From 7932f962aff0ac35dd53b84e483f405de81c0612 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 5 Nov 2020 15:07:58 -0600 Subject: Imported Scroller and used it with correlation page table --- wqflask/wqflask/templates/correlation_page.html | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index bc0b592c..06499ec6 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -215,6 +215,7 @@ + + @@ -331,10 +333,10 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "High P ?", + 'title': "High P ", 'type': "natural-minus-na", 'data': "lrs_score", - 'width': "60px", + 'width': "65px", 'orderSequence': [ "desc", "asc"] }, { @@ -344,10 +346,10 @@ 'data': "lrs_location" }, { - 'title': "Effect Size ?", + 'title': "Effect Size ", 'type': "natural-minus-na", 'data': "additive", - 'width': "85px", + 'width': "90px", 'orderSequence': [ "desc", "asc"] }{% elif dataset.type == 'Publish' %}, { @@ -400,7 +402,7 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "High P ?", + 'title': "High P ", 'type': "natural-minus-na", 'data': "lrs_score", 'width': "80px", @@ -413,7 +415,7 @@ 'data': "lrs_location" }, { - 'title': "Effect Size ?", + 'title': "Effect Size ", 'type': "natural-minus-na", 'width': "120px", 'data': "additive", -- cgit v1.2.3 From db0e80bef73eb163bfb747ec4d137d5c5069ade8 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 13 Nov 2020 13:40:40 -0600 Subject: Added cdn imports for fontawesome to correlation page and changed superscript i's to fontawesome icons for the glossary links in column headers --- wqflask/wqflask/templates/correlation_page.html | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index bb7d3df6..6ea86609 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -4,6 +4,7 @@ + {% endblock %} {% block content %} @@ -145,7 +146,8 @@ - + + -- cgit v1.2.3 From 76d5b24b3d2e0b5e6be5b1cf4c125a9a812ff57a Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 13 Nov 2020 15:25:32 -0600 Subject: Switched to using boolean casting to check if various trait attributes exist --- wqflask/wqflask/correlation/show_corr_results.py | 59 ++++++++++++------------ 1 file changed, 29 insertions(+), 30 deletions(-) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 17d3de54..87dd7597 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -494,61 +494,60 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap results_dict['mean'] = "N/A" results_dict['lrs_score'] = "N/A" results_dict['additive'] = "N/A" - if trait.description_display: + if bool(trait.description_display): results_dict['description'] = trait.description_display - if trait.mean and trait.mean != "": + if bool(trait.mean): results_dict['mean'] = float(trait.mean) if trait.LRS_score_repr != "N/A": results_dict['lrs_score'] = "%.1f" % float(trait.LRS_score_repr) results_dict['lrs_location'] = trait.LRS_location_repr - if trait.additive and trait.additive != "": + if bool(trait.additive): results_dict['additive'] = "%0.3f" % float(trait.additive) results_dict['sample_r'] = "%0.3f" % float(trait.sample_r) results_dict['num_overlap'] = trait.num_overlap results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) - if trait.lit_corr == "" or trait.lit_corr == 0: - results_dict['lit_corr'] = "--" - else: + results_dict['lit_corr'] = "--" + results_dict['tissue_corr'] = "--" + results_dict['tissue_pvalue'] = "--" + if bool(trait.lit_corr): results_dict['lit_corr'] = "%0.3f" % float(trait.lit_corr) - if trait.tissue_corr == "" or trait.tissue_corr == 0: - results_dict['tissue_corr'] = "--" - results_dict['tissue_pvalue'] = "--" - else: + if bool(trait.tissue_corr): results_dict['tissue_corr'] = "%0.3f" % float(trait.tissue_corr) results_dict['tissue_pvalue'] = "%0.3e" % float(trait.tissue_pvalue) elif target_dataset.type == "Publish": results_dict['abbreviation_display'] = "N/A" - if trait.abbreviation: - results_dict['abbreviation_display'] = trait.abbreviation results_dict['description'] = "N/A" - if trait.description_display: - results_dict['description'] = trait.description_display - results_dict['authors'] = trait.authors - authors_list = trait.authors.split(',') - if len(authors_list) > 6: - results_dict['authors_display'] = ", ".join(authors_list[:6]) + ", et al." + results_dict['authors_display'] = "N/A" + results_dict['additive'] = "N/A" + if for_api: + results_dict['pubmed_id'] = "N/A" + results_dict['year'] = "N/A" else: - results_dict['authors_display'] = trait.authors - if trait.pubmed_id: + results_dict['pubmed_link'] = "N/A" + results_dict['pubmed_text'] = "N/A" + + if bool(trait.abbreviation): + results_dict['abbreviation_display'] = trait.abbreviation + if bool(trait.description_display): + results_dict['description'] = trait.description_display + if bool(trait.authors): + authors_list = trait.authors.split(',') + if len(authors_list) > 6: + results_dict['authors_display'] = ", ".join(authors_list[:6]) + ", et al." + else: + results_dict['authors_display'] = trait.authors + if bool(trait.pubmed_id): if for_api: results_dict['pubmed_id'] = trait.pubmed_id results_dict['year'] = trait.pubmed_text else: results_dict['pubmed_link'] = trait.pubmed_link results_dict['pubmed_text'] = trait.pubmed_text - else: - if for_api: - results_dict['pubmed_id'] = "N/A" - results_dict['year'] = "N/A" - else: - results_dict['pubmed_link'] = "N/A" - results_dict['pubmed_text'] = "N/A" + results_dict['lrs_score'] = trait.LRS_score_repr results_dict['lrs_location'] = trait.LRS_location_repr - if trait.additive and trait.additive != "": + if bool(trait.additive): results_dict['additive'] = "%0.3f" % float(trait.additive) - else: - results_dict['additive'] = "N/A" results_dict['sample_r'] = "%0.3f" % trait.sample_r results_dict['num_overlap'] = trait.num_overlap results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) -- cgit v1.2.3 From 678d9cd4e073c3936c34d3b9b54f1e6c590def27 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 13 Nov 2020 15:37:49 -0600 Subject: Switched to using f-strings instead of the older method of string formatting --- wqflask/wqflask/correlation/show_corr_results.py | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 87dd7597..1b801b1d 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -499,21 +499,21 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap if bool(trait.mean): results_dict['mean'] = float(trait.mean) if trait.LRS_score_repr != "N/A": - results_dict['lrs_score'] = "%.1f" % float(trait.LRS_score_repr) + results_dict['lrs_score'] = f"{float(trait.LRS_score_repr):.1f}" results_dict['lrs_location'] = trait.LRS_location_repr if bool(trait.additive): - results_dict['additive'] = "%0.3f" % float(trait.additive) - results_dict['sample_r'] = "%0.3f" % float(trait.sample_r) + results_dict['additive'] = f"{float(trait.additive):.3f}" + results_dict['sample_r'] = f"{float(trait.sample_r):.3f}" results_dict['num_overlap'] = trait.num_overlap - results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + results_dict['sample_p'] = f"{float(trait.sample_p):.3e}" results_dict['lit_corr'] = "--" results_dict['tissue_corr'] = "--" results_dict['tissue_pvalue'] = "--" if bool(trait.lit_corr): - results_dict['lit_corr'] = "%0.3f" % float(trait.lit_corr) + results_dict['lit_corr'] = f"{float(trait.lit_corr):.3f}" if bool(trait.tissue_corr): - results_dict['tissue_corr'] = "%0.3f" % float(trait.tissue_corr) - results_dict['tissue_pvalue'] = "%0.3e" % float(trait.tissue_pvalue) + results_dict['tissue_corr'] = f"{float(trait.tissue_corr):.3f}" + results_dict['tissue_pvalue'] = f"{float(trait.tissue_pvalue):.3e}" elif target_dataset.type == "Publish": results_dict['abbreviation_display'] = "N/A" results_dict['description'] = "N/A" @@ -547,15 +547,15 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap results_dict['lrs_score'] = trait.LRS_score_repr results_dict['lrs_location'] = trait.LRS_location_repr if bool(trait.additive): - results_dict['additive'] = "%0.3f" % float(trait.additive) - results_dict['sample_r'] = "%0.3f" % trait.sample_r + results_dict['additive'] = f"{float(trait.additive):.3f}" + results_dict['sample_r'] = f"{float(trait.sample_r):.3f}" results_dict['num_overlap'] = trait.num_overlap - results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + results_dict['sample_p'] = f"{float(trait.sample_p):.3e}" else: results_dict['location'] = trait.location_repr - results_dict['sample_r'] = "%0.3f" % trait.sample_r + results_dict['sample_r'] = f"{float(trait.sample_r):.3f}" results_dict['num_overlap'] = trait.num_overlap - results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + results_dict['sample_p'] = f"{float(trait.sample_p):.3e}" results_list.append(results_dict) -- cgit v1.2.3 From ceeae6fd087d91637c5007e0433ce347048fa96d Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Tue, 17 Nov 2020 22:31:10 +0300 Subject: use better function names --- .../tests/wqflask/marker_regression/test_gemma_mapping.py | 14 +++++++------- .../tests/wqflask/marker_regression/test_rqtl_mapping.py | 2 +- .../tests/wqflask/marker_regression/test_run_mapping.py | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index af20c1b8..4fafd95a 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -23,7 +23,7 @@ class MockDatasetGroup(AttributeSetter): class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") - def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): + def test_run_gemma_firstrun_set_false(self, mock_parse_loco): """add tests for gemma function where first run is set to false""" dataset = AttributeSetter( {"group": AttributeSetter({"genofile": "genofile.geno"})}) @@ -49,7 +49,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.run_mapping.random.choice") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): + def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): """add tests for run_gemma where first run is set to true""" chromosomes = [] for i in range(1, 5): @@ -140,7 +140,7 @@ class TestGemmaMapping(unittest.TestCase): '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") - def test_parse_gemma_output_obj_returned(self): + def test_parse_gemma_output(self): """add test for generating gemma output with obj returned""" file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 @@ -157,7 +157,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 self.assertEqual(results, expected) @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") - def test_parse_gemma_output_empty_return(self): + def test_parse_gemma_output_with_empty_return(self): """add tests for parse gemma output where nothing returned""" output_file_results = """chr\t today""" with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: @@ -167,7 +167,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.json") - def test_parse_loco_output_file_found(self, mock_json, mock_os): + def test_parse_loco_outputfile_found(self, mock_json, mock_os): """add tests for parse loco output file found""" mock_json.load.return_value = { "files": [["file_name", "user", "~/file1"], @@ -193,8 +193,8 @@ chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") - def test_parse_loco_output_file_not_found(self, mock_os): - """add tests for parse loco output file not found""" + def test_parse_loco_outputfile_not_found(self, mock_os): + """add tests for parse loco output where output file not found""" mock_os.path.isfile.return_value = False file_to_write = """{"files":["file_1","file_2"]}""" diff --git a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py index 9fd32a30..69f53721 100644 --- a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py @@ -17,7 +17,7 @@ class TestRqtlMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.rqtl_mapping.g") @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data_type_found(self,mock_logger,mock_db): + def test_get_trait_data(self,mock_logger,mock_db): """test for getting trait data_type return True""" caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py index 2af4c3e3..a134f551 100644 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -62,7 +62,7 @@ class TestRunMapping(unittest.TestCase): self.assertEqual(result_2, []) @mock.patch("wqflask.marker_regression.run_mapping.data_set") - def test_geno_db_exists(self, mock_data_set): + def test_if_geno_db_exists(self, mock_data_set): mock_data_set.create_dataset.side_effect = [ AttributeSetter({}), Exception()] results_no_error = geno_db_exists(self.dataset) -- cgit v1.2.3 From 9d3493f2e8ee2d2185854b95d2b13a5d2b4e38e1 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Wed, 18 Nov 2020 02:18:45 +0300 Subject: use f strings in marker_regression/plink_mapping --- wqflask/wqflask/marker_regression/plink_mapping.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 8d57d556..5d675c38 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -9,11 +9,11 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) def run_plink(this_trait, dataset, species, vals, maf): - plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(dataset.group.name, this_trait.name)) + plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_") gen_pheno_txt_file(dataset, vals) - plink_command = PLINK_COMMAND + ' --noweb --bfile %s/%s --no-pheno --no-fid --no-parents --no-sex --maf %s --out %s%s --assoc ' % ( - flat_files('mapping'), dataset.group.name, maf, TMPDIR, plink_output_filename) + + plink_command = f"{PLINK_COMMAND} --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc " logger.debug("plink_command:", plink_command) os.system(plink_command) @@ -29,12 +29,12 @@ def gen_pheno_txt_file(this_dataset, vals): """Generates phenotype file for GEMMA/PLINK""" current_file_data = [] - with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile: + with open(f"{flat_files('mapping')}/{this_dataset.group.name}.fam", "r") as outfile: for i, line in enumerate(outfile): split_line = line.split() current_file_data.append(split_line) - with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile: + with open(f"{flat_files('mapping')}/{this_dataset.group.name}.fam","w") as outfile: for i, line in enumerate(current_file_data): if vals[i] == "x": this_val = -9 @@ -44,8 +44,8 @@ def gen_pheno_txt_file(this_dataset, vals): def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): ped_sample_list = get_samples_from_ped_file(dataset) - output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb") - header = 'FID\tIID\t%s\n' % this_trait.name + output_file = open(f"{TMPDIR}{pheno_filename}.txt", "wb") + header = f"FID\tIID\t{this_trait.name}\n" output_file.write(header) new_value_list = [] @@ -65,7 +65,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): for i, sample in enumerate(ped_sample_list): j = i+1 value = new_value_list[i] - new_line += '%s\t%s\t%s\n'%(sample, sample, value) + new_line += f"{sample}\t{sample}\t{value}\n" if j%1000 == 0: output_file.write(newLine) @@ -78,7 +78,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): # get strain name from ped file in order def get_samples_from_ped_file(dataset): - ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name), "r") + ped_file= open(f"{flat_files('mapping')}{dataset.group.name}.ped","r") line = ped_file.readline() sample_list=[] @@ -98,7 +98,7 @@ def parse_plink_output(output_filename, species): threshold_p_value = 1 - result_fp = open("%s%s.qassoc"% (TMPDIR, output_filename), "rb") + result_fp = open(f"{TMPDIR}{output_filename}.qassoc","rb") line = result_fp.readline() -- cgit v1.2.3 From 77dff447c83a4b0824fe6626d16484cfd826ca77 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Wed, 18 Nov 2020 03:06:27 +0300 Subject: use f strings in marker_regression/qtlreaper_mapping.py --- .../wqflask/marker_regression/qtlreaper_mapping.py | 46 +++++++++++++--------- 1 file changed, 28 insertions(+), 18 deletions(-) diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 78b1f7b0..505ae295 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -17,22 +17,29 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo else: genofile_name = this_dataset.group.name - trait_filename = str(this_trait.name) + "_" + str(this_dataset.name) + "_pheno" + trait_filename =f"{str(this_trait.name)}_{str(this_dataset.name)}_pheno" gen_pheno_txt_file(samples, vals, trait_filename) - output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + output_filename = (f"{this_dataset.group.name}_GWA_"+ + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + ) bootstrap_filename = None permu_filename = None opt_list = [] if boot_check and num_bootstrap > 0: - bootstrap_filename = this_dataset.group.name + "_BOOTSTRAP_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" + + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + ) opt_list.append("-b") - opt_list.append("--n_bootstrap " + str(num_bootstrap)) - opt_list.append("--bootstrap_output " + webqtlConfig.GENERATED_IMAGE_DIR + bootstrap_filename + ".txt") + opt_list.append(f"--n_bootstrap{str(num_bootstrap)}") + opt_list.append(f"--bootstrap_output{webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") if num_perm > 0: - permu_filename = this_dataset.group.name + "_PERM_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + permu_filename =("{this_dataset.group.name}_PERM_" + + ''.join(random.choice(string.ascii_uppercase + + string.digits) for _ in range(6)) + ) opt_list.append("-n " + str(num_perm)) opt_list.append("--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt") if control_marker != "" and do_control == "true": @@ -40,13 +47,15 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo if manhattan_plot != True: opt_list.append("--interval 1") - reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'), - genofile_name, - TEMPDIR, - trait_filename, - " ".join(opt_list), - webqtlConfig.GENERATED_IMAGE_DIR, - output_filename) + reaper_command = (REAPER_COMMAND + + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'), + + genofile_name, + TEMPDIR, + trait_filename, + " ".join(opt_list), + webqtlConfig.GENERATED_IMAGE_DIR, + output_filename)) logger.debug("reaper_command:" + reaper_command) os.system(reaper_command) @@ -61,12 +70,13 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo suggestive = permu_vals[int(num_perm*0.37-1)] significant = permu_vals[int(num_perm*0.95-1)] - return marker_obs, permu_vals, suggestive, significant, bootstrap_vals, [output_filename, permu_filename, bootstrap_filename] + return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals, + [output_filename, permu_filename, bootstrap_filename]) def gen_pheno_txt_file(samples, vals, trait_filename): """Generates phenotype file for GEMMA""" - with open("{}/gn2/{}.txt".format(TEMPDIR, trait_filename), "w") as outfile: + with open(f"{TEMPDIR}/gn2/{trait_filename}.txt","w") as outfile: outfile.write("Trait\t") filtered_sample_list = [] @@ -90,7 +100,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): only_cm = False only_mb = False - with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, gwa_filename)) as output_file: + with open(f"{webqtlConfig.GENERATED_IMAGE_DIR}{gwa_filename}.txt") as output_file: for line in output_file: if line.startswith("ID\t"): if len(line.split("\t")) < 8: @@ -137,13 +147,13 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): permu_vals = [] if permu_filename: - with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, permu_filename)) as permu_file: + with open(f"{webqtlConfig.GENERATED_IMAGE_DIR}{permu_filename}.txt") as permu_file: for line in permu_file: permu_vals.append(float(line)) bootstrap_vals = [] if bootstrap_filename: - with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, bootstrap_filename)) as bootstrap_file: + with open(f"{webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") as bootstrap_file: for line in bootstrap_file: bootstrap_vals.append(int(line)) -- cgit v1.2.3 From cf4db5545efee6d9052153708fc05ca707ef1716 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 24 Nov 2020 12:51:17 -0600 Subject: Added html/css for new "Filter Samples by Value" feature and changed a couple class names to make more sense for being shared between both this feature and "Block Samples by Index" --- wqflask/wqflask/static/new/css/show_trait.css | 4 ++-- .../templates/show_trait_transform_and_filter.html | 23 ++++++++++++++++++++-- 2 files changed, 23 insertions(+), 4 deletions(-) diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 5e1a279b..39c6ba53 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -145,11 +145,11 @@ input.corr-location { display: inline; } -div.block-by-index-div { +div.block-div { margin-bottom: 10px; } -div.block-by-attribute-div { +div.block-div-2 { margin-top:10px; margin-bottom:10px; } diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index 0418d972..22c52d8c 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -4,7 +4,7 @@ Reset option as needed.

