From 0e502113445741ecc6fcddde5d6b03b851146c02 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 29 May 2019 12:35:37 -0500 Subject: Added info for fetching trait list --- doc/API_readme.md | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/doc/API_readme.md b/doc/API_readme.md index 96e8b246..64fc61f9 100644 --- a/doc/API_readme.md +++ b/doc/API_readme.md @@ -51,13 +51,6 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd ``` (I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary) -## Fetch Sample Data for Dataset ## -``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv -``` - -Returns a CSV file with sample/strain names as the columns and trait IDs as rows - ## Fetch Individual Dataset Info ## ### For mRNA Assay/"ProbeSet" ### @@ -78,12 +71,27 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/10001 { "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" } ``` +## Fetch Sample Data for Dataset ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv +``` + +Returns a CSV file with sample/strain names as the columns and trait IDs as rows + ## Fetch Sample Data for Single Trait ## ``` curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at [ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ] ``` +## Fetch Trait List for Dataset ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json +[ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ] +``` + +Both JSON and CSV formats can be specified, with CSV as default. There is also an optional "ids_only" parameter that will only return a list of trait IDs. + ## Fetch Trait Info (Name, Description, Location, etc) ## ### For mRNA Expression/"ProbeSet" ### ``` -- cgit v1.2.3 From 8237c44937590fd06030945a35aa1de24e29463b Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 29 May 2019 12:43:21 -0500 Subject: Added option to get traits from dataset to API --- wqflask/wqflask/api/router.py | 116 ++++++++++++++++++++++++++++++++++++++---- 1 file changed, 105 insertions(+), 11 deletions(-) diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 845873a0..4ecd6699 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -290,6 +290,106 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") +@app.route("/api/v_{}/traits/".format(version), methods=('GET',)) +@app.route("/api/v_{}/traits/.".format(version), methods=('GET',)) +def fetch_traits(dataset_name, file_format = "csv"): + trait_ids, _trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name) + if ('ids_only' in request.args) and (len(trait_ids) > 0): + if file_format == "json": + filename = dataset_name + "_trait_ids.json" + return flask.jsonify(trait_ids) + else: + filename = dataset_name + "_trait_ids.csv" + + si = StringIO.StringIO() + csv_writer = csv.writer(si) + csv_writer.writerows([[trait_id] for trait_id in trait_ids]) + output = make_response(si.getvalue()) + output.headers["Content-Disposition"] = "attachment; filename=" + filename + output.headers["Content-type"] = "text/csv" + return output + else: + if len(trait_ids) > 0: + if data_type == "ProbeSet": + query = """ + SELECT + ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias, + ProbeSetXRef.mean, ProbeSetXRef.se, ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.h2 + FROM + ProbeSet, ProbeSetXRef + WHERE + ProbeSetXRef.ProbeSetFreezeId = '{0}' AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id + ORDER BY + ProbeSet.Id + """ + + field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"] + elif data_type == "Geno": + query = """ + SELECT + Geno.Id, Geno.Name, Geno.Marker_Name, Geno.Chr, Geno.Mb, Geno.Sequence, Geno.Source + FROM + Geno, GenoXRef + WHERE + GenoXRef.GenoFreezeId = '{0}' AND + GenoXRef.GenoId = Geno.Id + ORDER BY + Geno.Id + """ + + field_list = ["Id", "Name", "Marker_Name", "Chr", "Mb", "Sequence", "Source"] + else: + query = """ + SELECT + PublishXRef.Id, PublishXRef.PhenotypeId, PublishXRef.PublicationId, PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive, PublishXRef.Sequence + FROM + PublishXRef + WHERE + PublishXRef.InbredSetId = {0} + ORDER BY + PublishXRef.Id + """ + + field_list = ["Id", "PhenotypeId", "PublicationId", "Locus", "LRS", "Additive", "Sequence"] + + if file_format == "json": + filename = dataset_name + "_traits.json" + + final_query = query.format(dataset_id) + + result_list = [] + for result in g.db.execute(final_query).fetchall(): + trait_dict = {} + for i, field in enumerate(field_list): + if result[i]: + trait_dict[field] = result[i] + result_list.append(trait_dict) + + return flask.jsonify(result_list) + elif file_format == "csv": + filename = dataset_name + "_traits.csv" + + results_list = [] + header_list = [] + header_list += field_list + results_list.append(header_list) + + final_query = query.format(dataset_id) + for result in g.db.execute(final_query).fetchall(): + results_list.append(result) + + si = StringIO.StringIO() + csv_writer = csv.writer(si) + csv_writer.writerows(results_list) + output = make_response(si.getvalue()) + output.headers["Content-Disposition"] = "attachment; filename=" + filename + output.headers["Content-type"] = "text/csv" + return output + else: + return return_error(code=400, source=request.url_rule.rule, title="Invalid Output Format", details="Current formats available are JSON and CSV, with CSV as default") + else: + return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @app.route("/api/v_{}/sample_data/".format(version)) @app.route("/api/v_{}/sample_data/.".format(version)) @@ -528,8 +628,6 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"): PublishXRef.Id = '{0}' AND PublishXRef.InbredSetId = '{1}' """.format(trait_name, group_id) - - logger.debug("QUERY:", pheno_query) pheno_results = g.db.execute(pheno_query) @@ -612,13 +710,6 @@ def get_genotypes(group_name, file_format="csv"): return output -@app.route("/api/v_{}/traits/".format(version), methods=('GET',)) -@app.route("/api/v_{}/traits/.".format(version), methods=('GET',)) -def get_traits(dataset_name, file_format = "json"): - #ZS: Need to check about the "start" and "stop" stuff since it seems to just limit the number of results to stop - start + 1 in Pjotr's elixir code - - NotImplemented - def return_error(code, source, title, details): json_ob = {"errors": [ { @@ -652,7 +743,7 @@ def get_dataset_trait_ids(dataset_name): dataset_id = results[0][2] return trait_ids, trait_names, data_type, dataset_id - elif "Publish" in dataset_name: + elif "Publish" in dataset_name or get_group_id(dataset_name): data_type = "Publish" dataset_name = dataset_name.replace("Publish", "") dataset_id = get_group_id(dataset_name) @@ -743,7 +834,10 @@ def get_group_id_from_dataset(dataset_name): result = g.db.execute(query).fetchone() - return result[0] + if len(result) > 0: + return result[0] + else: + return None def get_group_id(group_name): query = """ -- cgit v1.2.3 From 4241730a9e304ea272381456555d843d85f4cb04 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 31 May 2019 12:55:28 -0500 Subject: Minor changes --- doc/API_readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/API_readme.md b/doc/API_readme.md index 64fc61f9..6c88d413 100644 --- a/doc/API_readme.md +++ b/doc/API_readme.md @@ -90,7 +90,7 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json [ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ] ``` -Both JSON and CSV formats can be specified, with CSV as default. There is also an optional "ids_only" parameter that will only return a list of trait IDs. +Both JSON and CSV formats can be specified, with JSON as default. There is also an optional "ids_only" and "names_only" parameter that will only return a list of trait IDs or names, respectively. ## Fetch Trait Info (Name, Description, Location, etc) ## ### For mRNA Expression/"ProbeSet" ### -- cgit v1.2.3 From 84d165a30aaff2fcb4dd6b3bb7106ff0ceb495e9 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 31 May 2019 12:58:26 -0500 Subject: Added option to get just trait names from traits query, and also fixed sample_data query to avoid duplicates --- wqflask/wqflask/api/router.py | 20 +++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 4ecd6699..707e4e65 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -292,8 +292,8 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): @app.route("/api/v_{}/traits/".format(version), methods=('GET',)) @app.route("/api/v_{}/traits/.".format(version), methods=('GET',)) -def fetch_traits(dataset_name, file_format = "csv"): - trait_ids, _trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name) +def fetch_traits(dataset_name, file_format = "json"): + trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name) if ('ids_only' in request.args) and (len(trait_ids) > 0): if file_format == "json": filename = dataset_name + "_trait_ids.json" @@ -308,6 +308,20 @@ def fetch_traits(dataset_name, file_format = "csv"): output.headers["Content-Disposition"] = "attachment; filename=" + filename output.headers["Content-type"] = "text/csv" return output + elif ('names_only' in request.args) and (len(trait_ids) > 0): + if file_format == "json": + filename = dataset_name + "_trait_names.json" + return flask.jsonify(trait_names) + else: + filename = dataset_name + "_trait_names.csv" + + si = StringIO.StringIO() + csv_writer = csv.writer(si) + csv_writer.writerows([[trait_name] for trait_name in trait_names]) + output = make_response(si.getvalue()) + output.headers["Content-Disposition"] = "attachment; filename=" + filename + output.headers["Content-type"] = "text/csv" + return output else: if len(trait_ids) > 0: if data_type == "ProbeSet": @@ -534,7 +548,7 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): dataset_or_group = dataset_name pheno_query = """ - SELECT + SELECT DISTINCT Strain.Name, Strain.Name2, PublishData.value, PublishData.Id, PublishSE.error, NStrain.count FROM (PublishData, Strain, PublishXRef, PublishFreeze) -- cgit v1.2.3 From 34d962fe1e0dd5e30f067e7a30fcbd8931f2aacb Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 4 Jun 2019 11:20:28 -0500 Subject: Added GeneMANIA link Fixed issue that caused error when creating UCSC RefSeq link Fixed issue that sometimes caused an error for phenotype searches Changed some text on collections page --- wqflask/base/webqtlConfig.py | 2 +- wqflask/wqflask/show_trait/show_trait.py | 11 ++++++++--- wqflask/wqflask/templates/collections/view.html | 4 ++-- wqflask/wqflask/templates/search_result_page.html | 6 +++++- wqflask/wqflask/templates/show_trait_details.html | 6 ++++++ 5 files changed, 22 insertions(+), 7 deletions(-) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index b14cc4b0..a08acb0a 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -43,6 +43,7 @@ HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/homologene/?term=%s" GENOTATION_URL = "http://www.genotation.org/Getd2g.pl?gene_list=%s" GTEX_URL = "https://www.gtexportal.org/home/gene/%s" GENEBRIDGE_URL = "https://www.systems-genetics.org/modules_by_gene/%s?organism=%s" +GENEMANIA_URL = "https://genemania.org/search/%s/%s" UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgTracks?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s" BIOGPS_URL = "http://biogps.org/?org=%s#goto=genereport&id=%s" STRING_URL = "http://string-db.org/newstring_cgi/show_network_section.pl?identifier=%s" @@ -87,4 +88,3 @@ if not valid_path(JSON_GENODIR): PORTADDR = "http://50.16.251.170" INFOPAGEHREF = '/dbdoc/%s.html' CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' -SCRIPTFILE = 'main.py' diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 66d3a448..e10b31c0 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -257,7 +257,7 @@ class ShowTrait(object): self.genbank_link = webqtlConfig.GENBANK_ID % genbank_id self.genotation_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = None - self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = None + self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = self.genemania_link = None if self.this_trait.symbol: self.genotation_link = webqtlConfig.GENOTATION_URL % self.this_trait.symbol self.gtex_link = webqtlConfig.GTEX_URL % self.this_trait.symbol @@ -266,7 +266,10 @@ class ShowTrait(object): self.ebi_gwas_link = webqtlConfig.EBIGWAS_URL % self.this_trait.symbol if self.dataset.group.species == "mouse" or self.dataset.group.species == "human": - self.genebridge_link = webqtlConfig.GENEBRIDGE_URL % (self.this_trait.symbol, self.dataset.group.species) + if self.dataset.group.species == "mouse": + self.genemania_link = webqtlConfig.GENEMANIA_URL % ("mus-musculus", self.this_trait.symbol) + else: + self.genemania_link = webqtlConfig.GENEMANIA_URL % ("homo-sapiens", self.this_trait.symbol) if self.dataset.group.species == "mouse": self.aba_link = webqtlConfig.ABA_URL % self.this_trait.symbol @@ -282,8 +285,10 @@ class ShowTrait(object): self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('mm10', self.this_trait.refseq_transcriptid, chr, transcript_start, transcript_end) if self.dataset.group.species == "rat": + self.genemania_link = webqtlConfig.GENEMANIA_URL % ("rattus-norvegicus", self.this_trait.symbol) + query = """SELECT kgID, chromosome, txStart, txEnd - FROM GeneLink_rn33 + FROM GeneList_rn33 WHERE geneSymbol = '{}'""".format(self.this_trait.symbol) kgId, chr, transcript_start, transcript_end = g.db.execute(query).fetchall()[0] if len(g.db.execute(query).fetchall()) > 0 else None diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 8d22b2a8..7e1001fc 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -84,8 +84,8 @@ - - + +

diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index e20ea2d3..bf434452 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -324,7 +324,11 @@ 'width': "500px", 'data': null, 'render': function(data, type, row, meta) { - return decodeURIComponent(escape(data.description)) + try { + return decodeURIComponent(escape(data.description)) + } catch { + return escape(data.description) + } } }, { diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 09f36021..43efa314 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -88,6 +88,12 @@    {% endif %} + {% if genemania_link %} + + GeneMANIA + +    + {% endif %} {% if unigene_link %} UniGene -- cgit v1.2.3 From 1033685f2f5769a44f2daabee2f7779288465711 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 4 Jun 2019 12:29:53 -0500 Subject: Fixed issue with probability plot y axis digits --- wqflask/wqflask/static/new/javascript/plotly_probability_plot.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js index d52cb100..38c18d2b 100644 --- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js +++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js @@ -161,7 +161,7 @@ intercept_line['samples_all'] = [[first_x, last_x], [first_value, last_value]] } - if (Math.max(y_values['samples_all']) - Math.min(y_values['samples_all']) < 6){ + if (Math.max(...y_values['samples_all']) - Math.min(...y_values['samples_all']) < 4){ tick_digits = '.1f' } else { tick_digits = 'f' -- cgit v1.2.3 From bb4e9e78067a4a26c84581b5f1b86b8718a117bc Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 4 Jun 2019 12:49:17 -0500 Subject: Changed the logic for deciding y axis digits to deal with situations where the range is less tan 0.4; not sure if more than this needs to be accounted for --- wqflask/wqflask/static/new/javascript/plotly_probability_plot.js | 5 ++++- wqflask/wqflask/static/new/javascript/show_trait.js | 6 +++++- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js index 38c18d2b..a9c5676c 100644 --- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js +++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js @@ -161,8 +161,11 @@ intercept_line['samples_all'] = [[first_x, last_x], [first_value, last_value]] } - if (Math.max(...y_values['samples_all']) - Math.min(...y_values['samples_all']) < 4){ + val_range = Math.max(...y_values['samples_all']) - Math.min(...y_values['samples_all']) + if (val_range < 4){ tick_digits = '.1f' + } else if (val_range < 0.4) { + tick_digits = '.2f' } else { tick_digits = 'f' } diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 50765eda..8366ec0a 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -921,8 +921,12 @@ get_bar_range = function(sample_list){ } root.chart_range = get_bar_range(sample_lists[0]) -if (root.chart_range[1] - root.chart_range[0] < 4){ +val_range = root.chart_range[1] - root.chart_range[0] + +if (val_range < 4){ tick_digits = '.1f' +} else if (val_range < 0.4) { + tick_digits = '.2f' } else { tick_digits = 'f' } -- cgit v1.2.3 From 319cb6f8a9f3b57137cb13855eb84545a08399e8 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 4 Jun 2019 12:56:49 -0500 Subject: Updated drop-downs (this probably needs to be separated out of the git repository) --- .../new/javascript/dataset_menu_structure.json | 109 ++++++++++++--------- 1 file changed, 62 insertions(+), 47 deletions(-) diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index b2354f70..0d73213d 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -1335,7 +1335,7 @@ [ "None", "HCPPublish", - "HCP Phenotypes" + "HCP Private Phenotypes" ] ] }, @@ -1346,15 +1346,15 @@ "HLC_0311", "GSE9588 Human Liver Normal (Mar11) Both Sexes" ], - [ - "383", - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], [ "384", "HLCF_0311", "GSE9588 Human Liver Normal (Mar11) Females" + ], + [ + "383", + "HLCM_0311", + "GSE9588 Human Liver Normal (Mar11) Males" ] ], "Phenotypes": [ @@ -1529,6 +1529,11 @@ "mouse": { "AIL": { "Hippocampus mRNA": [ + [ + "874", + "UCSD_AIL_HIP_RNA-Seq_log2_0418", + "UCSD AIL Hippocampus (Apr18) RNA-Seq Log2" + ], [ "844", "UCSD_AIL_HIP_RNA-Seq_0418", @@ -1543,6 +1548,11 @@ ] ], "Prefrontal Cortex mRNA": [ + [ + "876", + "UCSD_AIL_PFC_RNA-Seq_log2_0418", + "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq Log2" + ], [ "846", "UCSD_AIL_PFC_RNA-Seq_0418", @@ -1550,6 +1560,11 @@ ] ], "Striatum mRNA": [ + [ + "875", + "UCSD_AIL_STR_RNA-Seq_log2_0418", + "UCSD AIL Striatum (Apr18) RNA-Seq Log2" + ], [ "845", "UCSD_AIL_STR_RNA-Seq_0418", @@ -1818,6 +1833,11 @@ ] ], "Striatum mRNA": [ + [ + "85", + "SA_M2_0905_P", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" + ], [ "84", "SA_M2_0905_R", @@ -1827,26 +1847,21 @@ "83", "SA_M2_0905_M", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" - ], - [ - "85", - "SA_M2_0905_P", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" ] ] }, "BHF2": { "Adipose mRNA": [ - [ - "196", - "UCLA_BHF2_ADIPOSE_MALE", - "UCLA BHF2 Adipose Male mlratio" - ], [ "197", "UCLA_BHF2_ADIPOSE_FEMALE", "UCLA BHF2 Adipose Female mlratio" ], + [ + "196", + "UCLA_BHF2_ADIPOSE_MALE", + "UCLA BHF2 Adipose Male mlratio" + ], [ "165", "UCLA_BHF2_ADIPOSE_0605", @@ -1854,16 +1869,16 @@ ] ], "Brain mRNA": [ - [ - "198", - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], [ "199", "UCLA_BHF2_BRAIN_FEMALE", "UCLA BHF2 Brain Female mlratio" ], + [ + "198", + "UCLA_BHF2_BRAIN_MALE", + "UCLA BHF2 Brain Male mlratio" + ], [ "166", "UCLA_BHF2_BRAIN_0605", @@ -1878,16 +1893,16 @@ ] ], "Liver mRNA": [ - [ - "200", - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], [ "201", "UCLA_BHF2_LIVER_FEMALE", "UCLA BHF2 Liver Female mlratio" ], + [ + "200", + "UCLA_BHF2_LIVER_MALE", + "UCLA BHF2 Liver Male mlratio" + ], [ "167", "UCLA_BHF2_LIVER_0605", @@ -2121,6 +2136,11 @@ "BR_U_1105_P", "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], + [ + "81", + "BR_U_0805_P", + "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" + ], [ "80", "BR_U_0805_M", @@ -2131,11 +2151,6 @@ "BR_U_0805_R", "UTHSC Brain mRNA U74Av2 (Aug05) RMA" ], - [ - "81", - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], [ "42", "CB_M_0204_P", @@ -2681,6 +2696,11 @@ "EPFLMouseLiverHFDRMA0413", "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" ], + [ + "848", + "EPFLMouseLiverHFCEx0413", + "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" + ], [ "432", "EPFLMouseLiverCDRMA0413", @@ -2691,11 +2711,6 @@ "EPFLMouseLiverCDEx0413", "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" ], - [ - "848", - "EPFLMouseLiverHFCEx0413", - "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" - ], [ "433", "EPFLMouseLiverBothExRMA0413", @@ -2849,15 +2864,15 @@ "HQFNeoc_0208_RankInv", "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv" ], - [ - "274", - "DevNeocortex_ILM6.2P3RInv_1110", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" - ], [ "275", "DevNeocortex_ILM6.2P14RInv_1110", "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" + ], + [ + "274", + "DevNeocortex_ILM6.2P3RInv_1110", + "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" ] ], "Nucleus Accumbens mRNA": [ @@ -3089,6 +3104,11 @@ ] ], "Ventral Tegmental Area mRNA": [ + [ + "230", + "VCUEtvsSal_0609_R", + "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA" + ], [ "229", "VCUEtOH_0609_R", @@ -3098,11 +3118,6 @@ "228", "VCUSal_0609_R", "VCU BXD VTA Sal M430 2.0 (Jun09) RMA" - ], - [ - "230", - "VCUEtvsSal_0609_R", - "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA" ] ] }, @@ -3134,7 +3149,7 @@ [ "None", "BXD-HarvestedPublish", - "BXD-Harvested Phenotypes" + "BXD-NIA-Longevity Phenotypes" ] ] }, -- cgit v1.2.3 From 66c6bbfcbbd5fb23145ec09956f4809e5f701bec Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 5 Jun 2019 13:01:36 -0500 Subject: Fixed issue that caused interval mapping to not work because the python implementation of the reaper Dataset object doesn't include the addinterval method (so for those situations I still use reaper) Fixed issue where the last chromosome wasn't displayed for mapping results (though still need to fix issue where points are drawn too far to the right when a specific range is viewed) --- wqflask/base/data_set.py | 9 +- wqflask/utility/gen_geno_ob.py | 270 +++++++++++---------- .../marker_regression/display_mapping_results.py | 6 +- .../wqflask/marker_regression/qtlreaper_mapping.py | 2 +- 4 files changed, 147 insertions(+), 140 deletions(-) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index b324ac74..1fd1792e 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -384,7 +384,7 @@ class DatasetGroup(object): [result.extend(l) for l in lists if l] return result - def read_genotype_file(self): + def read_genotype_file(self, use_reaper=False): '''Read genotype from .geno file instead of database''' #genotype_1 is Dataset Object without parents and f1 #genotype_2 is Dataset Object with parents and f1 (not for intercross) @@ -396,9 +396,12 @@ class DatasetGroup(object): full_filename = str(locate(self.genofile, 'genotype')) else: full_filename = str(locate(self.name + '.geno', 'genotype')) - #genotype_1.read(full_filename) - genotype_1 = gen_geno_ob.genotype(full_filename) + if use_reaper: + genotype_1 = reaper.Dataset() + genotype_1.read(full_filename) + else: + genotype_1 = gen_geno_ob.genotype(full_filename) if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 5824b0b3..5172369f 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,135 +1,137 @@ -from __future__ import absolute_import, division, print_function - -class genotype(object): - """ - Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure - """ - - def __init__(self, filename): - self.group = None - self.type = "riset" - self.prgy = [] - self.nprgy = 0 - self.mat = -1 - self.pat = 1 - self.het = 0 - self.unk = "U" - self.filler = False - self.mb_exists = False - - #ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary - self.cm_column = 2 - self.mb_column = 3 - - self.chromosomes = [] - - self.read_file(filename) - - def __iter__(self): - return iter(self.chromosomes) - - def __getitem__(self, index): - return self.chromosomes[index] - - def __len__(self): - return len(self.chromosomes) - - def read_file(self, filename): - - with open(filename, 'r') as geno_file: - lines = geno_file.readlines() - - this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers - chr_ob = None - for line in lines: - if line[0] == "#": - continue - elif line[0] == "@": - label = line.split(":")[0][1:] - if label == "name": - self.group = line.split(":")[1] - elif label == "filler": - if line.split(":")[1] == "yes": - self.filler = True - elif label == "type": - self.type = line.split(":")[1] - elif label == "mat": - self.mat = line.split(":")[1] - elif label == "pat": - self.pat = line.split(":")[1] - elif label == "het": - self.het = line.split(":")[1] - elif label == "unk": - self.unk = line.split(":")[1] - else: - continue - elif line[:3] == "Chr": - header_row = line.split("\t") - if header_row[2] == "Mb": - self.mb_exists = True - self.mb_column = 2 - self.cm_column = 3 - elif header_row[3] == "Mb": - self.mb_exists = True - self.mb_column = 3 - elif header_row[2] == "cM": - self.cm_column = 2 - - if self.mb_exists: - self.prgy = header_row[4:] - else: - self.prgy = header_row[3:] - self.nprgy = len(self.prgy) - else: - if line.split("\t")[0] != this_chr: - if this_chr != "": - self.chromosomes.append(chr_ob) - this_chr = line.split("\t")[0] - chr_ob = Chr(line.split("\t")[0], self) - chr_ob.add_marker(line.split("\t")) - -class Chr(object): - def __init__(self, name, geno_ob): - self.name = name - self.loci = [] - self.mb_exists = geno_ob.mb_exists - self.cm_column = geno_ob.cm_column - self.mb_column = geno_ob.mb_column - self.geno_ob = geno_ob - - def __iter__(self): - return iter(self.loci) - - def __getitem__(self, index): - return self.loci[index] - - def __len__(self): - return len(self.loci) - - def add_marker(self, marker_row): - self.loci.append(Locus(marker_row, self.geno_ob)) - -class Locus(object): - def __init__(self, marker_row, geno_ob): - self.chr = marker_row[0] - self.name = marker_row[1] - self.cM = float(marker_row[geno_ob.cm_column]) - self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None - - geno_table = { - geno_ob.mat: -1, - geno_ob.pat: 1, - geno_ob.het: 0, - geno_ob.unk: "U" - } - - self.genotype = [] - if geno_ob.mb_exists: - start_pos = 4 - else: - start_pos = 3 - for allele in marker_row[start_pos:]: - if allele in geno_table.keys(): - self.genotype.append(geno_table[allele]) - else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown +from __future__ import absolute_import, division, print_function + +class genotype(object): + """ + Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure + """ + + def __init__(self, filename): + self.group = None + self.type = "riset" + self.prgy = [] + self.nprgy = 0 + self.mat = -1 + self.pat = 1 + self.het = 0 + self.unk = "U" + self.filler = False + self.mb_exists = False + + #ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary + self.cm_column = 2 + self.mb_column = 3 + + self.chromosomes = [] + + self.read_file(filename) + + def __iter__(self): + return iter(self.chromosomes) + + def __getitem__(self, index): + return self.chromosomes[index] + + def __len__(self): + return len(self.chromosomes) + + def read_file(self, filename): + + with open(filename, 'r') as geno_file: + lines = geno_file.readlines() + + this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers + chr_ob = None + for line in lines: + if line[0] == "#": + continue + elif line[0] == "@": + label = line.split(":")[0][1:] + if label == "name": + self.group = line.split(":")[1] + elif label == "filler": + if line.split(":")[1] == "yes": + self.filler = True + elif label == "type": + self.type = line.split(":")[1] + elif label == "mat": + self.mat = line.split(":")[1] + elif label == "pat": + self.pat = line.split(":")[1] + elif label == "het": + self.het = line.split(":")[1] + elif label == "unk": + self.unk = line.split(":")[1] + else: + continue + elif line[:3] == "Chr": + header_row = line.split("\t") + if header_row[2] == "Mb": + self.mb_exists = True + self.mb_column = 2 + self.cm_column = 3 + elif header_row[3] == "Mb": + self.mb_exists = True + self.mb_column = 3 + elif header_row[2] == "cM": + self.cm_column = 2 + + if self.mb_exists: + self.prgy = header_row[4:] + else: + self.prgy = header_row[3:] + self.nprgy = len(self.prgy) + else: + if line.split("\t")[0] != this_chr: + if this_chr != "": + self.chromosomes.append(chr_ob) + this_chr = line.split("\t")[0] + chr_ob = Chr(line.split("\t")[0], self) + chr_ob.add_marker(line.split("\t")) + + self.chromosomes.append(chr_ob) + +class Chr(object): + def __init__(self, name, geno_ob): + self.name = name + self.loci = [] + self.mb_exists = geno_ob.mb_exists + self.cm_column = geno_ob.cm_column + self.mb_column = geno_ob.mb_column + self.geno_ob = geno_ob + + def __iter__(self): + return iter(self.loci) + + def __getitem__(self, index): + return self.loci[index] + + def __len__(self): + return len(self.loci) + + def add_marker(self, marker_row): + self.loci.append(Locus(marker_row, self.geno_ob)) + +class Locus(object): + def __init__(self, marker_row, geno_ob): + self.chr = marker_row[0] + self.name = marker_row[1] + self.cM = float(marker_row[geno_ob.cm_column]) + self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None + + geno_table = { + geno_ob.mat: -1, + geno_ob.pat: 1, + geno_ob.het: 0, + geno_ob.unk: "U" + } + + self.genotype = [] + if geno_ob.mb_exists: + start_pos = 4 + else: + start_pos = 3 + for allele in marker_row[start_pos:]: + if allele in geno_table.keys(): + self.genotype.append(geno_table[allele]) + else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown self.genotype.append("U") \ No newline at end of file diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 993fc2d9..e53e5279 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -236,9 +236,11 @@ class DisplayMappingResults(object): self.selectedChr = int(start_vars['selected_chr']) self.strainlist = start_vars['samples'] - self.genotype = self.dataset.group.read_genotype_file() + if self.mapping_method == "reaper" and self.manhattan_plot != True: - self.genotype = self.genotype.addinterval() + self.genotype = self.dataset.group.read_genotype_file(use_reaper=True) + else: + self.genotype = self.dataset.group.read_genotype_file() #Darwing Options try: diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 35bed8d8..d58c59c8 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -2,7 +2,7 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): - genotype = dataset.group.read_genotype_file() + genotype = dataset.group.read_genotype_file(use_reaper=True) if manhattan_plot != True: genotype = genotype.addinterval() -- cgit v1.2.3 From 65b33706d16abb7ef68a815fde5e3b1e69d4638f Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 5 Jun 2019 13:15:57 -0500 Subject: Issue where manhattan plot points went past the edge of the plot should be fixed now --- wqflask/wqflask/marker_regression/display_mapping_results.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index e53e5279..043e561a 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -1868,7 +1868,14 @@ class DisplayMappingResults(object): point_color = pid.grey else: point_color = pid.black - canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=point_color, font=symbolFont) + + final_x_pos = Xc-canvas.stringWidth("5",font=symbolFont)/2+1 + if final_x_pos > (xLeftOffset + plotWidth): + break + elif final_x_pos < xLeftOffset: + continue + else: + canvas.drawString("5", final_x_pos,Yc+2,color=point_color, font=symbolFont) else: LRSCoordXY.append((Xc, Yc)) -- cgit v1.2.3 From 067fb003a7ea9893d63454762183a514829069b1 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 5 Jun 2019 13:51:36 -0500 Subject: Additive effects now display for manhattan plots when available --- wqflask/wqflask/marker_regression/display_mapping_results.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 043e561a..b9050aea 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -1794,7 +1794,7 @@ class DisplayMappingResults(object): if self.manhattan_plot != True: canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - if not self.multipleInterval and not self.manhattan_plot and self.additiveChecked: + if not self.multipleInterval and self.additiveChecked: plusColor = self.ADDITIVE_COLOR_POSITIVE minusColor = self.ADDITIVE_COLOR_NEGATIVE for k, aPoint in enumerate(AdditiveCoordXY): -- cgit v1.2.3 From 38dd85ae47819190c5a3cc9e9a7269b44e92bb38 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 5 Jun 2019 16:13:41 -0500 Subject: Needed to replace single quotes with double quotes for JSON output --- wqflask/wqflask/api/router.py | 290 +++++++++++++++++++++--------------------- 1 file changed, 145 insertions(+), 145 deletions(-) diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 707e4e65..aab3d660 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -22,7 +22,7 @@ version = "pre1" @app.route("/api/v_{}/".format(version)) def hello_world(): - return flask.jsonify({'hello':'world'}) + return flask.jsonify({"hello":"world"}) @app.route("/api/v_{}/species".format(version)) def get_species_list(): @@ -31,10 +31,10 @@ def get_species_list(): species_list = [] for species in the_species: species_dict = { - 'Id' : species[0], - 'Name' : species[1], - 'FullName' : species[2], - 'TaxonomyId' : species[3] + "Id" : species[0], + "Name" : species[1], + "FullName" : species[2], + "TaxonomyId" : species[3] } species_list.append(species_dict) @@ -45,14 +45,14 @@ def get_species_list(): def get_species_info(species_name, file_format = "json"): results = g.db.execute("""SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species - WHERE (Name='{0}' OR FullName='{0}' OR SpeciesName='{0}');""".format(species_name)) + WHERE (Name="{0}" OR FullName="{0}" OR SpeciesName="{0}");""".format(species_name)) the_species = results.fetchone() species_dict = { - 'Id' : the_species[0], - 'Name' : the_species[1], - 'FullName' : the_species[2], - 'TaxonomyId' : the_species[3] + "Id" : the_species[0], + "Name" : the_species[1], + "FullName" : the_species[2], + "TaxonomyId" : the_species[3] } return flask.jsonify(species_dict) @@ -61,14 +61,14 @@ def get_species_info(species_name, file_format = "json"): @app.route("/api/v_{}//groups".format(version)) def get_groups_list(species_name=None): if species_name: - results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, - InbredSet.Name, InbredSet.FullName, InbredSet.public, + results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, + InbredSet.Name, InbredSet.FullName, InbredSet.public, InbredSet.MappingMethodId, InbredSet.GeneticType FROM InbredSet, Species WHERE InbredSet.SpeciesId = Species.Id AND - (Species.Name = '{0}' OR - Species.FullName='{0}' OR - Species.SpeciesName='{0}');""".format(species_name)) + (Species.Name = "{0}" OR + Species.FullName="{0}" OR + Species.SpeciesName="{0}");""".format(species_name)) else: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, @@ -80,14 +80,14 @@ def get_groups_list(species_name=None): groups_list = [] for group in the_groups: group_dict = { - 'Id' : group[0], - 'SpeciesId' : group[1], - 'DisplayName' : group[2], - 'Name' : group[3], - 'FullName' : group[4], - 'public' : group[5], - 'MappingMethodId' : group[6], - 'GeneticType' : group[7] + "Id" : group[0], + "SpeciesId" : group[1], + "DisplayName" : group[2], + "Name" : group[3], + "FullName" : group[4], + "public" : group[5], + "MappingMethodId" : group[6], + "GeneticType" : group[7] } groups_list.append(group_dict) @@ -106,32 +106,32 @@ def get_group_info(group_name, species_name = None, file_format = "json"): InbredSet.MappingMethodId, InbredSet.GeneticType FROM InbredSet, Species WHERE InbredSet.SpeciesId = Species.Id AND - (InbredSet.InbredSetName = '{0}' OR - InbredSet.Name = '{0}' OR - InbredSet.FullName = '{0}') AND - (Species.Name = '{1}' OR - Species.FullName='{1}' OR - Species.SpeciesName='{1}');""".format(group_name, species_name)) + (InbredSet.InbredSetName = "{0}" OR + InbredSet.Name = "{0}" OR + InbredSet.FullName = "{0}") AND + (Species.Name = "{1}" OR + Species.FullName="{1}" OR + Species.SpeciesName="{1}");""".format(group_name, species_name)) else: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, InbredSet.MappingMethodId, InbredSet.GeneticType FROM InbredSet - WHERE (InbredSet.InbredSetName = '{0}' OR - InbredSet.Name = '{0}' OR - InbredSet.FullName = '{0}');""".format(group_name)) + WHERE (InbredSet.InbredSetName = "{0}" OR + InbredSet.Name = "{0}" OR + InbredSet.FullName = "{0}");""".format(group_name)) group = results.fetchone() if group: group_dict = { - 'Id' : group[0], - 'SpeciesId' : group[1], - 'DisplayName' : group[2], - 'Name' : group[3], - 'FullName' : group[4], - 'public' : group[5], - 'MappingMethodId' : group[6], - 'GeneticType' : group[7] + "Id" : group[0], + "SpeciesId" : group[1], + "DisplayName" : group[2], + "Name" : group[3], + "FullName" : group[4], + "public" : group[5], + "MappingMethodId" : group[6], + "GeneticType" : group[7] } return flask.jsonify(group_dict) @@ -150,9 +150,9 @@ def get_datasets_for_group(group_name, species_name=None): FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Species WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND - (InbredSet.Name = '{0}' OR InbredSet.InbredSetName = '{0}' OR InbredSet.FullName = '{0}') AND + (InbredSet.Name = "{0}" OR InbredSet.InbredSetName = "{0}" OR InbredSet.FullName = "{0}") AND InbredSet.SpeciesId = Species.Id AND - (Species.SpeciesName = '{1}' OR Species.MenuName = '{1}' OR Species.FullName = '{1}'); + (Species.SpeciesName = "{1}" OR Species.MenuName = "{1}" OR Species.FullName = "{1}"); """.format(group_name, species_name)) else: results = g.db.execute(""" @@ -163,7 +163,7 @@ def get_datasets_for_group(group_name, species_name=None): FROM ProbeSetFreeze, ProbeFreeze, InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND - (InbredSet.Name = '{0}' OR InbredSet.InbredSetName = '{0}' OR InbredSet.FullName = '{0}'); + (InbredSet.Name = "{0}" OR InbredSet.InbredSetName = "{0}" OR InbredSet.FullName = "{0}"); """.format(group_name)) the_datasets = results.fetchall() @@ -172,17 +172,17 @@ def get_datasets_for_group(group_name, species_name=None): datasets_list = [] for dataset in the_datasets: dataset_dict = { - 'Id' : dataset[0], - 'ProbeFreezeId' : dataset[1], - 'AvgID' : dataset[2], - 'Short_Abbreviation' : dataset[3], - 'Long_Abbreviation' : dataset[4], - 'FullName' : dataset[5], - 'ShortName' : dataset[6], - 'CreateTime' : dataset[7], - 'public' : dataset[8], - 'confidentiality' : dataset[9], - 'DataScale' : dataset[10] + "Id" : dataset[0], + "ProbeFreezeId" : dataset[1], + "AvgID" : dataset[2], + "Short_Abbreviation" : dataset[3], + "Long_Abbreviation" : dataset[4], + "FullName" : dataset[5], + "ShortName" : dataset[6], + "CreateTime" : dataset[7], + "public" : dataset[8], + "confidentiality" : dataset[9], + "DataScale" : dataset[10] } datasets_list.append(dataset_dict) @@ -197,7 +197,7 @@ def get_datasets_for_group(group_name, species_name=None): def get_dataset_info(dataset_name, group_name = None, file_format="json"): #ZS: First get ProbeSet (mRNA expression) datasets and then get Phenotype datasets - datasets_list = [] #ZS: I figure I might as well return a list if there are multiple matches, though I don't know if this will actually happen in practice + datasets_list = [] #ZS: I figure I might as well return a list if there are multiple matches, though I don"t know if this will actually happen in practice probeset_query = """ SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, @@ -212,12 +212,12 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): """ if dataset_name.isdigit(): where_statement += """ - ProbeSetFreeze.Id = '{}' + ProbeSetFreeze.Id = "{}" """.format(dataset_name) else: where_statement += """ - (ProbeSetFreeze.Name = '{0}' OR ProbeSetFreeze.Name2 = '{0}' OR - ProbeSetFreeze.FullName = '{0}' OR ProbeSetFreeze.ShortName = '{0}') + (ProbeSetFreeze.Name = "{0}" OR ProbeSetFreeze.Name2 = "{0}" OR + ProbeSetFreeze.FullName = "{0}" OR ProbeSetFreeze.ShortName = "{0}") """.format(dataset_name) probeset_query += where_statement @@ -226,16 +226,16 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): if dataset: dataset_dict = { - 'dataset_type' : "mRNA expression", - 'id' : dataset[0], - 'name' : dataset[1], - 'full_name' : dataset[2], - 'short_name' : dataset[3], - 'data_scale' : dataset[4], - 'tissue_id' : dataset[5], - 'tissue' : dataset[6], - 'public' : dataset[7], - 'confidential' : dataset[8] + "dataset_type" : "mRNA expression", + "id" : dataset[0], + "name" : dataset[1], + "full_name" : dataset[2], + "short_name" : dataset[3], + "data_scale" : dataset[4], + "tissue_id" : dataset[5], + "tissue" : dataset[6], + "public" : dataset[7], + "confidential" : dataset[8] } datasets_list.append(dataset_dict) @@ -249,7 +249,7 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): WHERE PublishXRef.InbredSetId = InbredSet.Id AND PublishXRef.PhenotypeId = Phenotype.Id AND PublishXRef.PublicationId = Publication.Id AND - InbredSet.Name = '{0}' AND PublishXRef.Id = '{1}' + InbredSet.Name = "{0}" AND PublishXRef.Id = "{1}" """.format(group_name, dataset_name) logger.debug("QUERY:", pheno_query) @@ -260,25 +260,25 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): if dataset: if dataset[5]: dataset_dict = { - 'dataset_type' : "phenotype", - 'id' : dataset[0], - 'name' : dataset[1], - 'description' : dataset[2], - 'pubmed_id' : dataset[5], - 'title' : dataset[6], - 'year' : dataset[7] + "dataset_type" : "phenotype", + "id" : dataset[0], + "name" : dataset[1], + "description" : dataset[2], + "pubmed_id" : dataset[5], + "title" : dataset[6], + "year" : dataset[7] } elif dataset[4]: dataset_dict = { - 'dataset_type' : "phenotype", - 'id' : dataset[0], - 'name' : dataset[3], - 'description' : dataset[4] + "dataset_type" : "phenotype", + "id" : dataset[0], + "name" : dataset[3], + "description" : dataset[4] } else: dataset_dict = { - 'dataset_type' : "phenotype", - 'id' : dataset[0] + "dataset_type" : "phenotype", + "id" : dataset[0] } datasets_list.append(dataset_dict) @@ -290,11 +290,11 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/traits/".format(version), methods=('GET',)) -@app.route("/api/v_{}/traits/.".format(version), methods=('GET',)) +@app.route("/api/v_{}/traits/".format(version), methods=("GET",)) +@app.route("/api/v_{}/traits/.".format(version), methods=("GET",)) def fetch_traits(dataset_name, file_format = "json"): trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name) - if ('ids_only' in request.args) and (len(trait_ids) > 0): + if ("ids_only" in request.args) and (len(trait_ids) > 0): if file_format == "json": filename = dataset_name + "_trait_ids.json" return flask.jsonify(trait_ids) @@ -308,7 +308,7 @@ def fetch_traits(dataset_name, file_format = "json"): output.headers["Content-Disposition"] = "attachment; filename=" + filename output.headers["Content-type"] = "text/csv" return output - elif ('names_only' in request.args) and (len(trait_ids) > 0): + elif ("names_only" in request.args) and (len(trait_ids) > 0): if file_format == "json": filename = dataset_name + "_trait_names.json" return flask.jsonify(trait_names) @@ -332,7 +332,7 @@ def fetch_traits(dataset_name, file_format = "json"): FROM ProbeSet, ProbeSetXRef WHERE - ProbeSetXRef.ProbeSetFreezeId = '{0}' AND + ProbeSetXRef.ProbeSetFreezeId = "{0}" AND ProbeSetXRef.ProbeSetId = ProbeSet.Id ORDER BY ProbeSet.Id @@ -346,7 +346,7 @@ def fetch_traits(dataset_name, file_format = "json"): FROM Geno, GenoXRef WHERE - GenoXRef.GenoFreezeId = '{0}' AND + GenoXRef.GenoFreezeId = "{0}" AND GenoXRef.GenoId = Geno.Id ORDER BY Geno.Id @@ -422,8 +422,8 @@ def all_sample_data(dataset_name, file_format = "csv"): LEFT JOIN ProbeSetSE ON (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) WHERE - ProbeSetXRef.ProbeSetFreezeId = '{0}' AND - ProbeSetXRef.ProbeSetId = '{1}' AND + ProbeSetXRef.ProbeSetFreezeId = "{0}" AND + ProbeSetXRef.ProbeSetId = "{1}" AND ProbeSetXRef.DataId = ProbeSetData.Id AND ProbeSetData.StrainId = Strain.Id ORDER BY @@ -438,8 +438,8 @@ def all_sample_data(dataset_name, file_format = "csv"): LEFT JOIN GenoSE ON (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) WHERE - GenoXRef.GenoFreezeId = '{0}' AND - GenoXRef.GenoId = '{1}' AND + GenoXRef.GenoFreezeId = "{0}" AND + GenoXRef.GenoId = "{1}" AND GenoXRef.DataId = GenoData.Id AND GenoData.StrainId = Strain.Id ORDER BY @@ -457,8 +457,8 @@ def all_sample_data(dataset_name, file_format = "csv"): (NStrain.DataId = PublishData.Id AND NStrain.StrainId = PublishData.StrainId) WHERE - PublishXRef.InbredSetId = '{0}' AND - PublishXRef.PhenotypeId = '{1}' AND + PublishXRef.InbredSetId = "{0}" AND + PublishXRef.PhenotypeId = "{1}" AND PublishData.Id = PublishXRef.DataId AND PublishData.StrainId = Strain.Id ORDER BY @@ -511,9 +511,9 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): LEFT JOIN ProbeSetSE ON (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) WHERE - ProbeSet.Name = '{0}' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSet.Name = "{0}" AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetFreeze.Name = '{1}' AND + ProbeSetFreeze.Name = "{1}" AND ProbeSetXRef.DataId = ProbeSetData.Id AND ProbeSetData.StrainId = Strain.Id ORDER BY @@ -527,13 +527,13 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): sample_list = [] for sample in sample_data: sample_dict = { - 'sample_name' : sample[0], - 'sample_name_2' : sample[1], - 'value' : sample[2], - 'data_id' : sample[3], + "sample_name" : sample[0], + "sample_name_2" : sample[1], + "value" : sample[2], + "data_id" : sample[3], } if sample[4]: - sample_dict['se'] = sample[4] + sample_dict["se"] = sample[4] sample_list.append(sample_dict) return flask.jsonify(sample_list) @@ -559,9 +559,9 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): NStrain.StrainId = PublishData.StrainId) WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = '{1}' AND - (PublishFreeze.Id = '{0}' OR PublishFreeze.Name = '{0}' OR - PublishFreeze.ShortName = '{0}' OR PublishXRef.InbredSetId = '{0}') AND + PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = "{1}" AND + (PublishFreeze.Id = "{0}" OR PublishFreeze.Name = "{0}" OR + PublishFreeze.ShortName = "{0}" OR PublishXRef.InbredSetId = "{0}") AND PublishData.StrainId = Strain.Id ORDER BY Strain.Name @@ -574,15 +574,15 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): sample_list = [] for sample in sample_data: sample_dict = { - 'sample_name' : sample[0], - 'sample_name_2' : sample[1], - 'value' : sample[2], - 'data_id' : sample[3] + "sample_name" : sample[0], + "sample_name_2" : sample[1], + "value" : sample[2], + "data_id" : sample[3] } if sample[4]: - sample_dict['se'] = sample[4] + sample_dict["se"] = sample[4] if