest.TestCase):
+
+ @mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData")
+ def test_get_trait_symbol_and_tissue_values(self, mock_class):
+ """test for getting trait symbol and tissue_values"""
+ mock_class_instance = mock_class.return_value
+ mock_class_instance.gene_symbols = ["k1", "k2", "k3"]
+ mock_class_instance.get_symbol_values_pairs.return_value = {
+ "k1": ["v1", "v2", "v3"], "k2": ["v2", "v3"], "k3": ["k3"]}
+ results = get_trait_symbol_and_tissue_values(
+ symbol_list=["k1", "k2", "k3"])
+ mock_class.assert_called_with(gene_symbols=['k1', 'k2', 'k3'])
+ self.assertEqual({"k1": ["v1", "v2", "v3"], "k2": [
+ "v2", "v3"], "k3": ["k3"]}, results)
diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
new file mode 100644
index 00000000..33601990
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
@@ -0,0 +1,98 @@
+import unittest
+from unittest import mock
+from wqflask.correlation.show_corr_results import get_header_fields
+from wqflask.correlation.show_corr_results import generate_corr_json
+
+
+class AttributeSetter:
+ def __init__(self, trait_obj):
+ for key, value in trait_obj.items():
+ setattr(self, key, value)
+
+
+class TestShowCorrResults(unittest.TestCase):
+ def test_get_header_fields(self):
+ expected = [
+ ['Index',
+ 'Record',
+ 'Symbol',
+ 'Description',
+ 'Location',
+ 'Mean',
+ 'Sample rho',
+ 'N',
+ 'Sample p(rho)',
+ 'Lit rho',
+ 'Tissue rho',
+ 'Tissue p(rho)',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect'],
+
+ ['Index',
+ 'ID',
+ 'Location',
+ 'Sample r',
+ 'N',
+ 'Sample p(r)']
+
+ ]
+ result1 = get_header_fields("ProbeSet", "spearman")
+ result2 = get_header_fields("Other", "Other")
+ self.assertEqual(result1, expected[0])
+ self.assertEqual(result2, expected[1])
+
+ @mock.patch("wqflask.correlation.show_corr_results.hmac.data_hmac")
+ def test_generate_corr_json(self, mock_data_hmac):
+ mock_data_hmac.return_value = "hajsdiau"
+
+ dataset = AttributeSetter({"name": "the_name"})
+ this_trait = AttributeSetter(
+ {"name": "trait_test", "dataset": dataset})
+ target_dataset = AttributeSetter({"type": "Publish"})
+ corr_trait_1 = AttributeSetter({
+ "name": "trait_1",
+ "dataset": AttributeSetter({"name": "dataset_1"}),
+ "view": True,
+ "abbreviation": "T1",
+ "description_display": "Trait I description",
+ "authors": "JM J,JYEW",
+ "pubmed_id": "34n4nn31hn43",
+ "pubmed_text": "2016",
+ "pubmed_link": "https://www.load",
+ "lod_score": "",
+ "mean": "",
+ "LRS_location_repr": "BXBS",
+ "additive": "",
+ "sample_r": 10.5,
+ "num_overlap": 2,
+ "sample_p": 5
+
+
+
+
+ })
+ corr_results = [corr_trait_1]
+
+ dataset_type_other = {
+ "location": "cx-3-4",
+ "sample_4": 12.32,
+ "num_overlap": 3,
+ "sample_p": 10.34
+ }
+
+ expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "mean": "N/A", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]'
+
+ results1 = generate_corr_json(corr_results=corr_results, this_trait=this_trait,
+ dataset=dataset, target_dataset=target_dataset, for_api=True)
+ self.assertEqual(expected_results, results1)
+
+ def test_generate_corr_json_view_false(self):
+ trait = AttributeSetter({"view": False})
+ corr_results = [trait]
+ this_trait = AttributeSetter({"name": "trait_test"})
+ dataset = AttributeSetter({"name": "the_name"})
+
+ results_where_view_is_false = generate_corr_json(
+ corr_results=corr_results, this_trait=this_trait, dataset={}, target_dataset={}, for_api=False)
+ self.assertEqual(results_where_view_is_false, "[]")
diff --git a/wqflask/tests/unit/wqflask/snp_browser/__init__.py b/wqflask/tests/unit/wqflask/snp_browser/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/snp_browser/__init__.py
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
new file mode 100644
index 00000000..ce3e7b83
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -0,0 +1,105 @@
+import unittest
+from unittest import mock
+from wqflask import app
+from wqflask.snp_browser.snp_browser import get_gene_id
+from wqflask.snp_browser.snp_browser import get_gene_id_name_dict
+from wqflask.snp_browser.snp_browser import check_if_in_gene
+from wqflask.snp_browser.snp_browser import get_browser_sample_lists
+from wqflask.snp_browser.snp_browser import get_header_list
+
+
+class TestSnpBrowser(unittest.TestCase):
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ def test_get_header_list(self):
+ empty_columns = {"snp_source": "false", "conservation_score": "true", "gene_name": "false",
+ "transcript": "false", "exon": "false", "domain_2": "true", "function": "false", "function_details": "true"}
+ strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []}
+ expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore',
+ 'Domain 1', 'Domain 2', 'Details'],
+ ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
+ ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
+ 'conservation_score', 'domain_1', 'domain_2',
+ 'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
+
+ results_with_snp = get_header_list(
+ variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns)
+ results_with_indel = get_header_list(
+ variant_type="InDel", strains=strains, species="rat", empty_columns=[])
+ expected_results_with_indel = (
+ ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start',
+ 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
+ ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