-
+
+ + + + + + + + +
{% if sample_groups[0].attributes %} -
+
+ {% for attribute in sample_groups[0].attributes %} + {% if sample_groups[0].attributes[attribute].distinct_values|length <= 10 %} + + {% endif %} + {% endfor %} + + + + +
+ {% endif %}
- + + {% if sample_groups[0].attributes %} + + {% endif %}
- {% if sample_groups[0].attributes %} -
- - - - -
- {% endif %}
-- cgit v1.2.3 From a53302a077b8eea3591460a03a60c9621c3f4586 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Nov 2020 13:11:11 -0600 Subject: Substituted CDN link to the font-awesome CSS with the local guix profile link --- wqflask/wqflask/templates/search_result_page.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 8e2b06a4..35d8ed27 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -2,9 +2,9 @@ {% block title %}Search Results{% endblock %} {% block css %} + - {% endblock %} -- cgit v1.2.3 From c8a339616fb3dd3f63427378dc4285de9ad1ccef Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Nov 2020 13:11:48 -0600 Subject: Removed an unused console.timeEnd in the JS --- wqflask/wqflask/templates/search_result_page.html | 2 -- 1 file changed, 2 deletions(-) diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 35d8ed27..9a28a78e 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -440,8 +440,6 @@ 'processing': 'Loading...' } } ); - - console.timeEnd("Creating table"); $('.toggle-vis').on( 'click', function (e) { e.preventDefault(); -- cgit v1.2.3 From ab6681e545bd4c84e1f74107b90ea52f7d2ca24c Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Nov 2020 13:15:25 -0600 Subject: Added form options for changing manhattan plot color scheme + added necessary imports and hidden inputs --- wqflask/wqflask/templates/mapping_results.html | 47 +++++++++++++++++++++++--- 1 file changed, 42 insertions(+), 5 deletions(-) diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 28d93542..9542c29d 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -40,6 +40,9 @@ + {% if manhattan_plot == True %} + + {% endif %} @@ -55,7 +58,7 @@ -
+

Map Viewer: Whole Genome


Population: {{ dataset.group.species|capitalize }} {{ dataset.group.name }}
@@ -77,7 +80,7 @@ - - + @@ -114,11 +117,31 @@ -
Chr:  +
View: View:  to
Width:  + pixels (minimum=900)
+ {% if manhattan_plot == True and selectedChr == -1 %} + + + + + + +
+ Manhattan Plot Color Scheme:  + + + + + +
+ {% endif %}
{% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %} @@ -328,6 +351,9 @@ + {% if manhattan_plot == True and selectedChr == -1 %} + + {% endif %} @@ -423,7 +449,7 @@ var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results', - 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', + 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'color_scheme', 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'n_samples'] @@ -449,10 +475,21 @@ remap = function() { $('input[name=selected_chr]').val($('select[name=chromosomes]').val()); + $('input[name=color_scheme]').val($('select#color_scheme').val()); $('#marker_regression_form').attr('action', '/loading'); return $('#marker_regression_form').submit(); }; + {% if manhattan_plot == True and selectedChr == -1 %} + $('#color_scheme').change(function(){ + if ($(this).val() == "single"){ + $('#point_color_picker').show(); + } else { + $('#point_color_picker').hide(); + } + }); + {% endif %} + {% if mapping_method != "gemma" and mapping_method != "plink" %} $('#download_perm').click(function(){ perm_info_dict = { -- cgit v1.2.3 From a1563aee47a54d5ff4253e1da7e851afe28805c0 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Nov 2020 13:16:26 -0600 Subject: Added code for passing around form parameters related to manhattan plot coloration to run_mapping.py and views.py --- wqflask/wqflask/marker_regression/run_mapping.py | 7 ++++++- wqflask/wqflask/views.py | 2 ++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 31d6a67c..c474e0e0 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -138,7 +138,12 @@ class RunMapping(object): mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) - if start_vars['manhattan_plot'] == "true": + if start_vars['manhattan_plot']: + self.color_scheme = "alternating" + if "color_scheme" in start_vars: + self.color_scheme = start_vars['color_scheme'] + if self.color_scheme == "single": + self.manhattan_single_color = start_vars['manhattan_single_color'] self.manhattan_plot = True else: self.manhattan_plot = False diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index b7c4d142..7118bab7 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -718,6 +718,8 @@ def mapping_results_page(): 'maf', 'use_loco', 'manhattan_plot', + 'color_scheme', + 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', -- cgit v1.2.3 From d1740605ffd36e49b9560e81c0e085c58ef8b688 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Nov 2020 13:17:03 -0600 Subject: Added actual code for coloring manhattan plot differently to display_mapping_results.py --- .../marker_regression/display_mapping_results.py | 46 ++++++++++++++++++++-- 1 file changed, 43 insertions(+), 3 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 3f6de2b2..87910401 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -74,6 +74,34 @@ DARKVIOLET = ImageColor.getrgb("darkviolet") MEDIUMPURPLE = ImageColor.getrgb("mediumpurple") # ---- END: Define common colours ---- # +# ZS: List of distinct colors for manhattan plot if user selects "varied" +DISTINCT_COLOR_LIST = [ + ImageColor.getrgb("#FF0000"), + ImageColor.getrgb("#00FF00"), + ImageColor.getrgb("#0000FF"), + ImageColor.getrgb("#FFFF00"), + ImageColor.getrgb("#FF00FF"), + ImageColor.getrgb("#00FFFF"), + ImageColor.getrgb("#000000"), + ImageColor.getrgb("#800000"), + ImageColor.getrgb("#008000"), + ImageColor.getrgb("#000080"), + ImageColor.getrgb("#808000"), + ImageColor.getrgb("#800080"), + ImageColor.getrgb("#008080"), + ImageColor.getrgb("#808080"), + ImageColor.getrgb("#C00000"), + ImageColor.getrgb("#00C000"), + ImageColor.getrgb("#0000C0"), + ImageColor.getrgb("#C0C000"), + ImageColor.getrgb("#C000C0"), + ImageColor.getrgb("#00C0C0"), + ImageColor.getrgb("#C0C0C0"), + ImageColor.getrgb("#400000"), + ImageColor.getrgb("#004000"), + ImageColor.getrgb("#000040"), +] + # ---- FONT FILES ---- # VERDANA_FILE = "./wqflask/static/fonts/verdana.ttf" VERDANA_BOLD_FILE = "./wqflask/static/fonts/verdanab.ttf" @@ -293,6 +321,12 @@ class DisplayMappingResults(object): self.plotScale = "physic" self.manhattan_plot = start_vars['manhattan_plot'] + if self.manhattan_plot: + self.color_scheme = "alternating" + if 'color_scheme' in start_vars: + self.color_scheme = start_vars['color_scheme'] + if self.color_scheme == "single": + self.manhattan_single_color = ImageColor.getrgb("#" + start_vars['manhattan_single_color']) if 'permCheck' in list(start_vars.keys()): self.permChecked = start_vars['permCheck'] @@ -2424,10 +2458,16 @@ class DisplayMappingResults(object): Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max if self.manhattan_plot == True: - if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1): - point_color = RED + if self.color_scheme == "single": + point_color = self.manhattan_single_color + elif self.color_scheme == "varied": + point_color = DISTINCT_COLOR_LIST[previous_chr_as_int] else: - point_color = BLUE + if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1): + point_color = RED + else: + point_color = BLUE + im_drawer.text( text="5", xy=( -- cgit v1.2.3 From 60447282a0f0063513ab10251945df3ab2c2dbfd Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 00:03:07 +0300 Subject: add reference markdown and github button --- wqflask/wqflask/templates/reference.html | 1541 +----------------------------- 1 file changed, 53 insertions(+), 1488 deletions(-) diff --git a/wqflask/wqflask/templates/reference.html b/wqflask/wqflask/templates/reference.html index d95d22e3..78469d39 100644 --- a/wqflask/wqflask/templates/reference.html +++ b/wqflask/wqflask/templates/reference.html @@ -1,1497 +1,62 @@ {% extends "base.html" %} -{% block title %}References{% endblock %} -{% block content %} - -

 Papers and References to GeneNetwork

- -
- - -Highlighted References | -Key References | -Background References | - - -

- -2020 | -2019 | -2018 | -2017 | -2016 | -2015 | -2014 | -2013 | -2012 | -2011 | -2010 | -2009 | -2008 | -2007 | -2006 | -2005 | -2004 | -2003 | - -
- - - Google Scholar search for "genenetwork" OR "webqtl" generated: -
    -
  1. 1430 hits on 2016/09/08 -
  2. 1730 hits on 2017/10/17 -
  3. 2020 hits on 2019/05/13) -
- -Google Scholar search for "genenetwork.org" generated: - -
    -
  1. 1030 hits on 2019/05/13 -
  2. 105 hits from 2018/01/01 to 2019/05/13 -
- - - - -
- Highlighted References -
- -Please send us citations to articles that we may have missed. - -
    - -
  1. Mulligan MK, Mozhui K, Prins P, Williams RW (2017) GeneNetwork: A Toolbox for Systems Genetics. In Systems Genetics, Methods in Molecular Biology 1488:75-120 -[An updated primer in using GeneNetwork for molecular analysis of mouse and human cohorts.] -PDF version - -
    -
    - -
  2. Williams RW, Williams EG (2017) Resources for Systems Genetics. In Systems Genetics, Methods in Molecular Biology 1488:3-29. -[This review is intended to help you when making the hard choices about types of resources to use in system genetic studies. The short answer: embrace diversity in your resources. The computational barriers to joint analysis are now minimal.] -PDF version - -
    -
    - -
  3. Williams RW (2009) Herding cats: the sociology of data integration. Frontier in Neuroscience 3(2):154-6. -[An short but amusing commentary on predictive (someday perhaps even precision) medicine and how to get there using genetic reference populations such as the BXD and Collaborative Cross families.] -PDF version - -
    -
    - - -
  4. -Pinelli M, Carissimo A, Cutillo L, Lai CH, Mutarelli M, Moretti MN, Singh MV, Karali M, Carrella D, Pizzo M, Russo F, Ferrari S, Ponzin D, Angelini C, Banfi S, di Bernardo D (2016) An atlas of gene expression and gene co-regulation in the human retina.Nucleic Acids Res. 2016 Jul 8;44(12):5773-84 -RETINA database, and see the PDF. These data are now in GeneNetwork (Species = Human, Group = Retina). - - -
    -
    - - -
  5. -Williams EG, Wu Y, Pooja J, Dubuis S, Blattmann P, Argmann CA, Houten SM, Amariuta T, Wolski W, Zamboni N, Aebersold R, Auwerx J (2016) Systems proteomics and trans-omic integration illuminate new mechanisms in mitochondrial function. Science 352(6291):aad0189 -HTML version, PDF - -
    -
    - - - -
  6. -Sloan Z, Arends D, Broman KW, Centeno A, Furlotte N, Nijveen H, Yan L, Zhou X, Williams RW, Prins P (2016) GenetNetwork: framework for web-based genetics. The Journal of Open Source Software http://joss.theoj.org/papers/10.21105/joss.00025 (http://dx.doi.org/10.21105/joss.00025) -HTML version - -
    -
    - -
  7. Alam G, Miller DB, O'Callaghan JP, Lu L, Williams RW, Jones BC (2016) MPTP neurotoxicity is highly concordant between the sexes among BXD recombinant inbred mouse strains. Neurotoxicology in press -PDF version - -
    -
    - - -
  8. Merkwirth C, Jovaisaite V, Durieux J, Matilainen O, Jordan SD, Quiros PM, Steffen KK, Williams EG, Mouchiroud L, Tronnes SU, Murillo V, Wolff SC, Shaw RJ, Auwerx J, Dillin A (2016) Two conserved histone demethylases regulate mitochondrial stress-induced longevity. Cell 165:1209-1223 -
    -
    - - -
  9. Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW (2016). Joint mouse-human phenome-wide association to test gene function and disease risk. Nature Communications 7:10464 -[Best reference on the BXD family of strains and the wide range of phenotypes that have been generated over the past 40 years.] - -PDF version and the - -Supplementary Tables in one Excel file - - -
    -
    - - -
  10. Xue Y, Li J, Yan L, Lu L, Liao FF (2015) Genetic variability to diet-induced hippocampal dysfunction in BXD recombinant inbred (RI) mouse strains. Behav Brain Res 292:83-94 -
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    - -
  11. Chaum E, Winborn CS, Bhattacharya S (2015) Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Mamm Genome 26:210-221 -
    -
    - -
  12. Cheng Q, Seltzer Z, Sima C, Lakschevitz FS, Glogauer M. (2015) Quantitative Trait Loci and Candidate Genes for Neutrophil Recruitment in Sterile Inflammation Mapped in AXB-BXA Recombinant Inbred Mice. PLoS One 10:e0124117 -
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  13. Scott RE, Ghule PN, Stein JL, Stein GS (2015) Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis. J Cell Physiol 230:2533-42 -
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  14. Williams EG, Auwerx J (2015) The convergence of systems and reductionist approaches in complex trait analysis. Cell 162:23-32. -
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  15. Wu Y, Williams EG, Dubuis S, Mottis A, Jovaisaite V, Houten SM, Argmann CA, Faridi P, Wolski W, Kutalik Z, Zamboni N, Auwerx J, Aebersold R (2014) Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell 158:1415-1430 -
    -
    +{% block title %}Reference{% endblock %} -
  16. -Hayes SK, Hager R, Grencis RK (2014) Sex-dependent genetics effects on immune responses to parasitic nematodes. BMC Genomics 15:193 -
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    - -
  17. Harenza JL, Muldoon PP, De Biasi M, Damaj MI, Miles MF (2014) Genetic variation within the Chrna7 gene modulates nicotine reward-like phenotypes in mice. Genes Brain Behav 13:213-225 -
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    - - -
  18. -Ye R, Carneiro AM, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B, Blakely RD (2014) Evaluation of heritable determinants of blood and brain serotonin homeostasis using recombinant inbred mice. Genes Brain Behav. 13:247-260 +{% block css %} + +{% endblock %} -
    -
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  19. -Houtkooper RH, Mouchiroud L, Ryu D, Moullan N, Katsyuba E, Knott G, Williams RW, Auwerx J (2013) Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 497:451-457 PDF version +{% block content %} -
    -
    +
    + Edit on Github +
    + +
    + {{ rendered_markdown|safe }} + + + +
    + + {% endblock %} + -- cgit v1.2.3 From 2681d11a9c39a3291db03521e5b7f73ed672533c Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 00:04:22 +0300 Subject: register references blueprint --- wqflask/wqflask/__init__.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index 874cde17..39a36fa3 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -7,6 +7,7 @@ from flask import g from flask import Flask from utility import formatting from wqflask.markdown_routes import glossary_blueprint +from wqflask.markdown_routes import references_blueprint app = Flask(__name__) @@ -19,6 +20,7 @@ app.jinja_env.globals.update( # Registering blueprints app.register_blueprint(glossary_blueprint, url_prefix="/glossary") +app.register_blueprint(references_blueprint,url_prefix="/references") @app.before_request def before_request(): @@ -39,4 +41,4 @@ from wqflask import db_info from wqflask import user_login from wqflask import user_session -import wqflask.views +import wqflask.views -- cgit v1.2.3 From 23d27c88bcc085bac3fb14b534cf1d4a7f11f22a Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 00:07:01 +0300 Subject: modify references links --- wqflask/wqflask/markdown_routes.py | 33 ++++++++++++++++++++++++++++++++- wqflask/wqflask/templates/base.html | 2 +- wqflask/wqflask/views.py | 5 ----- 3 files changed, 33 insertions(+), 7 deletions(-) diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 7a9fac41..60d4374c 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -9,7 +9,10 @@ from flask import Blueprint from flask import render_template glossary_blueprint = Blueprint('glossary_blueprint', __name__) - +references_blueprint=Blueprint("references_blueprint",__name__) +environments_blueprint=Blueprint("environments_blueprint",__name__) +links_blueprint=Blueprint("links_blueprint",__name__) +policies_blueprint=Blueprint("policies_blueprint",__name__) def render_markdown(file_name): """Try to fetch the file name from Github and if that fails, try to @@ -22,6 +25,7 @@ look for it inside the file system if md_content.status_code == 200: return markdown.Markdown().convert(md_content.content.decode("utf-8")) + # TODO: Add fallback on our git server by checking the mirror. # Content not available @@ -32,8 +36,35 @@ look for it inside the file system "Please reach out to the gn2 team to have a look at this") + + @glossary_blueprint.route('/') def glossary(): return render_template( "glossary.html", rendered_markdown=render_markdown("general/glossary/glossary.md")), 200 + + +@references_blueprint.route('/') +def references(): + return render_template( + "reference.html", + rendered_markdown=render_markdown("general/glossary/glossary.md")), 200 + + + +@environments_blueprint.route("/") +def references(): + return render_template("environments.html",rendered_markdown=render_markdown("general/environments/environments.md")) + + +@links_blueprint.route("/") +def links(): + return rendered_template("links.html",rendered_markdown=render_markdown("general/links/links.md")) + + +policies_blueprint.route("/") +def policies(): + return rendered_template("policies.html",rendered_markdown=rendered_markdown("general/policies/policies.md")) + + diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 0e572fcf..ca6c9d9b 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -64,7 +64,7 @@
    20. -
    • References
      • +
    • References
    • Tutorials/Primers
    • Glossary of Term
    • FAQ
      • diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index bf2e9026..060c5a7b 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -301,11 +301,6 @@ def news(): doc = Docs("news", request.args) return render_template("docs.html", **doc.__dict__) -@app.route("/references") -def references(): - doc = Docs("references", request.args) - # return render_template("reference.html") - return render_template("docs.html", **doc.__dict__) @app.route("/intro") def intro(): -- cgit v1.2.3 From d0550bfee7e4eaf986d797c9ebadc7b8bc59f891 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 00:10:33 +0300 Subject: modify github button --- wqflask/wqflask/templates/reference.html | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/wqflask/wqflask/templates/reference.html b/wqflask/wqflask/templates/reference.html index 78469d39..0ba7d7d5 100644 --- a/wqflask/wqflask/templates/reference.html +++ b/wqflask/wqflask/templates/reference.html @@ -15,10 +15,6 @@
      {{ rendered_markdown|safe }} - -
      -{% endblock %} - +{% endblock %} \ No newline at end of file -- cgit v1.2.3 From a0bb3633c0288e9636e8abb1185d051ac02ea446 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 12:41:14 +0300 Subject: move css to markdown and add references --- wqflask/wqflask/static/new/css/markdown.css | 33 +++++++++++++++++ wqflask/wqflask/templates/reference.html | 56 ----------------------------- wqflask/wqflask/templates/references.html | 30 ++++++++++++++++ 3 files changed, 63 insertions(+), 56 deletions(-) delete mode 100644 wqflask/wqflask/templates/reference.html create mode 100644 wqflask/wqflask/templates/references.html diff --git a/wqflask/wqflask/static/new/css/markdown.css b/wqflask/wqflask/static/new/css/markdown.css index 91167908..d8dd4776 100644 --- a/wqflask/wqflask/static/new/css/markdown.css +++ b/wqflask/wqflask/static/new/css/markdown.css @@ -11,3 +11,36 @@ margin-right: auto; margin-left: auto; } +#markdown { + background: red; +} + + + + .github-btn{ + margin:20px 10px; + display: flex; + width: 90vw; + justify-content: flex-end; + } + .github-btn a{ + display: inline-block; + align-self:center; + text-decoration: none; + transition-property:all; + transition-duration:0.5s; + padding:8px 12px; + color:#fff; + /*background: #27407a;*/ + background: blue; + border-radius: 20px; + background: red; + /*text-align: center;*/ + + + } + .github-btn a:hover{ + + background: #333; + + } diff --git a/wqflask/wqflask/templates/reference.html b/wqflask/wqflask/templates/reference.html deleted file mode 100644 index e04deed5..00000000 --- a/wqflask/wqflask/templates/reference.html +++ /dev/null @@ -1,56 +0,0 @@ -{% extends "base.html" %} - -{% block title %}Reference{% endblock %} - -{% block css %} - -{% endblock %} - -{% block content %} - -
      - Edit on Github -
      - -
      - {{ rendered_markdown|safe }} - -
      - - - -{% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/references.html b/wqflask/wqflask/templates/references.html new file mode 100644 index 00000000..5e86d95b --- /dev/null +++ b/wqflask/wqflask/templates/references.html @@ -0,0 +1,30 @@ +{% extends "base.html" %} + +{% block title %}Reference{% endblock %} + +{% block css %} + +{% endblock %} + +{% block content %} + +
      + Edit on Github +
      + +
      + {{ rendered_markdown|safe }} + +
      + + + +{% endblock %} \ No newline at end of file -- cgit v1.2.3 From 98b9fa88028704d504d3186e0dc032152b535181 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 13:53:47 +0300 Subject: delete templates/links page --- wqflask/wqflask/templates/links.html | 451 ----------------------------------- 1 file changed, 451 deletions(-) delete mode 100644 wqflask/wqflask/templates/links.html diff --git a/wqflask/wqflask/templates/links.html b/wqflask/wqflask/templates/links.html deleted file mode 100644 index 6ff7fc6c..00000000 --- a/wqflask/wqflask/templates/links.html +++ /dev/null @@ -1,451 +0,0 @@ -{% extends "base.html" %} -{% block title %}Links{% endblock %} -{% block content %} - - - - -
      - - -