sample[5]: - sample_dict['n_cases'] = sample[5] + sample_dict["n_cases"] = sample[5] sample_list.append(sample_dict) return flask.jsonify(sample_list) @@ -596,15 +596,15 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): def get_trait_info(dataset_name, trait_name, file_format = "json"): probeset_query = """ SELECT - ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias, + ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias, ProbeSetXRef.mean, ProbeSetXRef.se, ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze WHERE - ProbeSet.Name = '{0}' AND + ProbeSet.Name = "{0}" AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetFreeze.Name = '{1}' + ProbeSetFreeze.Name = "{1}" """.format(trait_name, dataset_name) probeset_results = g.db.execute(probeset_query) @@ -612,19 +612,19 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"): trait_info = probeset_results.fetchone() if trait_info: trait_dict = { - 'id' : trait_info[0], - 'name' : trait_info[1], - 'symbol' : trait_info[2], - 'description' : trait_info[3], - 'chr' : trait_info[4], - 'mb' : trait_info[5], - 'alias' :trait_info[6], - 'mean' : trait_info[7], - 'se' : trait_info[8], - 'locus' : trait_info[9], - 'lrs' : trait_info[10], - 'p_value' : trait_info[11], - 'additive' : trait_info[12] + "id" : trait_info[0], + "name" : trait_info[1], + "symbol" : trait_info[2], + "description" : trait_info[3], + "chr" : trait_info[4], + "mb" : trait_info[5], + "alias" :trait_info[6], + "mean" : trait_info[7], + "se" : trait_info[8], + "locus" : trait_info[9], + "lrs" : trait_info[10], + "p_value" : trait_info[11], + "additive" : trait_info[12] } return flask.jsonify(trait_dict) @@ -639,8 +639,8 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"): FROM PublishXRef WHERE - PublishXRef.Id = '{0}' AND - PublishXRef.InbredSetId = '{1}' + PublishXRef.Id = "{0}" AND + PublishXRef.InbredSetId = "{1}" """.format(trait_name, group_id) pheno_results = g.db.execute(pheno_query) @@ -648,17 +648,17 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"): trait_info = pheno_results.fetchone() if trait_info: trait_dict = { - 'id' : trait_info[0], - 'locus' : trait_info[1], - 'lrs' : trait_info[2], - 'additive' : trait_info[3] + "id" : trait_info[0], + "locus" : trait_info[1], + "lrs" : trait_info[2], + "additive" : trait_info[3] } return flask.jsonify(trait_dict) else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/correlation".format(version), methods=('GET',)) +@app.route("/api/v_{}/correlation".format(version), methods=("GET",)) def get_corr_results(): results = correlation.do_correlation(request.args) @@ -667,12 +667,12 @@ def get_corr_results(): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") -@app.route("/api/v_{}/mapping".format(version), methods=('GET',)) +@app.route("/api/v_{}/mapping".format(version), methods=("GET",)) def get_mapping_results(): results = mapping.do_mapping_for_api(request.args) if len(results) > 0: - filename = "mapping_" + datetime.datetime.utcnow().strftime('%b_%d_%Y_%I:%M%p') + ".csv" + filename = "mapping_" + datetime.datetime.utcnow().strftime("%b_%d_%Y_%I:%M%p") + ".csv" si = StringIO.StringIO() csv_writer = csv.writer(si) @@ -692,28 +692,28 @@ def get_genotypes(group_name, file_format="csv"): if file_format == "csv" or file_format == "geno": filename = group_name + ".geno" - if os.path.isfile('{0}/{1}.geno'.format(flat_files('genotype'), group_name)): + if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)): output_lines = [] - with open('{0}/{1}.geno'.format(flat_files('genotype'), group_name)) as genofile: + with open("{0}/{1}.geno".format(flat_files("genotype"), group_name)) as genofile: for line in genofile: if line[0] == "#" or line[0] == "@": output_lines.append([line.strip()]) else: output_lines.append(line.split()) - csv_writer = csv.writer(si, delimiter = '\t', escapechar = "\\", quoting = csv.QUOTE_NONE) + csv_writer = csv.writer(si, delimiter = "\t", escapechar = "\\", quoting = csv.QUOTE_NONE) else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") else: filename = group_name + ".bimbam" - if os.path.isfile('{0}/{1}.geno'.format(flat_files('genotype'), group_name)): + if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)): output_lines = [] - with open('{0}/{1}_geno.txt'.format(flat_files('genotype/bimbam'), group_name)) as genofile: + with open("{0}/{1}_geno.txt".format(flat_files("genotype/bimbam"), group_name)) as genofile: for line in genofile: output_lines.append([line.strip() for line in line.split(",")]) - csv_writer = csv.writer(si, delimiter = ',') + csv_writer = csv.writer(si, delimiter = ",") else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @@ -747,7 +747,7 @@ def get_dataset_trait_ids(dataset_name): WHERE Geno.Id = GenoXRef.GenoId AND GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoFreeze.Name = '{0}' + GenoFreeze.Name = "{0}" """.format(dataset_name) results = g.db.execute(query).fetchall() @@ -768,7 +768,7 @@ def get_dataset_trait_ids(dataset_name): FROM PublishXRef WHERE - PublishXRef.InbredSetId = '{0}' + PublishXRef.InbredSetId = "{0}" """.format(dataset_id) results = g.db.execute(query).fetchall() @@ -787,7 +787,7 @@ def get_dataset_trait_ids(dataset_name): WHERE ProbeSet.Id = ProbeSetXRef.ProbeSetId AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetFreeze.Name = '{0}' + ProbeSetFreeze.Name = "{0}" """.format(dataset_name) results = g.db.execute(query).fetchall() @@ -857,7 +857,7 @@ def get_group_id(group_name): query = """ SELECT InbredSet.Id FROM InbredSet - WHERE InbredSet.Name = '{}' + WHERE InbredSet.Name = "{}" """.format(group_name) group_id = g.db.execute(query).fetchone() -- cgit v1.2.3 From c898381788574b70a3f85c145eb8fcd5d7af7ca0 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 5 Jun 2019 16:26:19 -0500 Subject: Ensured that a string is returned for SQL fields that can potentially be null --- wqflask/wqflask/api/router.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index aab3d660..64552fa5 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -63,7 +63,7 @@ def get_groups_list(species_name=None): if species_name: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - InbredSet.MappingMethodId, InbredSet.GeneticType + ISNULL(InbredSet.MappingMethodId, "None"), ISNULL(InbredSet.GeneticType, "None") FROM InbredSet, Species WHERE InbredSet.SpeciesId = Species.Id AND (Species.Name = "{0}" OR @@ -72,7 +72,7 @@ def get_groups_list(species_name=None): else: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - InbredSet.MappingMethodId, InbredSet.GeneticType + ISNULL(InbredSet.MappingMethodId, "None"), ISNULL(InbredSet.GeneticType, "None") FROM InbredSet;""") the_groups = results.fetchall() @@ -103,7 +103,7 @@ def get_group_info(group_name, species_name = None, file_format = "json"): if species_name: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - InbredSet.MappingMethodId, InbredSet.GeneticType + ISNULL(InbredSet.MappingMethodId, "None"), ISNULL(InbredSet.GeneticType, "None") FROM InbredSet, Species WHERE InbredSet.SpeciesId = Species.Id AND (InbredSet.InbredSetName = "{0}" OR @@ -115,7 +115,7 @@ def get_group_info(group_name, species_name = None, file_format = "json"): else: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - InbredSet.MappingMethodId, InbredSet.GeneticType + ISNULL(InbredSet.MappingMethodId, "None"), ISNULL(InbredSet.GeneticType, "None") FROM InbredSet WHERE (InbredSet.InbredSetName = "{0}" OR InbredSet.Name = "{0}" OR -- cgit v1.2.3 From c0aa776c39b00d8a7a90f304db0560d9bc2d0646 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 6 Jun 2019 12:45:02 -0500 Subject: Replaced ISNULL with IFNULL (which is the correct version for MySQL) Changed the query form for getting a species' groups --- wqflask/wqflask/api/router.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 64552fa5..8e2cbbdc 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -58,12 +58,12 @@ def get_species_info(species_name, file_format = "json"): return flask.jsonify(species_dict) @app.route("/api/v_{}/groups".format(version)) -@app.route("/api/v_{}//groups".format(version)) +@app.route("/api/v_{}/groups/".format(version)) def get_groups_list(species_name=None): if species_name: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - ISNULL(InbredSet.MappingMethodId, "None"), ISNULL(InbredSet.GeneticType, "None") + IFNULL(InbredSet.MappingMethodId, "None"), IFNULL(InbredSet.GeneticType, "None") FROM InbredSet, Species WHERE InbredSet.SpeciesId = Species.Id AND (Species.Name = "{0}" OR @@ -72,7 +72,7 @@ def get_groups_list(species_name=None): else: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - ISNULL(InbredSet.MappingMethodId, "None"), ISNULL(InbredSet.GeneticType, "None") + IFNULL(InbredSet.MappingMethodId, "None"), IFNULL(InbredSet.GeneticType, "None") FROM InbredSet;""") the_groups = results.fetchall() @@ -103,7 +103,7 @@ def get_group_info(group_name, species_name = None, file_format = "json"): if species_name: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - ISNULL(InbredSet.MappingMethodId, "None"), ISNULL(InbredSet.GeneticType, "None") + IFNULL(InbredSet.MappingMethodId, "None"), IFNULL(InbredSet.GeneticType, "None") FROM InbredSet, Species WHERE InbredSet.SpeciesId = Species.Id AND (InbredSet.InbredSetName = "{0}" OR @@ -115,7 +115,7 @@ def get_group_info(group_name, species_name = None, file_format = "json"): else: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, - ISNULL(InbredSet.MappingMethodId, "None"), ISNULL(InbredSet.GeneticType, "None") + IFNULL(InbredSet.MappingMethodId, "None"), IFNULL(InbredSet.GeneticType, "None") FROM InbredSet WHERE (InbredSet.InbredSetName = "{0}" OR InbredSet.Name = "{0}" OR -- cgit v1.2.3 From 9e892146abeeeff5ef4d08f6773a2272fe752e0c Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 6 Jun 2019 15:34:07 -0500 Subject: Made some changes to REST API, including adding limit_to option to mapping --- wqflask/wqflask/api/mapping.py | 263 ++++++++++++++++++++++------------------- wqflask/wqflask/api/router.py | 63 +++++++--- 2 files changed, 188 insertions(+), 138 deletions(-) diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index 83c61796..d830cefc 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -1,122 +1,141 @@ -from __future__ import absolute_import, division, print_function - -import string - -from base import data_set -from base import webqtlConfig -from base.trait import GeneralTrait, retrieve_sample_data - -from utility import helper_functions -from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping - -import utility.logger -logger = utility.logger.getLogger(__name__ ) - -def do_mapping_for_api(start_vars): - assert('db' in start_vars) - assert('trait_id' in start_vars) - - dataset = data_set.create_dataset(dataset_name = start_vars['db']) - dataset.group.get_markers() - this_trait = GeneralTrait(dataset = dataset, name = start_vars['trait_id']) - this_trait = retrieve_sample_data(this_trait, dataset) - - samples = [] - vals = [] - - for sample in dataset.group.samplelist: - in_trait_data = False - for item in this_trait.data: - if this_trait.data[item].name == sample: - value = str(this_trait.data[item].value) - samples.append(item) - vals.append(value) - in_trait_data = True - break - if not in_trait_data: - vals.append("x") - - mapping_params = initialize_parameters(start_vars, dataset, this_trait) - - covariates = "" #ZS: It seems to take an empty string as default. This should probably be changed. - - if mapping_params['mapping_method'] == "gemma": - header_row = ["name", "chr", "Mb", "lod_score", "p_value"] - if mapping_params['use_loco'] == "True": #ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api - result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0] - else: - result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf']) - elif mapping_params['mapping_method'] == "rqtl": - header_row = ["name", "chr", "Mb", "lod_score"] - if mapping_params['num_perm'] > 0: - _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], - mapping_params['perm_check'], mapping_params['num_perm'], - mapping_params['do_control'], mapping_params['control_marker'], - mapping_params['manhattan_plot'], mapping_params['pair_scan']) - else: - result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], - mapping_params['perm_check'], mapping_params['num_perm'], - mapping_params['do_control'], mapping_params['control_marker'], - mapping_params['manhattan_plot'], mapping_params['pair_scan']) - - output_rows = [] - output_rows.append(header_row) - for marker in result_markers: - this_row = [marker[header] for header in header_row] - output_rows.append(this_row) - - return output_rows - - -def initialize_parameters(start_vars, dataset, this_trait): - mapping_params = {} - mapping_params['mapping_method'] = "gemma" - if 'method' in start_vars: - mapping_params['mapping_method'] = start_vars['method'] - - if mapping_params['mapping_method'] == "rqtl": - mapping_params['rqtl_method'] = "hk" - mapping_params['rqtl_model'] = "normal" - mapping_params['do_control'] = False - mapping_params['control_marker'] = "" - mapping_params['manhattan_plot'] = True - mapping_params['pair_scan'] = False - if 'rqtl_method' in start_vars: - mapping_params['rqtl_method'] = start_vars['rqtl_method'] - if 'rqtl_model' in start_vars: - mapping_params['rqtl_model'] = start_vars['rqtl_model'] - if 'control_marker' in start_vars: - mapping_params['control_marker'] = start_vars['control_marker'] - mapping_params['do_control'] = True - if 'pair_scan' in start_vars: - if start_vars['pair_scan'].lower() == "true": - mapping_params['pair_scan'] = True - - if 'interval_mapping' in start_vars: - if start_vars['interval_mapping'].lower() == "true": - mapping_params['manhattan_plot'] = False - elif 'manhattan_plot' in start_vars: - if start_vars['manhattan_plot'].lower() != "true": - mapping_params['manhattan_plot'] = False - - mapping_params['maf'] = 0.01 - if 'maf' in start_vars: - mapping_params['maf'] = start_vars['maf'] # Minor allele frequency - - mapping_params['use_loco'] = False - if 'use_loco' in start_vars: - if start_vars['use_loco'].lower() != "false": - mapping_params['use_loco'] = start_vars['use_loco'] - - mapping_params['num_perm'] = 0 - mapping_params['perm_check'] = False - if 'num_perm' in start_vars: - try: - mapping_params['num_perm'] = int(start_vars['num_perm']) - mapping_params['perm_check'] = "ON" - except: - mapping_params['perm_check'] = False - - return mapping_params - - +from __future__ import absolute_import, division, print_function + +import string + +from base import data_set +from base import webqtlConfig +from base.trait import GeneralTrait, retrieve_sample_data + +from utility import helper_functions +from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping + +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +def do_mapping_for_api(start_vars): + assert('db' in start_vars) + assert('trait_id' in start_vars) + + dataset = data_set.create_dataset(dataset_name = start_vars['db']) + dataset.group.get_markers() + this_trait = GeneralTrait(dataset = dataset, name = start_vars['trait_id']) + this_trait = retrieve_sample_data(this_trait, dataset) + + samples = [] + vals = [] + + for sample in dataset.group.samplelist: + in_trait_data = False + for item in this_trait.data: + if this_trait.data[item].name == sample: + value = str(this_trait.data[item].value) + samples.append(item) + vals.append(value) + in_trait_data = True + break + if not in_trait_data: + vals.append("x") + + mapping_params = initialize_parameters(start_vars, dataset, this_trait) + + covariates = "" #ZS: It seems to take an empty string as default. This should probably be changed. + + if mapping_params['mapping_method'] == "gemma": + header_row = ["name", "chr", "Mb", "lod_score", "p_value"] + if mapping_params['use_loco'] == "True": #ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api + result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0] + else: + result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf']) + elif mapping_params['mapping_method'] == "rqtl": + header_row = ["name", "chr", "cM", "lod_score"] + if mapping_params['num_perm'] > 0: + _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], + mapping_params['perm_check'], mapping_params['num_perm'], + mapping_params['do_control'], mapping_params['control_marker'], + mapping_params['manhattan_plot'], mapping_params['pair_scan']) + else: + result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], + mapping_params['perm_check'], mapping_params['num_perm'], + mapping_params['do_control'], mapping_params['control_marker'], + mapping_params['manhattan_plot'], mapping_params['pair_scan']) + + if mapping_params['limit_to']: + result_markers = result_markers[:mapping_params['limit_to']] + + if mapping_params['format'] == "csv": + output_rows = [] + output_rows.append(header_row) + for marker in result_markers: + this_row = [marker[header] for header in header_row] + output_rows.append(this_row) + + return output_rows, mapping_params['format'] + elif mapping_params['format'] == "json": + return result_markers, mapping_params['format'] + else: + return result_markers, None + + + +def initialize_parameters(start_vars, dataset, this_trait): + mapping_params = {} + + mapping_params['format'] = "json" + if 'format' in start_vars: + mapping_params['format'] = start_vars['format'] + + mapping_params['limit_to'] = False + if 'limit_to' in start_vars: + if start_vars['limit_to'].isdigit(): + mapping_params['limit_to'] = int(start_vars['limit_to']) + + mapping_params['mapping_method'] = "gemma" + if 'method' in start_vars: + mapping_params['mapping_method'] = start_vars['method'] + + if mapping_params['mapping_method'] == "rqtl": + mapping_params['rqtl_method'] = "hk" + mapping_params['rqtl_model'] = "normal" + mapping_params['do_control'] = False + mapping_params['control_marker'] = "" + mapping_params['manhattan_plot'] = True + mapping_params['pair_scan'] = False + if 'rqtl_method' in start_vars: + mapping_params['rqtl_method'] = start_vars['rqtl_method'] + if 'rqtl_model' in start_vars: + mapping_params['rqtl_model'] = start_vars['rqtl_model'] + if 'control_marker' in start_vars: + mapping_params['control_marker'] = start_vars['control_marker'] + mapping_params['do_control'] = True + if 'pair_scan' in start_vars: + if start_vars['pair_scan'].lower() == "true": + mapping_params['pair_scan'] = True + + if 'interval_mapping' in start_vars: + if start_vars['interval_mapping'].lower() == "true": + mapping_params['manhattan_plot'] = False + elif 'manhattan_plot' in start_vars: + if start_vars['manhattan_plot'].lower() != "true": + mapping_params['manhattan_plot'] = False + + mapping_params['maf'] = 0.01 + if 'maf' in start_vars: + mapping_params['maf'] = start_vars['maf'] # Minor allele frequency + + mapping_params['use_loco'] = True + if 'use_loco' in start_vars: + if (start_vars['use_loco'].lower() == "false") or (start_vars['use_loco'].lower() == "no"): + mapping_params['use_loco'] = False + + mapping_params['num_perm'] = 0 + mapping_params['perm_check'] = False + if 'num_perm' in start_vars: + try: + mapping_params['num_perm'] = int(start_vars['num_perm']) + mapping_params['perm_check'] = "ON" + except: + mapping_params['perm_check'] = False + + return mapping_params + + diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 8e2cbbdc..cbff6e83 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -293,7 +293,7 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): @app.route("/api/v_{}/traits/".format(version), methods=("GET",)) @app.route("/api/v_{}/traits/.".format(version), methods=("GET",)) def fetch_traits(dataset_name, file_format = "json"): - trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name) + trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args) if ("ids_only" in request.args) and (len(trait_ids) > 0): if file_format == "json": filename = dataset_name + "_trait_ids.json" @@ -367,6 +367,10 @@ def fetch_traits(dataset_name, file_format = "json"): field_list = ["Id", "PhenotypeId", "PublicationId", "Locus", "LRS", "Additive", "Sequence"] + if 'limit_to' in request.args: + limit_number = request.args['limit_to'] + query += "LIMIT " + str(limit_number) + if file_format == "json": filename = dataset_name + "_traits.json" @@ -408,7 +412,7 @@ def fetch_traits(dataset_name, file_format = "json"): @app.route("/api/v_{}/sample_data/".format(version)) @app.route("/api/v_{}/sample_data/.".format(version)) def all_sample_data(dataset_name, file_format = "csv"): - trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name) + trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args) if len(trait_ids) > 0: sample_list = get_samplelist(dataset_name) @@ -496,7 +500,7 @@ def all_sample_data(dataset_name, file_format = "csv"): output.headers["Content-type"] = "text/csv" return output else: - return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + return return_error(code=415, source=request.url_rule.rule, title="Unsupported file format", details="") else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @@ -669,25 +673,35 @@ def get_corr_results(): @app.route("/api/v_{}/mapping".format(version), methods=("GET",)) def get_mapping_results(): - results = mapping.do_mapping_for_api(request.args) + results, format = mapping.do_mapping_for_api(request.args) if len(results) > 0: - filename = "mapping_" + datetime.datetime.utcnow().strftime("%b_%d_%Y_%I:%M%p") + ".csv" + if format == "csv": + filename = "mapping_" + datetime.datetime.utcnow().strftime("%b_%d_%Y_%I:%M%p") + ".csv" - si = StringIO.StringIO() - csv_writer = csv.writer(si) - csv_writer.writerows(results) - output = make_response(si.getvalue()) - output.headers["Content-Disposition"] = "attachment; filename=" + filename - output.headers["Content-type"] = "text/csv" + si = StringIO.StringIO() + csv_writer = csv.writer(si) + csv_writer.writerows(results) + output = make_response(si.getvalue()) + output.headers["Content-Disposition"] = "attachment; filename=" + filename + output.headers["Content-type"] = "text/csv" - return output + return output + elif format == "json": + return flask.jsonify(results) + else: + return return_error(code=415, source=request.url_rule.rule, title="Unsupported Format", details="") else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @app.route("/api/v_{}/genotypes/".format(version)) @app.route("/api/v_{}/genotypes/.".format(version)) def get_genotypes(group_name, file_format="csv"): + limit_num = None + if 'limit_to' in request.args: + if request.args['limit_to'].isdigit(): + limit_num = int(request.args['limit_to']) + si = StringIO.StringIO() if file_format == "csv" or file_format == "geno": filename = group_name + ".geno" @@ -695,11 +709,15 @@ def get_genotypes(group_name, file_format="csv"): if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)): output_lines = [] with open("{0}/{1}.geno".format(flat_files("genotype"), group_name)) as genofile: + i = 0 for line in genofile: if line[0] == "#" or line[0] == "@": output_lines.append([line.strip()]) else: + if i >= limit_num: + break output_lines.append(line.split()) + i += 1 csv_writer = csv.writer(si, delimiter = "\t", escapechar = "\\", quoting = csv.QUOTE_NONE) else: @@ -710,8 +728,12 @@ def get_genotypes(group_name, file_format="csv"): if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)): output_lines = [] with open("{0}/{1}_geno.txt".format(flat_files("genotype/bimbam"), group_name)) as genofile: + i = 0 for line in genofile: + if i >= limit_num: + break output_lines.append([line.strip() for line in line.split(",")]) + i += 1 csv_writer = csv.writer(si, delimiter = ",") else: @@ -736,7 +758,13 @@ def return_error(code, source, title, details): return flask.jsonify(json_ob) -def get_dataset_trait_ids(dataset_name): +def get_dataset_trait_ids(dataset_name, start_vars): + + if 'limit_to' in start_vars: + limit_string = "LIMIT " + str(start_vars['limit_to']) + else: + limit_string = "" + if "Geno" in dataset_name: data_type = "Geno" #ZS: Need to pass back the dataset type query = """ @@ -748,7 +776,8 @@ def get_dataset_trait_ids(dataset_name): Geno.Id = GenoXRef.GenoId AND GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoFreeze.Name = "{0}" - """.format(dataset_name) + {1} + """.format(dataset_name, limit_string) results = g.db.execute(query).fetchall() @@ -769,7 +798,8 @@ def get_dataset_trait_ids(dataset_name): PublishXRef WHERE PublishXRef.InbredSetId = "{0}" - """.format(dataset_id) + {1} + """.format(dataset_id, limit_string) results = g.db.execute(query).fetchall() @@ -788,7 +818,8 @@ def get_dataset_trait_ids(dataset_name): ProbeSet.Id = ProbeSetXRef.ProbeSetId AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND ProbeSetFreeze.Name = "{0}" - """.format(dataset_name) + {1} + """.format(dataset_name, limit_string) results = g.db.execute(query).fetchall() -- cgit v1.2.3 From 3659ceb0ee7058e41cd0b789558b07d7e8bf415e Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 7 Jun 2019 13:08:47 -0500 Subject: Global search and correlation results can handle null expression now --- wqflask/utility/type_checking.py | 2 +- wqflask/wqflask/correlation/show_corr_results.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py index 220e5f62..f15b17e2 100644 --- a/wqflask/utility/type_checking.py +++ b/wqflask/utility/type_checking.py @@ -27,7 +27,7 @@ def get_float(vars,name,default=None): if name in vars: if is_float(vars[name]): return float(vars[name]) - return None + return default def get_int(vars,name,default=None): if name in vars: diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 1aa7945d..6e9abcd6 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -83,7 +83,7 @@ class CorrelationResults(object): assert('corr_sample_method' in start_vars) assert('corr_samples_group' in start_vars) assert('corr_dataset' in start_vars) - assert('min_expr' in start_vars) + #assert('min_expr' in start_vars) assert('corr_return_results' in start_vars) if 'loc_chr' in start_vars: assert('min_loc_mb' in start_vars) -- cgit v1.2.3 From f92100ca1eceb1a5440fc08d950a4001ed3b6b73 Mon Sep 17 00:00:00 2001 From: zsloan Date: Sun, 9 Jun 2019 11:01:53 -0500 Subject: Added fix for error when records don't have mean expression in global search --- wqflask/wqflask/gsearch.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 62398154..5910d77b 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -78,7 +78,10 @@ class GSearch(object): this_trait['location_repr'] = 'N/A' if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): this_trait['location_repr'] = 'Chr%s: %.6f' % (line[8], float(line[9])) - this_trait['mean'] = '%.3f' % line[10] + try: + this_trait['mean'] = '%.3f' % line[10] + except: + this_trait['mean'] = "N/A" this_trait['LRS_score_repr'] = "N/A" if line[11] != "" and line[11] != None: this_trait['LRS_score_repr'] = '%3.1f' % line[11] -- cgit v1.2.3 From dca78fcaa95dbbd2cb2f5e51461525b0f9f1b3e6 Mon Sep 17 00:00:00 2001 From: zsloan Date: Sun, 9 Jun 2019 13:21:22 -0500 Subject: Fixed issue that caused heatmap to not work (needed to tell it to use reaper for generating genotype object) Fixed issue that caused *all* collection page functions to not load correctly (datatables wasn't loading correctly due to a new column being added) --- wqflask/wqflask/heatmap/heatmap.py | 2 +- wqflask/wqflask/templates/collections/view.html | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 9d33961c..28c5ce12 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -120,7 +120,7 @@ class Heatmap(object): self.dataset.group.get_markers() this_trait = trait_db[0] #this_db = trait_db[1] - genotype = self.dataset.group.read_genotype_file() + genotype = self.dataset.group.read_genotype_file(use_reaper=True) samples, values, variances, sample_aliases = this_trait.export_informative() trimmed_samples = [] diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 7e1001fc..268bbe1f 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -182,6 +182,7 @@ { "type": "natural", "width": 50 }, { "type": "natural" }, { "type": "natural", "width": 120 }, + { "type": "natural", "width": 120 }, { "type": "natural" }, { "type": "natural", "width": 130 }, { "type": "natural", "width": 35 }, -- cgit v1.2.3 From a5f6f1e7a892b16922eb2467950fa5145894c759 Mon Sep 17 00:00:00 2001 From: zsloan Date: Sun, 9 Jun 2019 20:09:15 -0500 Subject: Fixed javascript error with phenotype global search --- wqflask/wqflask/templates/gsearch_pheno.html | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index 7dc22a88..7e2e6997 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -134,7 +134,11 @@ 'width': "25%", 'data': null, 'render': function(data, type, row, meta) { - return decodeURIComponent(escape(data.description)) + try { + return decodeURIComponent(escape(data.description)) + } except { + return escape(data.description) + } } }, { -- cgit v1.2.3 From 573b9e154244da07c1ac639b4158cfba74cec180 Mon Sep 17 00:00:00 2001 From: zsloan Date: Sun, 9 Jun 2019 20:17:38 -0500 Subject: Issue with encoding should be fixed for both global searches now --- wqflask/wqflask/templates/gsearch_gene.html | 6 +++++- wqflask/wqflask/templates/gsearch_pheno.html | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 4672f161..9984c0b6 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -158,7 +158,11 @@ 'type': "natural", 'data': null, 'render': function(data, type, row, meta) { - return decodeURIComponent(escape(data.description)) + try { + return decodeURIComponent(escape(data.description)) + } catch { + return escape(data.description)) + } } }, { diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index 7e2e6997..a34c2796 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -136,7 +136,7 @@ 'render': function(data, type, row, meta) { try { return decodeURIComponent(escape(data.description)) - } except { + } catch { return escape(data.description) } } -- cgit v1.2.3 From 2078f74984501419229d995cf0fa72294e45d6ea Mon Sep 17 00:00:00 2001 From: zsloan Date: Sun, 9 Jun 2019 20:41:54 -0500 Subject: Had an extra parenthesis to remove --- wqflask/wqflask/templates/gsearch_gene.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 9984c0b6..97b09929 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -161,7 +161,7 @@ try { return decodeURIComponent(escape(data.description)) } catch { - return escape(data.description)) + return escape(data.description) } } }, -- cgit v1.2.3 From 467a3141abd2ed358f80bcb420402b258d112da3 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 12 Jun 2019 20:36:58 -0500 Subject: Fixed error when zooming in on chromosome for rat mapping results --- wqflask/wqflask/marker_regression/display_mapping_results.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index b9050aea..cafbf38c 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2215,7 +2215,8 @@ class DisplayMappingResults(object): this_row = [] #container for the cells of each row selectCheck = HT.Input(type="checkbox", name="searchResult", Class="checkbox", onClick="highlight(this)").__str__() #checkbox for each row - webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__() + #ZS: May want to get this working again later + #webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__() if theGO["GeneID"] != "": geneSymbolNCBI = HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % theGO["GeneID"], theGO["GeneSymbol"], Class="normalsize", target="_blank").__str__() @@ -2256,7 +2257,7 @@ class DisplayMappingResults(object): this_row = [selectCheck.__str__(), str(gIndex+1), - webqtlSearch.__str__() + geneSymbolNCBI, + geneSymbolNCBI, theGO["TxStart"], HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)).__str__(), avgExprVal, -- cgit v1.2.3 From 0a69a6cda09b4014eaa4f0b94beb00de39c4983e Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 14 Jun 2019 13:43:10 -0500 Subject: Added some metadata to top of global search results --- wqflask/wqflask/gsearch.py | 3 +++ wqflask/wqflask/templates/gsearch_gene.html | 3 ++- wqflask/wqflask/templates/gsearch_pheno.html | 7 ++++--- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 5910d77b..8df8c9a3 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -61,6 +61,7 @@ class GSearch(object): with Bench("Running query"): logger.sql(sql) re = g.db.execute(sql).fetchall() + trait_list = [] with Bench("Creating trait objects"): for i, line in enumerate(re): @@ -100,6 +101,7 @@ class GSearch(object): trait_list.append(this_trait) + self.trait_count = len(trait_list) self.trait_list = json.dumps(trait_list) elif self.type == "phenotype": @@ -186,4 +188,5 @@ class GSearch(object): trait_list.append(this_trait) + self.trait_count = len(trait_list) self.trait_list = json.dumps(trait_list) diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 97b09929..62a2944c 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -9,7 +9,8 @@
-