+ 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
+
+ self.assertEqual(expected_results, results_with_snp)
+ self.assertEqual(expected_results_with_indel, results_with_indel)
+
+ @mock.patch("wqflask.snp_browser.snp_browser.g")
+ def test_get_gene_id(self, mock_db):
+ mock_db.db.execute.return_value.fetchone.return_value = "517d729f-aa13-4413-a885-40a3f7ff768a"
+ db_query_value = """
+ SELECT
+ geneId
+ FROM
+ GeneList
+ WHERE
+ SpeciesId = c9c0f59e-1259-4cba-91e6-831ef1a99c83 AND geneSymbol = 'INSR'
+ """
+ results = get_gene_id(
+ species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR")
+ mock_db.db.execute.assert_called_once_with(db_query_value)
+ self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a")
+
+ @mock.patch("wqflask.snp_browser.snp_browser.g")
+ def test_gene_id_name_dict(self, mock_db):
+ no_gene_names = []
+ self.assertEqual("", get_gene_id_name_dict(
+ species_id="fregb343bui43g4", gene_name_list=no_gene_names))
+ gene_name_list = ["GH1", "GH2", "GH3"]
+ mock_db.db.execute.return_value.fetchall.side_effect = [[], [("fsdf43-fseferger-f22", "GH1"), ("1sdf43-fsewferger-f22", "GH2"),
+ ("fwdj43-fstferger-f22", "GH3")]]
+ no_results = get_gene_id_name_dict(
+ species_id="ret3-32rf32", gene_name_list=gene_name_list)
+ results_found = get_gene_id_name_dict(
+ species_id="ret3-32rf32", gene_name_list=gene_name_list)
+ expected_found = {'GH1': 'fsdf43-fseferger-f22',
+ 'GH2': '1sdf43-fsewferger-f22', 'GH3': 'fwdj43-fstferger-f22'}
+ db_query_value = """
+ SELECT
+ geneId, geneSymbol
+ FROM
+ GeneList
+ WHERE
+ SpeciesId = ret3-32rf32 AND geneSymbol in ('GH1','GH2','GH3')
+ """
+ mock_db.db.execute.assert_called_with(db_query_value)
+ self.assertEqual(results_found, expected_found)
+ self.assertEqual(no_results, {})
+
+ @mock.patch("wqflask.snp_browser.snp_browser.g")
+ def test_check_if_in_gene(self, mock_db):
+ mock_db.db.execute.return_value.fetchone.side_effect = [
+ ("fsdf-232sdf-sdf", "GHA"), ""]
+ results_found = check_if_in_gene(
+ species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr="CH1", mb=12.09)
+ db_query_value = """SELECT geneId, geneSymbol
+ FROM GeneList
+ WHERE SpeciesId = 517d729f-aa13-4413-a885-40a3f7ff768a AND chromosome = 'CH1' AND
+ (txStart < 12.09 AND txEnd > 12.09); """
+ gene_not_found = check_if_in_gene(
+ species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr="CH1", mb=12.09)
+ mock_db.db.execute.assert_called_with(db_query_value)
+ self.assertEqual(gene_not_found, "")
+
+ @mock.patch("wqflask.snp_browser.snp_browser.g")
+ def test_get_browser_sample_lists(self, mock_db):
+ mock_db.db.execute.return_value.fetchall.return_value = []
+
+ results = get_browser_sample_lists(species_id="12")
+ self.assertEqual(results, {'mouse': [], 'rat': []})
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py
new file mode 100644
index 00000000..4f91d8ca
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_server_side.py
@@ -0,0 +1,31 @@
+import unittest
+
+from wqflask.server_side import ServerSideTable
+
+
+class TestServerSideTableTests(unittest.TestCase):
+ """
+ Test the ServerSideTable class
+
+ test table:
+ first, second, third
+ 'd', 4, 'zz'
+ 'b', 2, 'aa'
+ 'c', 1, 'ss'
+ """
+
+ def test_get_page(self):
+ rows_count = 3
+ table_rows = [
+ {'first': 'd', 'second': 4, 'third': 'zz'},
+ {'first': 'b', 'second': 2, 'third': 'aa'},
+ {'first': 'c', 'second': 1, 'third': 'ss'},
+ ]
+ headers = ['first', 'second', 'third']
+ request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
+
+ test_page = ServerSideTable(rows_count, table_rows, headers, request_args).get_page()
+ self.assertEqual(test_page['sEcho'], '1')
+ self.assertEqual(test_page['iTotalRecords'], 'nan')
+ self.assertEqual(test_page['iTotalDisplayRecords'], '3')
+ self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}])
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
index f15b17e2..6b029317 100644
--- a/wqflask/utility/type_checking.py
+++ b/wqflask/utility/type_checking.py
@@ -23,20 +23,20 @@ def is_str(value):
except:
return False
-def get_float(vars,name,default=None):
- if name in vars:
- if is_float(vars[name]):
- return float(vars[name])
+def get_float(vars_obj,name,default=None):
+ if name in vars_obj:
+ if is_float(vars_obj[name]):
+ return float(vars_obj[name])
return default
-def get_int(vars,name,default=None):
- if name in vars:
- if is_int(vars[name]):
- return float(vars[name])
+def get_int(vars_obj,name,default=None):
+ if name in vars_obj:
+ if is_int(vars_obj[name]):
+ return float(vars_obj[name])
return default
-def get_string(vars,name,default=None):
- if name in vars:
- if not vars[name] is None:
- return str(vars[name])
+def get_string(vars_obj,name,default=None):
+ if name in vars_obj:
+ if not vars_obj[name] is None:
+ return str(vars_obj[name])
return default
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index b883e361..fd7691d4 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -71,34 +71,6 @@ def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pears
return corr_result
-###########################################################################
-#Input: cursor, symbolList (list), dataIdDict(Dict)
-#output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
-# key is symbol, value is one list of expression values of one probeSet;
-#function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
-#Attention! All keys are lower case!