      Links for Exploring Networks of Genes and Phenotypes

      - - -
      GeneNetwork and WebQTL have integrated links to the following resources
      -
      -
      GN PARTNERS, DEVELOPMENT SITES, AND MIRRORS
      - -
      - -
      - -
      KEY RESOURCES CONNECTED WITH GENENETWORK
      -
      - -
      - -
      - -
      Resources for Analysis of Single Genes, SNPs, mRNAs, and Proteins
      -
      -
      -Harvester retrieves summary data on any one of 57,000 proteins from several bioinformatic resources. -[Added Dec 22, 2004; last site review Sept 19, 2008 by RWW.] -
      - -
      -GSCAN: the Oxford Wellcome Trust Genome Viewer retrieves mapping data for many mouse experimental mapping populations including the Heterogenous Stock, the Pre-Collaborative Cross mice, and Mouse Diversity Panel. -[Added Oct 13, 2010; last site review Oct 13, 2010 by RWW.] -
      - - - - -
      -NIF: The Neuroscience Information Framework retrieves summary from a wide variety of neuroscience and bioinformatic resources. -[Added Dec 3, 2009; last site review Dec 3, 2009 by RWW.] -
      -
      -Genomics of aging resources. A collection of databases and tools designed to help researchers understand the genetics of human ageing through a combination of functional genomics and evolutionary biology. -[Added Feb 28, 2010; last site review Feb 28, 2010 by RWW.] -
      -
      -Human Disease Gene Database from Cardiff (requires log in) -[Added Nov 5, 2009; last site review Nov 5, 2009 by RWW.] -
      -
      -SNPnexus database of human SNPs is designed to simplify and assist in the selection of functionally relevant SNPs for large-scale genotyping studies of multifactorial disorders.[Added Jan 15, 2010; last site review Jan 15, 2010 by RWW.] -
      -
      -SNPedia is a wiki investigating human genetics. We share information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA.[Added Jan 15, 2010; last site review Jan 15, 2010 by RWW.] -
      -
      -Genoglyphix Browser includes extensive data on human copy number variants as well as maps of low copy number repeat regions. -[Added Nov 5, 2009; last site review Nov 5, 2009 by RWW.] -
      -
      -Human Protein Reference DB: a manually curated resource with data on 20,000 proteins. Very effective interface and rich data. -[Added Oct 30, 2005; last site review Sept 19, 2008 by RWW.] -
      -
      -x:map is a terrific visual display tool for exploring Affymetrix Exon array data sets for mouse and human transcriptomes. -[Added April 18, 2008; last site review Sept 19, 2008 by RWW.] -
      -
      -iHOP retrieves PubMed sentences that report interactions between a reference gene and associate genes and proteins. It allows the assembly of complex graphs that plot the literature interactions of genes. Effective interface for humans and machines. -[Added Dec 25, 2004; last site review Sept 19, 2008 by RWW.] -
      -
      -Human Protein Atlas displays expression and localization of proteins in a large variety of normal human tissues and cancer cells as high resolution images of immunohistochemically stained tissues and cell lines. -[Added Sept 22, 2007; last site review Sept 22, 2007 by RWW.] -
      -
      -GoPubMed is a simple tool that searches PubMed and sorts the results by GO and MeSH terms. -[Added July 5, 2007 by RWW; last site review Sept 19, 2008 by RWW.] -
      -
      -AceView and the Alternative Splicing and Transcript Diversity database provide excellent resources for systematic information about the many alternative transcripts produced from single genes. -[Added Jan 1, 2005; last site review Sept 19, 2008 by RWW.] -
      - -
      -MGI and RGD are reference sites for mouse and rat genetics, respectively. -[Added Dec 22, 2004; last site review Sept 19, 2008 by RWW.] -
      - - -
      -GenAtlas provides summary data for approximately 19300 human genes and has a useful link that will fetch 10 Kb of upstream sequence for promoter analysis. -[Added Jan 9, 2005; last site review Sept 19, 2008 by RWW.] -
      -
      -PromoLign aligns homologous regions of mouse and human promoters and highlights SNPs and transcription factor binding sites. Check the quick tutorial to see how to extract key data. This site requires an SVG plugin that may not be supported by some browsers and operating systems. -[Added May 10, 2005; FAILED: last site review Sept 19, 2008 by RWW.] -
      -
      -CGAP SNP Viewer allows users to view SNPs in the context of transcripts, ORFs and protein motifs for either human or mouse genes. Try the Ahr gene in mouse as an example. -[Added April 10, 2006; last site review Sept 19, 2008 by RWW.] -
      -
      -Synapse Database (SynDB) is a comprehensive database of genes and proteins associated with the neuronal or neuromuscular synapse. Many Trait Data and Analysis pages provide links to SynDB. -[Added May 29, 2005; last site review Sept 19, 2008 by RWW.] -
      -
      -Synapse Database at University of Pennsylvania is a comprehensive database of roughly 200 genes and proteins associated with the synapse. -[Added Nov 26, 2006; last site review Sept 19, 2008 by RWW.] -
      -
      -Singapore Bio Databases and Tool. -[Added Dec 22, 2004; Dragon Genome Explorer site FAILED last site review, changed link; Sept 19, 2008 by RWW.] -
      -
      - MutDB and SNPs3D provide great data on functional SNPs in human genes. To analyze the functional impact of non-synonymous SNPs you will also find SNP Analyzer useful because it evaluates SNP impact in terms of the whole protein structural context. -[Added Dec 22, 2004; last site review Sept 19, 2008 by RWW.] -
      -
      -Alternative Splicing Project provides great summaries and output graphs on splice variants in human, mouse, and Drosophila. -[Added Nov 8, 2005; last site review Sept 19, 2008 by RWW.] -
      -
      - -
      - -
      Resources on Imprinting and Parental Origin Effects
      -
      -
      -Geneimprint is a portal into the burgeoning field of genomic imprinting, collecting relevant articles and reviews, press reports, video and audio lectures, and genetic information -[Added June 23, 2010 by RWW; last site review June 23, 2010 by RWW.] -
      -
      -Catalogue of Parent of Origin Effects provides a list of imprinted and putatively imprinted genes with commentary by Ian Morison (University of Otago, New Zealand). Database was last updated in 2008. -[Added June 23, 2010 by RWW; last site review June 23, 2010 by RWW.] -
      -
      - -
      - -
      Resources for the Spatial Analysis of Gene and Protein Expression
      -
      -
      -UBC Bioinformatic and Gene Expression Links is a very extensive and well curated collection of on-line resources for the analysis of biological data sets. -[Added May 24, 2007 by RWW; last site review Sept 19, 2008 by RWW.] -
      -
      -The mamep GeneExpression Links image database of whole-mounted in situ hybridization of mid-gestation mouse embryos. Try entering the symbol Ptch1. -[Added May 28, 2007 by RWW.] -
      -
      -The Genes to Cognition databases have a focus on proteins expressed in several key cellular compartments related to synpase function. -[Added Aug 9, 2007 by RWW.] -
      - -
      -Cerebellar Development Transcriptome Database. Expression data for the mouse cerebellum, both microarray and in situ. -[Added Sept 1, 2010; last site review Sept 1, 2010 by RWW.] -
      - - -
      -Several excellent resources can be used to explore patterns of gene expression primarily in C57BL/6J mice. This strain is one of the parents of the BXD, AXB/BXA, BXH, and CXB genetic reference populations that are key resources in the Gene Network and its companion site, the Mouse Brain Library. -
        -
      • BGEM and GENSAT provide images of gene expression in brains of embryos, neonates, and adult mice (roughly 2008 genes as of July 2005). -
        -
        -
      • GenePaint and GeneAtlas are companion sites that also provide expression data in embryos, neonates, and adults at high spatial resolution. GeneAtlas has excellent but slow image searching and matching capabilities. -
        -
        -
      • Allen Brain Atlas has expression data for ~12000 transcripts (adult males in the sagittal plane). -
        -
        -
      • EMAP (Edinburgh Mouse Atlas Project) provides data on expression of ~800 genes during development (in situ, immunohistochemistry, and reporter knock-in expression patterns). Most data are from wholemounts between Theiler stages 11 and 20 (embryonic days E7 to E13). EMAP can be used as a Java WebStart application. -
        -
        -
      • Mouse Atlas of Gene Expression is a massive SAGE library. The Atlas has quantified the normal state for many tissues by determining the number and identity of genes expressed throughout development. The scope of the project encompasses multiple stages of development of C57BL/6J mouse, from the single cell zygote to the adult, and includes an extensive initial collection of 200 tissues. DiscoverySpace is a WebStart application for use with The Mouse Atlas of Gene Expression. -
        -
        -
      • Mahoney Center maintains a rich image collection for ~1000 transcription factors expressed in brain (developmental stages, coronal plane). -[Added Dec 22, 2004; sites reviewed last on Sept 26, 2005 by RWW.] -
        -
        -
      -
      -
      - -
      - -
      Resources for the Analysis of Sets and Networks of Transcripts, Genes, Proteins, and SNPs
      -
      -
      -GeneMANIA helps you predict the function of your favourite genes and gene sets. Powerful and fast computational methods and a great use of Cytoscape Web. (2010 PDF). -[Added July 1, 2010; last site review Aug 8, 2010 by RWW.] -
      -
      -ToppGene Suite A one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network -[Added Jan 16, 2010; last site review Jan 16, 2010 by RWW.] -
      -
      -WikiPathways (WGCNA) is an open, public platform dedicated to the curation of biological pathways by and for the scientific community. -[Added Nov 12, 2009; last site review Nov 12, 2009 by RWW.] -
      -
      -Pathway Commons (WGCNA) is a search tool to find and visualize public biological pathway information. This site collates from several major sites. -[Added Nov 12, 2009; last site review Nov 12, 2009 by RWW.] -
      -
      -Sanger Mouse Genome Project SNP Finder provides access to SNP and indels generated by sequencing 17 strains of mice (plus C57BL/6J). Marvelous. -[Added Nov 18, 2009; last site review Nov 18, 2009 by RWW.] -
      -
      -Weighted Gene Coexpression Network Analysis (WGCNA) is a collection of R functions to perform weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. See the recent paper on WGCNA. -[Added Aug 21, 2009; last site review Aug 21, 2009 by RWW.] -
      -
      -GenomeNet is a terrific site for the analysis of molecular networks. Download the very effective KegArray 0.2.6beta package (May 2005) for exploratory data analysis of microarray data set. This package is as good as most commerical software and includes with built-in linkage to the KEGG databases. Versions are available for Mac OS X and Windows. -[Added Jan 3, 2005; last site review Aug 5, 2005 by RWW.] -
      -
      -Expression Profiler at http://ep.ebi.ac.uk/ is a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Tools in the Expression Profiler allow you to perform cluster analysis, pattern discovery, pattern visualization, study and search Gene Ontology categories, generate sequence logos, extract regulatory sequences, study protein interactions, as well as to link analysis results to external tools and databases. -[Added May 20, 2008; last site review May 20, 2008 by RWW.] -
      -
      -BioGRID: the Biological General Repository for Interaction Datasets is a freely accessible database of protein and genetic interactions from Mt. Sinai, Toronto. -[Added July 28, 2007; last site review July 28, 2007 by RWW.] -
      -
      -CisMols Analyzer at Cincinnati Children's Hospital (Aronow and colleagues) is a server and database for the analysis of cis element co-occurences in the promoters of a list of genes. The PolyDoms Analyzer is a tool for scanning through gene lists for those members of a pathway, ontolog, or disease that contain potentially harmful protein-coding SNPs. GenomeTraFaC is a comparative genomics-based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq Gene Orthologs. -[Added Sept 23, 2006; last site review Sept 23, 2006 by RWW.] -
      -
      -PolymiRTS database that searches for microRNA (miRNA) targets in transcripts that overlap SNPs. This database will also search for genes with associated phenotype variants that may have variants in miRNA target sequence (Yan Cui, Lei Bao and colleagues). - [Added Sept 23, 2006; last site review Sept 23, 2006 by RWW.] -
      -
      -MSigDB: The Molecular Signature Database is part of the Broad Institute Gene Set Enrichment Analysis suite. MSigDB contains large numbers of static and partly annotated sets of genes/transcripts. Registration is not actually required to download data sets. - [Added Jan 18, 2007; last site review Jan 18, 2007 by RWW.] -
      -
      -C-INIA MAGIC-B microarray knowledgebase from the Department of Pharmacology, University of Colorado, Denver, part of the NIAAA INIA project. Extensive public and privated brain array data sets in a powerful analytic web environment. - [Added May 31, 2007 by RWW.] -
      -
      -GenMAPP 2.0 (2004), the Gene Map Annotation and Pathway Prolifer, is a free Windows application (simple registration required) with which you can visualize expression and other genomic data sets on maps of biological pathways. Very flexible suite of programs that you can also use to make custom gene annotation maps (and more). -[Added Aug 5, 2005; last site review Aug 5, 2005 by RWW.] -
      -
      -BIND and STRING and IntAct are great sites that provide access to well curated data on protein-protein interactions. BIND and IntAct focus on experimentally verified interactions whereas STRING and preBIND incorporate inferred interaction based on other data types, including gene expression. Links to BIND and STRING have been added to the Trait Data and Analysis forms on the GeneNetwork BETA site. -[Added Aug 21, 2005; last site reviews Aug 27, 2005 by RWW.] -
      -
      -Microarray Module Maps is a great site that databases a large number of coexpression modules defined using many cancer array studies. -[Added Aug 26, 2005; last site review Aug 26, 2005 by RWW.] -
      -
      -The Gene Ontology Consortium maintains a well annotated list of open resources for the analysis of large expression data sets and gene ontologies. Note that there are several different lists, each with valuable links. -[Added July 15, 2005; last site review July 15, 2005 by RWW.] -
      -
      -Prioritizer: Prioritizer is a stand-alone Java program that uses a functional human gene network, available at www.genenetwork.nl, to prioritize positional candidate genes that reside within susceptibility loci, by assuming that real disease genes, residing within different loci are functionally closely related within the gene network. -
      -
      -eQTL Explorer is a Java WebStart application that has also been designed for the calculation and display of QTL maps for large rat data sets, particuarly those generated using the HXB strains. Locations of QTLs for both mRNA traits and conventional physiological traits are displayed on chromosome ideograms. High precision QTL maps can also be generated. A password is required to gain access to the primary data files. -[Added January 7, 2006; last site review Jan 7, 2006 by RWW.] -
      -
      -Clique-GO Analysis is a novel tool for extracting cliques of coregulated transcripts. The current data requires Affymetrix U74Av2 probe set IDs as input. Try "103370_at" (the gene Lin7c) as an example. -[Added Jan 4, 2005; last site review Jan 4, 2005 by RWW.] -
      -
      -Gemma and ErmineJ are powerful resources for analysis and metaanalysis of gene expression data sets at UBC. Pavlidis and colleagues also provide updated GO data for common microarray platforms. -[Added Jan 4, 2005; last site review June 7, 2007 by RWW.] -
      -
      -Cytoscape is one of several SBML-compatible open source programs for visualizing molecular interaction networks and overlaying these networks with gene expression profiles and other data sets to generate and test specific hypotheses. -[Added Jan 5, 2005; last site review Jan 5, 2005 by RWW.] -
      -
      -Pathway Searcher provides fast access to gene/protein interaction pathways. An intuitive interface. -[Added Dec 30, 2004; last site review Dec 30, 2004 by RWW.] -
      -
      -Gene Sorter is a tool for generating and sorting sets of genes using a wide variety of information integrated into UCSC's Genome Brower. -[Added Dec 31, 2004; last site review Dec 31, 2004 by RWW.] -
      -
      -oPPOSUM is a tool for finding over-represented transcription factor binding sites in lists of mouse and human genes. It handles about 100 out of greater than 600 TFBSs. -[Added Jan 27, 2005; last site review Nov 21, 2005 by RWW.] -
      -
      -MOTIF and PAINT search for motifs in submitted sequences or lists of genes. Paint makes use of the TRANSFAC Pro database. -[Added Dec 22, 2004; last site review Dec 25, 2004 by RWW.] -
      -
      -Arrowsmith provides a fast way to evaluate known interactions or common mechanisms between two genes or proteins. It carries out a sophisticated comparison of the current PubMed database. -[Added Dec 22, 2004; last site review June 7, 2007 by RWW.] -
      -
      -Chilibot applies natural-language processing to the PubMed database to hunt for directed relationships among pairs or sets of genes, proteins, and keywords. [Added Dec 30, 2004; last site review Aug 13, 2009 by RWW.] -
      -
      -Mouse Imprinting Resources: -The Harwell Mouse Imprinting Resource, -Duke University - Jirtle's Laboratory, -RIKEN Candidate Imprinted Transcript Maps, and -Imprinted Gene Catalogue - University of Otago. -[Added Oct 20, 2006; last site review Oct 20, 2006 by RWW.] -
      -
      - -
      - -
      Resources for the Analysis of Phenotypes in Genetic Reference Populations
      -
      -
      -MBL is a extensive image database of brain sections from genetic reference populations of mice, including the BXD, AXB, CXB, BXH strains included in WebQTL. The MBL is a companion database of WebQTL. -[Added Dec 22, 2004; last site review Aug 6, 2005 by RWW.] -
      -
      -MPAD Mouse Phenome Association Database v 1.0, by Eleazar Eskin and Hyun Min Kang. This resource performs genome-wide association mapping. Phenotype data sets are derived from the Mouse Phenome Project set of standard mouse strains. The permutation procedures account for the genetic relations among these strains and provide much more appropriate genome-wide significance thresholds than previous mouse association mapping methods. -[Added Nov 19, 2006; last site review Nov 19, 2006 by RWW. Link broken June 2007 probably due to move from UCSD to UCLA; check with EE.] -
      -
      -GScan at the Wellcome Trust, Oxford, is a sophisticated viewer and analysis tool with which to explore the genetic control of diverse phenotypes (including array data) generated using heterogeneous stock mice (Flint, Mott, and colleagues). -[Added May 28, 2007 by RWW.] -
      -
      -Phenome Project provides access to a wide variety of phenotype data many common and wild inbred strains of mice. -[Added Dec 22, 2004; last site review Dec 25, 2004 by RWW.] -
      -
      - -
      - -
      QTL Mapping Resources
      -
      -
      -QSB: QSB is a stand-alone JAVA program with a sophisticated GUI developed for genetical genomics or systems genetics, an emerging field that combines quantitative genetics and genomics. QSB stands for QTL mapping, Sequence polymorphism analysis (or SNP analysis) and Bayesian network analysis. QSB takes marker and array data from a segregating population as input and identifies significant QTLs and then evaluated networks of candidate genes associated with these QTLs. -[Added July 29, 2005; last site review Jan 7, 2006 by RWW.] -
      -
      -Positional Medline (PosMed) is a knowledge-based ranking system of candidate genes within QTL intervals for human, mouse, rat, Arabidopsis, and rice. -[Added Nov 4, 2009; last site review Nov 4, 2009 by RWW.] -
      -
      Genome - Phenome Superbrain Project integrates various databases to build a comprehensive computerized encyclopedia of omic sciences in several species, including mouse, rat, human, and arabidopsis, etc. The goal is to evolve this intelligent system into a form of artificial intelligence that can solve a researcher's problems by exploiting a vast amount of information accumulated in documents and published data ranging from genomes to phenomes. [Added Sept 13, 2007; last site review Sept12, 2007 by RWW.] -
      -
      -QTL Reaper is software, written in C and compiled as a Python module, for rapidly scanning microarray expression data for QTLs. It is essentially the batch-oriented version of WebQTL. It requires, as input, expression data from members of a set of recombinant inbred lines and genotype information for the same lines. It searches for an association between each expression trait and all genotypes and evaluates that association by a permutation test. For the permutation test, it performs only as many permutations as are necessary to define the empirical P-value to a reasonable precision. It also performs bootstrap resampling to estimate the confidence region for the location of a putative QTL. -[Added Jan 27, 2005; last site review Jan 27, 2005 by KFM.] -
      -
      -QTLNetwork 2.0 is a software package ofr mapping QTLs with epistatic and GXE interaction effects in experimental populations including double-haploid, recombinant inbred, backcross, F2, IF2 and BxFy populations. The program provides graphical presentations of QTL mapping results. The software is programmed by C++ programming language under Microsoft Visual C++ 6.0 environment. It works with Microsoft Windows operating systems, including Windows 95/98, NT, 2000, XP, 2003server. A new version of QTLNetwork is under developing, and its functions will be extended to include linkage group construction and marker-assisted virtual breeding.[Added June 21, 2007.] -
      -
      -MouseHapMap project genotypes from Mark Daly and colleagues. Approximately 140,000 SNPs across 49 strains. Updated Feb 2006.used to explore the Oxford Wellcome Heterogeneous stock QTL mapping project population. It currently includes mapping data for 100+ phenotypes typed across 2000 animals and 13,000 SNPs. -[Added May 10, 2006; last site review May 10, 2006 by RWW.] -
      -
      -A valuable list of Software for QTL Data Analysis and Gene Expression Microarray Software is managed by Brian Yandell at University of Wisconsin. -[Added May 16, 2006; last site review May 16, 2006 by RWW.] -
      -
      -GSCAN DB is a browser used to explore the Oxford Wellcome Heterogeneous stock QTL mapping project population. It currently includes mapping data for 100+ phenotypes typed across 2000 animals and 13,000 SNPs. -[Added May 10, 2006; last site review May 10, 2006 by RWW.] -
      -
      -The Wellcome Trust-CTC SNP Data Set consists of high density SNP data for approximately 490 strains of mice at 13,377 SNPs. These data fiels were processed slightly to generate many of the mouse mapping files used in WebQTL. -[Added Sept 27, 2005; last site review Sept 27, 2005 by RWW.] -
      -
      -The NIEHS-Perlegen Mouse Strain Resequencing Project provides links to SNP data for up to 15 strains of mice. Very high density data for many chromosomes. These data are integrated to some extent in the GeneNetwork. -[Added Sept 25, 2005; last site review Sept 25, 2005 by RWW.] -
      -
      - -
      - -
      Affymetrix Array Annotation Resources
      -
      -
      -Affy MOE430A and MOE430B Annotation files are explained more clearly that Affymetrix has ever done by Earl F Glynn at the Stowers Institute. (efg@stowers-insitute.org). -[Added July 17, 2006; last site review June 7, 2007 by RWW. This Oct 7, 2005 file caused Grace Wheeler's Mac internet connection to break.] -
      -
      - -
      - -
      Information about this HTML page:
      -
      -