You searched for {{ terms }}.

+

GN searched 754 datasets and 39765944 traits across 10 species, and found {{ trait_count }} results that match your query. + You can filter these results by adding key words in the fields below and you can also sort results on most columns.

To study a record, click on its Record ID below.
Check records below and click Add button to add to selection.

diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index a34c2796..2a0e5c0c 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -9,7 +9,8 @@
-

You searched for {{ terms }}.

+

GN searched 51 datasets and 13763 traits across 10 species, and found {{ trait_count }} results that match your query. + You can filter these results by adding key words in the fields below and you can also sort results on most columns.

To study a record, click on its ID below.
Check records below and click Add button to add to selection.

@@ -28,8 +29,8 @@
-
- +
+
-- cgit v1.2.3 From e424d8cebee099e9e5732351247c98fa9580d963 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 18 Jun 2019 10:55:27 -0500 Subject: Phenotype results with long descriptions/authors look much better now + added some links to index page --- wqflask/wqflask/templates/base.html | 2 ++ wqflask/wqflask/templates/gsearch_pheno.html | 16 +++++++++++---- wqflask/wqflask/templates/index_page_orig.html | 1 + wqflask/wqflask/templates/search_result_page.html | 24 +++++++++++++++-------- 4 files changed, 31 insertions(+), 12 deletions(-) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 2c1f67d4..21fc99d3 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -65,6 +65,8 @@
  • News
    • +
  • FAQ
    • +
  • Glossary of Term
  • References
  • Policies
  • Links
    • diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index 2a0e5c0c..fd06b771 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -135,10 +135,10 @@ 'width': "25%", 'data': null, 'render': function(data, type, row, meta) { - try { + try { return decodeURIComponent(escape(data.description)) - } catch { - return escape(data.description) + } catch { + return data.description } } }, @@ -146,7 +146,15 @@ 'title': "Authors", 'type': "natural", 'width': "25%", - 'data': "authors" + 'data': null, + 'render': function(data, type, row, meta) { + author_list = data.authors.split(",") + if (author_list.length >= 6) { + return author_list.slice(0, 6).join(",") + ", et al." + } else{ + return data.authors + } + } }, { 'title': "Year", diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 4b95e7f9..79342452 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -246,6 +246,7 @@

    GeneNetwork v1:

    • Main website at UTHSC
      • +
    • Time Machine: Full GN versions from 2009 to 2016 (mm9)
    • Website at the HZI (Germany)
    • Amazon Cloud (EC2)
      • diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index bf434452..b31d2d00 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -119,7 +119,7 @@
      -
      +

Loading...
@@ -321,21 +321,29 @@ { 'title': "Description", 'type': "natural", - 'width': "500px", + 'width': "25%", 'data': null, 'render': function(data, type, row, meta) { - try { - return decodeURIComponent(escape(data.description)) - } catch { - return escape(data.description) + try { + return decodeURIComponent(escape(data.description)) + } catch { + return data.description } } }, { 'title': "Authors", 'type': "natural", - 'width': "300px", - 'data': "authors" + 'width': "25%", + 'data': null, + 'render': function(data, type, row, meta) { + author_list = data.authors.split(",") + if (author_list.length >= 6) { + return author_list.slice(0, 6).join(",") + ", et al." + } else{ + return data.authors + } + } }, { 'title': "Year", -- cgit v1.2.3 From 21529db361812860286faf7f3fc4b08e9637b687 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 18 Jun 2019 13:17:27 -0500 Subject: Changed the text displayed on search results page Added some links to index page Removed footer from search results page --- wqflask/wqflask/templates/index_page_orig.html | 3 +- wqflask/wqflask/templates/search_result_page.html | 40 ++++++----------------- 2 files changed, 11 insertions(+), 32 deletions(-) diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 79342452..30e3f2f6 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -183,6 +183,7 @@
  • Genome browser at UTHSC
  • Galaxy at UTHSC
  • Systems Genetics @ EPFL
    • +
  • UTHSC Bayesian Network Web Server
    • @@ -247,8 +248,6 @@ diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index b31d2d00..61a533f7 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -37,15 +37,16 @@ {% elif word.key|lower == "position" %} with target genes on chromosome {% if word.search_term[0].split('chr')|length > 1 %}{{ word.search_term[0].split('chr')[1] }}{% elif word.search_term[0].split('CHR')|length > 1 %}{{ word.search_term[0].split('CHR')[1] }}{% else %}{{ word.search_term[0] }}{% endif %} between {{ word.search_term[1] }} and {{ word.search_term[2] }} Mb{% if loop.last %}.{% else %} and {% endif %} {% else %} - that match the TERM{{ word.search_term[0] }}{% if loop.last %},{% else %} and {% endif %} + {% if word.search_term[0] == "*" %} in the dataset.{% else %}{% if loop.first %}that match:
    {% endif %}"{{ word.search_term[0] }}"{% if loop.last %}{% else %} and {% endif %}{% endif %} {% endif %} {% endfor %} - and found {{ results|count }} records. +
    + {{ results|count }} records are shown below.

    -

    To study a record click on its ID below, and to view the whole description {% if dataset.type == "Publish" %}or list of authors {% endif %} hover over the table cell. Check records below and click Add button to add to selection.

    + -
    + @@ -104,21 +105,19 @@

    - - + + -
    -
    -
    + - +
    - +

    Loading...
    @@ -411,25 +410,6 @@ } } ); - if (trait_list.length > 20) { - $('#trait_table').append( - '' + - '' + - '' + - '' + - '' + - ' ' + - '' + - '' + - '' + - '' + - '' + - '' + - '' + - '' - ); - } - console.timeEnd("Creating table"); $('#redraw').click(function() { -- cgit v1.2.3 From 172bf33d20d6f42650b415571c1185af4cbd22c5 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 18 Jun 2019 15:39:36 -0500 Subject: Fixed issue with sorting involving 0's on trait page Fixed links to dataset info pages in search results and correlation results pages --- wqflask/base/data_set.py | 41 ++++++++++++++--------- wqflask/wqflask/templates/correlation_page.html | 4 +-- wqflask/wqflask/templates/search_result_page.html | 2 +- wqflask/wqflask/templates/show_trait.html | 4 +-- 4 files changed, 31 insertions(+), 20 deletions(-) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1fd1792e..4fee5c7a 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -289,7 +289,6 @@ class DatasetGroup(object): self.parlist = None self.get_f1_parent_strains() - self.accession_id = self.get_accession_id() self.mapping_id, self.mapping_names = self.get_mapping_methods() self.species = webqtlDatabaseFunction.retrieve_species(self.name) @@ -299,20 +298,6 @@ class DatasetGroup(object): self._datasets = None self.genofile = None - def get_accession_id(self): - results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where - InbredSet.Name = %s and - PublishFreeze.InbredSetId = InbredSet.Id and - InfoFiles.InfoPageName = PublishFreeze.Name and - PublishFreeze.public > 0 and - PublishFreeze.confidentiality < 1 order by - PublishFreeze.CreateTime desc""", (self.name)).fetchone() - - if results != None: - return str(results[0]) - else: - return "None" - def get_mapping_methods(self): mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0] @@ -510,6 +495,7 @@ class DataSet(object): self.check_confidentiality() self.retrieve_other_names() self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype + self.accession_id = self.get_accession_id() if get_samplelist == True: self.group.get_samplelist() self.species = species.TheSpecies(self) @@ -524,6 +510,31 @@ class DataSet(object): def riset(): Weve_Renamed_This_As_Group + def get_accession_id(self): + if self.type == "Publish": + results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where + InbredSet.Name = %s and + PublishFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = PublishFreeze.Name and + PublishFreeze.public > 0 and + PublishFreeze.confidentiality < 1 order by + PublishFreeze.CreateTime desc""", (self.group.name)).fetchone() + elif self.type == "Geno": + results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where + InbredSet.Name = %s and + GenoFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = GenoFreeze.ShortName and + GenoFreeze.public > 0 and + GenoFreeze.confidentiality < 1 order by + GenoFreeze.CreateTime desc""", (self.group.name)).fetchone() + else: + results = None + + if results != None: + return str(results[0]) + else: + return "None" + def retrieve_other_names(self): """This method fetches the the dataset names in search_result. diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 7cc998bb..32f5e774 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -12,8 +12,8 @@
    -

    Values of record {{ this_trait.name }} in the {{ dataset.fullname }} - dataset were compared to all records in the {{ target_dataset.fullname }} +

    Values of record {{ this_trait.name }} in the {{ dataset.fullname }} + dataset were compared to all records in the {{ target_dataset.fullname }} dataset. The top {{ return_number }} correlations ranked by the {{ formatted_corr_type }} are displayed. You can resort this list by clicking the headers. Select the Record ID to open the trait data and analysis page. diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 61a533f7..374347bd 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -13,7 +13,7 @@

    -

    We searched {{ dataset.fullname }} +

    We searched {{ dataset.fullname }} to find all records {% for word in search_terms %} {% if word.key|lower == "rif" %} diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 378f91b1..d5473bca 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -183,10 +183,10 @@ var x = getValue(a); var y = getValue(b); - if (x == 'x' || x == '') { + if (x == 'x' || x === '') { return 1; } - else if (y == 'x' || y == '') { + else if (y == 'x' || y === '') { return -1; } else { -- cgit v1.2.3 From 4a7c35204863066dc387637bd0f8af7d274cde55 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 24 Jun 2019 12:09:35 -0500 Subject: Got non-LOCO GEMMA mapping working with gemma-wrapper (so caching should work for that now) Fixed position digits and row highlighting on interval analyst table Updated default MAF to 0.05 Updated footer text --- wqflask/base/data_set.py | 2 +- .../marker_regression/display_mapping_results.py | 10 +-- wqflask/wqflask/marker_regression/gemma_mapping.py | 73 +++++++++++----------- wqflask/wqflask/show_trait/show_trait.py | 2 +- wqflask/wqflask/templates/base.html | 42 ++++++++----- wqflask/wqflask/templates/mapping_results.html | 8 ++- 6 files changed, 74 insertions(+), 63 deletions(-) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4fee5c7a..d766e284 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -433,7 +433,7 @@ def datasets(group_name, this_group = None): and InbredSet.Name like %s and ProbeSetFreeze.public > %s and ProbeSetFreeze.confidentiality < 1 - ORDER BY Tissue.Name) + ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC) ''' % (group_name, webqtlConfig.PUBLICTHRESH, group_name, webqtlConfig.PUBLICTHRESH, "'" + group_name + "'", webqtlConfig.PUBLICTHRESH)) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index cafbf38c..41cdf819 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2127,7 +2127,7 @@ class DisplayMappingResults(object): tableIterationsCnt = tableIterationsCnt + 1 this_row = [] #container for the cells of each row - selectCheck = HT.Input(type="checkbox", name="searchResult", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") #checkbox for each row + selectCheck = HT.Input(type="checkbox", name="selectCheck", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") #checkbox for each row geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0 tenPercentLength = geneLength*0.0001 @@ -2213,7 +2213,7 @@ class DisplayMappingResults(object): elif self.dataset.group.species == 'rat': for gIndex, theGO in enumerate(geneCol): this_row = [] #container for the cells of each row - selectCheck = HT.Input(type="checkbox", name="searchResult", Class="checkbox", onClick="highlight(this)").__str__() #checkbox for each row + selectCheck = HT.Input(type="checkbox", name="selectCheck", Class="checkbox trait_checkbox").__str__() #checkbox for each row #ZS: May want to get this working again later #webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__() @@ -2240,14 +2240,14 @@ class DisplayMappingResults(object): #Mouse Gene if theGO['mouseGene']: mouseChr = theGO['mouseGene']["Chromosome"] - mouseTxStart = theGO['mouseGene']["TxStart"] + mouseTxStart = "%0.6f" % theGO['mouseGene']["TxStart"] else: mouseChr = mouseTxStart = "" #the chromosomes for human 1 are 1qXX.XX if theGO['humanGene']: humanChr = theGO['humanGene']["Chromosome"] - humanTxStart = theGO['humanGene']["TxStart"] + humanTxStart = "%0.6f" % theGO['humanGene']["TxStart"] else: humanChr = humanTxStart = "" @@ -2258,7 +2258,7 @@ class DisplayMappingResults(object): this_row = [selectCheck.__str__(), str(gIndex+1), geneSymbolNCBI, - theGO["TxStart"], + "%0.6f" % theGO["TxStart"], HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)).__str__(), avgExprVal, mouseChr, diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 0f37e711..4e3c203d 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -73,50 +73,51 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf gwa_output_filename) else: - generate_k_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk -outdir %s/gn2/ -o %s' % (flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - trait_filename, - flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - k_output_filename) - #generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), - # genofile_name, - # flat_files('genotype/bimbam'), - # trait_filename, - # flat_files('genotype/bimbam'), - # genofile_name, - # TEMPDIR, - # k_output_filename) + # generate_k_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk -outdir %s/gn2/ -o %s' % (flat_files('genotype/bimbam'), + # genofile_name, + # TEMPDIR, + # trait_filename, + # flat_files('genotype/bimbam'), + # genofile_name, + # TEMPDIR, + # k_output_filename) + generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + trait_filename, + flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + k_output_filename) logger.debug("k_command:" + generate_k_command) os.system(generate_k_command) - gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -k %s/gn2/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - trait_filename, - flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - k_output_filename, - maf) + # gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -k %s/gn2/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'), + # genofile_name, + # TEMPDIR, + # trait_filename, + # flat_files('genotype/bimbam'), + # genofile_name, + # TEMPDIR, + # k_output_filename, + # maf) - #gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (flat_files('genotype/bimbam'), - # genofile_name, - # flat_files('genotype/bimbam'), - # genofile_name) + gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + trait_filename) if covariates != "": - gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'), - this_dataset.group.name, - webqtlConfig.GENERATED_IMAGE_DIR, - genofile_name) - else: - gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR, - genofile_name) + gemma_command += ' -c %s/%s_covariates.txt' % (flat_files('mapping'), this_dataset.group.name) + # gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'), + # this_dataset.group.name, + # webqtlConfig.GENERATED_IMAGE_DIR, + # genofile_name) + # else: + # gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR, + # genofile_name) logger.debug("gemma_command:" + gemma_command) diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index e10b31c0..5178ece8 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -168,7 +168,7 @@ class ShowTrait(object): hddn['control_marker'] = self.nearest_marker #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2 hddn['do_control'] = False - hddn['maf'] = 0.01 + hddn['maf'] = 0.05 hddn['compare_traits'] = [] hddn['export_data'] = "" hddn['export_format'] = "excel" diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 21fc99d3..3fd9faf5 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -127,27 +127,35 @@ JOSS


    -

    GeneNetwork is supported by:

    -
      -
    • - +

      GeneNetwork support from:

      +
        +
      • + The UT Center for Integrative and Translational Genomics - +
        • -
      • NIAAA - Integrative Neuroscience Initiative on Alcoholism - (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425) +
      • + NIGMS + Systems Genetics and Precision Medicine Project (R01 GM123489, 2017-2021)
        • -
      • - NIDA, NIMH - , and - NIAAA (P20-DA 21131) +
      • + NIDA + NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
        • -
      • NCI MMHCC (U01CA105417) and - NCRR - BIRN - (U24 RR021760) +
      • + NIA + Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018) +
        • +
      • + NIAAA + Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017) +
        • +
      • + NIDA, NIMH, and NIAAA + (P20-DA 21131, 2001-2012) +
        • +
      • + NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)
      diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index ba4d4d7c..00a7b811 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -262,7 +262,7 @@

      Interval Analyst

      -
    IndexRecordSymbolDescriptionLocationMeanMax LRS ?Max LRS LocationAdditive Effect ?
    +
    {% for header in gene_table_header %} @@ -322,6 +322,7 @@ - - + + + + {% endblock %} diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 251a816f..286f6c1f 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -17,7 +17,7 @@ --> -
    +
    {{ flash_me() }} diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 00a7b811..be285d15 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -9,7 +9,7 @@ {% endblock %} {% from "base_macro.html" import header %} {% block content %} -
    +
    diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index b1442b7f..f5978196 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -8,7 +8,7 @@ {% endblock %} {% block content %} -
    +
    diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index ea7c5123..19b0e0f5 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -39,7 +39,7 @@ -
    +
    -- cgit v1.2.3 From 823169d970d8b64e955f7316e6df87c5204b4864 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 1 Aug 2019 12:08:33 -0500 Subject: Made some more aesthetic changes to various pages and charts/figures Added some information to the mapping loading page --- wqflask/base/trait.py | 17 +++-- wqflask/wqflask/show_trait/show_trait.py | 83 ++++++++++++---------- .../new/javascript/plotly_probability_plot.js | 19 ++--- .../wqflask/static/new/javascript/show_trait.js | 73 +++++++++++-------- .../new/javascript/show_trait_mapping_tools.js | 2 +- wqflask/wqflask/templates/base.html | 2 +- wqflask/wqflask/templates/correlation_matrix.html | 2 +- wqflask/wqflask/templates/index_page_orig.html | 8 +-- wqflask/wqflask/templates/loading.html | 20 +++++- .../wqflask/templates/new_security/login_user.html | 83 ++++++++++------------ wqflask/wqflask/templates/search_result_page.html | 11 +-- wqflask/wqflask/views.py | 10 +++ 12 files changed, 194 insertions(+), 136 deletions(-) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 0527449b..39dd075e 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -3,6 +3,7 @@ from __future__ import absolute_import, division, print_function import string import resource import codecs +import requests import redis Redis = redis.StrictRedis() @@ -120,11 +121,17 @@ class GeneralTrait(object): @property def alias_fmt(self): '''Return a text formatted alias''' - if self.alias: - alias = string.replace(self.alias, ";", " ") - alias = string.join(string.split(alias), ", ") - else: - alias = 'Not available' + + alias = 'Not available' + if self.symbol: + response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol) + alias_list = json.loads(response.content) + alias = "; ".join(alias_list) + + if alias == 'Not available': + if self.alias: + alias = string.replace(self.alias, ";", " ") + alias = string.join(string.split(alias), ", ") return alias diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 1dd80962..f1f5840f 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -142,40 +142,6 @@ class ShowTrait(object): self.qnorm_vals = quantile_normalize_vals(self.sample_groups) self.z_scores = get_z_scores(self.sample_groups) - # Todo: Add back in the ones we actually need from below, as we discover we need them - hddn = OrderedDict() - - if self.dataset.group.allsamples: - hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ') - - hddn['trait_id'] = self.trait_id - hddn['dataset'] = self.dataset.name - hddn['temp_trait'] = False - if self.temp_trait: - hddn['temp_trait'] = True - hddn['group'] = self.temp_group - hddn['species'] = self.temp_species - hddn['use_outliers'] = False - hddn['method'] = "gemma" - hddn['selected_chr'] = -1 - hddn['mapping_display_all'] = True - hddn['suggestive'] = 0 - hddn['num_perm'] = 0 - hddn['manhattan_plot'] = "" - hddn['control_marker'] = "" - if not self.temp_trait: - if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish": - hddn['control_marker'] = self.nearest_marker - #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2 - hddn['do_control'] = False - hddn['maf'] = 0.05 - hddn['compare_traits'] = [] - hddn['export_data'] = "" - hddn['export_format'] = "excel" - - # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self - self.hddn = hddn - self.temp_uuid = uuid.uuid4() self.sample_group_types = OrderedDict() @@ -216,18 +182,61 @@ class ShowTrait(object): sample_column_width = max_samplename_width * 8 - if self.num_values >= 500: + if self.num_values >= 5000: self.maf = 0.01 else: self.maf = 0.05 trait_symbol = None + short_description = None if not self.temp_trait: if self.this_trait.symbol: trait_symbol = self.this_trait.symbol + short_description = trait_symbol + + elif self.this_trait.post_publication_abbreviation: + short_description = self.this_trait.post_publication_abbreviation + + elif self.this_trait.pre_publication_abbreviation: + short_description = self.this_trait.pre_publication_abbreviation + + # Todo: Add back in the ones we actually need from below, as we discover we need them + hddn = OrderedDict() + + if self.dataset.group.allsamples: + hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ') + hddn['primary_samples'] = string.join(self.primary_sample_names, ',') + hddn['trait_id'] = self.trait_id + hddn['dataset'] = self.dataset.name + hddn['temp_trait'] = False + if self.temp_trait: + hddn['temp_trait'] = True + hddn['group'] = self.temp_group + hddn['species'] = self.temp_species + hddn['use_outliers'] = False + hddn['method'] = "gemma" + hddn['selected_chr'] = -1 + hddn['mapping_display_all'] = True + hddn['suggestive'] = 0 + hddn['num_perm'] = 0 + hddn['manhattan_plot'] = "" + hddn['control_marker'] = "" + if not self.temp_trait: + if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish": + hddn['control_marker'] = self.nearest_marker + #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2 + hddn['do_control'] = False + hddn['maf'] = 0.05 + hddn['compare_traits'] = [] + hddn['export_data'] = "" + hddn['export_format'] = "excel" + + # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self + self.hddn = hddn js_data = dict(trait_id = self.trait_id, trait_symbol = trait_symbol, + short_description = short_description, unit_type = trait_units, dataset_type = self.dataset.type, data_scale = self.dataset.data_scale, @@ -396,6 +405,8 @@ class ShowTrait(object): sample_group_type='primary', header="%s Only" % (self.dataset.group.name)) self.sample_groups = (primary_samples,) + + self.primary_sample_names = primary_sample_names self.dataset.group.allsamples = all_samples_ordered def quantile_normalize_vals(sample_groups): @@ -493,7 +504,7 @@ def get_genofiles(this_dataset): return jsondata['genofile'] def get_table_widths(sample_groups, has_num_cases=False): - stats_table_width = 200 + stats_table_width = 250 if len(sample_groups) > 1: stats_table_width = 450 diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js index a9c5676c..cc4195e4 100644 --- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js +++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js @@ -171,22 +171,23 @@ } var layout = { - title: js_data.trait_id, + title: "Trait " + js_data.trait_id + ": " + js_data.short_description + "", margin: { - l: 65, + l: 100, r: 30, t: 80, - b: 80 + b: 60 }, xaxis: { - title: "Normal Theoretical Quantiles", + title: "Normal Theoretical Quantiles", range: [first_x, last_x], zeroline: false, visible: true, linecolor: 'black', linewidth: 1, titlefont: { - size: 16 + family: "arial", + size: 20 }, ticklen: 4, tickfont: { @@ -194,19 +195,21 @@ } }, yaxis: { - title: "Data Quantiles", + title: "Data Quantiles", zeroline: false, visible: true, linecolor: 'black', linewidth: 1, titlefont: { - size: 16 + family: "arial", + size: 20 }, ticklen: 4, tickfont: { size: 16 }, - tickformat: tick_digits + tickformat: tick_digits, + automargin: true }, hovermode: "closest" } diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 8366ec0a..48b6da5e 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -30,11 +30,11 @@ Stat_Table_Rows = [ }, { vn: "min", pretty: "Minimum", - digits: 2 + digits: 3 }, { vn: "max", pretty: "Maximum", - digits: 2 + digits: 3 } ] @@ -67,7 +67,7 @@ Stat_Table_Rows.push( digits: 3 }, { vn: "interquartile", - pretty: "Interquartile Range", + pretty: "Interquartile Range", url: "http://www.genenetwork.org/glossary.html#Interquartile", digits: 3 }, { @@ -334,9 +334,9 @@ update_prob_plot = function() { make_table = function() { var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1; if (js_data.trait_symbol != null) { - header = "
    "; + header = ""; } else { - header = ""; + header = ""; } _ref = js_data.sample_group_types; for (key in _ref) { @@ -990,12 +990,13 @@ var hist_trace = { root.histogram_data = [hist_trace]; root.histogram_layout = { bargap: 0.05, - title: js_data.trait_id, + title: "Trait " + js_data.trait_id + ": " + js_data.short_description + "", xaxis: { autorange: true, - title: "Value", + title: "Value", titlefont: { - size: 16 + family: "arial", + size: 20 }, ticklen: 4, tickfont: { @@ -1004,23 +1005,25 @@ root.histogram_layout = { }, yaxis: { autorange: true, - title: "Count", + title: "Count", titlefont: { - size: 16 + family: "arial", + size: 20 }, showline: true, ticklen: 4, tickfont: { size: 16 - } + }, + automargin: true }, width: 500, height: 600, margin: { - l: 50, + l: 70, r: 30, t: 100, - b: 60 + b: 50 } }; @@ -1036,25 +1039,34 @@ $('.histogram_samples_group').change(function() { }); root.box_layout = { - title: js_data.trait_id, xaxis: { showline: true, + titlefont: { + family: "arial", + size: 20 + }, tickfont: { size: 16 }, }, yaxis: { - title: js_data.unit_type, + title: "" + js_data.unit_type +"", autorange: true, showline: true, + titlefont: { + family: "arial", + size: 20 + }, ticklen: 4, tickfont: { size: 16 }, - tickformat: tick_digits + tickformat: tick_digits, + zeroline: false, + automargin: true }, margin: { - l: 50, + l: 90, r: 30, t: 30, b: 80 @@ -1122,7 +1134,7 @@ if (full_sample_lists.length > 1) { { type: 'box', y: get_sample_vals(full_sample_lists[0]), - name: sample_group_list[0], + name: "Trait " + js_data.trait_id + "", boxpoints: 'Outliers', jitter: 0.5, whiskerwidth: 0.2, @@ -1150,28 +1162,36 @@ $('.box_plot_tab').click(function() { // Violin Plot root.violin_layout = { - title: js_data.trait_id, xaxis: { showline: true, + titlefont: { + family: "arial", + size: 20 + }, tickfont: { size: 16 } }, yaxis: { - title: js_data.unit_type, + title: ""+js_data.unit_type+"", autorange: true, showline: true, + titlefont: { + family: "arial", + size: 20 + }, ticklen: 4, tickfont: { size: 16 }, tickformat: tick_digits, - zeroline: false + zeroline: false, + automargin: true }, margin: { - l: 50, + l: 90, r: 30, - t: 80, + t: 30, b: 80 } }; @@ -1239,14 +1259,11 @@ if (full_sample_lists.length > 1) { box: { visible: true }, - line: { - color: 'green', - }, meanline: { visible: true }, - name: sample_group_list[0], - x0: sample_group_list[0] + name: "Trait " + js_data.trait_id + "", + x0: "Trait " + js_data.trait_id + "" } ] } diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index 8001dfc9..8db9522c 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -156,7 +156,7 @@ 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', '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'] + 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples'] $("#rqtl_geno_compute").on("click", (function(_this) { return function() { diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 80bbd7f5..2366bdec 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -94,7 +94,7 @@
    - diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 7e67ece2..34a15c6a 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -10,7 +10,7 @@