-###########################################################################
-def get_symbol_value_pairs(tissue_data):
- id_list = [tissue_data[symbol.lower()].data_id for item in tissue_data]
-
- symbol_value_pairs = {}
- value_list=[]
-
- query = """SELECT value, id
- FROM TissueProbeSetData
- WHERE Id IN {}""".format(create_in_clause(id_list))
-
- try :
- results = g.db.execute(query).fetchall()
- for result in results:
- value_list.append(result.value)
- symbol_value_pairs[symbol] = value_list
- except:
- symbol_value_pairs[symbol] = None
-
- return symbol_value_pairs
-
-
########################################################################################################
#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 0d0894a4..c4ea2921 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -28,9 +28,9 @@ class SearchResultPage(object):
#maxReturn = 3000
def __init__(self, kw):
- """This class gets invoked after hitting submit on the main menu (in
-views.py).
-
+ """
+ This class gets invoked after hitting submit on the main menu (in
+ views.py).
"""
###########################################
@@ -86,7 +86,6 @@ views.py).
else:
self.gen_search_result()
-
def gen_search_result(self):
"""
Get the info displayed in the search result table from the set of results computed in
@@ -161,7 +160,14 @@ views.py).
trait_dict[key] = trait_dict[key].decode('utf-8')
trait_list.append(trait_dict)
- self.trait_list = json.dumps(trait_list)
+ self.trait_list = trait_list
+
+ if this_trait.dataset.type == "ProbeSet":
+ self.header_data_names = ['index', 'display_name', 'symbol', 'description', 'location', 'mean', 'lrs_score', 'lrs_location', 'additive']
+ elif this_trait.dataset.type == "Publish":
+ self.header_data_names = ['index', 'display_name', 'description', 'mean', 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive']
+ elif this_trait.dataset.type == "Geno":
+ self.header_data_names = ['index', 'display_name', 'location']
def search(self):
"""
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
new file mode 100644
index 00000000..5f764767
--- /dev/null
+++ b/wqflask/wqflask/server_side.py
@@ -0,0 +1,93 @@
+# handles server side table processing
+
+
+
+class ServerSideTable(object):
+ """
+ This class is used to do server-side processing
+ on the DataTables table such as paginating, sorting,
+ filtering(not implemented) etc. This takes the load off
+ the client-side and reduces the size of data interchanged.
+
+ Usage:
+ ServerSideTable(table_data, request_values)
+ where,
+ `table_data` must have data members
+ `rows_count` as number of rows in the table,
+ `table_rows` as data rows of the table,
+ `header_data_names` as headers names of the table.
+
+ `request_values` must have request arguments values
+ including the DataTables server-side processing arguments.
+
+ Have a look at snp_browser_table() function in
+ wqflask/wqflask/views.py for reference use.
+ """
+
+ def __init__(self, rows_count, table_rows, header_data_names, request_values):
+ self.request_values = request_values
+ self.sEcho = self.request_values['sEcho']
+
+ self.rows_count = rows_count
+ self.table_rows = table_rows
+ self.header_data_names = header_data_names
+
+ self.sort_rows()
+ self.paginate_rows()
+
+ def sort_rows(self):
+ """
+ Sorts the rows taking in to account the column (or columns) that the
+ user has selected.
+ """
+ def is_reverse(str_direction):
+ """ Maps the 'desc' and 'asc' words to True or False. """
+ return True if str_direction == 'desc' else False
+
+ if (self.request_values['iSortCol_0'] != "") and (int(self.request_values['iSortingCols']) > 0):
+ for i in range(0, int(self.request_values['iSortingCols'])):
+ column_number = int(self.request_values['iSortCol_' + str(i)])
+ column_name = self.header_data_names[column_number - 1]
+ sort_direction = self.request_values['sSortDir_' + str(i)]
+ self.table_rows = sorted(self.table_rows,
+ key=lambda x: x[column_name],
+ reverse=is_reverse(sort_direction))
+
+ def paginate_rows(self):
+ """
+ Selects a subset of the filtered and sorted data based on if the table
+ has pagination, the current page and the size of each page.