      This text originally generated by RWW, Dec 21, 2004. Updated by EJC, Feb 27, 2005; by RWW, July 15, Sept 25. -

      Management of GeneNetwork access and trait pages. -

      -
      - -
      - -{% endblock %} -- cgit v1.2.3 From 76ef7a0479473c0716e7178c524f4a3ae02df16c Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 14:45:49 +0300 Subject: remove static views form wqflask/view.py --- wqflask/wqflask/views.py | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 060c5a7b..cc2dc341 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -307,17 +307,7 @@ def intro(): doc = Docs("intro", request.args) return render_template("docs.html", **doc.__dict__) -@app.route("/policies") -def policies(): - doc = Docs("policies", request.args) - #return render_template("policies.html") - return render_template("docs.html", **doc.__dict__) -@app.route("/links") -def links(): - #doc = Docs("links", request.args) - #return render_template("docs.html", **doc.__dict__) - return render_template("links.html") @app.route("/tutorials") def tutorials(): -- cgit v1.2.3 From 7a669eb9b9674ebffba8917f42833c71bfe36255 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 15:01:42 +0300 Subject: add css for container --- wqflask/wqflask/static/new/css/markdown.css | 72 ++++++++++++++++++----------- 1 file changed, 46 insertions(+), 26 deletions(-) diff --git a/wqflask/wqflask/static/new/css/markdown.css b/wqflask/wqflask/static/new/css/markdown.css index d8dd4776..ad665835 100644 --- a/wqflask/wqflask/static/new/css/markdown.css +++ b/wqflask/wqflask/static/new/css/markdown.css @@ -2,7 +2,10 @@ padding: 20px; } -#markdown h2, #markdown h3, #markdown h4, #markdown h5 { +#markdown h2, +#markdown h3, +#markdown h4, +#markdown h5 { font-weight: bold; } @@ -11,36 +14,53 @@ margin-right: auto; margin-left: auto; } -#markdown { - background: red; + + + +.github-btn { + margin: 20px 10px; + display: flex; + width: 90vw; + justify-content: flex-end; } +.github-btn a { + display: inline-block; + align-self: center; + text-decoration: none; + transition-property: all; + transition-duration: 0.5s; + padding: 8px 12px; + color: #fff; + /*background: #27407a;*/ + background: blue; + border-radius: 20px; + + /*text-align: center;*/ + +} - .github-btn{ - margin:20px 10px; - display: flex; - width: 90vw; - justify-content: flex-end; - } - .github-btn a{ - display: inline-block; - align-self:center; - text-decoration: none; - transition-property:all; - transition-duration:0.5s; - padding:8px 12px; - color:#fff; - /*background: #27407a;*/ - background: blue; - border-radius: 20px; - background: red; - /*text-align: center;*/ +.github-btn a:hover { + background: #333; - } - .github-btn a:hover{ +} - background: #333; - } +.container { +width:80vw; +margin: auto; +max-width:80vw; + +} + +.container p { + font-size: 17px; + word-spacing: 0.2em; +} +@media(max-width:650px){ + .container{ + width: 100vw; + } +} \ No newline at end of file -- cgit v1.2.3 From 419532807eff4cd28eb011a777a3a28b1c99d90d Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 15:03:44 +0300 Subject: build url for functions --- wqflask/wqflask/templates/base.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index ca6c9d9b..fefb519c 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -68,8 +68,8 @@
    • Tutorials/Primers
    • Glossary of Term
    • FAQ
      • -
    • Policies
      • -
    • Links
      • +
    • Policies
      • +
    • Links
    • Environments
    • GN1 News
    -- cgit v1.2.3 From 828cb4d0b327bcb441dc523f4d825f660f371e01 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 15:04:30 +0300 Subject: add policies page --- wqflask/wqflask/templates/policies.html | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/wqflask/wqflask/templates/policies.html b/wqflask/wqflask/templates/policies.html index 83b6b3c0..ef481de2 100644 --- a/wqflask/wqflask/templates/policies.html +++ b/wqflask/wqflask/templates/policies.html @@ -1,18 +1,21 @@ {% extends "base.html" %} -{% block title %}Policies{% endblock %} + +{% block title %}Links{% endblock %} + +{% block css %} + +{% endblock %} + {% block content %} - - - -
    -

    WebQTL Conditions of Use

    - -

    -
    +
    + Edit on Github +
    + +
    + {{ rendered_markdown|safe }} + +
    + {% endblock %} \ No newline at end of file -- cgit v1.2.3 From 6ae545167f59b40ecd0cee2bebb1276b34fa7c5b Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 15:06:05 +0300 Subject: register view,policies blueprint --- wqflask/wqflask/__init__.py | 4 ++++ wqflask/wqflask/templates/references.html | 25 ++++++++++++++++++------- 2 files changed, 22 insertions(+), 7 deletions(-) diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index 39a36fa3..d7da3755 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -8,6 +8,8 @@ from flask import Flask from utility import formatting from wqflask.markdown_routes import glossary_blueprint from wqflask.markdown_routes import references_blueprint +from wqflask.markdown_routes import links_blueprint +from wqflask.markdown_routes import policies_blueprint app = Flask(__name__) @@ -21,6 +23,8 @@ app.jinja_env.globals.update( # Registering blueprints app.register_blueprint(glossary_blueprint, url_prefix="/glossary") app.register_blueprint(references_blueprint,url_prefix="/references") +app.register_blueprint(links_blueprint,url_prefix="/links") +app.register_blueprint(policies_blueprint,url_prefix="/policies") @app.before_request def before_request(): diff --git a/wqflask/wqflask/templates/references.html b/wqflask/wqflask/templates/references.html index 5e86d95b..c10576d8 100644 --- a/wqflask/wqflask/templates/references.html +++ b/wqflask/wqflask/templates/references.html @@ -3,13 +3,13 @@ {% block title %}Reference{% endblock %} {% block css %} - + {% endblock %} {% block content %}
    - Edit on Github + Edit on Github
    @@ -18,12 +18,23 @@
    -- cgit v1.2.3 From 2a346d94a978c8a7faf0d1435220816efc3c2c64 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 15:07:42 +0300 Subject: add edit button in glossary page --- wqflask/wqflask/templates/glossary.html | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/wqflask/wqflask/templates/glossary.html b/wqflask/wqflask/templates/glossary.html index 146c7e86..395bcfea 100644 --- a/wqflask/wqflask/templates/glossary.html +++ b/wqflask/wqflask/templates/glossary.html @@ -8,9 +8,11 @@ {% block content %} +
    + Edit on Github +
    - - [Edit on Github] + {{ rendered_markdown|safe }}
    {% endblock %} -- cgit v1.2.3 From 416cb0cd272001651a3d9eb43500067ef524819d Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 15:09:37 +0300 Subject: add endpoint for polices,environments and policies --- wqflask/wqflask/markdown_routes.py | 51 ++++++++++++++++++++++---------------- 1 file changed, 29 insertions(+), 22 deletions(-) diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 60d4374c..5170fcf0 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -9,23 +9,31 @@ from flask import Blueprint from flask import render_template glossary_blueprint = Blueprint('glossary_blueprint', __name__) -references_blueprint=Blueprint("references_blueprint",__name__) -environments_blueprint=Blueprint("environments_blueprint",__name__) -links_blueprint=Blueprint("links_blueprint",__name__) -policies_blueprint=Blueprint("policies_blueprint",__name__) +references_blueprint = Blueprint("references_blueprint", __name__) +environments_blueprint = Blueprint("environments_blueprint", __name__) +links_blueprint = Blueprint("links_blueprint", __name__) +policies_blueprint = Blueprint("policies_blueprint", __name__) -def render_markdown(file_name): +#for debug +github_url = ("https://raw.githubusercontent.com/" + "genenetwork/gn-docs/master/general/glossary/glossary.md") + + + +def render_markdown(file_name,github_url="https://raw.githubusercontent.com/Alexanderlacuna/gn-docs/feature/add-markdown-pages/"): + + md_content=requests.get(f"{github_url}{file_name}") """Try to fetch the file name from Github and if that fails, try to look for it inside the file system - +po """ - github_url = ("https://raw.githubusercontent.com/" - "genenetwork/gn-docs/master/") - md_content = requests.get(f"{github_url}{file_name}") + # github_url = ("https://raw.githubusercontent.com/" + # "genenetwork/gn-docs/master/") + # md_content = requests.get(f"{github_url}{file_name}") if md_content.status_code == 200: + # print(md_content.content.decode("utf-8")) return markdown.Markdown().convert(md_content.content.decode("utf-8")) - # TODO: Add fallback on our git server by checking the mirror. # Content not available @@ -36,8 +44,6 @@ look for it inside the file system "Please reach out to the gn2 team to have a look at this") - - @glossary_blueprint.route('/') def glossary(): return render_template( @@ -48,23 +54,24 @@ def glossary(): @references_blueprint.route('/') def references(): return render_template( - "reference.html", - rendered_markdown=render_markdown("general/glossary/glossary.md")), 200 - + "references.html", + rendered_markdown=render_markdown("general/references/references.md")), 200 @environments_blueprint.route("/") -def references(): - return render_template("environments.html",rendered_markdown=render_markdown("general/environments/environments.md")) +def environments(): + return render_template("environments.html", rendered_markdown=render_markdown("general/links/links.md")) @links_blueprint.route("/") def links(): - return rendered_template("links.html",rendered_markdown=render_markdown("general/links/links.md")) + return render_template( + "links.html", + rendered_markdown=render_markdown("general/links/links.md")), 200 -policies_blueprint.route("/") +@policies_blueprint.route("/") def policies(): - return rendered_template("policies.html",rendered_markdown=rendered_markdown("general/policies/policies.md")) - - + return render_template( + "links.html", + rendered_markdown=render_markdown("general/policies/policies.md")), 200 -- cgit v1.2.3 From 52eea81494a507eb69751dea54f98270b53d9844 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 15:10:46 +0300 Subject: add links page --- wqflask/wqflask/templates/links.html | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 wqflask/wqflask/templates/links.html diff --git a/wqflask/wqflask/templates/links.html b/wqflask/wqflask/templates/links.html new file mode 100644 index 00000000..7b092839 --- /dev/null +++ b/wqflask/wqflask/templates/links.html @@ -0,0 +1,21 @@ +{% extends "base.html" %} + +{% block title %}Links{% endblock %} + +{% block css %} + +{% endblock %} + +{% block content %} + +
    + Edit on Github +
    + +
    + {{ rendered_markdown|safe }} + +
    + + +{% endblock %} \ No newline at end of file -- cgit v1.2.3 From c58751a8aa7ab0277096d91bb3e50c3ef0d62aab Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 15:18:04 +0300 Subject: add re-used css to markdown.css for easy maintenance and reusability --- wqflask/wqflask/templates/references.html | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/wqflask/wqflask/templates/references.html b/wqflask/wqflask/templates/references.html index c10576d8..e05c8440 100644 --- a/wqflask/wqflask/templates/references.html +++ b/wqflask/wqflask/templates/references.html @@ -17,25 +17,5 @@
- {% endblock %} \ No newline at end of file -- cgit v1.2.3 From 8a0e79d3186e340bc438dd07b4c2992f81c3e6d7 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 17:09:43 +0300 Subject: add environment markdown --- wqflask/wqflask/templates/environment.html | 37 ++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 wqflask/wqflask/templates/environment.html diff --git a/wqflask/wqflask/templates/environment.html b/wqflask/wqflask/templates/environment.html new file mode 100644 index 00000000..a331d494 --- /dev/null +++ b/wqflask/wqflask/templates/environment.html @@ -0,0 +1,37 @@ +{% extends "base.html" %} + +{% block title %}Glossary{% endblock %} + +{% block css %} + +{% endblock %} + +{% block content %} + +
+ Edit on Github +
+
+ +
{{ rendered_markdown|safe }}
+
+ + +{% endblock %} -- cgit v1.2.3 From b0c1d59d4e5a9580b4d15664a53845969db32d0a Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 17:11:55 +0300 Subject: remove environment from /wqflask/views.py --- wqflask/wqflask/templates/links.html | 2 +- wqflask/wqflask/views.py | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/wqflask/wqflask/templates/links.html b/wqflask/wqflask/templates/links.html index 7b092839..ef481de2 100644 --- a/wqflask/wqflask/templates/links.html +++ b/wqflask/wqflask/templates/links.html @@ -9,7 +9,7 @@ {% block content %}
- Edit on Github + Edit on Github
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index cc2dc341..6cdce248 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -321,10 +321,10 @@ def credits(): #return render_template("docs.html", **doc.__dict__) return render_template("credits.html") -@app.route("/environments") -def environments(): - doc = Docs("environments", request.args) - return render_template("docs.html", **doc.__dict__) +# @app.route("/environments") +# def environments(): +# doc = Docs("environments", request.args) +# return render_template("docs.html", **doc.__dict__) #return render_template("environments.html", **doc.__dict__) @app.route("/update_text", methods=('POST',)) -- cgit v1.2.3 From d8fb319272a4833ed3045cdc5ed46e0e204f78e1 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 17:13:24 +0300 Subject: add and register environments blueprint --- wqflask/wqflask/__init__.py | 2 ++ wqflask/wqflask/templates/base.html | 2 +- wqflask/wqflask/templates/references.html | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index d7da3755..f44b4bfd 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -10,6 +10,7 @@ from wqflask.markdown_routes import glossary_blueprint from wqflask.markdown_routes import references_blueprint from wqflask.markdown_routes import links_blueprint from wqflask.markdown_routes import policies_blueprint +from wqflask.markdown_routes import environments_blueprint app = Flask(__name__) @@ -25,6 +26,7 @@ app.register_blueprint(glossary_blueprint, url_prefix="/glossary") app.register_blueprint(references_blueprint,url_prefix="/references") app.register_blueprint(links_blueprint,url_prefix="/links") app.register_blueprint(policies_blueprint,url_prefix="/policies") +app.register_blueprint(environments_blueprint,url_prefix="/environments") @app.before_request def before_request(): diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index fefb519c..8ba5d0d5 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -70,7 +70,7 @@
  • FAQ
  • Policies
  • Links
    • -
  • Environments
    • +
  • Environments
  • GN1 News
    • diff --git a/wqflask/wqflask/templates/references.html b/wqflask/wqflask/templates/references.html index e05c8440..e2f152e3 100644 --- a/wqflask/wqflask/templates/references.html +++ b/wqflask/wqflask/templates/references.html @@ -9,7 +9,7 @@ {% block content %}
    - Edit on Github + Edit on Github
    -- cgit v1.2.3 From 66f4ab80a5dbfa8634c3a5df91a59a9119f57b2c Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 17:18:35 +0300 Subject: add table extension to support conversion of markdown tables to HTML --- wqflask/wqflask/markdown_routes.py | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 5170fcf0..073370c7 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -20,7 +20,24 @@ github_url = ("https://raw.githubusercontent.com/" + +def render_markdown_table(file_name,github_url="https://raw.githubusercontent.com/Alexanderlacuna/gn-docs/feature/add-markdown-pages/"): + + md_content=md_content=requests.get(f"{github_url}{file_name}") + if md_content.status_code==200: + return markdown.markdown(md_content.content.decode("utf-8"), extensions=['tables']) + return (f"\nContent for {file_name} not available. " + "Please check " + "(here to see where content exists)" + "[https://github.com/genenetwork/gn-docs]. " + "Please reach out to the gn2 team to have a look at this") + + + + def render_markdown(file_name,github_url="https://raw.githubusercontent.com/Alexanderlacuna/gn-docs/feature/add-markdown-pages/"): + github_url = ("https://raw.githubusercontent.com/" + "genenetwork/gn-docs/master/") md_content=requests.get(f"{github_url}{file_name}") """Try to fetch the file name from Github and if that fails, try to @@ -60,7 +77,7 @@ def references(): @environments_blueprint.route("/") def environments(): - return render_template("environments.html", rendered_markdown=render_markdown("general/links/links.md")) + return render_template("environment.html", rendered_markdown=render_markdown_table("general/environments/environments.md")),200 @links_blueprint.route("/") -- cgit v1.2.3 From 41988f8e92ea5a273e22a7176481cf2f4bd88b5b Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 17:22:44 +0300 Subject: delete environments html pagE --- wqflask/wqflask/templates/environments.html | 83 ----------------------------- 1 file changed, 83 deletions(-) delete mode 100644 wqflask/wqflask/templates/environments.html diff --git a/wqflask/wqflask/templates/environments.html b/wqflask/wqflask/templates/environments.html deleted file mode 100644 index 5ef91a95..00000000 --- a/wqflask/wqflask/templates/environments.html +++ /dev/null @@ -1,83 +0,0 @@ -{% extends "base.html" %} - -{% block title %}Environments{% endblock %} - -{% block content %} -
    -