    Correlation Matrix

    -
    Lower left cells list Pearson product-moment correlations; upper right cells list Spearman rank order correlations. Each cell also contains the n of cases. Values ranging from 0.4 to 1.0 range from dark blue to white, while values ranging from -0.4 to -1.0 range from orange to white. Select any cell to generate a scatter plot. Select trait labels for more information.
    +
    Lower left cells list Pearson product-moment correlations; upper right cells list Spearman rank order correlations. Each cell also contains the n of cases. Values ranging from 0.4 to 1.0 range from orange to white, while values ranging from -0.4 to -1.0 range from dark blue to white. Select any cell to generate a scatter plot. Select trait labels for more information.
    {% if lowest_overlap < 8 %}
    Caution: This matrix of correlations contains some cells with small sample sizes of fewer than 8.
    diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 286f6c1f..ed91a886 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -28,7 +28,7 @@

    Select and search

    - +
    @@ -199,9 +199,9 @@

    Github

    @@ -241,7 +241,7 @@

    GeneNetwork v2:

    GeneNetwork v1:

      diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 25560249..3eb061e5 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -7,10 +7,24 @@
      -
      +
      + {% if start_vars.tool_used == "Mapping" %} +

      Computing the Map

      +
      + n = {{ start_vars.num_vals }} +
      + Method = {{ start_vars.method }} +
      + {% if start_vars.transform != "" %} + transform = {{ start_vars.transform }} +
      + {% endif %} + MAF = {{ start_vars.maf }} + {% else %}

      Loading {{ start_vars.tool_used }} Results...

      + {% endif %}
      -
      +
      @@ -22,5 +36,5 @@ \ No newline at end of file diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html index 27b20ebf..c9aaf028 100644 --- a/wqflask/wqflask/templates/new_security/login_user.html +++ b/wqflask/wqflask/templates/new_security/login_user.html @@ -2,53 +2,11 @@ {% block title %}Register{% endblock %} {% block content %} -
      +
      {{ flash_me() }} -
      -

          Login

      -
      - - -
      - -

      Don't have an account?

      - - {% if es_server: %} - Create a new account - {% else: %} -
      -

      You cannot create an account at this moment.
      - Please try again later.

      -
      - {% endif %} - -
      -

      Login with external services

      - - {% if external_login: %} -
      - {% if external_login["github"]: %} - Login with Github - {% else %} -

      Github login is not available right now

      - {% endif %} - - {% if external_login["orcid"]: %} - Login with ORCID - {% else %} -

      ORCID login is not available right now

      - {% endif %} -
      - {% else: %} -
      -

      Sorry, you cannot login with Github or ORCID at this time.

      -
      - {% endif %} -
      - -

      Already have an account? Sign in here.

      +

      Already have an account? Sign in here.

      {% if es_server: %} @@ -69,7 +27,6 @@
      -
      @@ -87,6 +44,42 @@
    +
    + +

    Don't have an account?

    + + {% if es_server: %} + Create a new account + {% else: %} +
    +

    You cannot create an account at this moment.
    + Please try again later.

    +
    + {% endif %} + +
    +

    Login with external services

    + + {% if external_login: %} +
    + {% if external_login["github"]: %} + Login with Github + {% else %} +

    Github login is not available right now

    + {% endif %} + + {% if external_login["orcid"]: %} + Login with ORCID + {% else %} +

    ORCID login is not available right now

    + {% endif %} +
    + {% else: %} +
    +

    Sorry, you cannot login with Github or ORCID at this time.

    +
    + {% endif %} + {% else: %}
    diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index f5978196..2dded69f 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -13,7 +13,7 @@
    -

    We searched {{ dataset.fullname }} +

    Search Results: We searched {{ dataset.fullname }} to find all records {% for word in search_terms %} {% if word.key|lower == "rif" %} @@ -249,6 +249,7 @@ 'columns': [ { 'data': null, + 'width': "30px", 'orderDataType': "dom-checkbox", 'orderSequence': [ "desc", "asc"], 'render': function(data, type, row, meta) { @@ -258,12 +259,14 @@ { 'title': "Index", 'type': "natural", + 'width': "30px", 'data': "index" }, { 'title': "Record", 'type': "natural", 'data': null, + 'width': "60px", 'orderDataType': "dom-inner-text", 'render': function(data, type, row, meta) { return '' + data.name + '' @@ -277,7 +280,6 @@ { 'title': "Description", 'type': "natural", - 'width': "300px", 'data': null, 'render': function(data, type, row, meta) { try { @@ -290,12 +292,13 @@ { 'title': "Location", 'type': "natural", - 'width': "140px", + 'width': "120px", 'data': "location" }, { 'title': "Mean", 'type': "natural", + 'width': "40px", 'data': "mean", 'orderSequence': [ "desc", "asc"] }, @@ -308,7 +311,7 @@ { 'title': "Max LRS Location", 'type': "natural", - 'width': "140px", + 'width': "120px", 'data': "lrs_location" }, { diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index fe858d52..7b585b03 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -560,6 +560,7 @@ def loading_page(): logger.info(request.url) initial_start_vars = request.form start_vars_container = {} + num_vals = 0 #ZS: So it can be displayed on loading page if 'wanted_inputs' in initial_start_vars: wanted = initial_start_vars['wanted_inputs'].split(",") start_vars = {} @@ -567,6 +568,15 @@ def loading_page(): if key in wanted or key.startswith(('value:')): start_vars[key] = value + if 'primary_samples' in start_vars: + samples = start_vars['primary_samples'].split(",") + for sample in samples: + value = start_vars.get('value:' + sample) + if value != "x": + num_vals += 1 + + start_vars['num_vals'] = num_vals + start_vars_container['start_vars'] = start_vars else: start_vars_container['start_vars'] = initial_start_vars -- cgit v1.2.3 From d49507350119c79c1ffb09b054d08b7545703a18 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 1 Aug 2019 15:04:06 -0500 Subject: Replaced loading bar with a gif that should work in Safari --- wqflask/wqflask/templates/loading.html | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 3eb061e5..4c30664b 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -6,8 +6,8 @@ {% endfor %}

    -
    -
    +
    +
    {% if start_vars.tool_used == "Mapping" %}

    Computing the Map


    @@ -23,10 +23,17 @@ {% else %}

    Loading {{ start_vars.tool_used }} Results...

    {% endif %} +

    +
    + +
    -- cgit v1.2.3 From eb2fb5c936ff8e2351ef3c1f9cf4968790528bdb Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 1 Aug 2019 15:16:39 -0500 Subject: Added wikidata aliases Fixed year to not be a hyperlink when no pubmed id Fixed first column width so it doesn't go onto two lines for trait details --- wqflask/base/trait.py | 16 +++++++++++----- wqflask/wqflask/templates/show_trait_details.html | 12 +++++++++--- 2 files changed, 20 insertions(+), 8 deletions(-) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 39dd075e..a0679041 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -122,17 +122,23 @@ class GeneralTrait(object): def alias_fmt(self): '''Return a text formatted alias''' + alias = 'Not available' + if self.alias: + alias = string.replace(self.alias, ";", " ") + alias = string.join(string.split(alias), ", ") + + return alias + + @property + def wikidata_alias_fmt(self): + '''Return a text formatted alias''' + alias = 'Not available' if self.symbol: response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol) alias_list = json.loads(response.content) alias = "; ".join(alias_list) - if alias == 'Not available': - if self.alias: - alias = string.replace(self.alias, ";", " ") - alias = string.join(string.split(alias), ", ") - return alias diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index e6c68591..7714a1ab 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -1,6 +1,6 @@
    Trait: " + js_data.trait_id + " - " + js_data.trait_symbol + "
    Statistic
    Trait " + js_data.trait_id + " - " + js_data.trait_symbol + "
    Statistic
    Trait: " + js_data.trait_id + "
    Statistic
    Trait " + js_data.trait_id + "
    Statistic
    - + {% if this_trait.dataset.type == 'Publish' %} @@ -18,7 +18,7 @@ - + {% else %} @@ -35,8 +35,14 @@ {% endif %} - + + {% if this_trait.alias_fmt != "Not Available" %} + + + + + {% endif %} {% endif %} {% if this_trait.dataset.type != 'Publish' %} -- cgit v1.2.3 From 1fd5271ebd12cff537e8ce68d9f8d706e531eb51 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 1 Aug 2019 17:13:07 -0500 Subject: Updated aliases to get all species aliases and remove duplicates --- wqflask/base/trait.py | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index a0679041..58169b5c 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -135,9 +135,20 @@ class GeneralTrait(object): alias = 'Not available' if self.symbol: - response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol) - alias_list = json.loads(response.content) - alias = "; ".join(alias_list) + human_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.upper()) + mouse_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.capitalize()) + other_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.lower()) + alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content) + + filtered_aliases = [] + seen = set() + for item in alias_list: + if item in seen: + continue + else: + filtered_aliases.append(item) + seen.add(item) + alias = "; ".join(filtered_aliases) return alias -- cgit v1.2.3 From 3b626057ffebddf2829fbddb50445cf4934b0580 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 2 Aug 2019 10:47:18 -0500 Subject: Added the gif for the loading screen --- wqflask/wqflask/static/gif/89.gif | Bin 0 -> 27183 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 wqflask/wqflask/static/gif/89.gif diff --git a/wqflask/wqflask/static/gif/89.gif b/wqflask/wqflask/static/gif/89.gif new file mode 100644 index 00000000..e9b3279d Binary files /dev/null and b/wqflask/wqflask/static/gif/89.gif differ -- cgit v1.2.3 From 8f9dcc4b53e4149d5ac7c698bb0b3bb88e36cf64 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 2 Aug 2019 10:50:05 -0500 Subject: Fixed issue where resizing correlation page could make buttons get pushed down --- wqflask/wqflask/templates/correlation_page.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 32f5e774..fea60dfa 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -4,7 +4,7 @@ {% endblock %} {% block content %} -
    +

    Correlation Table

    Trait: {{ this_trait.name }} -- cgit v1.2.3 From 5a886b90383f19c646cb5da8b2b9b0fdd0d9713e Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 2 Aug 2019 11:02:53 -0500 Subject: Fixed issue where zooming into chromosomes or range didn't work with reaper --- wqflask/wqflask/templates/mapping_results.html | 3 +++ 1 file changed, 3 insertions(+) diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index be285d15..98931166 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -20,6 +20,9 @@ {% if gwa_filename is defined %} {% endif %} + {% if reaper_version is defined %} + + {% endif %} -- cgit v1.2.3 From bb46f3adb391cbeb4b530869b3a900d2d6004d5b Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 2 Aug 2019 12:24:20 -0500 Subject: Fixed issue that caused heatmap to not work --- wqflask/wqflask/heatmap/heatmap.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 28c5ce12..37454dfb 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -127,7 +127,7 @@ class Heatmap(object): trimmed_values = [] for i in range(0, len(samples)): if samples[i] in self.dataset.group.samplelist: - trimmed_samples.append(samples[i]) + trimmed_samples.append(str(samples[i])) trimmed_values.append(values[i]) reaper_results = genotype.regression(strains = trimmed_samples, -- cgit v1.2.3 From 256f6cffe7e88e6414914188df5c34899999a151 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 2 Aug 2019 13:22:42 -0500 Subject: Updated phenogen link in mapping results --- wqflask/wqflask/marker_regression/display_mapping_results.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 6498f039..ddf6dd50 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -1417,9 +1417,9 @@ class DisplayMappingResults(object): if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - PHENOGEN_HREF = "https://phenogen.ucdenver.edu/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) + PHENOGEN_HREF = "https://phenogen.org/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) else: - PHENOGEN_HREF = "https://phenogen.ucdenver.edu/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) + PHENOGEN_HREF = "https://phenogen.org/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen" gifmap.areas.append(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE)) canvas.drawRect(xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_PHENOGEN_REGION_COLOR, fillColor=self.CLICKABLE_PHENOGEN_REGION_COLOR) -- cgit v1.2.3 From 52bf76b7238a4b3395e667c0dc8bff5cc409cc58 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 7 Aug 2019 11:49:20 -0500 Subject: Changed rn3 to rn6 for a couple external links on the trait page Made some text bold on trait page details --- .../marker_regression/display_mapping_results.py | 6 +- .../wqflask/marker_regression/qtlreaper_mapping.py | 3 +- wqflask/wqflask/marker_regression/run_mapping.py | 87 ++++++++++++---------- wqflask/wqflask/search_results.py | 79 ++++++++++++++------ wqflask/wqflask/show_trait/show_trait.py | 4 +- .../wqflask/static/new/javascript/show_trait.js | 3 +- wqflask/wqflask/templates/mapping_results.html | 56 ++++++++------ wqflask/wqflask/templates/search_result_page.html | 7 ++ wqflask/wqflask/templates/show_trait_details.html | 24 +++--- wqflask/wqflask/views.py | 18 ++++- 10 files changed, 181 insertions(+), 106 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index ddf6dd50..ea1ca5ed 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -146,7 +146,7 @@ class DisplayMappingResults(object): self.dataset = start_vars['dataset'] self.this_trait = start_vars['this_trait'] - self.n_samples = len(start_vars['vals']) + self.n_samples = start_vars['num_vals'] self.species = start_vars['species'] self.genofile_string = "" if 'genofile_string' in start_vars: @@ -168,8 +168,8 @@ class DisplayMappingResults(object): self.mapmodel_rqtl_geno = start_vars['model'] self.pair_scan = start_vars['pair_scan'] - if self.mapping_method != "gemma" and self.mapping_method != "plink": - self.js_data = start_vars['js_data'] + #if self.mapping_method != "gemma" and self.mapping_method != "plink": + self.js_data = start_vars['js_data'] self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table if self.dataset.group.species == "rat": diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index b74a1c4d..809d0ce4 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -95,7 +95,8 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): marker['chr'] = line.split("\t")[2] marker['cM'] = float(line.split("\t")[3]) marker['Mb'] = float(line.split("\t")[4]) - marker['p_value'] = float(line.split("\t")[7]) + if float(line.split("\t")[7]) != 1: + marker['p_value'] = float(line.split("\t")[7]) marker['lrs_value'] = float(line.split("\t")[5]) marker['lod_score'] = marker['lrs_value'] / 4.61 marker['additive'] = float(line.split("\t")[6]) diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 676df391..7f6bb0a5 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -85,6 +85,8 @@ class RunMapping(object): self.samples.append(sample) self.vals.append(value) + self.num_vals = start_vars['num_vals'] + #ZS: Check if genotypes exist in the DB in order to create links for markers if "geno_db_exists" in start_vars: self.geno_db_exists = start_vars['geno_db_exists'] @@ -311,14 +313,32 @@ class RunMapping(object): else: self.qtl_results = [] + self.qtl_results_for_browser = [] highest_chr = 1 #This is needed in order to convert the highest chr to X/Y for marker in results: + browser_marker = dict( + chr = str(marker['chr']), + rs = marker['name'], + ps = marker['Mb']*1000000 + ) + if 'p_value' in marker: + browser_marker['p_wald'] = marker['p_value'] + else: + if 'lrs_value' in marker and marker['lrs_value'] > 0: + browser_marker['p_wald'] = -math.log10(marker['lrs_value']/4.16) + elif 'lod_score' in marker and marker['lod_score'] > 0: + browser_marker['p_wald'] = -math.log10(marker['lod_score']) + else: + browser_marker['p_wald'] = 0 + self.qtl_results_for_browser.append(browser_marker) if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y": if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y": highest_chr = marker['chr'] if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): self.qtl_results.append(marker) + browser_files = write_input_for_browser(self.dataset, self.qtl_results_for_browser) + with Bench("Exporting Results"): export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type) @@ -330,50 +350,23 @@ class RunMapping(object): self.trimmed_markers = trim_markers_for_table(results) if self.mapping_method != "gemma": - self.json_data['chr'] = [] - self.json_data['pos'] = [] - self.json_data['lod.hk'] = [] - self.json_data['markernames'] = [] - - self.json_data['suggestive'] = self.suggestive - self.json_data['significant'] = self.significant - - #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary - for index, qtl in enumerate(self.qtl_results): - #if index<40: - # logger.debug("lod score is:", qtl['lod_score']) - if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y": - #logger.debug("changing to X") - self.json_data['chr'].append("X") - else: - self.json_data['chr'].append(str(qtl['chr'])) - self.json_data['pos'].append(qtl['Mb']) - if 'lrs_value' in qtl.keys(): - self.json_data['lod.hk'].append(str(qtl['lrs_value'])) - else: - self.json_data['lod.hk'].append(str(qtl['lod_score'])) - self.json_data['markernames'].append(qtl['name']) - - #Get chromosome lengths for drawing the interval map plot - chromosome_mb_lengths = {} - self.json_data['chrnames'] = [] - for key in self.species.chromosomes.chromosomes.keys(): - self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) - chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length - self.js_data = dict( - result_score_type = self.score_type, - json_data = self.json_data, - this_trait = self.this_trait.name, - data_set = self.dataset.name, - maf = self.maf, - manhattan_plot = self.manhattan_plot, - mapping_scale = self.mapping_scale, - chromosomes = chromosome_mb_lengths, - qtl_results = self.qtl_results, + #result_score_type = self.score_type, + #this_trait = self.this_trait.name, + #data_set = self.dataset.name, + #maf = self.maf, + #manhattan_plot = self.manhattan_plot, + #mapping_scale = self.mapping_scale, + #chromosomes = chromosome_mb_lengths, + #qtl_results = self.qtl_results, num_perm = self.num_perm, perm_results = self.perm_output, + browser_files = browser_files ) + else: + self.js_data = dict( + browser_files = browser_files + ) def run_rqtl_plink(self): # os.chdir("") never do this inside a webserver!! @@ -497,3 +490,17 @@ def trim_markers_for_table(markers): return trimmed_sorted_markers else: return sorted_markers + +def write_input_for_browser(this_dataset, markers): + file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + gwas_filename = file_base + "_GWAS" + annot_filename = file_base + "_ANNOT" + gwas_path = "{}/gn2/".format(TEMPDIR) + gwas_filename + annot_path = "{}/gn2/".format(TEMPDIR) + annot_filename + + with open(gwas_path + ".json", "w") as gwas_file, open(annot_path + ".json", "w") as annot_file: + gwas_file.write(json.dumps(markers)) + annot_file.write(json.dumps([])) + + return [gwas_filename, annot_filename] + #return [gwas_filename, annot_filename] \ No newline at end of file diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 444e1f40..e74fef80 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -25,7 +25,7 @@ from db import webqtlDatabaseFunction from wqflask import user_manager -from flask import render_template +from flask import render_template, Flask, g from utility import formatting from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string @@ -47,6 +47,7 @@ views.py). ########################################### self.uc_id = uuid.uuid4() + self.go_term = None logger.debug("uc_id:", self.uc_id) # contains a unique id logger.debug("kw is:", kw) # dict containing search terms @@ -157,25 +158,31 @@ views.py). combined_where_clause = "" previous_from_clauses = [] #The same table can't be referenced twice in the from clause for i, a_search in enumerate(self.search_terms): - the_search = self.get_search_ob(a_search) - if the_search != None: - get_from_clause = getattr(the_search, "get_from_clause", None) - if callable(get_from_clause): - from_clause = the_search.get_from_clause() - if from_clause in previous_from_clauses: - pass - else: - previous_from_clauses.append(from_clause) - combined_from_clause += from_clause - where_clause = the_search.get_where_clause() - combined_where_clause += "(" + where_clause + ")" - if (i+1) < len(self.search_terms): - if self.and_or == "and": - combined_where_clause += "AND" - else: - combined_where_clause += "OR" + if a_search['key'] == "GO": + self.go_term = a_search['search_term'][0] + gene_list = get_GO_symbols(a_search) + self.search_terms += gene_list + continue else: - self.search_term_exists = False + the_search = self.get_search_ob(a_search) + if the_search != None: + get_from_clause = getattr(the_search, "get_from_clause", None) + if callable(get_from_clause): + from_clause = the_search.get_from_clause() + if from_clause in previous_from_clauses: + pass + else: + previous_from_clauses.append(from_clause) + combined_from_clause += from_clause + where_clause = the_search.get_where_clause() + combined_where_clause += "(" + where_clause + ")" + if (i+1) < len(self.search_terms): + if self.and_or == "and": + combined_where_clause += "AND" + else: + combined_where_clause += "OR" + else: + self.search_term_exists = False if self.search_term_exists: combined_where_clause = "(" + combined_where_clause + ")" final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause) @@ -186,11 +193,19 @@ views.py). self.search_term_exists = False else: for a_search in self.search_terms: - the_search = self.get_search_ob(a_search) - if the_search != None: - self.results.extend(the_search.run()) + logger.debug("TERMS:", self.search_terms) + if a_search['key'] == "GO": + self.go_term = a_search['search_term'][0] + gene_list = get_GO_symbols(a_search) + self.search_terms += gene_list + self.search_terms.pop(0) + continue else: - self.search_term_exists = False + the_search = self.get_search_ob(a_search) + if the_search != None: + self.results.extend(the_search.run()) + else: + self.search_term_exists = False if self.search_term_exists: if the_search != None: @@ -218,9 +233,27 @@ views.py). else: return None +def get_GO_symbols(a_search): + query = """SELECT genes + FROM GORef + WHERE goterm='{0}:{1}'""".format(a_search['key'], a_search['search_term'][0]) + + gene_list = g.db.execute(query).fetchone()[0].strip().split() + + new_terms = [] + for gene in gene_list: + this_term = dict(key=None, + separator=None, + search_term=[gene]) + + new_terms.append(this_term) + + return new_terms + def insert_newlines(string, every=64): """ This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """ lines = [] for i in xrange(0, len(string), every): lines.append(string[i:i+every]) return '\n'.join(lines) + diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index f1f5840f..b0a46b32 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -107,7 +107,7 @@ class ShowTrait(object): blatsequence += '%3EProbe_' + string.strip(seqt[1]) + '%0A' + string.strip(seqt[0]) + '%0A' if self.dataset.group.species == "rat": - self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence) + self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn6', blatsequence) self.UTHSC_BLAT_URL = "" elif self.dataset.group.species == "mouse": self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm10', blatsequence) @@ -314,7 +314,7 @@ class ShowTrait(object): if chr and transcript_start and transcript_end and kgId: transcript_start = int(transcript_start*1000000) # Convert to bases from megabases transcript_end = int(transcript_end*1000000) - self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('rn3', kgId, chr, transcript_start, transcript_end) + self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('rn6', kgId, chr, transcript_start, transcript_end) if self.this_trait.geneid and (self.dataset.group.species == "mouse" or self.dataset.group.species == "rat" or self.dataset.group.species == "human"): self.biogps_link = webqtlConfig.BIOGPS_URL % (self.dataset.group.species, self.this_trait.geneid) diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 48b6da5e..53158885 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -940,6 +940,7 @@ if (js_data.num_values < 256) { root.bar_layout = { title: js_data.trait_id, xaxis: { + type: 'category', titlefont: { size: 16 }, @@ -947,7 +948,7 @@ if (js_data.num_values < 256) { ticklen: 4, tickfont: { size: 16 - } + }, }, yaxis: { title: js_data.unit_type, diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 98931166..b8b64761 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -3,9 +3,11 @@ {% block css %} + + - + {% endblock %} {% from "base_macro.html" import header %} {% block content %} @@ -29,6 +31,7 @@ {% for sample in samples %} {% endfor %} + @@ -153,11 +156,9 @@
  • GN1 Map
    • - {% if mapping_method != "gemma" and mapping_method != "plink" %} -
  • - Vector Map +
  • + Genome Browser
    • - {% endif %}
    @@ -177,19 +178,31 @@ {% endif %}
    - {% if mapping_method != "gemma" and mapping_method != "plink" %} -
    -
    -
    -
    +
    +
    +
    + + + + + +
    +
    - {% endif %}

    {% if selectedChr == -1 %} -
    +

    Mapping Statistics


    @@ -307,20 +320,14 @@ + - {% if mapping_method != "gemma" and mapping_method != "plink" %} - {% endif %} - {% if mapping_method != "gemma" and mapping_method != "plink" %} - - - - - {% endif %} + {% endblock %} diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 2dded69f..8dfa37a8 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -15,6 +15,9 @@

    Search Results: We searched {{ dataset.fullname }} to find all records + {% if go_term is not none %} + with Gene Ontology ID GO:{{ go_term }}. + {% else %} {% for word in search_terms %} {% if word.key|lower == "rif" %} with GeneRIF containing {{ word.search_term[0] }}{% if loop.last %}.{% else %} and {% endif %} @@ -40,9 +43,13 @@ {% if word.search_term[0] == "*" %} in the dataset.{% else %}{% if loop.first %}that match:
    {% endif %}"{{ word.search_term[0] }}"{% if loop.last %}{% else %} and {% endif %}{% endif %} {% endif %} {% endfor %} + {% endif %}
    {{ results|count }} records are shown below.