+ """
+ def requires_pagination():
+ """ Check if the table is going to be paginated """
+ if self.request_values['iDisplayStart'] != "":
+ if int(self.request_values['iDisplayLength']) != -1:
+ return True
+ return False
+
+ if not requires_pagination():
+ return
+
+ start = int(self.request_values['iDisplayStart'])
+ length = int(self.request_values['iDisplayLength'])
+
+ # if search returns only one page
+ if len(self.table_rows) <= length:
+ # display only one page
+ self.table_rows = self.table_rows[start:]
+ else:
+ limit = -len(self.table_rows) + start + length
+ if limit < 0:
+ # display pagination
+ self.table_rows = self.table_rows[start:limit]
+ else:
+ # display last page of pagination
+ self.table_rows = self.table_rows[start:]
+
+ def get_page(self):
+ output = {}
+ output['sEcho'] = str(self.sEcho)
+ output['iTotalRecords'] = str(float('Nan'))
+ output['iTotalDisplayRecords'] = str(self.rows_count)
+ output['data'] = self.table_rows
+ return output
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 6c3fcf53..a52399a2 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -4,7 +4,7 @@ import string
from PIL import (Image)
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
from base import species
from base import webqtlConfig
@@ -14,21 +14,21 @@ class SnpBrowser(object):
def __init__(self, start_vars):
self.strain_lists = get_browser_sample_lists()
self.initialize_parameters(start_vars)
- self.limit_number = 10000
if self.first_run == "false":
self.filtered_results = self.get_browser_results()
+ self.table_rows = self.get_table_rows()
+ self.rows_count = len(self.table_rows)
- if len(self.filtered_results) <= self.limit_number:
- self.table_rows = self.get_table_rows()
- else:
- self.empty_columns = None
+ del self.filtered_results
+
+ if 'sEcho' not in start_vars:
self.table_rows = []
if self.limit_strains == "true":
- self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
+ self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
else:
- self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
+ self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
def initialize_parameters(self, start_vars):
if 'first_run' in start_vars:
@@ -368,19 +368,19 @@ class SnpBrowser(object):
#ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc)
self.empty_columns = {
- "snp_source": "false",
- "conservation_score": "false",
- "gene_name": "false",
- "transcript": "false",
- "exon": "false",
- "domain_2": "false",
- "function": "false",
- "function_details": "false"
- }
+ "snp_source": "false",
+ "conservation_score": "false",
+ "gene_name": "false",
+ "transcript": "false",
+ "exon": "false",
+ "domain_2": "false",
+ "function": "false",
+ "function_details": "false"
+ }
the_rows = []
for i, result in enumerate(self.filtered_results):
- this_row = []
+ this_row = {}
if self.variant_type == "SNP":
snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[:14]
allele_value_list = result[14:]
@@ -520,13 +520,10 @@ class SnpBrowser(object):
"source_name": str(source_name)
}
#this_row = [indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name]
- else:
- this_row = {}
the_rows.append(this_row)
return the_rows
-
def include_record(self, domain, function, snp_source, conservation_score):
""" Decide whether to add this record """
@@ -674,9 +671,13 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
empty_field_count = 0 #ZS: This is an awkward way of letting the javascript know the index where the allele value columns start; there's probably a better way of doing this
header_fields = []
+ header_data_names = []
if variant_type == "SNP":
header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details'])
+ header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details']
+
header_fields.append(strain_list)
+ header_data_names += strain_list
if empty_columns != None:
if empty_columns['snp_source'] == "false":
@@ -703,11 +704,16 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
if empty_columns['function_details'] == "false":
empty_field_count += 1
header_fields[0].remove('Details')
+
+ for col in empty_columns.keys():
+ if empty_columns[col] == "false":
+ header_data_names.remove(col)
elif variant_type == "InDel":
header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
+ header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']
- return header_fields, empty_field_count
+ return header_fields, empty_field_count, header_data_names
def get_effect_details_by_category(effect_name = None, effect_value = None):
gene_list = []
@@ -868,8 +874,6 @@ def get_gene_id_name_dict(species_id, gene_name_list):
if len(results) > 0:
for item in results:
gene_id_name_dict[item[1]] = item[0]
- else:
- pass
return gene_id_name_dict
@@ -883,7 +887,7 @@ def check_if_in_gene(species_id, chr, mb):
query = """SELECT geneId,geneSymbol
FROM GeneList
WHERE chromosome = '{0}' AND
- (txStart < {1} AND txEnd > {1}); """.format(species_id, chr, mb)
+ (txStart < {1} AND txEnd > {1}); """.format(chr, mb)
result = g.db.execute(query).fetchone()
diff --git a/wqflask/wqflask/static/new/css/snp_browser.css b/wqflask/wqflask/static/new/css/snp_browser.css
index 30fe9a59..a7942d2a 100644
--- a/wqflask/wqflask/static/new/css/snp_browser.css
+++ b/wqflask/wqflask/static/new/css/snp_browser.css
@@ -6,6 +6,10 @@ table.dataTable thead th {
vertical-align: bottom;
}
+table.dataTable tbody tr.selected {
+ background-color: #ffee99;
+}
+
table.dataTable thead .sorting,
table.dataTable thead .sorting_asc,
table.dataTable thead .sorting_desc,
@@ -18,7 +22,7 @@ table.dataTable thead .sorting_desc_disabled {