    System Properties

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Operating System
    Ubuntu12.04.5 LTS 64-bithttp://www.ubuntu.com/Free software licenses (mainly GPL)
    Database
    MySQL5.5.40http://www.mysql.com/GPL (version 2) or proprietary
    Python
    Python2.7.3http://www.python.org/Python Software Foundation License
    Flask0.9http://flask.pocoo.org/BSD
    Jinja22.6http://jinja.pocoo.org/BSD
    NumPy1.7.0http://www.numpy.org/BSD-new
    SciPy0.11.0http://www.scipy.org/BSD-new
    JavaScript / CSS
    jQuery1.10.2http://jquery.com/MIT
    Bootstrap2.3.1http://getbootstrap.com/MIT License (Apache License 2.0 prior to 3.1.0)
    DataTables1.9.4http://www.datatables.net/MIT
    CKEditor4.4.5http://ckeditor.com/GPL, LGPL and MPL
    -
    -{% endblock %} -- cgit v1.2.3 From da73052c84d5566bf3d221d90f93688db125181d Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 18:13:00 +0300 Subject: add facilities page --- wqflask/wqflask/markdown_routes.py | 10 ++++++++-- wqflask/wqflask/templates/facilities.html | 21 +++++++++++++++++++++ 2 files changed, 29 insertions(+), 2 deletions(-) create mode 100644 wqflask/wqflask/templates/facilities.html diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 073370c7..7765af36 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -13,6 +13,7 @@ references_blueprint = Blueprint("references_blueprint", __name__) environments_blueprint = Blueprint("environments_blueprint", __name__) links_blueprint = Blueprint("links_blueprint", __name__) policies_blueprint = Blueprint("policies_blueprint", __name__) +facilities_blueprint=Blueprint("facilities",__name__) #for debug github_url = ("https://raw.githubusercontent.com/" @@ -36,8 +37,8 @@ def render_markdown_table(file_name,github_url="https://raw.githubusercontent.co def render_markdown(file_name,github_url="https://raw.githubusercontent.com/Alexanderlacuna/gn-docs/feature/add-markdown-pages/"): - github_url = ("https://raw.githubusercontent.com/" - "genenetwork/gn-docs/master/") + # github_url = ("https://raw.githubusercontent.com/" + # "genenetwork/gn-docs/master/") md_content=requests.get(f"{github_url}{file_name}") """Try to fetch the file name from Github and if that fails, try to @@ -92,3 +93,8 @@ def policies(): return render_template( "links.html", rendered_markdown=render_markdown("general/policies/policies.md")), 200 + + +@facilities_blueprint.route("/") +def facilities(): + return render_template("facilities",rendered_markdown=render_markdown("general/policies/policies.md")), 200 \ No newline at end of file diff --git a/wqflask/wqflask/templates/facilities.html b/wqflask/wqflask/templates/facilities.html new file mode 100644 index 00000000..5be0c96d --- /dev/null +++ b/wqflask/wqflask/templates/facilities.html @@ -0,0 +1,21 @@ +{% extends "base.html" %} + +{% block title %}Facilities{% endblock %} + +{% block css %} + +{% endblock %} + +{% block content %} + +
    + Edit on Github +
    + +
    + {{ rendered_markdown|safe }} + +
    + + +{% endblock %} \ No newline at end of file -- cgit v1.2.3 From 6ab58b529aca9c12bb26865a1d81a15aaad1fd5d Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 18:14:03 +0300 Subject: add and register facilities blueprint --- wqflask/wqflask/__init__.py | 2 ++ wqflask/wqflask/markdown_routes.py | 8 ++++---- wqflask/wqflask/templates/base.html | 1 + 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index f44b4bfd..0b69ec40 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -11,6 +11,7 @@ from wqflask.markdown_routes import references_blueprint from wqflask.markdown_routes import links_blueprint from wqflask.markdown_routes import policies_blueprint from wqflask.markdown_routes import environments_blueprint +from wqflask.markdown_routes import facilities_blueprint app = Flask(__name__) @@ -27,6 +28,7 @@ app.register_blueprint(references_blueprint,url_prefix="/references") app.register_blueprint(links_blueprint,url_prefix="/links") app.register_blueprint(policies_blueprint,url_prefix="/policies") app.register_blueprint(environments_blueprint,url_prefix="/environments") +app.register_blueprint(facilities_blueprint,url_prefix="/facilities") @app.before_request def before_request(): diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 7765af36..d00628b9 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -13,7 +13,7 @@ references_blueprint = Blueprint("references_blueprint", __name__) environments_blueprint = Blueprint("environments_blueprint", __name__) links_blueprint = Blueprint("links_blueprint", __name__) policies_blueprint = Blueprint("policies_blueprint", __name__) -facilities_blueprint=Blueprint("facilities",__name__) +facilities_blueprint=Blueprint("facilities_blueprint",__name__) #for debug github_url = ("https://raw.githubusercontent.com/" @@ -37,8 +37,8 @@ def render_markdown_table(file_name,github_url="https://raw.githubusercontent.co def render_markdown(file_name,github_url="https://raw.githubusercontent.com/Alexanderlacuna/gn-docs/feature/add-markdown-pages/"): - # github_url = ("https://raw.githubusercontent.com/" - # "genenetwork/gn-docs/master/") + github_url = ("https://raw.githubusercontent.com/" + "genenetwork/gn-docs/master/") md_content=requests.get(f"{github_url}{file_name}") """Try to fetch the file name from Github and if that fails, try to @@ -97,4 +97,4 @@ def policies(): @facilities_blueprint.route("/") def facilities(): - return render_template("facilities",rendered_markdown=render_markdown("general/policies/policies.md")), 200 \ No newline at end of file + return render_template("facilities.html",rendered_markdown=render_markdown("general/help/facilities.md")), 200 \ No newline at end of file diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 8ba5d0d5..faa59deb 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -70,6 +70,7 @@
  • FAQ
  • Policies
  • Links
    • +
  • Facilities
  • Environments
  • GN1 News
    • -- cgit v1.2.3 From 4f449007d7f4afe4b141851772fa694ced4e77e3 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 21:28:37 +0300 Subject: refactor render_markdown function in wqflask/markdown_routes.py --- wqflask/wqflask/markdown_routes.py | 45 +++++++---------------------- wqflask/wqflask/static/new/css/markdown.css | 17 ++++++----- 2 files changed, 19 insertions(+), 43 deletions(-) diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index d00628b9..0445ded1 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -13,47 +13,22 @@ references_blueprint = Blueprint("references_blueprint", __name__) environments_blueprint = Blueprint("environments_blueprint", __name__) links_blueprint = Blueprint("links_blueprint", __name__) policies_blueprint = Blueprint("policies_blueprint", __name__) -facilities_blueprint=Blueprint("facilities_blueprint",__name__) +facilities_blueprint = Blueprint("facilities_blueprint", __name__) -#for debug -github_url = ("https://raw.githubusercontent.com/" - "genenetwork/gn-docs/master/general/glossary/glossary.md") +# for debug +# https://raw.githubusercontent.com/Alexanderlacuna/gn-docs/feature/add-markdown-pages/ - - -def render_markdown_table(file_name,github_url="https://raw.githubusercontent.com/Alexanderlacuna/gn-docs/feature/add-markdown-pages/"): - - md_content=md_content=requests.get(f"{github_url}{file_name}") - if md_content.status_code==200: - return markdown.markdown(md_content.content.decode("utf-8"), extensions=['tables']) - return (f"\nContent for {file_name} not available. " - "Please check " - "(here to see where content exists)" - "[https://github.com/genenetwork/gn-docs]. " - "Please reach out to the gn2 team to have a look at this") - - - - -def render_markdown(file_name,github_url="https://raw.githubusercontent.com/Alexanderlacuna/gn-docs/feature/add-markdown-pages/"): +def render_markdown(file_name): github_url = ("https://raw.githubusercontent.com/" "genenetwork/gn-docs/master/") - - md_content=requests.get(f"{github_url}{file_name}") - """Try to fetch the file name from Github and if that fails, try to -look for it inside the file system -po - """ - # github_url = ("https://raw.githubusercontent.com/" - # "genenetwork/gn-docs/master/") - # md_content = requests.get(f"{github_url}{file_name}") + + md_content = requests.get(f"{github_url}{file_name}") if md_content.status_code == 200: - # print(md_content.content.decode("utf-8")) - return markdown.Markdown().convert(md_content.content.decode("utf-8")) + return markdown.markdown(md_content.content.decode("utf-8"), extensions=['tables']) + # return markdown.Markdown().convert(md_content.content.decode("utf-8")) # TODO: Add fallback on our git server by checking the mirror. - # Content not available return (f"\nContent for {file_name} not available. " "Please check " @@ -78,7 +53,7 @@ def references(): @environments_blueprint.route("/") def environments(): - return render_template("environment.html", rendered_markdown=render_markdown_table("general/environments/environments.md")),200 + return render_template("environment.html", rendered_markdown=render_markdown_table("general/environments/environments.md")), 200 @links_blueprint.route("/") @@ -97,4 +72,4 @@ def policies(): @facilities_blueprint.route("/") def facilities(): - return render_template("facilities.html",rendered_markdown=render_markdown("general/help/facilities.md")), 200 \ No newline at end of file + return render_template("facilities.html", rendered_markdown=render_markdown("general/help/facilities.md")), 200 diff --git a/wqflask/wqflask/static/new/css/markdown.css b/wqflask/wqflask/static/new/css/markdown.css index ad665835..6d76c190 100644 --- a/wqflask/wqflask/static/new/css/markdown.css +++ b/wqflask/wqflask/static/new/css/markdown.css @@ -35,7 +35,7 @@ /*background: #27407a;*/ background: blue; border-radius: 20px; - + /*text-align: center;*/ @@ -49,18 +49,19 @@ .container { -width:80vw; -margin: auto; -max-width:80vw; - + width: 80vw; + margin: auto; + max-width: 80vw; + } .container p { font-size: 17px; - word-spacing: 0.2em; + word-spacing: 0.2em; } -@media(max-width:650px){ - .container{ + +@media(max-width:650px) { + .container { width: 100vw; } } \ No newline at end of file -- cgit v1.2.3 From 001b10077517b24e0eecc16819c77f0eb3c31dc1 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 21:33:39 +0300 Subject: PEP8 format and remove unnecessary comments --- wqflask/wqflask/markdown_routes.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 0445ded1..093dffeb 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -15,10 +15,6 @@ links_blueprint = Blueprint("links_blueprint", __name__) policies_blueprint = Blueprint("policies_blueprint", __name__) facilities_blueprint = Blueprint("facilities_blueprint", __name__) -# for debug -# https://raw.githubusercontent.com/Alexanderlacuna/gn-docs/feature/add-markdown-pages/ - - def render_markdown(file_name): github_url = ("https://raw.githubusercontent.com/" "genenetwork/gn-docs/master/") -- cgit v1.2.3 From f900a574be30590cca0e9c962bfecf25121e4ab0 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 21:40:15 +0300 Subject: delete environment endpoint in wqflask/views.py --- wqflask/wqflask/views.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 6cdce248..91d0842c 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -321,12 +321,6 @@ def credits(): #return render_template("docs.html", **doc.__dict__) return render_template("credits.html") -# @app.route("/environments") -# def environments(): -# doc = Docs("environments", request.args) -# return render_template("docs.html", **doc.__dict__) - #return render_template("environments.html", **doc.__dict__) - @app.route("/update_text", methods=('POST',)) def update_page(): update_text(request.form) -- cgit v1.2.3 From 8a74593bfda0d9e5e681046044c262713073164b Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 22:55:39 +0300 Subject: pep8 format for blue_print,url_prefix --- wqflask/wqflask/__init__.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index 0b69ec40..0564cfa7 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -24,11 +24,11 @@ app.jinja_env.globals.update( # Registering blueprints app.register_blueprint(glossary_blueprint, url_prefix="/glossary") -app.register_blueprint(references_blueprint,url_prefix="/references") -app.register_blueprint(links_blueprint,url_prefix="/links") -app.register_blueprint(policies_blueprint,url_prefix="/policies") -app.register_blueprint(environments_blueprint,url_prefix="/environments") -app.register_blueprint(facilities_blueprint,url_prefix="/facilities") +app.register_blueprint(references_blueprint, url_prefix="/references") +app.register_blueprint(links_blueprint, url_prefix="/links") +app.register_blueprint(policies_blueprint, url_prefix="/policies") +app.register_blueprint(environments_blueprint, url_prefix="/environments") +app.register_blueprint(facilities_blueprint, url_prefix="/facilities") @app.before_request def before_request(): -- cgit v1.2.3 From 63c90d88499c2cda1b3da0960e179856aaba05c9 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 23:00:53 +0300 Subject: add doc string for render_markdown in wqflask/markdown_routes.py --- wqflask/wqflask/markdown_routes.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 093dffeb..7e6c7948 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -16,6 +16,8 @@ policies_blueprint = Blueprint("policies_blueprint", __name__) facilities_blueprint = Blueprint("facilities_blueprint", __name__) def render_markdown(file_name): + """Try to fetch the file name from Github and if that fails, try to +look for it inside the file system """ github_url = ("https://raw.githubusercontent.com/" "genenetwork/gn-docs/master/") -- cgit v1.2.3 From b86f0f6200cb435cea91077352d5d95f610162a6 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 23:35:00 +0300 Subject: use css block in templates and remove comments --- wqflask/wqflask/markdown_routes.py | 3 ++- wqflask/wqflask/static/new/css/markdown.css | 7 ------- wqflask/wqflask/templates/environment.html | 2 -- wqflask/wqflask/templates/facilities.html | 3 +-- wqflask/wqflask/templates/links.html | 4 +--- wqflask/wqflask/templates/policies.html | 4 +--- wqflask/wqflask/templates/references.html | 3 +-- 7 files changed, 6 insertions(+), 20 deletions(-) diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 7e6c7948..25eabe66 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -15,6 +15,7 @@ links_blueprint = Blueprint("links_blueprint", __name__) policies_blueprint = Blueprint("policies_blueprint", __name__) facilities_blueprint = Blueprint("facilities_blueprint", __name__) + def render_markdown(file_name): """Try to fetch the file name from Github and if that fails, try to look for it inside the file system """ @@ -51,7 +52,7 @@ def references(): @environments_blueprint.route("/") def environments(): - return render_template("environment.html", rendered_markdown=render_markdown_table("general/environments/environments.md")), 200 + return render_template("environment.html", rendered_markdown=render_markdown("general/environments/environments.md")), 200 @links_blueprint.route("/") diff --git a/wqflask/wqflask/static/new/css/markdown.css b/wqflask/wqflask/static/new/css/markdown.css index 6d76c190..91b72cb8 100644 --- a/wqflask/wqflask/static/new/css/markdown.css +++ b/wqflask/wqflask/static/new/css/markdown.css @@ -15,8 +15,6 @@ margin-left: auto; } - - .github-btn { margin: 20px 10px; display: flex; @@ -32,13 +30,8 @@ transition-duration: 0.5s; padding: 8px 12px; color: #fff; - /*background: #27407a;*/ background: blue; border-radius: 20px; - - /*text-align: center;*/ - - } .github-btn a:hover { diff --git a/wqflask/wqflask/templates/environment.html b/wqflask/wqflask/templates/environment.html index a331d494..f378e0b8 100644 --- a/wqflask/wqflask/templates/environment.html +++ b/wqflask/wqflask/templates/environment.html @@ -19,7 +19,6 @@ {% endblock %} diff --git a/wqflask/wqflask/templates/facilities.html b/wqflask/wqflask/templates/facilities.html index 5be0c96d..63f110dd 100644 --- a/wqflask/wqflask/templates/facilities.html +++ b/wqflask/wqflask/templates/facilities.html @@ -3,7 +3,7 @@ {% block title %}Facilities{% endblock %} {% block css %} - + {% endblock %} {% block content %} @@ -17,5 +17,4 @@
    - {% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/links.html b/wqflask/wqflask/templates/links.html index ef481de2..94d8eab7 100644 --- a/wqflask/wqflask/templates/links.html +++ b/wqflask/wqflask/templates/links.html @@ -3,7 +3,7 @@ {% block title %}Links{% endblock %} {% block css %} - + {% endblock %} {% block content %} @@ -16,6 +16,4 @@ {{ rendered_markdown|safe }}
    - - {% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/policies.html b/wqflask/wqflask/templates/policies.html index ef481de2..94d8eab7 100644 --- a/wqflask/wqflask/templates/policies.html +++ b/wqflask/wqflask/templates/policies.html @@ -3,7 +3,7 @@ {% block title %}Links{% endblock %} {% block css %} - + {% endblock %} {% block content %} @@ -16,6 +16,4 @@ {{ rendered_markdown|safe }}
    - - {% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/references.html b/wqflask/wqflask/templates/references.html index e2f152e3..8dcf4493 100644 --- a/wqflask/wqflask/templates/references.html +++ b/wqflask/wqflask/templates/references.html @@ -3,7 +3,7 @@ {% block title %}Reference{% endblock %} {% block css %} - + {% endblock %} {% block content %} @@ -17,5 +17,4 @@