    + {% if go_term is not none %} +

    The associated genes include:

    {% for word in search_terms %}{{ word.search_term[0] }}{% endfor %}

    + {% endif %} diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 7714a1ab..bb0b62fe 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -1,40 +1,40 @@
    Species and GroupSpecies and Group {{ this_trait.dataset.group.species }}, {{ this_trait.dataset.group.name }}
    Journal{{ this_trait.journal }} ({{ this_trait.year }}){{ this_trait.journal }} ({% if this_trait.pubmed_id %}{{ this_trait.year }}{% else %}{{ this_trait.year }}{% endif %})
    Aliases{{ this_trait.alias_fmt|replace(",",";") }}Wikidata: {{ this_trait.wikidata_alias_fmt|replace(",",";") }}
    GeneNetwork: {{ this_trait.alias_fmt|replace(",",";") }}
    - + {% if this_trait.dataset.type == 'Publish' %} - + - + - + - + {% else %} - + {% endif %} {% if this_trait.dataset.type == 'ProbeSet' %} {% if this_trait.symbol != None %} - + {% endif %} - + {% if this_trait.alias_fmt != "Not Available" %} @@ -46,12 +46,12 @@ {% endif %} {% if this_trait.dataset.type != 'Publish' %} - + {% endif %} - + {% if this_trait.probe_set_specificity %} - + - + - {% for header in target_dataset.header_fields %} - {% if header == 'Year' %} + {% for header in header_fields %} - {% elif header == 'Max LRS' %} - - {% elif header == 'Max LRS Location' %} - - {% elif header == 'Location' %} - - {% elif header == 'Mean' %} - - {% elif header == 'Additive Effect' %} - - {% elif header == 'Index' %} - - {% elif header == 'N' %} - - {% else %} - - {% endif %} {% endfor %} - {% if target_dataset.type == "ProbeSet" %} - {% if corr_method == 'pearson' %} - - - - - - - {% else %} - - - - - - - {% endif %} - {% elif target_dataset.type == "Publish" %} - {% if corr_method == 'pearson' %} - - - - {% else %} - - - - {% endif %} - {% elif target_dataset.type == "Geno" %} - {% if corr_method == 'pearson' %} - - - - {% else %} - - - - {% endif %} - {% endif %} @@ -190,9 +135,6 @@ - - - @@ -208,6 +150,9 @@ {% endif %} + + + {% elif target_dataset.type == "Publish" %} @@ -398,15 +343,15 @@ { "type": "natural", "width": "15%" }, { "type": "natural" }, { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] }, { "type": "natural" }, { "type": "scientific" }, { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] }, { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] }, - { "type": "scientific" } + { "type": "scientific" }, + { "type": "natural" }, + { "type": "natural" }, + { "type": "natural" } ], "createdRow": function ( row, data, index ) { $('td', row).eq(4).attr('title', $('td', row).eq(4).text()); @@ -416,14 +361,11 @@ } }, "order": [[12, "asc" ]], - "sDom": "BRZtir", + "sDom": "tir", "iDisplayLength": -1, "autoWidth": false, "deferRender": true, "bSortClasses": false, - "scrollY": "800px", - "scrollCollapse": false, - "scroller": true, "paging": false, "orderClasses": true } diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 5706c870..48ed0ec5 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -36,7 +36,7 @@
    - +
    @@ -48,7 +48,7 @@
    - +
    @@ -58,7 +58,7 @@
    - +
    @@ -67,7 +67,7 @@
    - +
    -- cgit v1.2.3 From d9ceb094bd6887d81faf37dc93388d3df200e9b7 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 29 Aug 2019 16:03:35 -0500 Subject: Fixed remaining issue where columns didn't show up right and the mean/r filter didn't work right for non-ProbeSet target datasets --- wqflask/wqflask/correlation/show_corr_results.py | 17 ++++++++++-- wqflask/wqflask/templates/correlation_page.html | 35 +++++++++++------------- 2 files changed, 31 insertions(+), 21 deletions(-) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 1fa47920..0db8fa38 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -150,6 +150,13 @@ class CorrelationResults(object): self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method) + if self.target_dataset.type == "ProbeSet": + self.filter_cols = [7, 6] + elif self.target_dataset.type == "Publish": + self.filter_cols = [6, 0] + else: + self.filter_cols = [4, 0] + self.correlation_results = [] self.correlation_data = {} @@ -583,7 +590,10 @@ def get_header_fields(data_type, corr_method): 'Year', 'Sample r', 'N', - 'Sample p(r)'] + 'Sample p(r)', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] else: header_fields = ['Index', 'Record', @@ -592,7 +602,10 @@ def get_header_fields(data_type, corr_method): 'Year', 'Sample rho', 'N', - 'Sample p(rho)'] + 'Sample p(rho)', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] else: if corr_method == "pearson": header_fields = ['Index', diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index fffdfd75..cbd2ab46 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -161,12 +161,12 @@ {{ trait.pubmed_text }} -
    - - + + + {% elif target_dataset.type == "Geno" %} @@ -233,38 +233,37 @@ //$.fn.dataTableExt.afnFiltering.push( $.fn.dataTable.ext.search.push( function( settings, data, dataIndex ) { - var r_column = 10; + var r_column = {{ filter_cols[0] }}; var r_greater = parseFloat($('input[name=r_greater_select]').val()) var r_less = parseFloat($('input[name=r_less_select]').val()); var r_and_or = $('#r_and_or').val(); - var mean_column = 6; + var mean_column = {{ filter_cols[1] }}; var mean_greater = parseFloat($('input[name=mean_greater_select]').val()); var mean_less = parseFloat($('input[name=mean_less_select]').val()); var mean_and_or = $('#mean_and_or').val(); - if (r_and_or == "and" && mean_and_or == "and"){ - if ( (data[r_column] >= r_greater && data[r_column] <= r_less) && (data[mean_column] > mean_greater && data[mean_column] < mean_less) ){ + if ( (data[r_column] >= r_greater && data[r_column] <= r_less) && {% if filter_cols[1] != 0 %}(data[mean_column] > mean_greater && data[mean_column] < mean_less){% else %} true{% endif %} ){ return true } else { return false } } else if (r_and_or == "and" && mean_and_or == "or"){ - if ( (data[r_column] >= r_greater && data[r_column] <= r_less) && (data[mean_column] >= mean_greater || data[mean_column] <= mean_less) ){ + if ( (data[r_column] >= r_greater && data[r_column] <= r_less) && {% if filter_cols[1] != 0 %}(data[mean_column] >= mean_greater || data[mean_column] <= mean_less){% else %} true{% endif %} ){ return true } else { return false } } else if (r_and_or == "or" && mean_and_or == "and") { - if ( (data[r_column] >= r_greater || data[r_column] <= r_less) && (data[mean_column] >= mean_greater && data[mean_column] <= mean_less) ){ + if ( (data[r_column] >= r_greater || data[r_column] <= r_less) && {% if filter_cols[1] != 0 %}(data[mean_column] >= mean_greater && data[mean_column] <= mean_less){% else %} true{% endif %} ){ return true } else { return false } } else { - if ( (data[r_column] >= r_greater || data[r_column] <= r_less) && (data[mean_column] >= mean_greater || data[mean_column] <= mean_less) ){ + if ( (data[r_column] >= r_greater || data[r_column] <= r_less) && {% if filter_cols[1] != 0 %}(data[mean_column] >= mean_greater || data[mean_column] <= mean_less){% else %} true{% endif %} ){ return true } else { return false @@ -360,7 +359,7 @@ $('td', row).eq(4).text($('td', row).eq(4).text() + '...') } }, - "order": [[12, "asc" ]], + "order": [[9, "asc" ]], "sDom": "tir", "iDisplayLength": -1, "autoWidth": false, @@ -395,11 +394,11 @@ { "type": "natural", "width": "12%" }, { "type": "natural" }, { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] }, + { "type": "scientific" }, { "type": "natural" }, - { "type": "scientific" } + { "type": "natural" }, + { "type": "natural" } ], "createdRow": function ( row, data, index ) { $('td', row).eq(3).attr('title', $('td', row).eq(3).text()); @@ -413,12 +412,10 @@ $('td', row).eq(4).text($('td', row).eq(4).text() + '...') } }, - "order": [[11, "asc" ]], - "sDom": "Btir", + "order": [[8, "asc" ]], + "sDom": "tir", "autoWidth": false, - "bDeferRender": true, - "scrollY": "800px", - "scrollCollapse": false + "bDeferRender": true } {% elif target_dataset.type == "Geno" %} table_conf = { -- cgit v1.2.3 From c540d661c9603f33b46edf2f6c8fd6b95bab8b38 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 29 Aug 2019 17:09:46 -0500 Subject: Fixed issue where LOD to LRS conversions weren't showing up correctly in the table Fixed issue where non-LOCO GEMMA wasn't working correctly --- .../wqflask/marker_regression/display_mapping_results.py | 10 +++++----- wqflask/wqflask/marker_regression/gemma_mapping.py | 2 +- wqflask/wqflask/marker_regression/run_mapping.py | 16 ++++++++-------- wqflask/wqflask/templates/mapping_results.html | 4 ++-- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 1d5843d4..911219f4 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -229,10 +229,10 @@ class DisplayMappingResults(object): self.covariates = start_vars['covariates'] if 'maf' in start_vars.keys(): self.maf = start_vars['maf'] + if 'output_files' in start_vars.keys(): + self.output_files = start_vars['output_files'] if 'use_loco' in start_vars.keys() and self.mapping_method == "gemma": self.use_loco = start_vars['use_loco'] - if self.use_loco == "True": - self.output_files = start_vars['output_files'] if 'reaper_version' in start_vars.keys() and self.mapping_method == "reaper": self.reaper_version = start_vars['reaper_version'] @@ -1702,7 +1702,7 @@ class DisplayMappingResults(object): #ZS: Needed to pass to genome browser js_data = json.loads(self.js_data) if self.LRS_LOD == "LRS": - js_data['max_score'] = LRS_LOD_Max/4.16 + js_data['max_score'] = LRS_LOD_Max/4.61 else: js_data['max_score'] = LRS_LOD_Max self.js_data = json.dumps(js_data) @@ -2068,9 +2068,9 @@ class DisplayMappingResults(object): ######################################### myCanvas = pid.PILCanvas(size=(400,300)) if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS": - perm_output = [value*4.16 for value in self.perm_output] + perm_output = [value*4.61 for value in self.perm_output] elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD": - perm_output = [value/4.16 for value in self.perm_output] + perm_output = [value/4.61 for value in self.perm_output] else: perm_output = self.perm_output diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 8d59a392..5b34e837 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -109,7 +109,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf return marker_obs, gwa_output_filename else: marker_obs = parse_loco_output(this_dataset, gwa_output_filename) - return marker_obs + return marker_obs, gwa_output_filename def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename): """Generates phenotype file for GEMMA""" diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index af5d0206..56d901fc 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -181,18 +181,18 @@ class RunMapping(object): self.dataset.group.get_markers() if self.mapping_method == "gemma": self.first_run = True - self.output_files= None + self.output_files = None + if 'output_files' in start_vars: + self.output_files = start_vars['output_files'] if 'first_run' in start_vars: #ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) self.first_run = False - if 'output_files' in start_vars: - self.output_files = start_vars['output_files'] self.score_type = "-log(p)" self.manhattan_plot = True with Bench("Running GEMMA"): if self.use_loco == "True": marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) else: - marker_obs = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run) + marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) results = marker_obs elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() @@ -397,7 +397,7 @@ class RunMapping(object): if self.mapping_method != "gemma": if self.score_type == "LRS": - significant_for_browser = self.significant / 4.16 + significant_for_browser = self.significant / 4.61 else: significant_for_browser = self.significant @@ -521,15 +521,15 @@ def trim_markers_for_figure(markers): else: filtered_markers.append(marker) else: - if marker[score_type] < 4.16: + if marker[score_type] < 4.61: if low_counter % 20 == 0: filtered_markers.append(marker) low_counter += 1 - elif 4.16 <= marker[score_type] < (2*4.16): + elif 4.61 <= marker[score_type] < (2*4.61): if med_counter % 10 == 0: filtered_markers.append(marker) med_counter += 1 - elif (2*4.16) <= marker[score_type] <= (3*4.16): + elif (2*4.61) <= marker[score_type] <= (3*4.61): if high_counter % 2 == 0: filtered_markers.append(marker) high_counter += 1 diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 189f8abc..373bae1e 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -250,11 +250,11 @@ {% if 'lod_score' in marker %} {% else %} - + {% endif %} {% else %} {% if 'lod_score' in marker %} - + {% else %} {% endif %} -- cgit v1.2.3 From 4bd1db34b109bff3b9abdcc161472885e9ae700d Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 6 Sep 2019 03:29:12 -0500 Subject: Fix name of javascript-twitter-post-fetcher --- wqflask/utility/tools.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 31ab2046..ec9f01bd 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -289,11 +289,14 @@ assert_dir(TEMPDIR) JS_GUIX_PATH = get_setting("JS_GUIX_PATH") assert_dir(JS_GUIX_PATH) assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom') + CSS_PATH = "UNKNOWN" # assert_dir(JS_PATH) -JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher")) + +JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher")) assert_dir(JS_TWITTER_POST_FETCHER_PATH) assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") + JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape")) assert_dir(JS_CYTOSCAPE_PATH) assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js') -- cgit v1.2.3 From cc12fe06593f4957fb2b5b641ebe7e5cf43453b1 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 9 Sep 2019 16:22:15 -0500 Subject: Add option to hide columns in correlation results Increased width of permutation histogram Increased a couple table widths that had crowded header text on certain browers (maybe just Safari) --- wqflask/utility/tools.py | 5 ++-- .../marker_regression/display_mapping_results.py | 2 +- wqflask/wqflask/templates/correlation_page.html | 28 ++++++++++++---------- wqflask/wqflask/templates/mapping_results.html | 2 +- 4 files changed, 20 insertions(+), 17 deletions(-) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 31ab2046..a2eb0817 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -105,7 +105,7 @@ def js_path(module=None): try_guix = get_setting("JS_GUIX_PATH")+"/"+module if valid_path(try_guix): return try_guix - raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)" + raise Exception("No JS path found for "+module+" (if not in Guix check JS_GN_PATH)") def reaper_command(guess=None): return get_setting("REAPER_COMMAND",guess) @@ -291,7 +291,8 @@ assert_dir(JS_GUIX_PATH) assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom') CSS_PATH = "UNKNOWN" # assert_dir(JS_PATH) -JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher")) +#JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher")) +JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher")) assert_dir(JS_TWITTER_POST_FETCHER_PATH) assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape")) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 911219f4..2834f1c3 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2066,7 +2066,7 @@ class DisplayMappingResults(object): ######################################### # Permutation Graph ######################################### - myCanvas = pid.PILCanvas(size=(400,300)) + myCanvas = pid.PILCanvas(size=(500,300)) if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS": perm_output = [value*4.61 for value in self.perm_output] elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD": diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index cbd2ab46..9e986eda 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -2,6 +2,7 @@ {% block css %} + {% endblock %} {% block content %}
    @@ -188,10 +189,9 @@ - - - - + + + - - - + + + + - - - - + + +
    Species and GroupSpecies and Group {{ this_trait.dataset.group.species }}, {{ this_trait.dataset.group.name }}
    PhenotypePhenotype
    {{ this_trait.description_fmt }}
    AuthorsAuthors
    {{ this_trait.authors }}
    TitleTitle
    {{ this_trait.title }}
    JournalJournal {{ this_trait.journal }} ({% if this_trait.pubmed_id %}{{ this_trait.year }}{% else %}{{ this_trait.year }}{% endif %})
    TissueTissue {{ this_trait.dataset.tissue }}
    Gene SymbolGene Symbol {{ this_trait.symbol }}
    AliasesAliases Wikidata: {{ this_trait.wikidata_alias_fmt|replace(",",";") }}
    LocationLocation {{ this_trait.location_fmt }}
    DatabaseDatabase {{ dataset.fullname }} @@ -60,7 +60,7 @@
    Target ScoreTarget Score BLAT Specificity @@ -75,7 +75,7 @@ {% endif %} {% if this_trait.pubmed_id or this_trait.geneid or this_trait.omim or this_trait.symbol %}
    Resource LinksResource Links {% if pubmed_link %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 7b585b03..aa64a910 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -639,7 +639,8 @@ def mapping_results_page(): 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', - 'reaper_version' + 'reaper_version', + 'num_vals' ) start_vars = {} for key, value in initial_start_vars.iteritems(): @@ -670,8 +671,8 @@ def mapping_results_page(): if template_vars.no_results: rendered_template = render_template("mapping_error.html") else: - if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink": - template_vars.js_data = json.dumps(template_vars.js_data, + #if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink": + template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") @@ -808,6 +809,17 @@ def get_temp_data(): temp_uuid = request.args['key'] return flask.jsonify(temp_data.TempData(temp_uuid).get_all()) +@app.route("/browser_input", methods=('GET',)) +def browser_inputs(): + """ Returns JSON from tmp directory for the purescript genome browser""" + + filename = request.args['filename'] + + with open("{}/gn2/".format(TEMPDIR) + filename + ".json", "r") as the_file: + file_contents = json.load(the_file) + + return flask.jsonify(file_contents) + ########################################################################## def json_default_handler(obj): -- cgit v1.2.3 From eb710ee13c5c1d138a75c5689ae7158b8a8f40cb Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 7 Aug 2019 14:55:30 -0500 Subject: Fixed issue with non-LOCO GEMMA mapping --- wqflask/wqflask/marker_regression/gemma_mapping.py | 35 +++---------- wqflask/wqflask/views.py | 60 +++++++++++----------- 2 files changed, 37 insertions(+), 58 deletions(-) diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 895d4ac6..1d9bbb43 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -73,14 +73,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf gwa_output_filename) else: - # generate_k_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk -outdir %s/gn2/ -o %s' % (flat_files('genotype/bimbam'), - # genofile_name, - # TEMPDIR, - # trait_filename, - # flat_files('genotype/bimbam'), - # genofile_name, - # TEMPDIR, - # k_output_filename) generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), genofile_name, TEMPDIR, @@ -93,31 +85,18 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf logger.debug("k_command:" + generate_k_command) os.system(generate_k_command) - # gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -k %s/gn2/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'), - # genofile_name, - # TEMPDIR, - # trait_filename, - # flat_files('genotype/bimbam'), - # genofile_name, - # TEMPDIR, - # k_output_filename, - # maf) - - gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), + gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), + genofile_name, + flat_files('genotype/bimbam'), genofile_name, TEMPDIR, trait_filename) if covariates != "": - gemma_command += ' -c %s/%s_covariates.txt' % (flat_files('mapping'), this_dataset.group.name) - # gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'), - # this_dataset.group.name, - # webqtlConfig.GENERATED_IMAGE_DIR, - # genofile_name) - # else: - # gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR, - # genofile_name) + gemma_command += ' -c %s/%s_covariates.txt > %s/gn2/%s.json' % (flat_files('mapping'), this_dataset.group.name, TEMPDIR, gwa_output_filename) + else: + gemma_command += ' > %s/gn2/%s.json' % (TEMPDIR, gwa_output_filename) logger.debug("gemma_command:" + gemma_command) @@ -127,7 +106,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf marker_obs = parse_loco_output(this_dataset, gwa_output_filename) return marker_obs, gwa_output_filename else: - marker_obs = parse_gemma_output(genofile_name) + marker_obs = parse_loco_output(this_dataset, gwa_output_filename) return marker_obs def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename): diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index aa64a910..fbcaefc1 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -671,36 +671,36 @@ def mapping_results_page(): if template_vars.no_results: rendered_template = render_template("mapping_error.html") else: - #if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink": - template_vars.js_data = json.dumps(template_vars.js_data, - default=json_default_handler, - indent=" ") - - result = template_vars.__dict__ - - if result['pair_scan']: - with Bench("Rendering template"): - img_path = result['pair_scan_filename'] - logger.info("img_path:", img_path) - initial_start_vars = request.form - logger.info("initial_start_vars:", initial_start_vars) - imgfile = open(TEMPDIR + img_path, 'rb') - imgdata = imgfile.read() - imgB64 = imgdata.encode("base64") - bytesarray = array.array('B', imgB64) - result['pair_scan_array'] = bytesarray - rendered_template = render_template("pair_scan_results.html", **result) - else: - gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__ - #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) - #logger.info("pickled result length:", len(pickled_result)) - #Redis.set(key, pickled_result) - #Redis.expire(key, 1*60) - - with Bench("Rendering template"): - if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"): - gn1_template_vars.pop('qtlresults', None) - rendered_template = render_template("mapping_results.html", **gn1_template_vars) + #if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink": + template_vars.js_data = json.dumps(template_vars.js_data, + default=json_default_handler, + indent=" ") + + result = template_vars.