table.dataTable thead th{
border-right: 1px solid white;
color: white;
- background-color: royalblue;
+ background-color: #369;
}
table.dataTable tbody td {
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index 3d756303..1b944d4f 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -118,7 +118,6 @@
};
};
data = [make_data('samples_primary'), make_data('samples_other')];
- console.log("THE DATA IS:", data);
d3.select("#prob_plot_container svg").datum(data).call(chart);
if (js_data.trait_symbol != null) {
$("#prob_plot_title").html("<h3>" + js_data.trait_symbol + ": " + js_data.trait_id + "</h3>");
diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
index 2552fb04..508f5bf2 100644
--- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js
+++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
@@ -1,5 +1,3 @@
-console.log("THE FILES:", js_data.browser_files)
-
snps_filename = "/browser_input?filename=" + js_data.browser_files[0]
annot_filename = "/browser_input?filename=" + js_data.browser_files[1]
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 9ffef4f8..05dcfda5 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -1,4 +1,4 @@
-change_buttons = function() {
+change_buttons = function(check_node = 0) {
var button, buttons, item, num_checked, text, _i, _j, _k, _l, _len, _len2, _len3, _len4, _results, _results2;
buttons = ["#add", "#remove"];
@@ -6,7 +6,7 @@ change_buttons = function() {
table_api = $('#trait_table').DataTable();
check_cells = table_api.column(0).nodes().to$();
for (let i = 0; i < check_cells.length; i++) {
- if (check_cells[i].childNodes[0].checked){
+ if (check_cells[i].childNodes[check_node].checked){
num_checked += 1
}
}
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 2b8a4d30..b8ffa8e8 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -94,25 +94,7 @@ add = function() {
$('#add_to_collection').click(add);
sample_lists = js_data.sample_lists;
sample_group_types = js_data.sample_group_types;
-d3.select("#select_compare_trait").on("click", (function(_this) {
- return function() {
- $('.scatter-matrix-container').remove();
- return open_trait_selection();
- };
-})(this));
-$(".select_covariates").click(function () {
- open_covariate_selection();
-});
-$(".remove_covariates").click(function () {
- $("input[name=covariates]").val("")
- $(".selected-covariates").val("")
-});
-d3.select("#clear_compare_trait").on("click", (function(_this) {
- return function() {
- return $('.scatter-matrix-container').remove();
- };
-})(this));
open_trait_selection = function() {
return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) {
return function() {
@@ -225,6 +207,8 @@ update_histogram = function() {
if ($('input[name="transform"]').val() != ""){
root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
}
Plotly.newPlot('histogram', root.histogram_data, root.histogram_layout, root.modebar_options);
@@ -273,6 +257,8 @@ update_bar_chart = function() {
if ($('input[name="transform"]').val() != ""){
root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
}
root.bar_data[0]['y'] = trait_vals
@@ -314,6 +300,8 @@ update_box_plot = function() {
if ($('input[name="transform"]').val() != ""){
root.box_layout['yaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.box_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
}
Plotly.newPlot('box_plot', root.box_data, root.box_layout, root.modebar_options)
@@ -345,6 +333,8 @@ update_violin_plot = function() {
if ($('input[name="transform"]').val() != ""){
root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
}
Plotly.newPlot('violin_plot', root.violin_data, root.violin_layout, root.modebar_options)
@@ -467,15 +457,15 @@ edit_data_change = function() {
if (is_number(sample_val) && sample_val !== "") {
sample_val = parseFloat(sample_val);
sample_sets[table].add_value(sample_val);
- if (typeof var_nodes === 'undefined'){
- sample_var = null;
- } else {
+ try {
sample_var = var_nodes[_j].childNodes[0].value
if (is_number(sample_var)) {
sample_var = parseFloat(sample_var)
} else {
sample_var = null;
}
+ } catch {
+ sample_var = null;
}
sample_dict = {
value: sample_val,
@@ -832,6 +822,7 @@ reset_samples_table = function() {
};
$('.reset').click(function() {
reset_samples_table();
+ $('input[name="transform"]').val("");
edit_data_change();
});
@@ -1321,7 +1312,7 @@ if (js_data.num_values < 256) {
margin: {
l: left_margin,
r: 30,
- t: 30,
+ t: 100,
b: bottom_margin
}
};
diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js
index 4df03412..6c443ab3 100644
--- a/wqflask/wqflask/static/new/javascript/stats.js
+++ b/wqflask/wqflask/static/new/javascript/stats.js
@@ -91,8 +91,6 @@ Stats = (function() {
Stats.prototype.interquartile = function() {
var iq, length, q1, q3;
length = this.the_values.length;
- console.log("in interquartile the_values are:", this.the_values);
- console.log("length is:", length);
if (js_data.dataset_type == "ProbeSet" && js_data.data_scale == "linear_positive") {
q1 = Math.log2(this.the_values[Math.floor(length * .25)]);
q3 = Math.log2(this.the_values[Math.floor(length * .75)]);
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 2fb37832..c2256e47 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -245,7 +245,7 @@
<button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
<button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
<button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
- <button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
+ {% if geno_db_exists == "True" %}<button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>{% endif %}