    - {% endblock %} \ No newline at end of file -- cgit v1.2.3 From cd27138b6cc963450851417ef06303027da51419 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Fri, 27 Nov 2020 00:15:18 +0300 Subject: remove commented code --- wqflask/wqflask/markdown_routes.py | 1 - 1 file changed, 1 deletion(-) diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 25eabe66..601845d7 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -26,7 +26,6 @@ look for it inside the file system """ if md_content.status_code == 200: return markdown.markdown(md_content.content.decode("utf-8"), extensions=['tables']) - # return markdown.Markdown().convert(md_content.content.decode("utf-8")) # TODO: Add fallback on our git server by checking the mirror. # Content not available return (f"\nContent for {file_name} not available. " -- cgit v1.2.3 From 78fd4d4a89a02fc5233a1f5bbdfd3946ec08f3b7 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 26 Nov 2020 16:06:59 -0600 Subject: Changed the way the chromosome colors for the "color by chr" manhattan plot option are stored to using a list comprehension on a list of the just the hex strings --- .../marker_regression/display_mapping_results.py | 32 ++++------------------ 1 file changed, 6 insertions(+), 26 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 87910401..08c2d750 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -75,32 +75,12 @@ MEDIUMPURPLE = ImageColor.getrgb("mediumpurple") # ---- END: Define common colours ---- # # ZS: List of distinct colors for manhattan plot if user selects "varied" -DISTINCT_COLOR_LIST = [ - ImageColor.getrgb("#FF0000"), - ImageColor.getrgb("#00FF00"), - ImageColor.getrgb("#0000FF"), - ImageColor.getrgb("#FFFF00"), - ImageColor.getrgb("#FF00FF"), - ImageColor.getrgb("#00FFFF"), - ImageColor.getrgb("#000000"), - ImageColor.getrgb("#800000"), - ImageColor.getrgb("#008000"), - ImageColor.getrgb("#000080"), - ImageColor.getrgb("#808000"), - ImageColor.getrgb("#800080"), - ImageColor.getrgb("#008080"), - ImageColor.getrgb("#808080"), - ImageColor.getrgb("#C00000"), - ImageColor.getrgb("#00C000"), - ImageColor.getrgb("#0000C0"), - ImageColor.getrgb("#C0C000"), - ImageColor.getrgb("#C000C0"), - ImageColor.getrgb("#00C0C0"), - ImageColor.getrgb("#C0C0C0"), - ImageColor.getrgb("#400000"), - ImageColor.getrgb("#004000"), - ImageColor.getrgb("#000040"), -] +COLOR_CODES = ["#FF0000", "#00FF00", "#0000FF", "#FFFF00", "#FF00FF", "#00FFFF", + "#000000", "#800000", "#008000", "#000080", "#808000", "#800080", + "#008080", "#808080", "#C00000", "#00C000", "#0000C0", "#C0C000", + "#C000C0", "#00C0C0", "#C0C0C0", "#400000", "#004000", "#000040"] + +DISTINCT_COLOR_LIST = [ImageColor.getrgb(color) for color in COLOR_CODES] # ---- FONT FILES ---- # VERDANA_FILE = "./wqflask/static/fonts/verdana.ttf" -- cgit v1.2.3 From e396706f5c2bbb1bef21bcc8180565015aee3fb0 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Fri, 27 Nov 2020 12:59:18 +0300 Subject: add edit image --- wqflask/wqflask/static/images/edit.png | Bin 0 -> 2452 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 wqflask/wqflask/static/images/edit.png diff --git a/wqflask/wqflask/static/images/edit.png b/wqflask/wqflask/static/images/edit.png new file mode 100644 index 00000000..571b08cd Binary files /dev/null and b/wqflask/wqflask/static/images/edit.png differ -- cgit v1.2.3 From 5c4a2727f013785c8818864c0520321ef8d60dce Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Fri, 27 Nov 2020 13:00:47 +0300 Subject: add new github button and css --- wqflask/wqflask/static/new/css/markdown.css | 27 +++++++++++++-------------- wqflask/wqflask/templates/environment.html | 11 ++++++++--- wqflask/wqflask/templates/facilities.html | 12 ++++++++---- wqflask/wqflask/templates/glossary.html | 11 ++++++++--- wqflask/wqflask/templates/links.html | 11 ++++++++--- wqflask/wqflask/templates/policies.html | 12 ++++++++---- wqflask/wqflask/templates/references.html | 19 +++++++++---------- 7 files changed, 62 insertions(+), 41 deletions(-) diff --git a/wqflask/wqflask/static/new/css/markdown.css b/wqflask/wqflask/static/new/css/markdown.css index 91b72cb8..311962c1 100644 --- a/wqflask/wqflask/static/new/css/markdown.css +++ b/wqflask/wqflask/static/new/css/markdown.css @@ -15,29 +15,28 @@ margin-left: auto; } -.github-btn { +.github-btn-container { margin: 20px 10px; display: flex; width: 90vw; justify-content: flex-end; } -.github-btn a { - display: inline-block; - align-self: center; - text-decoration: none; - transition-property: all; - transition-duration: 0.5s; - padding: 8px 12px; - color: #fff; - background: blue; - border-radius: 20px; +.github-btn { + border: 3px solid #357ebd; + background: lightgrey; + padding: 6px 8px; + border-radius: 16px; } -.github-btn a:hover { - - background: #333; +.github-btn a { + font-weight: bold; + color: #357ebd; +} +.github-btn a img { + height: 40px; + width: 40px; } diff --git a/wqflask/wqflask/templates/environment.html b/wqflask/wqflask/templates/environment.html index f378e0b8..183518a5 100644 --- a/wqflask/wqflask/templates/environment.html +++ b/wqflask/wqflask/templates/environment.html @@ -8,9 +8,14 @@ {% block content %} -
    - Edit on Github -
    +
    +
    + + Edit on Github inner + + +
    +
    {{ rendered_markdown|safe }}
    diff --git a/wqflask/wqflask/templates/facilities.html b/wqflask/wqflask/templates/facilities.html index 63f110dd..652746a7 100644 --- a/wqflask/wqflask/templates/facilities.html +++ b/wqflask/wqflask/templates/facilities.html @@ -8,10 +8,14 @@ {% block content %} -
    - Edit on Github -
    - +
    +
    + + Edit on Github inner + + +
    +
    {{ rendered_markdown|safe }} diff --git a/wqflask/wqflask/templates/glossary.html b/wqflask/wqflask/templates/glossary.html index 395bcfea..f536d977 100644 --- a/wqflask/wqflask/templates/glossary.html +++ b/wqflask/wqflask/templates/glossary.html @@ -8,9 +8,14 @@ {% block content %} -
    - Edit on Github -
    +
    +
    + + Edit on Github inner + + +
    +
    {{ rendered_markdown|safe }} diff --git a/wqflask/wqflask/templates/links.html b/wqflask/wqflask/templates/links.html index 94d8eab7..cf524496 100644 --- a/wqflask/wqflask/templates/links.html +++ b/wqflask/wqflask/templates/links.html @@ -8,9 +8,14 @@ {% block content %} -
    - Edit on Github -
    +
    +
    + + Edit on Github inner + + +
    +
    {{ rendered_markdown|safe }} diff --git a/wqflask/wqflask/templates/policies.html b/wqflask/wqflask/templates/policies.html index 94d8eab7..420493ad 100644 --- a/wqflask/wqflask/templates/policies.html +++ b/wqflask/wqflask/templates/policies.html @@ -8,10 +8,14 @@ {% block content %} -
    - Edit on Github -
    - +
    +
    + + Edit on Github inner + + +
    +
    {{ rendered_markdown|safe }} diff --git a/wqflask/wqflask/templates/references.html b/wqflask/wqflask/templates/references.html index 8dcf4493..caf87244 100644 --- a/wqflask/wqflask/templates/references.html +++ b/wqflask/wqflask/templates/references.html @@ -1,20 +1,19 @@ {% extends "base.html" %} - {% block title %}Reference{% endblock %} - {% block css %} {% endblock %} - {% block content %} - -
    - Edit on Github -
    - +
    +
    + + Edit on Github inner + + +
    +
    - {{ rendered_markdown|safe }} - + {{ rendered_markdown|safe }}
    {% endblock %} \ No newline at end of file -- cgit v1.2.3 From a4842a8d54f891dcb59d29aa53a0e442f8f0e0c2 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Fri, 27 Nov 2020 13:33:47 +0300 Subject: update to edit text in static templates --- wqflask/wqflask/templates/environment.html | 2 +- wqflask/wqflask/templates/facilities.html | 2 +- wqflask/wqflask/templates/glossary.html | 2 +- wqflask/wqflask/templates/links.html | 2 +- wqflask/wqflask/templates/policies.html | 2 +- wqflask/wqflask/templates/references.html | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/wqflask/wqflask/templates/environment.html b/wqflask/wqflask/templates/environment.html index 183518a5..94b31464 100644 --- a/wqflask/wqflask/templates/environment.html +++ b/wqflask/wqflask/templates/environment.html @@ -11,7 +11,7 @@
    - Edit on Github inner + Edit Text
    diff --git a/wqflask/wqflask/templates/facilities.html b/wqflask/wqflask/templates/facilities.html index 652746a7..a022b657 100644 --- a/wqflask/wqflask/templates/facilities.html +++ b/wqflask/wqflask/templates/facilities.html @@ -11,7 +11,7 @@
    - Edit on Github inner + Edit Text
    diff --git a/wqflask/wqflask/templates/glossary.html b/wqflask/wqflask/templates/glossary.html index f536d977..752c4b12 100644 --- a/wqflask/wqflask/templates/glossary.html +++ b/wqflask/wqflask/templates/glossary.html @@ -11,7 +11,7 @@
    - Edit on Github inner + Edit Text
    diff --git a/wqflask/wqflask/templates/links.html b/wqflask/wqflask/templates/links.html index cf524496..072e8429 100644 --- a/wqflask/wqflask/templates/links.html +++ b/wqflask/wqflask/templates/links.html @@ -11,7 +11,7 @@
    - Edit on Github inner + Edit Text
    diff --git a/wqflask/wqflask/templates/policies.html b/wqflask/wqflask/templates/policies.html index 420493ad..4e0985d3 100644 --- a/wqflask/wqflask/templates/policies.html +++ b/wqflask/wqflask/templates/policies.html @@ -11,7 +11,7 @@
    - Edit on Github inner + Edit Text
    diff --git a/wqflask/wqflask/templates/references.html b/wqflask/wqflask/templates/references.html index caf87244..f723a1e8 100644 --- a/wqflask/wqflask/templates/references.html +++ b/wqflask/wqflask/templates/references.html @@ -7,7 +7,7 @@
    - Edit on Github inner + Edit Text
    -- cgit v1.2.3 From 1cabb7810a8b2ab5171e1547e154244978fb37d4 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Fri, 27 Nov 2020 14:23:21 +0300 Subject: edit css for static page --- wqflask/wqflask/static/new/css/markdown.css | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/static/new/css/markdown.css b/wqflask/wqflask/static/new/css/markdown.css index 311962c1..dca3e31d 100644 --- a/wqflask/wqflask/static/new/css/markdown.css +++ b/wqflask/wqflask/static/new/css/markdown.css @@ -23,13 +23,17 @@ } .github-btn { + display: flex; + justify-content: center; border: 3px solid #357ebd; background: lightgrey; - padding: 6px 8px; + padding: 3px 4px; + width: 200px; border-radius: 16px; } .github-btn a { + align-self: center; font-weight: bold; color: #357ebd; } @@ -37,6 +41,7 @@ .github-btn a img { height: 40px; width: 40px; + padding-left:5px; } -- cgit v1.2.3 From 7f35213b64707e7c61affb6fa376f561200ac1d6 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Fri, 27 Nov 2020 19:59:17 +0300 Subject: move tests to unit folder --- .../marker_regression/test_gemma_mapping.py | 205 +++++++++++++++ .../marker_regression/test_plink_mapping.py | 84 ++++++ .../marker_regression/test_qtlreaper_mapping.py | 21 ++ .../wqflask/marker_regression/test_rqtl_mapping.py | 48 ++++ .../wqflask/marker_regression/test_run_mapping.py | 284 +++++++++++++++++++++ .../marker_regression/test_gemma_mapping.py | 205 --------------- .../marker_regression/test_plink_mapping.py | 84 ------ .../marker_regression/test_qtlreaper_mapping.py | 21 -- .../wqflask/marker_regression/test_rqtl_mapping.py | 48 ---- .../wqflask/marker_regression/test_run_mapping.py | 284 --------------------- 10 files changed, 642 insertions(+), 642 deletions(-) create mode 100644 wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py create mode 100644 wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py create mode 100644 wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py create mode 100644 wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py create mode 100644 wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py delete mode 100644 wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py delete mode 100644 wqflask/tests/wqflask/marker_regression/test_plink_mapping.py delete mode 100644 wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py delete mode 100644 wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py delete mode 100644 wqflask/tests/wqflask/marker_regression/test_run_mapping.py diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py new file mode 100644 index 00000000..5b621264 --- /dev/null +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -0,0 +1,205 @@ +# test for wqflask/marker_regression/gemma_mapping.py +import unittest +import random +from unittest import mock +from wqflask.marker_regression.gemma_mapping import run_gemma +from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file +from wqflask.marker_regression.gemma_mapping import gen_covariates_file +from wqflask.marker_regression.gemma_mapping import parse_gemma_output +from wqflask.marker_regression.gemma_mapping import parse_loco_output + + +class AttributeSetter: + def __init__(self, obj): + for key, val in obj.items(): + setattr(self, key, val) + + +class MockGroup(AttributeSetter): + def get_samplelist(self): + return None + + +class TestGemmaMapping(unittest.TestCase): + + @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") + def test_run_gemma_firstrun_set_false(self, mock_parse_loco): + """add tests for gemma function where first run is set to false""" + dataset = AttributeSetter( + {"group": AttributeSetter({"genofile": "genofile.geno"})}) + + output_file = "file1" + mock_parse_loco.return_value = [] + this_trait = AttributeSetter({"name": "t1"}) + + result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ + ], covariates="", use_loco=True, first_run=False, output_files=output_file) + + expected_results = ([], "file1") + self.assertEqual(expected_results, result) + + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") + @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug") + @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/") + @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") + @mock.patch("wqflask.marker_regression.gemma_mapping.logger") + @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") + @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") + @mock.patch("wqflask.marker_regression.run_mapping.random.choice") + @mock.patch("wqflask.marker_regression.gemma_mapping.os") + @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") + def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): + """add tests for run_gemma where first run is set to true""" + chromosomes = [] + for i in range(1, 5): + chromosomes.append(AttributeSetter({"name": f"CH{i}"})) + chromo = AttributeSetter({"chromosomes": chromosomes}) + dataset_group = MockGroup( + {"name": "GP1", "genofile": "file_geno"}) + dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", + "species": AttributeSetter({"chromosomes": chromo})}) + trait = AttributeSetter({"name": "trait1"}) + samples = [] + mock_gen_pheno_txt.return_value = None + mock_os.path.isfile.return_value = True + mock_gen_covar.return_value = None + mock_choice.return_value = "R" + mock_flat_files.return_value = "/home/genotype/bimbam" + mock_parse_loco.return_value = [] + results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ + ], vals=[], covariates="", use_loco=True) + system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), + mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] + mock_os.system.assert_has_calls(system_calls) + mock_gen_pheno_txt.assert_called_once() + mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") + mock_os.path.isfile.assert_called_once_with( + ('/home/user/imgfile_output.assoc.txt')) + self.assertEqual(mock_logger.debug.call_count, 2) + self.assertEqual(mock_flat_files.call_count, 4) + self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) + + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") + def test_gen_pheno_txt_file(self): + """add tests for generating pheno txt file""" + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ + "x", "w", "q", "we", "R"], trait_filename="fitr.re") + mock_open.assert_called_once_with( + '/home/user/data/gn2/fitr.re.txt', 'w') + filehandler = mock_open() + values = ["x", "w", "q", "we", "R"] + write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call( + 'q\n'), mock.call('we\n'), mock.call('R\n')] + + filehandler.write.assert_has_calls(write_calls) + + @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") + @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait") + @mock.patch("wqflask.marker_regression.gemma_mapping.create_dataset") + def test_gen_covariates_file(self, create_dataset, create_trait, flat_files): + """add tests for generating covariates files""" + covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2" + samplelist = ["X1", "X2", "X3", "X4"] + create_dataset_side_effect = [] + create_trait_side_effect = [] + + for i in range(4): + create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'})) + create_trait_side_effect.append( + AttributeSetter({"data": [f'data_{i}']})) + + create_dataset.side_effect = create_trait_side_effect + create_trait.side_effect = create_trait_side_effect + + group = MockGroup({"name": "group_X", "samplelist": samplelist}) + this_dataset = AttributeSetter({"group": group}) + flat_files.return_value = "Home/Genenetwork" + + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_covariates_file(this_dataset=this_dataset, covariates=covariates, + samples=["x1", "x2", "X3"]) + + create_dataset.assert_has_calls( + [mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')]) + mock_calls = [] + trait_names = ["X1", "Y1", "M1", "V1"] + + for i, trait in enumerate(create_trait_side_effect): + mock_calls.append( + mock.call(dataset=trait, name=trait_names[i], cellid=None)) + + create_trait.assert_has_calls(mock_calls) + + flat_files.assert_called_once_with('mapping') + mock_open.assert_called_once_with( + 'Home/Genenetwork/group_X_covariates.txt', 'w') + filehandler = mock_open() + filehandler.write.assert_has_calls([mock.call( + '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) + + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") + def test_parse_gemma_output(self): + """add test for generating gemma output with obj returned""" + file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7 +X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 +125\tgn9\t433575\tQ\tE\tA\tP\tMMB\tCDE\t0.67 +""" + with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open: + results = parse_gemma_output(genofile_name="gema_file") + expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, + {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] + mock_open.assert_called_once_with( + "/home/user/img/gema_file_output.assoc.txt") + self.assertEqual(results, expected) + + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") + def test_parse_gemma_output_with_empty_return(self): + """add tests for parse gemma output where nothing returned""" + output_file_results = """chr\t today""" + with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: + results = parse_gemma_output(genofile_name="gema_file") + self.assertEqual(results, []) + + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") + @mock.patch("wqflask.marker_regression.gemma_mapping.os") + @mock.patch("wqflask.marker_regression.gemma_mapping.json") + def test_parse_loco_outputfile_found(self, mock_json, mock_os): + """add tests for parse loco output file found""" + mock_json.load.return_value = { + "files": [["file_name", "user", "~/file1"], + ["file_name", "user", "~/file2"]] + } + return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" + return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" + mock_os.path.isfile.return_value = True + file_to_write = """{"files":["file_1","file_2"]}""" + with mock.patch("builtins.open") as mock_open: + + handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open( + read_data=return_file_1).return_value, mock.mock_open(read_data=return_file_2).return_value) + mock_open.side_effect = handles + results = parse_loco_output( + this_dataset={}, gwa_output_filename=".xw/") + expected_results = [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, { + 'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] + + self.assertEqual(expected_results, results) + + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") + @mock.patch("wqflask.marker_regression.gemma_mapping.os") + def test_parse_loco_outputfile_not_found(self, mock_os): + """add tests for parse loco output where output file not found""" + + mock_os.path.isfile.return_value = False + file_to_write = """{"files":["file_1","file_2"]}""" + + with mock.patch("builtins.open", mock.mock_open(read_data=file_to_write)) as mock_open: + results = parse_loco_output( + this_dataset={}, gwa_output_filename=".xw/") + self.assertEqual(results, []) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py new file mode 100644 index 00000000..428f45b9 --- /dev/null +++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py @@ -0,0 +1,84 @@ +# test for wqflask/marker_regression/plink_mapping.py +import unittest +from unittest import mock +from wqflask.marker_regression.plink_mapping import build_line_list +from wqflask.marker_regression.plink_mapping import get_samples_from_ped_file +from wqflask.marker_regression.plink_mapping import flat_files +from wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink +from wqflask.marker_regression.plink_mapping import parse_plink_output + + +class AttributeSetter: + def __init__(self, obj): + for key, val in obj.items(): + setattr(self, key, val) +class TestPlinkMapping(unittest.TestCase): + + def test_build_line_list(self): + """testing for building line list""" + line_1 = "this is line one test" + irregular_line = " this is an, irregular line " + exp_line1 = ["this", "is", "line", "one", "test"] + + results = build_line_list(irregular_line) + self.assertEqual(exp_line1, build_line_list(line_1)) + self.assertEqual([], build_line_list()) + self.assertEqual(["this", "is", "an,", "irregular", "line"], results) + + @mock.patch("wqflask.marker_regression.plink_mapping.flat_files") + def test_get_samples_from_ped_file(self, mock_flat_files): + """test for getting samples from ped file""" + dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) + file_sample = """Expected_1\tline test +Expected_2\there + Expected_3\tthree""" + mock_flat_files.return_value = "/home/user/" + with mock.patch("builtins.open", mock.mock_open(read_data=file_sample)) as mock_open: + results = get_samples_from_ped_file(dataset) + mock_flat_files.assert_called_once_with("mapping") + mock_open.assert_called_once_with("/home/user/n_1.ped", "r") + self.assertEqual( + ["Expected_1", "Expected_2", "Expected_3"], results) + + @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") + @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file") + def test_gen_pheno_txt_file_plink(self, mock_samples): + """test for getting gen_pheno txt file""" + mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"] + + trait = AttributeSetter({"name": "TX"}) + dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) + vals = ["value=K1", "value=K2", "value=K3"] + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + results = gen_pheno_txt_file_plink(this_trait=trait, dataset=dataset, + vals=vals, pheno_filename="ph_file") + mock_open.assert_called_once_with( + "/home/user/data/ph_file.txt", "wb") + filehandler = mock_open() + calls_expected = [mock.call('FID\tIID\tTX\n'), + mock.call('Expected_1\tExpected_1\tK1\nExpected_2\tExpected_2\tK2\nExpected_3\tExpected_3\tK3\n')] + + filehandler.write.assert_has_calls(calls_expected) + + filehandler.close.assert_called_once() + + @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") + @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list") + def test_parse_plink_output(self, mock_line_list): + """test for parsing plink output""" + chromosomes = [0, 34, 110, 89, 123, 23, 2] + species = AttributeSetter( + {"name": "S1", "chromosomes": AttributeSetter({"chromosomes": chromosomes})}) + + fake_file = """0 AACCAT T98.6 0.89\n2 AATA B45 0.3\n121 ACG B56.4 NA""" + + mock_line_list.side_effect = [["0", "AACCAT", "T98.6", "0.89"], [ + "2", "AATA", "B45", "0.3"], ["121", "ACG", "B56.4", "NA"]] + with mock.patch("builtins.open", mock.mock_open(read_data=fake_file)) as mock_open: + parse_results = parse_plink_output( + output_filename="P1_file", species=species) + mock_open.assert_called_once_with( + "/home/user/data/P1_file.qassoc", "rb") + expected = (2, {'AACCAT': 0.89, 'AATA': 0.3}) + + self.assertEqual(parse_results, expected) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py new file mode 100644 index 00000000..b47f877a --- /dev/null +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -0,0 +1,21 @@ +import unittest +from unittest import mock +from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file + +#issues some methods in genofile object are not defined +#modify samples should equal to vals +class TestQtlReaperMapping(unittest.TestCase): + @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") + def test_gen_pheno_txt_file(self): + vals=["V1","x","V4","V3","x"] + samples=["S1","S2","S3","S4","S5"] + trait_filename="trait_file" + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename) + mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w") + filehandler=mock_open() + write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')] + + filehandler.write.assert_has_calls(write_calls) + + diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py new file mode 100644 index 00000000..69f53721 --- /dev/null +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -0,0 +1,48 @@ +import unittest +from unittest import mock +from wqflask import app +from wqflask.marker_regression.rqtl_mapping import get_trait_data_type +from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype +from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names + +class TestRqtlMapping(unittest.TestCase): + + def setUp(self): + self.app_context=app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + + @mock.patch("wqflask.marker_regression.rqtl_mapping.g") + @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") + def test_get_trait_data(self,mock_logger,mock_db): + """test for getting trait data_type return True""" + caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" + mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + results=get_trait_data_type("traid_id") + mock_db.db.execute.assert_called_with(caller_value) + self.assertEqual(results,"fer434f") + + def test_sanitize_rqtl_phenotype(self): + """test for sanitizing rqtl phenotype""" + vals=['f',"x","r","x","x"] + results=sanitize_rqtl_phenotype(vals) + expected_phenotype_string='c(f,NA,r,NA,NA)' + + self.assertEqual(results,expected_phenotype_string) + + def test_sanitize_rqtl_names(self): + """test for sanitzing rqtl names""" + vals=['f',"x","r","x","x"] + expected_sanitized_name="c('f',NA,'r',NA,NA)" + results=sanitize_rqtl_names(vals) + self.assertEqual(expected_sanitized_name,results) + + + + + + + diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py new file mode 100644 index 00000000..4129cc0c --- /dev/null +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -0,0 +1,284 @@ +import unittest +import datetime +from unittest import mock + +from wqflask.marker_regression.run_mapping import get_genofile_samplelist +from wqflask.marker_regression.run_mapping import geno_db_exists +from wqflask.marker_regression.run_mapping import write_input_for_browser +from wqflask.marker_regression.run_mapping import export_mapping_results +from wqflask.marker_regression.run_mapping import trim_markers_for_figure +from wqflask.marker_regression.run_mapping import get_perm_strata +from wqflask.marker_regression.run_mapping import get_chr_lengths + + +class AttributeSetter: + def __init__(self, obj): + for k, v in obj.items(): + setattr(self, k, v) + + +class MockGroup(AttributeSetter): + + def get_genofiles(self): + return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}] + + +class TestRunMapping(unittest.TestCase): + def setUp(self): + + self.group = MockGroup( + {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"}) + chromosomes = { + "3": AttributeSetter({ + "name": "C1", + "length": "0.04" + }), + "4": AttributeSetter({ + "name": "C2", + "length": "0.03" + }), + "5": AttributeSetter({ + "name": "C4", + "length": "0.01" + }) + } + self.dataset = AttributeSetter( + {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"}) + + self.chromosomes = AttributeSetter({"chromosomes": chromosomes}) + self.trait = AttributeSetter( + {"symbol": "IGFI", "chr": "X1", "mb": 123313}) + + def tearDown(self): + self.dataset = AttributeSetter( + {"group": {"location": "~/genofiles/g1_file"}}) + + def test_get_genofile_samplelist(self): + + results_1 = get_genofile_samplelist(self.dataset) + self.assertEqual(results_1, ["S1", "S2", "S3", "S4"]) + self.group.genofile = "~/genofiles/g2_file" + result_2 = get_genofile_samplelist(self.dataset) + self.assertEqual(result_2, []) + + @mock.patch("wqflask.marker_regression.run_mapping.data_set") + def test_if_geno_db_exists(self, mock_data_set): + mock_data_set.create_dataset.side_effect = [ + AttributeSetter({}), Exception()] + results_no_error = geno_db_exists(self.dataset) + results_with_error = geno_db_exists(self.dataset) + + self.assertEqual(mock_data_set.create_dataset.call_count, 2) + self.assertEqual(results_with_error, "False") + self.assertEqual(results_no_error, "True") + + def test_trim_markers_for_figure(self): + + markers = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":0.5 + }, + { + "name": "MK2", + "chr": "C2", + "cM": "15", + "Mb": "10000", + "genotypes": [], + "lod_score":0.7 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":1 + }] + + marker_2 = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "p_wald":4.6 + }] + results = trim_markers_for_figure(markers) + result_2 = trim_markers_for_figure(marker_2) + expected = [ + { + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":0.5 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":1 + } + + ] + self.assertEqual(results, expected) + self.assertEqual(result_2, marker_2) + + def test_export_mapping_results(self): + """test for exporting mapping results""" + datetime_mock = mock.Mock(wraps=datetime.datetime) + datetime_mock.now.return_value = datetime.datetime( + 2019, 9, 1, 10, 12, 12) + + markers = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":3 + }, + { + "name": "MK2", + "chr": "C2", + "cM": "15", + "Mb": "10000", + "genotypes": [], + "lod_score":7 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":7 + }] + + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + + with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock): + export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers, + results_path="~/results", mapping_scale="physic", score_type="-log(p)") + + write_calls = [ + mock.call('Time/Date: 09/01/19 / 10:12:12\n'), + mock.call('Population: Human GP1_\n'), mock.call( + 'Data Set: dataser_1\n'), + mock.call('Gene Symbol: IGFI\n'), mock.call( + 'Location: X1 @ 123313 Mb\n'), + mock.call('\n'), mock.call('Name,Chr,'), + mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'), + mock.call(',Additive'), mock.call(',Dominance'), + mock.call('\n'), mock.call('MK1,C1,'), + mock.call('12000,'), mock.call('1,'), + mock.call('3'), mock.call(',VA'), + mock.call(',TT'), mock.call('\n'), + mock.call('MK2,C2,'), mock.call('10000,'), + mock.call('15,'), mock.call('7'), + mock.call('\n'), mock.call('MK1,C3,'), + mock.call('1,'), mock.call('45,'), + mock.call('7'), mock.call(',VE'), + mock.call(',Tt') + + ] + mock_open.assert_called_once_with("~/results", "w+") + filehandler = mock_open() + filehandler.write.assert_has_calls(write_calls) + + @mock.patch("wqflask.marker_regression.run_mapping.random.choice") + def test_write_input_for_browser(self, mock_choice): + """test for writing input for browser""" + mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"] + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + expected = ['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT'] + + results = write_input_for_browser( + this_dataset=self.dataset, gwas_results={}, annotations={}) + self.assertEqual(results, expected) + + def test_get_perm_strata(self): + categorical_vars = ["C1", "C2", "W1"] + used_samples = ["S1", "S2"] + sample_list = AttributeSetter({"sample_attribute_values": { + "S1": { + "C1": "c1_value", + "C2": "c2_value", + "W1": "w1_value" + + }, + "S2": { + "W1": "w2_value", + "W2": "w2_value" + + }, + "S3": { + + "C1": "c1_value", + "C2": "c2_value" + + }, + + }}) + + results = get_perm_strata(this_trait={}, sample_list=sample_list, + categorical_vars=categorical_vars, used_samples=used_samples) + self.assertEqual(results, [2, 1]) + + def test_get_chr_length(self): + """test for getting chromosome length""" + chromosomes = AttributeSetter({"chromosomes": self.chromosomes}) + dataset = AttributeSetter({"species": chromosomes}) + results = get_chr_lengths( + mapping_scale="physic", mapping_method="reaper", dataset=dataset, qtl_results=[]) + chr_lengths = [] + for key, chromo in self.chromosomes.chromosomes.items(): + chr_lengths.append({"chr": chromo.name, "size": chromo.length}) + + self.assertEqual(chr_lengths, results) + + qtl_results = [{ + "chr": "16", + "cM": "0.2" + }, + { + "chr": "12", + "cM": "0.5" + }, + { + "chr": "18", + "cM": "0.1" + }, + { + "chr": "22", + "cM": "0.4" + }, + ] + + result_with_other_mapping_scale = get_chr_lengths( + mapping_scale="other", mapping_method="reaper", dataset=dataset, qtl_results=qtl_results) + expected_value = [{'chr': '1', 'size': '0'}, { + 'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}] + + self.assertEqual(result_with_other_mapping_scale, expected_value) diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py deleted file mode 100644 index 4fafd95a..00000000 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ /dev/null @@ -1,205 +0,0 @@ -# test for wqflask/marker_regression/gemma_mapping.py -import unittest -import random -from unittest import mock -from wqflask.marker_regression.gemma_mapping import run_gemma -from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file -from wqflask.marker_regression.gemma_mapping import gen_covariates_file -from wqflask.marker_regression.gemma_mapping import parse_gemma_output -from wqflask.marker_regression.gemma_mapping import parse_loco_output - - -class AttributeSetter: - def __init__(self, obj): - for key, val in obj.items(): - setattr(self, key, val) - - -class MockDatasetGroup(AttributeSetter): - def get_samplelist(self): - return None - - -class TestGemmaMapping(unittest.TestCase): - - @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") - def test_run_gemma_firstrun_set_false(self, mock_parse_loco): - """add tests for gemma function where first run is set to false""" - dataset = AttributeSetter( - {"group": AttributeSetter({"genofile": "genofile.geno"})}) - - output_file = "file1" - mock_parse_loco.return_value = [] - this_trait = AttributeSetter({"name": "t1"}) - - result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ - ], covariates="", use_loco=True, first_run=False, output_files=output_file) - - expected_results = ([], "file1") - self.assertEqual(expected_results, result) - - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") - @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug") - @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/") - @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") - @mock.patch("wqflask.marker_regression.gemma_mapping.logger") - @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") - @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") - @mock.patch("wqflask.marker_regression.run_mapping.random.choice") - @mock.patch("wqflask.marker_regression.gemma_mapping.os") - @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): - """add tests for run_gemma where first run is set to true""" - chromosomes = [] - for i in range(1, 5): - chromosomes.append(AttributeSetter({"name": f"CH{i}"})) - chromo = AttributeSetter({"chromosomes": chromosomes}) - dataset_group = MockDatasetGroup( - {"name": "GP1", "genofile": "file_geno"}) - dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", - "species": AttributeSetter({"chromosomes": chromo})}) - trait = AttributeSetter({"name": "trait1"}) - samples = [] - mock_gen_pheno_txt.return_value = None - mock_os.path.isfile.return_value = True - mock_gen_covar.return_value = None - mock_choice.return_value = "R" - mock_flat_files.return_value = "/home/genotype/bimbam" - mock_parse_loco.return_value = [] - results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ - ], vals=[], covariates="", use_loco=True) - system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), - mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] - mock_os.system.assert_has_calls(system_calls) - mock_gen_pheno_txt.assert_called_once() - mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") - mock_os.path.isfile.assert_called_once_with( - ('/home/user/imgfile_output.assoc.txt')) - self.assertEqual(mock_logger.debug.call_count, 2) - self.assertEqual(mock_flat_files.call_count, 4) - self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) - - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): - """add tests for generating pheno txt file""" - with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ - "x", "w", "q", "we", "R"], trait_filename="fitr.re") - mock_open.assert_called_once_with( - '/home/user/data/gn2/fitr.re.txt', 'w') - filehandler = mock_open() - values = ["x", "w", "q", "we", "R"] - write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call( - 'q\n'), mock.call('we\n'), mock.call('R\n')] - - filehandler.write.assert_has_calls(write_calls) - - @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") - @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait") - @mock.patch("wqflask.marker_regression.gemma_mapping.create_dataset") - def test_gen_covariates_file(self, create_dataset, create_trait, flat_files): - """add tests for generating covariates files""" - covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2" - samplelist = ["X1", "X2", "X3", "X4"] - create_dataset_side_effect = [] - create_trait_side_effect = [] - - for i in range(4): - create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'})) - create_trait_side_effect.append( - AttributeSetter({"data": [f'data_{i}']})) - - create_dataset.side_effect = create_trait_side_effect - create_trait.side_effect = create_trait_side_effect - - group = MockDatasetGroup({"name": "group_X", "samplelist": samplelist}) - this_dataset = AttributeSetter({"group": group}) - flat_files.return_value = "Home/Genenetwork" - - with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_covariates_file(this_dataset=this_dataset, covariates=covariates, - samples=["x1", "x2", "X3"]) - - create_dataset.assert_has_calls( - [mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')]) - mock_calls = [] - trait_names = ["X1", "Y1", "M1", "V1"] - - for i, trait in enumerate(create_trait_side_effect): - mock_calls.append( - mock.call(dataset=trait, name=trait_names[i], cellid=None)) - - create_trait.assert_has_calls(mock_calls) - - flat_files.assert_called_once_with('mapping') - mock_open.assert_called_once_with( - 'Home/Genenetwork/group_X_covariates.txt', 'w') - filehandler = mock_open() - filehandler.write.assert_has_calls([mock.call( - '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) - - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") - def test_parse_gemma_output(self): - """add test for generating gemma output with obj returned""" - file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7 -X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 -125\tgn9\t433575\tQ\tE\tA\tP\tMMB\tCDE\t0.67 -""" - with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open: - results = parse_gemma_output(genofile_name="gema_file") - expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, - {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] - mock_open.assert_called_once_with( - "/home/user/img/gema_file_output.assoc.txt") - self.assertEqual(results, expected) - - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") - def