__dict__ + + if result['pair_scan']: + with Bench("Rendering template"): + img_path = result['pair_scan_filename'] + logger.info("img_path:", img_path) + initial_start_vars = request.form + logger.info("initial_start_vars:", initial_start_vars) + imgfile = open(TEMPDIR + img_path, 'rb') + imgdata = imgfile.read() + imgB64 = imgdata.encode("base64") + bytesarray = array.array('B', imgB64) + result['pair_scan_array'] = bytesarray + rendered_template = render_template("pair_scan_results.html", **result) + else: + gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__ + #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) + #logger.info("pickled result length:", len(pickled_result)) + #Redis.set(key, pickled_result) + #Redis.expire(key, 1*60) + + with Bench("Rendering template"): + if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"): + gn1_template_vars.pop('qtlresults', None) + rendered_template = render_template("mapping_results.html", **gn1_template_vars) return rendered_template -- cgit v1.2.3 From 183997c17e7572d69227aacde15408e8577073e1 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 7 Aug 2019 14:57:48 -0500 Subject: Added Christian's genome browser, but still need to clean things up a bunch since now it has to create two separate marker lists --- .../static/new/javascript/init_genome_browser.js | 73 +++ .../css/purescript_genetics_browser_v01.css | 1 + .../js/purescript-genetics-browser_v01.js | 659 +++++++++++++++++++++ 3 files changed, 733 insertions(+) create mode 100644 wqflask/wqflask/static/new/javascript/init_genome_browser.js create mode 100644 wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript_genetics_browser_v01.css create mode 100644 wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser_v01.js diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js new file mode 100644 index 00000000..64a300bc --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js @@ -0,0 +1,73 @@ +console.log("THE FILES:", js_data.browser_files) + +snps_filename = "/browser_input?filename=" + js_data.browser_files[0] +annot_filename = "/browser_input?filename=" + js_data.browser_files[1] + +localUrls = +{ + snps: snps_filename, + annotations: null +}; + +var vscaleWidth = 90.0; +var legendWidth = 140.0; +var score = { min: 0.0, max: 30.0, sig: 4 }; +var gwasPadding = { top: 35.0, + bottom: 35.0, + left: vscaleWidth, + right: legendWidth }; +var gwasHeight = 420.0; +var genePadding = { top: 10.0, + bottom: 35.0, + left: vscaleWidth, + right: legendWidth }; +var geneHeight = 140.0; + + +var config = +{ trackHeight: 400.0, + padding: gwasPadding, + score: score, + urls: localUrls, + tracks: { + gwas: { + trackHeight: gwasHeight, + padding: gwasPadding, + snps: { + radius: 3.75, + lineWidth: 1.0, + color: { outline: "#FFFFFF", + fill: "#00008B" }, + pixelOffset: {x: 0.0, y: 0.0} + }, + annotations: { + radius: 5.5, + outline: "#000000", + snpColor: "#0074D9", + geneColor: "#FF4136" + }, + score: score, + legend: { + fontSize: 14, + hPad: 0.2, + vPad: 0.2 + }, + vscale: { + color: "#000000", + hPad: 0.125, + numSteps: 3, + fonts: { labelSize: 18, scaleSize: 16 } + }, + } + }, + chrs: { + chrBG1: "#FFFFFF", + chrBG2: "#DDDDDD", + chrLabels: { fontSize: 16 }, + }, + initialChrs: { left: "1", right: "19" } +}; + +GenomeBrowser.main(config)(); + +document.getElementById("controls").style.visibility = "visible"; \ No newline at end of file diff --git a/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript_genetics_browser_v01.css b/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript_genetics_browser_v01.css new file mode 100644 index 00000000..135292ac --- /dev/null +++ b/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript_genetics_browser_v01.css @@ -0,0 +1 @@ +body,html{max-width:100%;overflow-x:hidden}#browser{position:absolute;margin:0}#info-line{border:1px solid #aaa;padding:2px;position:absolute;right:0;top:1px;min-width:14%;font-size:9pt}#controls{visibility:hidden;position:absolute;top:4px;left:100px;z-index:1000}#controls>button{border:1px solid #aaa;border-radius:2px;padding-left:6px;padding-right:6px;height:23px;min-width:20px}button#scrollRight,button#zoomIn{margin-left:-2px;margin-right:4px}#infoBox{position:absolute;display:inline-block;z-index:10000;visibility:hidden;padding:5px;border:2px solid grey;border-radius:5%;background-color:#fff;min-height:100px;min-width:10px;max-width:80%;margin-top:9.7em;font-family:sans-serif}#infoBox>div{float:left;margin:1em 1.2em}#infoBox>div>p{margin:.1em} \ No newline at end of file diff --git a/wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser_v01.js b/wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser_v01.js new file mode 100644 index 00000000..acd590a5 --- /dev/null +++ b/wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser_v01.js @@ -0,0 +1,659 @@ +parcelRequire=function(e,r,t,n){var i,o="function"==typeof parcelRequire&&parcelRequire,u="function"==typeof require&&require;function f(t,n){if(!r[t]){if(!e[t]){var i="function"==typeof parcelRequire&&parcelRequire;if(!n&&i)return i(t,!0);if(o)return o(t,!0);if(u&&"string"==typeof t)return u(t);var c=new Error("Cannot find module '"+t+"'");throw c.code="MODULE_NOT_FOUND",c}p.resolve=function(r){return e[t][1][r]||r},p.cache={};var l=r[t]=new f.Module(t);e[t][0].call(l.exports,p,l,l.exports,this)}return r[t].exports;function p(e){return f(p.resolve(e))}}f.isParcelRequire=!0,f.Module=function(e){this.id=e,this.bundle=f,this.exports={}},f.modules=e,f.cache=r,f.parent=o,f.register=function(r,t){e[r]=[function(e,r){r.exports=t},{}]};for(var c=0;c="0"&&r[u]<="9"?"\\&":"";return"\\"+n.charCodeAt(0).toString(10)+c})+'"'},exports.showArrayImpl=function(r){return 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Error("Failed pattern match at Data.Ordering (line 21, column 1 - line 24, column 18): "+[n.constructor.name,e.constructor.name])}}),c=function(n){if(n instanceof i)return t.value;if(n instanceof o)return o.value;if(n instanceof t)return i.value;throw new Error("Failed pattern match at Data.Ordering (line 33, column 1 - line 33, column 31): "+[n.constructor.name])},f=new n.Eq(function(n){return function(e){return n instanceof t&&e instanceof t||(n instanceof i&&e instanceof i||n instanceof o&&e instanceof o)}});module.exports={LT:t,GT:i,EQ:o,invert:c,eqOrdering:f,semigroupOrdering:a,showOrdering:u}; +},{"../Data.Eq/index.js":"Pq4F","../Data.Semigroup/index.js":"EsAJ","../Data.Show/index.js":"mFY7"}],"+BUG":[function(require,module,exports) { +"use strict";exports.intSub=function(n){return function(t){return n-t|0}},exports.numSub=function(n){return function(t){return n-t}}; +},{}],"Vm8y":[function(require,module,exports) { +"use strict";exports.intAdd=function(n){return function(t){return n+t|0}},exports.intMul=function(n){return function(t){return n*t|0}},exports.numAdd=function(n){return function(t){return n+t}},exports.numMul=function(n){return function(t){return n*t}}; +},{}],"11NF":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Data.Symbol/index.js"),e=require("../Data.Unit/index.js"),u=require("../Record.Unsafe/index.js"),t=require("../Type.Data.Row/index.js"),o=require("../Type.Data.RowList/index.js"),i=function(n,r,e,u){this.addRecord=n,this.mulRecord=r,this.oneRecord=e,this.zeroRecord=u},c=function(n,r,e,u){this.add=n,this.mul=r,this.one=e,this.zero=u},f=function(n){return n.zeroRecord},a=function(n){return n.zero},d=new c(function(n){return function(n){return e.unit}},function(n){return function(n){return e.unit}},e.unit,e.unit),l=new i(function(n){return function(n){return function(n){return{}}}},function(n){return function(n){return function(n){return{}}}},function(n){return function(n){return{}}},function(n){return function(n){return{}}}),s=new c(n.numAdd,n.numMul,1,0),R=new c(n.intAdd,n.intMul,1,0),m=function(n){return n.oneRecord},y=function(n){return n.one},x=function(n){return n.mulRecord},v=function(n){return n.mul},P=function(n){return n.addRecord},S=function(n){return function(n){return new c(P(n)(o.RLProxy.value),x(n)(o.RLProxy.value),m(n)(o.RLProxy.value)(t.RProxy.value),f(n)(o.RLProxy.value)(t.RProxy.value))}},g=function(n){return n.add},w=function(n){return new c(function(r){return function(e){return function(u){return g(n)(r(u))(e(u))}}},function(r){return function(e){return function(u){return v(n)(r(u))(e(u))}}},function(r){return y(n)},function(r){return a(n)})},L=function(n){return function(e){return function(e){return function(c){return new i(function(t){return function(t){return function(i){var f=P(e)(o.RLProxy.value)(t)(i),a=r.reflectSymbol(n)(r.SProxy.value),d=u.unsafeSet(a),l=u.unsafeGet(a);return 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strict";var n=require("./foreign.js"),r=require("../Data.Semiring/index.js"),e=require("../Data.Symbol/index.js"),i=require("../Data.Unit/index.js"),u=require("../Record.Unsafe/index.js"),t=require("../Type.Data.RowList/index.js"),o=function(n,r){this.SemiringRecord0=n,this.subRecord=r},c=function(n,r){this.Semiring0=n,this.sub=r},f=function(n){return n.subRecord},s=function(n){return n.sub},g=new c(function(){return r.semiringUnit},function(n){return function(n){return i.unit}}),m=new o(function(){return r.semiringRecordNil},function(n){return function(n){return function(n){return{}}}}),d=function(n){return function(i){return function(c){return function(g){return new o(function(){return r.semiringRecordCons(n)(i)(c.SemiringRecord0())(g.Semiring0())},function(r){return function(r){return function(i){var o=f(c)(t.RLProxy.value)(r)(i),m=e.reflectSymbol(n)(e.SProxy.value),d=u.unsafeSet(m),R=u.unsafeGet(m);return d(s(g)(R(r))(R(i)))(o)}}})}}}},R=function(n){return function(e){return new c(function(){return r.semiringRecord(n)(e.SemiringRecord0())},f(e)(t.RLProxy.value))}},a=new c(function(){return r.semiringNumber},n.numSub),S=new c(function(){return r.semiringInt},n.intSub),b=function(n){return new c(function(){return r.semiringFn(n.Semiring0())},function(r){return function(e){return function(i){return s(n)(r(i))(e(i))}}})},l=function(n){return function(e){return s(n)(r.zero(n.Semiring0()))(e)}};module.exports={Ring:c,sub:s,negate:l,RingRecord:o,subRecord:f,ringInt:S,ringNumber:a,ringUnit:g,ringFn:b,ringRecord:R,ringRecordNil:m,ringRecordCons:d}; +},{"./foreign.js":"+BUG","../Data.Semiring/index.js":"11NF","../Data.Symbol/index.js":"4oJQ","../Data.Unit/index.js":"NhVk","../Record.Unsafe/index.js":"KG04","../Type.Data.RowList/index.js":"XaXP"}],"r4Vb":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),r=require("../Data.Eq/index.js"),e=require("../Data.Ordering/index.js"),t=require("../Data.Ring/index.js"),u=require("../Data.Semiring/index.js"),o=require("../Data.Symbol/index.js"),i=require("../Record.Unsafe/index.js"),c=require("../Type.Data.RowList/index.js"),a=function(n,r){this.EqRecord0=n,this.compareRecord=r},f=function(n,r){this.Eq10=n,this.compare1=r},l=function(n,r){this.Eq0=n,this.compare=r},s=new l(function(){return r.eqVoid},function(n){return function(n){return e.EQ.value}}),d=new l(function(){return r.eqUnit},function(n){return function(n){return e.EQ.value}}),m=new l(function(){return r.eqString},n.ordStringImpl(e.LT.value)(e.EQ.value)(e.GT.value)),T=new a(function(){return r.eqRowNil},function(n){return function(n){return function(n){return e.EQ.value}}}),v=new l(function(){return e.eqOrdering},function(n){return function(r){if(n instanceof e.LT&&r instanceof e.LT)return e.EQ.value;if(n instanceof e.EQ&&r instanceof e.EQ)return 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function(r){return function(e){return function(t){return Q(n)(r(e))(r(t))}}}},R=function(n){return function(r){return function(t){return Q(n)(r)(t)instanceof e.GT}}},O=function(n){return function(r){return function(t){return!(Q(n)(r)(t)instanceof e.LT)}}},x=function(n){return function(r){return function(e){return O(n)(e)(u.zero(r.Semiring0()))?u.one(r.Semiring0()):t.negate(r)(u.one(r.Semiring0()))}}},y=function(n){return function(r){return function(t){return Q(n)(r)(t)instanceof e.LT}}},S=function(n){return function(r){return function(t){return!(Q(n)(r)(t)instanceof e.GT)}}},D=function(n){return function(r){return function(t){var u=Q(n)(r)(t);if(u instanceof e.LT)return t;if(u instanceof e.EQ)return r;if(u instanceof e.GT)return r;throw new Error("Failed pattern match at Data.Ord (line 167, column 3 - line 170, column 12): "+[u.constructor.name])}}},I=function(n){return function(r){return function(t){var u=Q(n)(r)(t);if(u instanceof e.LT)return r;if(u instanceof e.EQ)return r;if(u instanceof e.GT)return t;throw new Error("Failed pattern match at Data.Ord (line 158, column 3 - line 161, column 12): "+[u.constructor.name])}}},j=function(t){return new l(function(){return r.eqArray(t.Eq0())},(u=function(n){return function(r){var u=Q(t)(n)(r);if(u instanceof e.EQ)return 0;if(u instanceof e.LT)return 1;if(u instanceof e.GT)return-1;throw new Error("Failed pattern match at Data.Ord (line 65, column 7 - line 68, column 17): "+[u.constructor.name])}},function(r){return function(e){return Q(q)(0)(n.ordArrayImpl(u)(r)(e))}}));var u},b=new f(function(){return r.eq1Array},function(n){return Q(j(n))}),A=function(n){return function(t){return function(u){return function(f){return new a(function(){return r.eqRowCons(n.EqRecord0())(t)(u)(f.Eq0())},function(t){return function(t){return function(a){var l=o.reflectSymbol(u)(o.SProxy.value),s=Q(f)(i.unsafeGet(l)(t))(i.unsafeGet(l)(a));return r.notEq(e.eqOrdering)(s)(e.EQ.value)?s:h(n)(c.RLProxy.value)(t)(a)}}})}}}},C=function(n){return function(r){return function(e){return function(t){return I(n)(e)(D(n)(r)(t))}}}},N=function(n){return function(r){return function(e){return function(t){return!y(n)(t)(r)&&!R(n)(t)(e)}}}},F=function(n){return function(r){return function(e){return O(n)(e)(u.zero(r.Semiring0()))?e:t.negate(r)(e)}}};module.exports={Ord:l,compare:Q,Ord1:f,compare1:L,lessThan:y,lessThanOrEq:S,greaterThan:R,greaterThanOrEq:O,comparing:G,min:I,max:D,clamp:C,between:N,abs:F,signum:x,OrdRecord:a,compareRecord:h,ordBoolean:p,ordInt:q,ordNumber:E,ordString:m,ordChar:w,ordUnit:d,ordVoid:s,ordArray:j,ordOrdering:v,ord1Array:b,ordRecordNil:T,ordRecordCons:A,ordRecord:g}; +},{"./foreign.js":"m7Aq","../Data.Eq/index.js":"Pq4F","../Data.Ordering/index.js":"5Eun","../Data.Ring/index.js":"E2qH","../Data.Semiring/index.js":"11NF","../Data.Symbol/index.js":"4oJQ","../Record.Unsafe/index.js":"KG04","../Type.Data.RowList/index.js":"XaXP"}],"kcUU":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),t=require("../Data.Ord/index.js"),r=require("../Data.Ordering/index.js"),e=require("../Data.Unit/index.js"),o=function(n,t,r){this.Ord0=n,this.bottom=t,this.top=r},u=function(n){return n.top},d=new o(function(){return t.ordUnit},e.unit,e.unit),i=new o(function(){return t.ordOrdering},r.LT.value,r.GT.value),b=new o(function(){return t.ordNumber},n.bottomNumber,n.topNumber),a=new o(function(){return t.ordInt},n.bottomInt,n.topInt),m=new o(function(){return t.ordChar},n.bottomChar,n.topChar),c=new o(function(){return t.ordBoolean},!1,!0),f=function(n){return n.bottom};module.exports={Bounded:o,bottom:f,top:u,boundedBoolean:c,boundedInt:a,boundedChar:m,boundedOrdering:i,boundedUnit:d,boundedNumber:b}; +},{"./foreign.js":"0C+G","../Data.Ord/index.js":"r4Vb","../Data.Ordering/index.js":"5Eun","../Data.Unit/index.js":"NhVk"}],"AXkC":[function(require,module,exports) { +"use strict";var n=require("../Data.Functor/index.js"),r=function(n){this.imap=n},t=new r(function(n){return function(r){return function(r){return n(r)}}}),i=new r(function(n){return function(r){return function(t){return function(i){return n(t(r(i)))}}}}),u=new r(function(n){return function(r){return function(r){return n(r)}}}),e=new r(function(n){return function(r){return function(r){return n(r)}}}),o=new r(function(n){return function(r){return function(r){return n(r)}}}),a=new r(function(n){return function(r){return function(r){return n(r)}}}),c=function(r){return function(t){return function(i){return n.map(r)(t)}}},f=new r(c(n.functorArray)),v=new 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t(function(){return n.ringRecordCons(i)(r)(e.RingRecord0())(u.Ring0())})}}}},o=function(t){return function(r){return new i(function(){return n.ringRecord(t)(r.RingRecord0())})}},c=new i(function(){return n.ringNumber}),R=new i(function(){return n.ringInt}),g=function(t){return new i(function(){return n.ringFn(t.Ring0())})};module.exports={CommutativeRing:i,CommutativeRingRecord:t,commutativeRingInt:R,commutativeRingNumber:c,commutativeRingUnit:r,commutativeRingFn:g,commutativeRingRecord:o,commutativeRingRecordNil:e,commutativeRingRecordCons:u}; +},{"../Data.Ring/index.js":"E2qH"}],"2IRB":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),i=require("../Data.CommutativeRing/index.js"),e=require("../Data.Eq/index.js"),t=require("../Data.Semiring/index.js"),r=function(n,i,e,t){this.CommutativeRing0=n,this.degree=i,this.div=e,this.mod=t},u=function(n){return n.mod},o=function(n){return function(i){return function(r){return function(o){var m,g=n,c=i,f=r,a=!1;function d(n,i,r,m){if(e.eq(n)(m)(t.zero(i.CommutativeRing0().Ring0().Semiring0())))return a=!0,r;g=n,c=i,f=m,o=u(i)(r)(m)}for(;!a;)m=d(g,c,f,o);return m}}}},m=new r(function(){return i.commutativeRingNumber},function(n){return 1},n.numDiv,function(n){return function(n){return 0}}),g=new r(function(){return i.commutativeRingInt},n.intDegree,n.intDiv,n.intMod),c=function(n){return n.div},f=function(n){return function(i){return function(r){return function(u){return e.eq(n)(r)(t.zero(i.CommutativeRing0().Ring0().Semiring0()))||e.eq(n)(u)(t.zero(i.CommutativeRing0().Ring0().Semiring0()))?t.zero(i.CommutativeRing0().Ring0().Semiring0()):c(i)(t.mul(i.CommutativeRing0().Ring0().Semiring0())(r)(u))(o(n)(i)(r)(u))}}}},a=function(n){return n.degree};module.exports={EuclideanRing:r,degree:a,div:c,mod:u,gcd:o,lcm:f,euclideanRingInt:g,euclideanRingNumber:m}; +},{"./foreign.js":"8EBw","../Data.CommutativeRing/index.js":"60TQ","../Data.Eq/index.js":"Pq4F","../Data.Semiring/index.js":"11NF"}],"TiEB":[function(require,module,exports) { +"use strict";var n=require("../Data.Boolean/index.js"),r=require("../Data.EuclideanRing/index.js"),e=require("../Data.Ordering/index.js"),i=require("../Data.Semigroup/index.js"),o=require("../Data.Symbol/index.js"),t=require("../Data.Unit/index.js"),u=require("../Record.Unsafe/index.js"),c=require("../Type.Data.RowList/index.js"),d=function(n,r){this.SemigroupRecord0=n,this.memptyRecord=r},m=function(n,r){this.Semigroup0=n,this.mempty=r},a=new m(function(){return i.semigroupUnit},t.unit),f=new m(function(){return i.semigroupString},""),p=new d(function(){return i.semigroupRecordNil},function(n){return{}}),s=new m(function(){return e.semigroupOrdering},e.EQ.value),g=new m(function(){return i.semigroupArray},[]),l=function(n){return n.memptyRecord},R=function(n){return function(r){return new m(function(){return i.semigroupRecord(n)(r.SemigroupRecord0())},l(r)(c.RLProxy.value))}},S=function(n){return n.mempty},w=function(n){return new m(function(){return i.semigroupFn(n.Semigroup0())},function(r){return S(n)})},y=function(n){return function(r){return function(e){return function(t){return new d(function(){return i.semigroupRecordCons(n)(e)(t.SemigroupRecord0())(r.Semigroup0())},function(e){var i=l(t)(c.RLProxy.value),d=o.reflectSymbol(n)(o.SProxy.value);return u.unsafeSet(d)(S(r))(i)})}}}},x=function(e){return function(o){return function t(u){if(u<=0)return S(e);if(1===u)return o;if(0===r.mod(r.euclideanRingInt)(u)(2)){var c=t(r.div(r.euclideanRingInt)(u)(2));return i.append(e.Semigroup0())(c)(c)}if(n.otherwise)return c=t(r.div(r.euclideanRingInt)(u)(2)),i.append(e.Semigroup0())(c)(i.append(e.Semigroup0())(c)(o));throw new Error("Failed pattern match at Data.Monoid (line 65, column 3 - line 65, column 17): "+[u.constructor.name])}}},h=function(n){return function(r){return function(e){if(r)return e;if(!r)return S(n);throw new Error("Failed pattern match at Data.Monoid (line 73, column 1 - line 73, column 49): "+[r.constructor.name,e.constructor.name])}}};module.exports={Monoid:m,mempty:S,power:x,guard:h,MonoidRecord:d,memptyRecord:l,monoidUnit:a,monoidOrdering:s,monoidFn:w,monoidString:f,monoidArray:g,monoidRecord:R,monoidRecordNil:p,monoidRecordCons:y}; +},{"../Data.Boolean/index.js":"ObQr","../Data.EuclideanRing/index.js":"2IRB","../Data.Ordering/index.js":"5Eun","../Data.Semigroup/index.js":"EsAJ","../Data.Symbol/index.js":"4oJQ","../Data.Unit/index.js":"NhVk","../Record.Unsafe/index.js":"KG04","../Type.Data.RowList/index.js":"XaXP"}],"5mN7":[function(require,module,exports) { +"use strict";var n=require("../Control.Alt/index.js"),e=require("../Control.Alternative/index.js"),t=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),o=require("../Control.Category/index.js"),i=require("../Control.Extend/index.js"),a=require("../Control.Monad/index.js"),c=require("../Control.MonadZero/index.js"),f=require("../Control.Plus/index.js"),l=require("../Data.Bounded/index.js"),s=require("../Data.Eq/index.js"),d=require("../Data.Function/index.js"),m=require("../Data.Functor/index.js"),w=require("../Data.Functor.Invariant/index.js"),y=require("../Data.Monoid/index.js"),p=require("../Data.Ord/index.js"),v=require("../Data.Ordering/index.js"),M=require("../Data.Semigroup/index.js"),b=require("../Data.Show/index.js"),q=require("../Data.Unit/index.js"),x=function(){function n(){}return n.value=new n,n}(),h=function(){function n(n){this.value0=n}return n.create=function(e){return new n(e)},n}(),j=function(n){return new b.Show(function(e){if(e instanceof h)return"(Just "+b.show(n)(e.value0)+")";if(e instanceof x)return"Nothing";throw new Error("Failed pattern match at Data.Maybe (line 205, column 1 - line 207, column 28): "+[e.constructor.name])})},D=function(n){return new M.Semigroup(function(e){return function(t){if(e instanceof x)return t;if(t instanceof x)return e;if(e instanceof h&&t instanceof h)return new h(M.append(n)(e.value0)(t.value0));throw new Error("Failed pattern match at Data.Maybe (line 174, column 1 - line 177, column 43): "+[e.constructor.name,t.constructor.name])}})},F=function(e){return function(r){return n.alt(e.Plus1().Alt0())(m.map(e.Plus1().Alt0().Functor0())(h.create)(r))(t.pure(e.Applicative0())(x.value))}},E=function(n){return new y.Monoid(function(){return D(n)},x.value)},A=function(n){return function(e){return function(t){if(t instanceof x)return n(q.unit);if(t instanceof h)return e(t.value0);throw new Error("Failed pattern match at Data.Maybe (line 230, column 1 - line 230, column 62): "+[n.constructor.name,e.constructor.name,t.constructor.name])}}},C=function(n){return function(e){return function(t){if(t instanceof x)return n;if(t instanceof h)return e(t.value0);throw new Error("Failed pattern match at Data.Maybe (line 217, column 1 - line 217, column 51): "+[n.constructor.name,e.constructor.name,t.constructor.name])}}},g=C(!0)(d.const(!1)),O=C(!1)(d.const(!0)),B=new m.Functor(function(n){return function(e){return e instanceof h?new h(n(e.value0)):x.value}}),J=new w.Invariant(w.imapF(B)),P=function(n){return A(n)(o.identity(o.categoryFn))},S=function(n){return C(n)(o.identity(o.categoryFn))},N=function(n){return function(n){if(n instanceof h)return n.value0;throw new Error("Failed pattern match at Data.Maybe (line 268, column 1 - line 268, column 46): "+[n.constructor.name])}},Z=new i.Extend(function(){return B},function(n){return function(e){return e instanceof x?x.value:new h(n(e))}}),I=function(n){return new s.Eq(function(e){return function(t){return e instanceof x&&t instanceof x||e instanceof h&&t instanceof h&&s.eq(n)(e.value0)(t.value0)}})},T=function(n){return