<br />
<br />
<div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;">
@@ -372,6 +372,20 @@
console.time("Creating table");
{% if selectedChr == -1 %}
$('#trait_table').DataTable( {
+ "drawCallback": function( settings ) {
+ $('#trait_table tr').off().on("click", function(event) {
+ if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') {
+ var obj =$(this).find('input');
+ obj.prop('checked', !obj.is(':checked'));
+ }
+ if ($(this).hasClass("selected")){
+ $(this).removeClass("selected")
+ } else {
+ $(this).addClass("selected")
+ }
+ {% if geno_db_exists == "True" %}change_buttons(check_node=1){% endif %}
+ });
+ },
"columns": [
{ "type": "natural", "width": "5%" },
{ "type": "natural", "width": "8%" },
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index f2334512..411a6628 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -3,7 +3,7 @@
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/font-awesome.min.css') }}" />
- <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scroller/css/scroller.dataTables.min.css') }}">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scrollerStyle/css/scroller.dataTables.min.css') }}">
<link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/css/all.min.css">
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
@@ -160,6 +160,16 @@
<script type="text/javascript" charset="utf-8">
$(document).ready( function () {
+
+ 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;
+ };
$('#trait_table tr').click(function(event) {
if (event.target.type !== 'checkbox') {
@@ -225,7 +235,7 @@
'data': null,
'width': "25px",
'orderDataType': "dom-checkbox",
- 'orderSequence': [ "desc", "asc"],
+ 'orderable': false,
'render': function(data, type, row, meta) {
return '<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + data.hmac + '">'
}
@@ -373,15 +383,33 @@
}{% endif %}
],
"order": [[1, "asc" ]],
- 'sDom': "itirp",
+ {% if dataset.type != 'Geno' %}
+ buttons: [
+ {
+ extend: 'columnsToggle',
+ columns: function( idx, data, node ) {
+ if (idx != 0) {
+ return true;
+ } else {
+ return false;
+ }
+ },
+ postfixButtons: [ 'colvisRestore' ]
+ }
+ ],
+ 'sDom': "Bpitirp",
+ {% else %}
+ 'sDom': "pitirp",
+ {% endif %}
'iDisplayLength': 500,
'deferRender': true,
'paging': true,
'orderClasses': true,
'processing': true,
- 'language': {
- 'loadingRecords': '&nbsp;',
- 'processing': 'Loading...'
+ 'bServerSide': true,
+ 'sAjaxSource': '/search_table'+getParams(window.location.href),
+ 'infoCallback': function(settings, start, end, max, total, pre) {
+ return "Showing " + start + " to " + (start + this.api().data().length - 1) + " of " + total + " entries";
}
} );
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 4f347d4e..865959b1 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -21,9 +21,6 @@
<li>
<a href="#violin_plot_tab" class="violin_plot_tab" data-toggle="tab">Violin Plot</a>
</li>
- <li>
- <a href="#scatterplot_matrix" data-toggle="tab">Scatterplot Matrix</a>
- </li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="stats_tab">
@@ -116,19 +113,6 @@
<div id="violin_plot"></div>
</div>
</div>
- <div class="tab-pane" id="scatterplot_matrix">
- <div class="btn-group scatterplot-btn-div">
- <button type="button" class="btn btn-default" id="select_compare_trait">
- <i class="icon-th-large"></i> Select Traits
- </button>
- <button type="button" class="btn btn-default" id="clear_compare_trait">
- <i class="icon-trash"></i> Clear
- </button>
- </div>
- <div id="scatterplot_container">
- <div id="comparison_scatterplot" class="qtlcharts"></div>
- </div>
- </div>
</div>
</div>
<div id="collections_holder_wrapper" style="display:none;">
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index a96b8e3b..b9aea570 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -15,7 +15,7 @@
<input type="hidden" name="first_run" value="{{ first_run }}">
<input type="hidden" name="chosen_strains_mouse" value="{{ chosen_strains_mouse|join(",") }}">
<input type="hidden" name="chosen_strains_rat" value="{{ chosen_strains_rat|join(",") }}">
- <div class="col-xs-4" style="padding-left: 0px;">
+ <div class="col-xs-4" style="width: 260px; padding-left: 30px; padding-right: 0px;">
<div class="form-group row" style="margin-bottom: 5px;">
<label for="snp_or_indel" style="text-align: right;" class="col-xs-4 col-form-label"><b>Type:</b></label>
<div class="col-xs-8">
@@ -74,7 +74,7 @@
</div>
</div>
</div>
- <div class="col-xs-4" style="padding-left: 0px;">
+ <div class="col-xs-4" style="width: 310px; padding-left: 0px; padding-right: 20px;">
<div class="form-group row" style="margin-bottom: 10px;">
<label for="strains" style="text-align: right;" class="col-xs-4 col-form-label"><b>Strains:</b></label>
<div class="col-xs-8">
@@ -107,8 +107,14 @@
</div>
</div>
</div>
+ <div class="form-group row">
+ <label class="col-xs-4 col-form-label"></label>
+ <div class="col-xs-8" style="margin-top: 65px;">
+ <input class="btn btn-primary" type="button" name="export_csv" value="Export to CSV">
+ </div>
+ </div>
</div>
- <div class="col-xs-4" style="padding-left: 20px;">
+ <div class="col-xs-4" style="width: 310px; padding-left: 20px;">
<div class="form-group row" style="margin-bottom: 5px;">
<label for="domain" style="text-align: right;" class="col-xs-4 col-form-label"><b>Domain:</b></label>
<div class="col-xs-8">
@@ -182,24 +188,21 @@
</div>
<div style="margin-top: 20px;">
- {% if filtered_results is defined %}
- {% if filtered_results|length > limit_number %}
- There are more than 10000 results. Consider limiting your search to a smaller range.