test_parse_gemma_output_with_empty_return(self): - """add tests for parse gemma output where nothing returned""" - output_file_results = """chr\t today""" - with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: - results = parse_gemma_output(genofile_name="gema_file") - self.assertEqual(results, []) - - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") - @mock.patch("wqflask.marker_regression.gemma_mapping.os") - @mock.patch("wqflask.marker_regression.gemma_mapping.json") - def test_parse_loco_outputfile_found(self, mock_json, mock_os): - """add tests for parse loco output file found""" - mock_json.load.return_value = { - "files": [["file_name", "user", "~/file1"], - ["file_name", "user", "~/file2"]] - } - return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" - return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" - mock_os.path.isfile.return_value = True - file_to_write = """{"files":["file_1","file_2"]}""" - with mock.patch("builtins.open") as mock_open: - - handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open( - read_data=return_file_1).return_value, mock.mock_open(read_data=return_file_2).return_value) - mock_open.side_effect = handles - results = parse_loco_output( - this_dataset={}, gwa_output_filename=".xw/") - expected_results = [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, { - 'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] - - self.assertEqual(expected_results, results) - - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") - @mock.patch("wqflask.marker_regression.gemma_mapping.os") - def test_parse_loco_outputfile_not_found(self, mock_os): - """add tests for parse loco output where output file not found""" - - mock_os.path.isfile.return_value = False - file_to_write = """{"files":["file_1","file_2"]}""" - - with mock.patch("builtins.open", mock.mock_open(read_data=file_to_write)) as mock_open: - results = parse_loco_output( - this_dataset={}, gwa_output_filename=".xw/") - self.assertEqual(results, []) diff --git a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py deleted file mode 100644 index 428f45b9..00000000 --- a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py +++ /dev/null @@ -1,84 +0,0 @@ -# test for wqflask/marker_regression/plink_mapping.py -import unittest -from unittest import mock -from wqflask.marker_regression.plink_mapping import build_line_list -from wqflask.marker_regression.plink_mapping import get_samples_from_ped_file -from wqflask.marker_regression.plink_mapping import flat_files -from wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink -from wqflask.marker_regression.plink_mapping import parse_plink_output - - -class AttributeSetter: - def __init__(self, obj): - for key, val in obj.items(): - setattr(self, key, val) -class TestPlinkMapping(unittest.TestCase): - - def test_build_line_list(self): - """testing for building line list""" - line_1 = "this is line one test" - irregular_line = " this is an, irregular line " - exp_line1 = ["this", "is", "line", "one", "test"] - - results = build_line_list(irregular_line) - self.assertEqual(exp_line1, build_line_list(line_1)) - self.assertEqual([], build_line_list()) - self.assertEqual(["this", "is", "an,", "irregular", "line"], results) - - @mock.patch("wqflask.marker_regression.plink_mapping.flat_files") - def test_get_samples_from_ped_file(self, mock_flat_files): - """test for getting samples from ped file""" - dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) - file_sample = """Expected_1\tline test -Expected_2\there - Expected_3\tthree""" - mock_flat_files.return_value = "/home/user/" - with mock.patch("builtins.open", mock.mock_open(read_data=file_sample)) as mock_open: - results = get_samples_from_ped_file(dataset) - mock_flat_files.assert_called_once_with("mapping") - mock_open.assert_called_once_with("/home/user/n_1.ped", "r") - self.assertEqual( - ["Expected_1", "Expected_2", "Expected_3"], results) - - @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") - @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file") - def test_gen_pheno_txt_file_plink(self, mock_samples): - """test for getting gen_pheno txt file""" - mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"] - - trait = AttributeSetter({"name": "TX"}) - dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) - vals = ["value=K1", "value=K2", "value=K3"] - with mock.patch("builtins.open", mock.mock_open()) as mock_open: - results = gen_pheno_txt_file_plink(this_trait=trait, dataset=dataset, - vals=vals, pheno_filename="ph_file") - mock_open.assert_called_once_with( - "/home/user/data/ph_file.txt", "wb") - filehandler = mock_open() - calls_expected = [mock.call('FID\tIID\tTX\n'), - mock.call('Expected_1\tExpected_1\tK1\nExpected_2\tExpected_2\tK2\nExpected_3\tExpected_3\tK3\n')] - - filehandler.write.assert_has_calls(calls_expected) - - filehandler.close.assert_called_once() - - @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") - @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list") - def test_parse_plink_output(self, mock_line_list): - """test for parsing plink output""" - chromosomes = [0, 34, 110, 89, 123, 23, 2] - species = AttributeSetter( - {"name": "S1", "chromosomes": AttributeSetter({"chromosomes": chromosomes})}) - - fake_file = """0 AACCAT T98.6 0.89\n2 AATA B45 0.3\n121 ACG B56.4 NA""" - - mock_line_list.side_effect = [["0", "AACCAT", "T98.6", "0.89"], [ - "2", "AATA", "B45", "0.3"], ["121", "ACG", "B56.4", "NA"]] - with mock.patch("builtins.open", mock.mock_open(read_data=fake_file)) as mock_open: - parse_results = parse_plink_output( - output_filename="P1_file", species=species) - mock_open.assert_called_once_with( - "/home/user/data/P1_file.qassoc", "rb") - expected = (2, {'AACCAT': 0.89, 'AATA': 0.3}) - - self.assertEqual(parse_results, expected) diff --git a/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py deleted file mode 100644 index b47f877a..00000000 --- a/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py +++ /dev/null @@ -1,21 +0,0 @@ -import unittest -from unittest import mock -from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file - -#issues some methods in genofile object are not defined -#modify samples should equal to vals -class TestQtlReaperMapping(unittest.TestCase): - @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): - vals=["V1","x","V4","V3","x"] - samples=["S1","S2","S3","S4","S5"] - trait_filename="trait_file" - with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename) - mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w") - filehandler=mock_open() - write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')] - - filehandler.write.assert_has_calls(write_calls) - - diff --git a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py deleted file mode 100644 index 69f53721..00000000 --- a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py +++ /dev/null @@ -1,48 +0,0 @@ -import unittest -from unittest import mock -from wqflask import app -from wqflask.marker_regression.rqtl_mapping import get_trait_data_type -from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype -from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names - -class TestRqtlMapping(unittest.TestCase): - - def setUp(self): - self.app_context=app.app_context() - self.app_context.push() - - def tearDown(self): - self.app_context.pop() - - - @mock.patch("wqflask.marker_regression.rqtl_mapping.g") - @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data(self,mock_logger,mock_db): - """test for getting trait data_type return True""" - caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] - results=get_trait_data_type("traid_id") - mock_db.db.execute.assert_called_with(caller_value) - self.assertEqual(results,"fer434f") - - def test_sanitize_rqtl_phenotype(self): - """test for sanitizing rqtl phenotype""" - vals=['f',"x","r","x","x"] - results=sanitize_rqtl_phenotype(vals) - expected_phenotype_string='c(f,NA,r,NA,NA)' - - self.assertEqual(results,expected_phenotype_string) - - def test_sanitize_rqtl_names(self): - """test for sanitzing rqtl names""" - vals=['f',"x","r","x","x"] - expected_sanitized_name="c('f',NA,'r',NA,NA)" - results=sanitize_rqtl_names(vals) - self.assertEqual(expected_sanitized_name,results) - - - - - - - diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py deleted file mode 100644 index a134f551..00000000 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ /dev/null @@ -1,284 +0,0 @@ -import unittest -import datetime -from unittest import mock - -from wqflask.marker_regression.run_mapping import get_genofile_samplelist -from wqflask.marker_regression.run_mapping import geno_db_exists -from wqflask.marker_regression.run_mapping import write_input_for_browser -from wqflask.marker_regression.run_mapping import export_mapping_results -from wqflask.marker_regression.run_mapping import trim_markers_for_figure -from wqflask.marker_regression.run_mapping import get_perm_strata -from wqflask.marker_regression.run_mapping import get_chr_lengths - - -class AttributeSetter: - def __init__(self, obj): - for k, v in obj.items(): - setattr(self, k, v) - - -class MockDataSetGroup(AttributeSetter): - - def get_genofiles(self): - return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}] - - -class TestRunMapping(unittest.TestCase): - def setUp(self): - - self.group = MockDataSetGroup( - {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"}) - chromosomes = { - "3": AttributeSetter({ - "name": "C1", - "length": "0.04" - }), - "4": AttributeSetter({ - "name": "C2", - "length": "0.03" - }), - "5": AttributeSetter({ - "name": "C4", - "length": "0.01" - }) - } - self.dataset = AttributeSetter( - {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"}) - - self.chromosomes = AttributeSetter({"chromosomes": chromosomes}) - self.trait = AttributeSetter( - {"symbol": "IGFI", "chr": "X1", "mb": 123313}) - - def tearDown(self): - self.dataset = AttributeSetter( - {"group": {"location": "~/genofiles/g1_file"}}) - - def test_get_genofile_samplelist(self): - - results_1 = get_genofile_samplelist(self.dataset) - self.assertEqual(results_1, ["S1", "S2", "S3", "S4"]) - self.group.genofile = "~/genofiles/g2_file" - result_2 = get_genofile_samplelist(self.dataset) - self.assertEqual(result_2, []) - - @mock.patch("wqflask.marker_regression.run_mapping.data_set") - def test_if_geno_db_exists(self, mock_data_set): - mock_data_set.create_dataset.side_effect = [ - AttributeSetter({}), Exception()] - results_no_error = geno_db_exists(self.dataset) - results_with_error = geno_db_exists(self.dataset) - - self.assertEqual(mock_data_set.create_dataset.call_count, 2) - self.assertEqual(results_with_error, "False") - self.assertEqual(results_no_error, "True") - - def test_trim_markers_for_figure(self): - - markers = [{ - "name": "MK1", - "chr": "C1", - "cM": "1", - "Mb": "12000", - "genotypes": [], - "dominance":"TT", - "additive":"VA", - "lod_score":0.5 - }, - { - "name": "MK2", - "chr": "C2", - "cM": "15", - "Mb": "10000", - "genotypes": [], - "lod_score":0.7 - }, - { - "name": "MK1", - "chr": "C3", - "cM": "45", - "Mb": "1", - "genotypes": [], - "dominance":"Tt", - "additive":"VE", - "lod_score":1 - }] - - marker_2 = [{ - "name": "MK1", - "chr": "C1", - "cM": "1", - "Mb": "12000", - "genotypes": [], - "dominance":"TT", - "additive":"VA", - "p_wald":4.6 - }] - results = trim_markers_for_figure(markers) - result_2 = trim_markers_for_figure(marker_2) - expected = [ - { - "name": "MK1", - "chr": "C1", - "cM": "1", - "Mb": "12000", - "genotypes": [], - "dominance":"TT", - "additive":"VA", - "lod_score":0.5 - }, - { - "name": "MK1", - "chr": "C3", - "cM": "45", - "Mb": "1", - "genotypes": [], - "dominance":"Tt", - "additive":"VE", - "lod_score":1 - } - - ] - self.assertEqual(results, expected) - self.assertEqual(result_2, marker_2) - - def test_export_mapping_results(self): - """test for exporting mapping results""" - datetime_mock = mock.Mock(wraps=datetime.datetime) - datetime_mock.now.return_value = datetime.datetime( - 2019, 9, 1, 10, 12, 12) - - markers = [{ - "name": "MK1", - "chr": "C1", - "cM": "1", - "Mb": "12000", - "genotypes": [], - "dominance":"TT", - "additive":"VA", - "lod_score":3 - }, - { - "name": "MK2", - "chr": "C2", - "cM": "15", - "Mb": "10000", - "genotypes": [], - "lod_score":7 - }, - { - "name": "MK1", - "chr": "C3", - "cM": "45", - "Mb": "1", - "genotypes": [], - "dominance":"Tt", - "additive":"VE", - "lod_score":7 - }] - - with mock.patch("builtins.open", mock.mock_open()) as mock_open: - - with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock): - export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers, - results_path="~/results", mapping_scale="physic", score_type="-log(p)") - - write_calls = [ - mock.call('Time/Date: 09/01/19 / 10:12:12\n'), - mock.call('Population: Human GP1_\n'), mock.call( - 'Data Set: dataser_1\n'), - mock.call('Gene Symbol: IGFI\n'), mock.call( - 'Location: X1 @ 123313 Mb\n'), - mock.call('\n'), mock.call('Name,Chr,'), - mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'), - mock.call(',Additive'), mock.call(',Dominance'), - mock.call('\n'), mock.call('MK1,C1,'), - mock.call('12000,'), mock.call('1,'), - mock.call('3'), mock.call(',VA'), - mock.call(',TT'), mock.call('\n'), - mock.call('MK2,C2,'), mock.call('10000,'), - mock.call('15,'), mock.call('7'), - mock.call('\n'), mock.call('MK1,C3,'), - mock.call('1,'), mock.call('45,'), - mock.call('7'), mock.call(',VE'), - mock.call(',Tt') - - ] - mock_open.assert_called_once_with("~/results", "w+") - filehandler = mock_open() - filehandler.write.assert_has_calls(write_calls) - - @mock.patch("wqflask.marker_regression.run_mapping.random.choice") - def test_write_input_for_browser(self, mock_choice): - """test for writing input for browser""" - mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"] - with mock.patch("builtins.open", mock.mock_open()) as mock_open: - expected = ['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT'] - - results = write_input_for_browser( - this_dataset=self.dataset, gwas_results={}, annotations={}) - self.assertEqual(results, expected) - - def test_get_perm_strata(self): - categorical_vars = ["C1", "C2", "W1"] - used_samples = ["S1", "S2"] - sample_list = AttributeSetter({"sample_attribute_values": { - "S1": { - "C1": "c1_value", - "C2": "c2_value", - "W1": "w1_value" - - }, - "S2": { - "W1": "w2_value", - "W2": "w2_value" - - }, - "S3": { - - "C1": "c1_value", - "C2": "c2_value" - - }, - - }}) - - results = get_perm_strata(this_trait={}, sample_list=sample_list, - categorical_vars=categorical_vars, used_samples=used_samples) - self.assertEqual(results, [2, 1]) - - def test_get_chr_length(self): - """test for getting chromosome length""" - chromosomes = AttributeSetter({"chromosomes": self.chromosomes}) - dataset = AttributeSetter({"species": chromosomes}) - results = get_chr_lengths( - mapping_scale="physic", mapping_method="reaper", dataset=dataset, qtl_results=[]) - chr_lengths = [] - for key, chromo in self.chromosomes.chromosomes.items(): - chr_lengths.append({"chr": chromo.name, "size": chromo.length}) - - self.assertEqual(chr_lengths, results) - - qtl_results = [{ - "chr": "16", - "cM": "0.2" - }, - { - "chr": "12", - "cM": "0.5" - }, - { - "chr": "18", - "cM": "0.1" - }, - { - "chr": "22", - "cM": "0.4" - }, - ] - - result_with_other_mapping_scale = get_chr_lengths( - mapping_scale="other", mapping_method="reaper", dataset=dataset, qtl_results=qtl_results) - expected_value = [{'chr': '1', 'size': '0'}, { - 'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}] - - self.assertEqual(result_with_other_mapping_scale, expected_value) -- cgit v1.2.3 From c96c1db5660367f1f86cfa76309c87866e79bf79 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Sat, 28 Nov 2020 16:23:53 +0300 Subject: modify test for plink mapping and rqtl_mapping --- wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py | 3 ++- wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py index 428f45b9..5eec93f1 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py @@ -14,8 +14,9 @@ class AttributeSetter: setattr(self, key, val) class TestPlinkMapping(unittest.TestCase): + def test_build_line_list(self): - """testing for building line list""" + """test for building line list""" line_1 = "this is line one test" irregular_line = " this is an, irregular line " exp_line1 = ["this", "is", "line", "one", "test"] diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index 69f53721..c585f1df 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -19,10 +19,10 @@ class TestRqtlMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") def test_get_trait_data(self,mock_logger,mock_db): """test for getting trait data_type return True""" - caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" + query_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] results=get_trait_data_type("traid_id") - mock_db.db.execute.assert_called_with(caller_value) + mock_db.db.execute.assert_called_with(query_value) self.assertEqual(results,"fer434f") def test_sanitize_rqtl_phenotype(self): -- cgit v1.2.3 From 668d6a97356030e0286365dad53c8d191c193290 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 2 Dec 2020 14:16:08 -0600 Subject: Made changes that should fix Heatmap errors + removed a console.log in panelutil.js --- wqflask/wqflask/static/new/javascript/lodheatmap.js | 6 ++++-- wqflask/wqflask/static/new/javascript/panelutil.js | 1 - 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/wqflask/wqflask/static/new/javascript/lodheatmap.js b/wqflask/wqflask/static/new/javascript/lodheatmap.js index 965a1d53..b82c95ad 100644 --- a/wqflask/wqflask/static/new/javascript/lodheatmap.js +++ b/wqflask/wqflask/static/new/javascript/lodheatmap.js @@ -44,7 +44,9 @@ lodheatmap = function() { _ref = data.chrnames; for (_i = 0, _len = _ref.length; _i < _len; _i++) { chr = _ref[_i]; - xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]]); + if (data.posByChr[chr[0]].length > 0){ + xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]]); + } } zmin = 0; zmax = 0; @@ -144,7 +146,7 @@ lodheatmap = function() { }).attr("stroke", "none").attr("stroke-width", "1").on("mouseover.paneltip", function(d) { yaxis.select("text#yaxis" + d.lodindex).attr("opacity", 1); d3.select(this).attr("stroke", "black"); - return celltip.show(d); + return celltip.show(d, this); }).on("mouseout.paneltip", function(d) { yaxis.select("text#yaxis" + d.lodindex).attr("opacity", 0); d3.select(this).attr("stroke", "none"); diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/wqflask/wqflask/static/new/javascript/panelutil.js index 3c715c81..ea55a7cf 100644 --- a/wqflask/wqflask/static/new/javascript/panelutil.js +++ b/wqflask/wqflask/static/new/javascript/panelutil.js @@ -159,7 +159,6 @@ chrscales = function(data, width, chrGap, leftMargin, pad4heatmap, mappingScale) if (mappingScale == "morgan") { max_pos = d3.max(data.posByChr[chr[0]]) - console.log("max_pos:", max_pos) data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], max_pos]).range([data.chrStart[i], data.chrEnd[i]]); } else { -- cgit v1.2.3