- {% else %}
+ {% if table_rows is defined %}
<table class="dataTable cell-border nowrap" id="results_table" style="float: left;">
<thead>
<tr>
<th></th>
{% if header_fields|length == 2 %}
{% for header in header_fields[0] %}
- <th data-export="{{ header }}">{{ header }}</th>
+ <th data-export="{{ header }}" name="{{ header }}">{{ header }}</th>
{% endfor %}
{% for strain in header_fields[1] %}
- <th data-export="{{ strain }}" style="align: center; text-align: center; line-height: 15px;">{% for letter in strain %}<div style="transform: rotate(90deg);">{{ letter }}</div>{% endfor %}</th>
+ <th data-export="{{ strain }}" name="{{ strain }}" style="align: center; text-align: center; line-height: 12px;">{% for letter in strain|reverse %}<div style="transform: rotate(270deg);">{{ letter }}</div>{% endfor %}</th>
{% endfor %}
{% else %}
{% for header in header_fields %}
- <th data-export="{{ header }}">{{ header }}</th>
+ <th data-export="{{ header }}" name="{{ header }}">{{ header }}</th>
{% endfor %}
{% endif %}
</tr>
@@ -208,7 +211,6 @@
<td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
</tbody>
</table>
- {% endif %}
{% endif %}
</div>
</div>
@@ -222,12 +224,24 @@
<script language="javascript" type="text/javascript" src="/static/new/javascript/typeahead_rn6.json"></script>
<script type='text/javascript'>
- var json_rows = {{ table_rows|safe }};
var empty_columns = {{ empty_columns|safe }};
+
+ var remain_field_count = 15 - {{ empty_field_count|safe }};
+ var total_field_count = 15 - {{ empty_field_count|safe }} + {{ allele_list|safe|length }};
</script>
<script language="javascript">
+ 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;
+ };
+
var substringMatcher = function(strs) {
return function findMatches(q, cb) {
var matches, substringRegex;
@@ -260,19 +274,20 @@
source: substringMatcher(rat_genes)
});
- {% if filtered_results is defined %}
+ {% if table_rows is defined %}
$("#results_table").DataTable( {
- 'data': json_rows,
{% if variant_type == "SNP" %}
'columns': [
{
'data': null,
+ 'className': 'dt-body-center',
'orderable': false,
'render': function(data, type, row, meta) {
- return '<input type="checkbox" name="trait_check">'
+ return '<input type="checkbox" class="checkbox" id="variant_checkbox" onchange="onVarinatCheck(this)" name="trait_check">'
}
}, {
- 'data': 'index'
+ 'data': 'index',
+ 'className': 'dt-body-right'
}, {
'data': null,
'render': function(data, type, row, meta) {
@@ -283,27 +298,30 @@
}
}
}, {
- 'data': 'chr'
+ 'data': 'chr',
+ 'className': 'dt-body-center'
}, {
- 'data': 'mb_formatted'
+ 'data': 'mb_formatted',
+ 'className': 'dt-body-right'
}, {
'data': 'alleles'
}, {% if empty_columns['snp_source'] == "true" %}{
'data': null,
'render': function(data, type, row, meta) {
if (data.snp_source == "Sanger/UCLA") {
- return '<a href="' + data.source_urls[0] + '">Sanger</a><a href="' + data.source_urls[1] + '">UCLA</a>'
+ return '<a href="' + data.source_urls[0] + '">Sanger</a>, <a href="' + data.source_urls[1] + '">UCLA</a>'
} else {
return data.snp_source
}
}
}, {% endif %} {% if empty_columns['conservation_score'] == "true" %}{
- 'data': 'conservation_score'
+ 'data': 'conservation_score',
+ 'className': 'dt-body-right'
}, {% endif %} {% if empty_columns['gene_name'] == "true" %}{
'data': null,
'render': function(data, type, row, meta) {
if (data.gene_name != "") {
- return '<i>' + data.gene_name + '</i><br><a href="' + data.gene_link + '">NCBI</a>'
+ return '<i>' + data.gene_name + '</i>, <a href="' + data.gene_link + '">NCBI</a>'
} else {
return data.gene_name
}
@@ -330,6 +348,7 @@
}, {% endif %} {% for item in allele_list %} {
'data': null,
'orderable': false,
+ 'className': 'dt-body-center',
'render': function(data, type, row, meta) {
if (typeof data.allele_value_list[{{ loop.index - 1 }}][0] !== "undefined") {
return data.allele_value_list[{{ loop.index - 1 }}][0]
@@ -339,12 +358,9 @@
}
}{% if loop.index < allele_list|length %},{% endif %}{% endfor %}
],
- 'createdRow': function( row, data, dataIndex) {
- $('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
- $('td', row).eq(1).attr("align", "right");
- for (i = {{ 15 - empty_field_count }}; i < ({{ 15 - empty_field_count }} + {{ allele_list|length }}); i++) {
+ 'createdRow': function(row, data, dataIndex) {
+ for (i = remain_field_count; i < total_field_count; i++) {
var this_allele = $('td', row).eq(i).text();
- $('td', row).eq(i).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
switch (this_allele) {
case "A":
$('td', row).eq(i).addClass('A_allele_color');
@@ -380,24 +396,29 @@
{
'data': null,
'render': function(data, type, row, meta) {
- return '<input type="checkbox" name="trait_check">'
+ return '<input type="checkbox" class="checkbox" id="variant_checkbox" onchange="onVarinatCheck(this)" name="trait_check">'
}
}, {
- 'data': 'index'
+ 'data': 'index',
+ 'className': 'dt-body-right'
}, {
'data': 'indel_name'
}, {
'data': 'indel_type'
}, {
- 'data': 'indel_chr'
+ 'data': 'indel_chr',
+ 'className': 'dt-body-center'
}, {
- 'data': 'indel_mb_s'
+ 'data': 'indel_mb_s',
+ 'className': 'dt-body-right'
}, {
- 'data': 'indel_mb_e'
+ 'data': 'indel_mb_e',
+ 'className': 'dt-body-right'
}, {
'data': 'indel_strand'
}, {
- 'data': 'indel_size'
+ 'data': 'indel_size',
+ 'className': 'dt-body-right'
}, {
'data': 'indel_sequence'
}, {
@@ -407,15 +428,28 @@
{% endif %}
'order': [[1, "asc" ]],
'sDom': "rtip",
- 'iDisplayLength': 500,
- 'processing': true,
- 'language': {
- 'loadingRecords': '&nbsp;',
- 'processing': 'Loading...'
+ 'iDisplayLength': 100,
+ 'bServerSide': true,
+ 'sAjaxSource': '/snp_browser_table'+getParams(window.location.href),
+ 'infoCallback': function(settings, start, end, max, total, pre) {
+ return "Showing " + start + " to " + (start + this.api().data().length - 1) + " of " + total + " entries";
}
});
{% endif %}
+ function onVarinatCheck(checkboxElem) {
+ if (checkboxElem.checked) {
+ if (!checkboxElem.parentElement.parentElement.classList.contains('selected')) {
+ checkboxElem.parentElement.parentElement.classList.add('selected')
+ }
+ }
+ else {
+ if (checkboxElem.parentElement.parentElement.classList.contains('selected')) {
+ checkboxElem.parentElement.parentElement.classList.remove('selected')
+ }
+ }
+ }
+
$("#species_select").change(function() {
this_species = $(this).val();
$("#strain_select").empty()
@@ -509,6 +543,40 @@
});
$("input[name=chosen_strains]").val(strain_list.join(","));
});
+
+
+
+ $("input[name=export_csv]").click(function() {
+ var csv = [];
+ var rows = document.querySelectorAll("table tr");
+
+ var headers = [];
+ var col_header = rows[0].querySelectorAll("th");
+ for(let i = 1; i < col_header.length; i++) {
+ headers.push(col_header[i].getAttribute("name"));
+ }
+ csv.push(headers.join(","));
+
+ for (let i = 1; i < rows.length; i++) {
+ var row = [], cols = rows[i].querySelectorAll("td");
+ var checkBox = rows[i].querySelector("input");
+
+ if(checkBox.checked == true) {
+ for (let j = 1; j < cols.length; j++)
+ row.push(cols[j].innerText);
+
+ csv.push(row.join(","));
+ }
+ }
+
+ var csvFile = new Blob([csv.join("\n")], {type: "text/csv"});
+ var downloadLink = document.createElement("a");
+ downloadLink.download = "variant_data.csv";
+ downloadLink.href = window.URL.createObjectURL(csvFile);
+ downloadLink.style.display = "none";
+ document.body.appendChild(downloadLink);
+ downloadLink.click();
+ });
</script>
{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 6b706b3f..e4834d53 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -26,6 +26,15 @@ import sqlalchemy
from wqflask import app
from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file
+from wqflask import group_manager
+from wqflask import resource_manager
+from wqflask import search_results
+from wqflask import export_traits
+from wqflask import gsearch
+from wqflask import update_search_results
+from wqflask import docs
+from wqflask import news
+from wqflask import server_side
from wqflask.submit_bnw import get_bnw_input
from base.data_set import create_dataset, DataSet # Used by YAML in marker_regression
from wqflask.show_trait import show_trait
@@ -220,6 +229,26 @@ def search_page():
else:
return render_template("search_error.html")
+@app.route("/search_table", methods=('GET',))
+def search_page_table():
+ logger.info("in search_page table")
+ logger.info(request.url)
+
+ logger.info("request.args is", request.args)
+ the_search = search_results.SearchResultPage(request.args)
+
+ logger.info(type(the_search.trait_list))
+ logger.info(the_search.trait_list)
+
+ current_page = server_side.ServerSideTable(
+ len(the_search.trait_list),
+ the_search.trait_list,
+ the_search.header_data_names,
+ request.args,
+ ).get_page()
+
+ return flask.jsonify(current_page)
+
@app.route("/gsearch", methods=('GET',))
def gsearchact():
logger.info(request.url)
@@ -890,6 +919,19 @@ def db_info_page():
return render_template("info_page.html", **template_vars.__dict__)
+@app.route("/snp_browser_table", methods=('GET',))
+def snp_browser_table():
+ logger.info(request.url)
+ snp_table_data = snp_browser.SnpBrowser(request.args)
+ current_page = server_side.ServerSideTable(
+ snp_table_data.rows_count,
+ snp_table_data.table_rows,
+ snp_table_data.header_data_names,
+ request.args,
+ ).get_page()
+
+ return flask.jsonify(current_page)
+
@app.route("/tutorial/WebQTLTour", methods=('GET',))
def tutorial_page():
#ZS: Currently just links to GN1