new p.Ord(function(){return I(n.Eq0())},function(e){return function(t){if(e instanceof x&&t instanceof x)return v.EQ.value;if(e instanceof x)return v.LT.value;if(t instanceof x)return v.GT.value;if(e instanceof h&&t instanceof h)return p.compare(n)(e.value0)(t.value0);throw new Error("Failed pattern match at Data.Maybe (line 194, column 1 - line 194, column 51): "+[e.constructor.name,t.constructor.name])}})},G=new s.Eq1(function(n){return s.eq(I(n))}),L=new p.Ord1(function(){return G},function(n){return p.compare(T(n))}),Q=function(n){return new l.Bounded(function(){return T(n.Ord0())},x.value,new h(l.top(n)))},U=new r.Apply(function(){return B},function(n){return function(e){if(n instanceof h)return m.map(B)(n.value0)(e);if(n instanceof x)return x.value;throw new Error("Failed pattern match at Data.Maybe (line 67, column 1 - line 69, column 30): "+[n.constructor.name,e.constructor.name])}}),k=new u.Bind(function(){return U},function(n){return function(e){if(n instanceof h)return e(n.value0);if(n instanceof x)return x.value;throw new Error("Failed pattern match at Data.Maybe (line 125, column 1 - line 127, column 28): "+[n.constructor.name,e.constructor.name])}}),z=new t.Applicative(function(){return U},h.create),H=new a.Monad(function(){return z},function(){return k}),K=new n.Alt(function(){return B},function(n){return function(e){return n instanceof x?e:n}}),R=new f.Plus(function(){return K},x.value),V=new e.Alternative(function(){return z},function(){return R}),W=new c.MonadZero(function(){return V},function(){return H});module.exports={Nothing:x,Just:h,maybe:C,"maybe'":A,fromMaybe:S,"fromMaybe'":P,isJust:O,isNothing:g,fromJust:N,optional:F,functorMaybe:B,applyMaybe:U,applicativeMaybe:z,altMaybe:K,plusMaybe:R,alternativeMaybe:V,bindMaybe:k,monadMaybe:H,monadZeroMaybe:W,extendMaybe:Z,invariantMaybe:J,semigroupMaybe:D,monoidMaybe:E,eqMaybe:I,eq1Maybe:G,ordMaybe:T,ord1Maybe:L,boundedMaybe:Q,showMaybe:j}; +},{"../Control.Alt/index.js":"lN+m","../Control.Alternative/index.js":"aHia","../Control.Applicative/index.js":"qYya","../Control.Apply/index.js":"QcLv","../Control.Bind/index.js":"7VcT","../Control.Category/index.js":"IAi2","../Control.Extend/index.js":"JIoJ","../Control.Monad/index.js":"U/Ix","../Control.MonadZero/index.js":"lD5R","../Control.Plus/index.js":"oMBg","../Data.Bounded/index.js":"kcUU","../Data.Eq/index.js":"Pq4F","../Data.Function/index.js":"ImXJ","../Data.Functor/index.js":"+0AE","../Data.Functor.Invariant/index.js":"AXkC","../Data.Monoid/index.js":"TiEB","../Data.Ord/index.js":"r4Vb","../Data.Ordering/index.js":"5Eun","../Data.Semigroup/index.js":"EsAJ","../Data.Show/index.js":"mFY7","../Data.Unit/index.js":"NhVk"}],"U/G5":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),e=require("../Control.Bind/index.js"),t=require("../Control.Monad/index.js"),o=require("../Data.Eq/index.js"),u=require("../Data.Functor/index.js"),i=require("../Data.HeytingAlgebra/index.js"),c=require("../Data.Monoid/index.js"),f=require("../Data.Ord/index.js"),j=require("../Data.Semigroup/index.js"),d=require("../Data.Semiring/index.js"),a=require("../Data.Show/index.js"),s=function(n){return n},C=function(n){return new a.Show(function(r){return"(Conj "+a.show(n)(r)+")"})},p=function(n){return new d.Semiring(function(r){return function(e){return i.conj(n)(r)(e)}},function(r){return function(e){return i.disj(n)(r)(e)}},i.ff(n),i.tt(n))},q=function(n){return new j.Semigroup(function(r){return function(e){return i.conj(n)(r)(e)}})},w=function(n){return n},x=function(n){return new c.Monoid(function(){return q(n)},i.tt(n))},l=new u.Functor(function(n){return function(r){return n(r)}}),m=function(n){return n},g=new o.Eq1(function(n){return o.eq(m(n))}),D=new f.Ord1(function(){return g},function(n){return f.compare(w(n))}),S=function(n){return n},A=new r.Apply(function(){return l},function(n){return function(r){return n(r)}}),h=new e.Bind(function(){return A},function(n){return function(r){return r(n)}}),v=new n.Applicative(function(){return A},s),y=new t.Monad(function(){return v},function(){return h});module.exports={Conj:s,eqConj:m,eq1Conj:g,ordConj:w,ord1Conj:D,boundedConj:S,showConj:C,functorConj:l,applyConj:A,applicativeConj:v,bindConj:h,monadConj:y,semigroupConj:q,monoidConj:x,semiringConj:p}; +},{"../Control.Applicative/index.js":"qYya","../Control.Apply/index.js":"QcLv","../Control.Bind/index.js":"7VcT","../Control.Monad/index.js":"U/Ix","../Data.Eq/index.js":"Pq4F","../Data.Functor/index.js":"+0AE","../Data.HeytingAlgebra/index.js":"paZe","../Data.Monoid/index.js":"TiEB","../Data.Ord/index.js":"r4Vb","../Data.Semigroup/index.js":"EsAJ","../Data.Semiring/index.js":"11NF","../Data.Show/index.js":"mFY7"}],"9bR7":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),e=require("../Control.Bind/index.js"),i=require("../Control.Monad/index.js"),t=require("../Data.Eq/index.js"),u=require("../Data.Functor/index.js"),o=require("../Data.HeytingAlgebra/index.js"),c=require("../Data.Monoid/index.js"),s=require("../Data.Ord/index.js"),f=require("../Data.Semigroup/index.js"),j=require("../Data.Semiring/index.js"),d=require("../Data.Show/index.js"),a=function(n){return n},D=function(n){return new d.Show(function(r){return"(Disj "+d.show(n)(r)+")"})},p=function(n){return new j.Semiring(function(r){return function(e){return o.disj(n)(r)(e)}},function(r){return function(e){return o.conj(n)(r)(e)}},o.tt(n),o.ff(n))},q=function(n){return new f.Semigroup(function(r){return function(e){return o.disj(n)(r)(e)}})},w=function(n){return n},x=function(n){return new c.Monoid(function(){return q(n)},o.ff(n))},l=new u.Functor(function(n){return function(r){return n(r)}}),m=function(n){return n},g=new t.Eq1(function(n){return t.eq(m(n))}),S=new s.Ord1(function(){return g},function(n){return s.compare(w(n))}),A=function(n){return n},h=new r.Apply(function(){return l},function(n){return function(r){return n(r)}}),v=new e.Bind(function(){return h},function(n){return function(r){return r(n)}}),y=new n.Applicative(function(){return h},a),C=new i.Monad(function(){return y},function(){return 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n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),e=require("../Control.Biapplicative/index.js"),t=require("../Control.Biapply/index.js"),u=require("../Data.Bifunctor/index.js"),i=require("../Data.Functor/index.js"),o=require("../Data.Newtype/index.js"),c=require("../Data.Show/index.js"),p=function(n){return n},f=function(n){return new c.Show(function(r){return"(Joker "+c.show(n)(r)+")"})},a=function(n){return n},l=new o.Newtype(function(n){return n},p),s=function(n){return new i.Functor(function(r){return function(e){return i.map(n)(r)(e)}})},w=function(n){return n},d=function(n){return new u.Bifunctor(function(r){return function(r){return function(e){return i.map(n)(r)(e)}}})},k=function(n){return new t.Biapply(function(){return d(n.Functor0())},function(e){return function(t){return r.apply(n)(e)(t)}})},J=function(r){return new e.Biapplicative(function(){return k(r.Apply0())},function(e){return function(e){return 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n=require("./foreign.js"),r=require("../Control.Applicative/index.js"),t=require("../Control.Apply/index.js"),u=require("../Control.Category/index.js"),e=require("../Data.Foldable/index.js"),i=require("../Data.Functor/index.js"),o=require("../Data.Maybe/index.js"),c=require("../Data.Maybe.First/index.js"),a=require("../Data.Maybe.Last/index.js"),f=require("../Data.Monoid.Additive/index.js"),l=require("../Data.Monoid.Conj/index.js"),p=require("../Data.Monoid.Disj/index.js"),s=require("../Data.Monoid.Dual/index.js"),d=require("../Data.Monoid.Multiplicative/index.js"),v=require("../Data.Traversable.Accum.Internal/index.js"),m=function(n,r,t,u){this.Foldable1=n,this.Functor0=r,this.sequence=t,this.traverse=u},y=function(n){return n.traverse},A=new m(function(){return e.foldableMultiplicative},function(){return d.functorMultiplicative},function(n){return function(r){return i.map(n.Apply0().Functor0())(d.Multiplicative)(r)}},function(n){return function(r){return function(t){return 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+},{"./foreign.js":"oRQn","../Control.Applicative/index.js":"qYya","../Control.Apply/index.js":"QcLv","../Control.Category/index.js":"IAi2","../Data.Foldable/index.js":"eVDl","../Data.Functor/index.js":"+0AE","../Data.Maybe/index.js":"5mN7","../Data.Maybe.First/index.js":"W/l6","../Data.Maybe.Last/index.js":"aQky","../Data.Monoid.Additive/index.js":"fHyj","../Data.Monoid.Conj/index.js":"U/G5","../Data.Monoid.Disj/index.js":"9bR7","../Data.Monoid.Dual/index.js":"ULyl","../Data.Monoid.Multiplicative/index.js":"y5cd","../Data.Traversable.Accum.Internal/index.js":"LbSr"}],"8nb9":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),t=require("../Control.Category/index.js"),u=require("../Data.Bifoldable/index.js"),e=require("../Data.Bifunctor/index.js"),i=require("../Data.Bifunctor.Clown/index.js"),o=require("../Data.Bifunctor.Flip/index.js"),c=require("../Data.Bifunctor.Joker/index.js"),f=require("../Data.Bifunctor.Product/index.js"),a=require("../Data.Bifunctor.Wrap/index.js"),l=require("../Data.Functor/index.js"),p=require("../Data.Traversable/index.js"),b=function(n,r,t,u){this.Bifoldable1=n,this.Bifunctor0=r,this.bisequence=t,this.bitraverse=u},s=function(n){return n.bitraverse},d=function(r){return function(t){return function(u){return function(e){return s(r)(t)(e)(n.pure(t))(u)}}}},F=function(r){return function(t){return function(u){return s(r)(t)(u)(n.pure(t))}}},v=function(r){return function(t){return function(u){return function(e){return s(r)(t)(n.pure(t))(e)(u)}}}},y=function(r){return function(t){return 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+},{"../Control.Applicative/index.js":"qYya","../Control.Apply/index.js":"QcLv","../Control.Category/index.js":"IAi2","../Data.Bifoldable/index.js":"wjQo","../Data.Bifunctor/index.js":"e2Wc","../Data.Bifunctor.Clown/index.js":"Wuz6","../Data.Bifunctor.Flip/index.js":"EM73","../Data.Bifunctor.Joker/index.js":"O/Oh","../Data.Bifunctor.Product/index.js":"U+97","../Data.Bifunctor.Wrap/index.js":"U78Q","../Data.Functor/index.js":"+0AE","../Data.Traversable/index.js":"n7EE"}],"ZgoH":[function(require,module,exports) { +"use strict";exports.mapWithIndexArray=function(r){return function(t){for(var n=t.length,e=Array(n),u=0;u=0&&r=0&&n0?n(r.pop()):t}}}},exports.pushAll=function(n){return function(t){return function(){return t.push.apply(t,n)}}},exports.shiftImpl=function(n){return function(t){return function(r){return function(){return r.length>0?n(r.shift()):t}}}},exports.unshiftAll=function(n){return function(t){return function(){return 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n=require("./foreign.js"),e=require("../Data.Function/index.js"),r=require("../Data.Functor/index.js"),u=require("../Data.Maybe/index.js"),t=require("../Data.Traversable/index.js"),i=require("../Data.Tuple/index.js"),o=require("../Data.Unfoldable1/index.js"),a=require("../Data.Unit/index.js"),f=function(n,e){this.Unfoldable10=n,this.unfoldr=e},l=function(n){return n.unfoldr},c=new f(function(){return o.unfoldable1Array},n.unfoldrArrayImpl(u.isNothing)(u.fromJust())(i.fst)(i.snd)),s=function(n){return function(e){return function(r){return l(n)(function(n){return n<=0?u.Nothing.value:new u.Just(new i.Tuple(r,n-1|0))})(e)}}},d=function(n){return function(e){return function(r){return function(u){return function(i){return t.sequence(r)(n)(s(e)(u)(i))}}}}},b=function(n){return l(n)(e.const(u.Nothing.value))(a.unit)},p=function(n){return l(n)(function(n){return 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n=require("./foreign.js"),r=require("../Control.Alt/index.js"),t=require("../Control.Applicative/index.js"),e=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),i=require("../Control.Category/index.js"),o=require("../Control.Lazy/index.js"),a=require("../Control.Monad.Rec.Class/index.js"),c=require("../Control.Monad.ST.Internal/index.js"),f=require("../Data.Array.ST/index.js"),l=require("../Data.Array.ST.Iterator/index.js"),s=require("../Data.Boolean/index.js"),p=require("../Data.Eq/index.js"),d=require("../Data.Foldable/index.js"),h=require("../Data.Function/index.js"),m=require("../Data.Functor/index.js"),v=require("../Data.HeytingAlgebra/index.js"),y=require("../Data.Maybe/index.js"),g=require("../Data.Ord/index.js"),A=require("../Data.Ordering/index.js"),q=require("../Data.Semigroup/index.js"),x=require("../Data.Traversable/index.js"),w=require("../Data.Tuple/index.js"),b=require("../Data.Unfoldable/index.js"),F=function(r){return function(t){return 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t?function(t){if(l(t)){if(t!==c(t))throw new Error(t+" is not an integer.");return new p(t)}return G(t.toString())}(t):"string"==typeof t?G(t):t}s.prototype.toArray=function(t){return $(this,t)},p.prototype.toArray=function(t){return $(this,t)},s.prototype.toString=function(t){if(void 0===t&&(t=10),10!==t)return F(this,t);for(var r,e=this.value,n=e.length,o=String(e[--n]);--n>=0;)r=String(e[n]),o+="0000000".slice(r.length)+r;return(this.sign?"-":"")+o},p.prototype.toString=function(t){return void 0===t&&(t=10),10!=t?F(this,t):String(this.value)},s.prototype.toJSON=p.prototype.toJSON=function(){return this.toString()},s.prototype.valueOf=function(){return parseInt(this.toString(),10)},s.prototype.toJSNumber=s.prototype.valueOf,p.prototype.valueOf=function(){return this.value},p.prototype.toJSNumber=p.prototype.valueOf;for(var K=0;K<1e3;K++)u[K]=new p(K),K>0&&(u[-K]=new p(-K));return u.one=u[1],u.zero=u[0],u.minusOne=u[-1],u.max=D,u.min=U,u.gcd=k,u.lcm=function(t,r){return t=H(t).abs(),r=H(r).abs(),t.divide(k(t,r)).multiply(r)},u.isInstance=function(t){return t instanceof s||t instanceof p},u.randBetween=function(t,r){var n=U(t=H(t),r=H(r)),o=D(t,r).subtract(n).add(1);if(o.isSmall)return n.add(Math.floor(Math.random()*o));for(var i=[],a=!0,u=o.value.length-1;u>=0;u--){var l=a?o.value[u]:e,f=c(Math.random()*l);i.unshift(f),f0?Math.floor(n):Math.ceil(n)}exports["fromBase'"]=function(r){return function(t){return function(u){return function(e){try{var o=n(e,u);return r(o)}catch(i){return t}}}}},exports["fromNumber'"]=function(t){return function(u){return function(e){try{var o=n(r(e));return t(o)}catch(i){return u}}}},exports.fromInt=function(r){return n(r)},exports.toBase=function(n){return function(r){return r.toString(n)}},exports.toNumber=function(n){return n.toJSNumber()},exports.biAdd=function(n){return function(r){return n.add(r)}},exports.biMul=function(n){return function(r){return n.multiply(r)}},exports.biSub=function(n){return function(r){return 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+},{"big-integer":"9xaU"}],"2lBd":[function(require,module,exports) { +"use strict";exports.fromNumberImpl=function(r){return function(n){return function(t){return(0|t)===t?r(t):n}}},exports.toNumber=function(r){return r},exports.fromStringAsImpl=function(r){return function(n){return function(t){var u;u=t<11?"[0-"+(t-1).toString()+"]":11===t?"[0-9a]":"[0-9a-"+String.fromCharCode(86+t)+"]";var o=new RegExp("^[\\+\\-]?"+u+"+$","i");return function(u){if(o.test(u)){var e=parseInt(u,t);return(0|e)===e?r(e):n}return n}}}},exports.toStringAs=function(r){return function(n){return n.toString(r)}},exports.quot=function(r){return function(n){return r/n|0}},exports.rem=function(r){return function(n){return r%n}},exports.pow=function(r){return function(n){return 0|Math.pow(r,n)}}; +},{}],"xYq2":[function(require,module,exports) { +"use strict";var n=require("../Data.Ring/index.js"),i=require("../Data.Semiring/index.js"),r=function(n,i){this.Ring0=n,this.recip=i},e=function(n){return n.recip},t=function(n){return function(r){return function(t){return i.mul(n.Ring0().Semiring0())(r)(e(n)(t))}}},u=function(n){return function(r){return function(t){return i.mul(n.Ring0().Semiring0())(e(n)(t))(r)}}},c=new r(function(){return n.ringNumber},function(n){return 1/n});module.exports={DivisionRing:r,recip:e,leftDiv:u,rightDiv:t,divisionringNumber:c}; +},{"../Data.Ring/index.js":"E2qH","../Data.Semiring/index.js":"11NF"}],"pJ2E":[function(require,module,exports) { +"use strict";exports.nan=NaN,exports.isNaN=isNaN,exports.infinity=1/0,exports.isFinite=isFinite,exports.readInt=function(t){return function(e){return parseInt(e,t)}},exports.readFloat=parseFloat; +},{}],"aQlK":[function(require,module,exports) { +"use strict";var i=require("./foreign.js");module.exports={nan:i.nan,isNaN:i.isNaN,infinity:i.infinity,isFinite:i.isFinite,readInt:i.readInt,readFloat:i.readFloat}; +},{"./foreign.js":"pJ2E"}],"9/+z":[function(require,module,exports) { +"use strict";exports.abs=Math.abs,exports.acos=Math.acos,exports.asin=Math.asin,exports.atan=Math.atan,exports.atan2=function(t){return function(r){return Math.atan2(t,r)}},exports.ceil=Math.ceil,exports.cos=Math.cos,exports.exp=Math.exp,exports.floor=Math.floor,exports.trunc=Math.trunc||function(t){return t<0?Math.ceil(t):Math.floor(t)},exports.log=Math.log,exports.max=function(t){return function(r){return Math.max(t,r)}},exports.min=function(t){return function(r){return Math.min(t,r)}},exports.pow=function(t){return function(r){return Math.pow(t,r)}},exports.remainder=function(t){return function(r){return t%r}},exports.round=Math.round,exports.sin=Math.sin,exports.sqrt=Math.sqrt,exports.tan=Math.tan,exports.e=Math.E,exports.ln2=Math.LN2,exports.ln10=Math.LN10,exports.log2e=Math.LOG2E,exports.log10e=Math.LOG10E,exports.pi=Math.PI,exports.tau=2*Math.PI,exports.sqrt1_2=Math.SQRT1_2,exports.sqrt2=Math.SQRT2; +},{}],"Rpaz":[function(require,module,exports) { +"use strict";var a=require("./foreign.js");module.exports={abs:a.abs,acos:a.acos,asin:a.asin,atan:a.atan,atan2:a.atan2,ceil:a.ceil,cos:a.cos,exp:a.exp,floor:a.floor,log:a.log,max:a.max,min:a.min,pow:a.pow,round:a.round,sin:a.sin,sqrt:a.sqrt,tan:a.tan,trunc:a.trunc,remainder:a.remainder,e:a.e,ln2:a.ln2,ln10:a.ln10,log2e:a.log2e,log10e:a.log10e,pi:a.pi,tau:a.tau,sqrt1_2:a.sqrt1_2,sqrt2:a.sqrt2}; +},{"./foreign.js":"9/+z"}],"xNJb":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),e=require("../Control.Category/index.js"),t=require("../Data.Boolean/index.js"),r=require("../Data.Bounded/index.js"),i=require("../Data.CommutativeRing/index.js"),u=require("../Data.DivisionRing/index.js"),o=require("../Data.Eq/index.js"),a=require("../Data.EuclideanRing/index.js"),c=require("../Data.Maybe/index.js"),f=require("../Data.Ord/index.js"),l=require("../Data.Ordering/index.js"),d=require("../Data.Ring/index.js"),s=require("../Data.Semiring/index.js"),m=require("../Data.Show/index.js"),v=require("../Global/index.js"),w=require("../Math/index.js"),g=function(n){return n},q=function(){function n(){}return n.value=new n,n}(),h=function(){function n(){}return n.value=new n,n}(),D=new m.Show(function(n){if(n instanceof q)return"Even";if(n instanceof h)return"Odd";throw new Error("Failed pattern match at Data.Int (line 112, column 1 - line 114, column 19): "+[n.constructor.name])}),b=function(n){if(n>=2&&n<=36)return new c.Just(n);if(t.otherwise)return 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+},{"./foreign.js":"2lBd","../Control.Category/index.js":"IAi2","../Data.Boolean/index.js":"ObQr","../Data.Bounded/index.js":"kcUU","../Data.CommutativeRing/index.js":"60TQ","../Data.DivisionRing/index.js":"xYq2","../Data.Eq/index.js":"Pq4F","../Data.EuclideanRing/index.js":"2IRB","../Data.Maybe/index.js":"5mN7","../Data.Ord/index.js":"r4Vb","../Data.Ordering/index.js":"5Eun","../Data.Ring/index.js":"E2qH","../Data.Semiring/index.js":"11NF","../Data.Show/index.js":"mFY7","../Global/index.js":"aQlK","../Math/index.js":"Rpaz"}],"g11n":[function(require,module,exports) { +"use strict";exports.fromCharArray=function(n){return n.join("")},exports.toCharArray=function(n){return n.split("")},exports.singleton=function(n){return n},exports._charAt=function(n){return function(t){return function(r){return function(u){return r>=0&&re.length)return t;var o=e.indexOf(r,u);return-1===o?t:n(o)}}}}},exports._lastIndexOf=function(n){return function(t){return function(r){return function(u){var 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e=require("./foreign.js"),r=require("../Data.Ordering/index.js"),l=function(e){return""===e},o=e._localeCompare(r.LT.value)(r.EQ.value)(r.GT.value);module.exports={null:l,localeCompare:o,replace:e.replace,replaceAll:e.replaceAll,split:e.split,toLower:e.toLower,toUpper:e.toUpper,trim:e.trim,joinWith:e.joinWith}; +},{"./foreign.js":"B+B2","../Data.Ordering/index.js":"5Eun"}],"Ph6A":[function(require,module,exports) { +"use strict";var n=require("../Control.Bind/index.js"),r=require("../Data.Eq/index.js"),t=require("../Data.Foldable/index.js"),e=require("../Data.Maybe/index.js"),i=require("../Data.Monoid/index.js"),o=require("../Data.Ord/index.js"),u=require("../Data.Semigroup/index.js"),c=require("../Data.Show/index.js"),a=require("../Data.String.CodeUnits/index.js"),f=require("../Data.String.Common/index.js"),p=require("../Data.Symbol/index.js"),m=function(n){return n},s=function(n){return n},l=function(n){this.nes=n},d=function(n){return f.toUpper(n)},S=function(n){return 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t=U(n.Foldable0())(r);return function(n){return m(t(n))}}},k=function(n){return""===n?e.Nothing.value:new e.Just(n)},A=function(r){return n.composeKleisliFlipped(e.bindMaybe)(k)(C(a.stripPrefix(r)))},B=function(r){return n.composeKleisliFlipped(e.bindMaybe)(k)(C(a.stripSuffix(r)))},J=function(n){return k(f.trim(n))},K=function(n){var r=e.fromJust(n);return function(n){return r(k(n))}},L=r.eqString,P=L,O=function(n){return C(a.contains(n))},z=function(n){return function(r){return n+r}};module.exports={nes:F,NonEmptyString:m,MakeNonEmpty:l,NonEmptyReplacement:s,fromString:k,unsafeFromString:K,toString:S,appendString:z,prependString:j,stripPrefix:A,stripSuffix:B,contains:O,localeCompare:R,replace:w,replaceAll:q,toLower:g,toUpper:d,trim:J,joinWith:U,join1With:W,joinWith1:M,liftS:C,eqNonEmptyString:L,ordNonEmptyString:h,semigroupNonEmptyString:x,showNonEmptyString:y,makeNonEmptyBad:v,nonEmptyNonEmpty:D,eqNonEmptyReplacement:P,ordNonEmptyReplacement:b,semigroupNonEmptyReplacement:N,showNonEmptyReplacement:E}; +},{"../Control.Bind/index.js":"7VcT","../Data.Eq/index.js":"Pq4F","../Data.Foldable/index.js":"eVDl","../Data.Maybe/index.js":"5mN7","../Data.Monoid/index.js":"TiEB","../Data.Ord/index.js":"r4Vb","../Data.Semigroup/index.js":"EsAJ","../Data.Show/index.js":"mFY7","../Data.String.CodeUnits/index.js":"6c6X","../Data.String.Common/index.js":"OSrc","../Data.Symbol/index.js":"4oJQ"}],"Zx+T":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),e=require("../Data.CommutativeRing/index.js"),r=require("../Data.Eq/index.js"),i=require("../Data.EuclideanRing/index.js"),t=require("../Data.Int/index.js"),o=require("../Data.Maybe/index.js"),u=require("../Data.Ord/index.js"),a=require("../Data.Ordering/index.js"),s=require("../Data.Ring/index.js"),d=require("../Data.Semiring/index.js"),m=require("../Data.Show/index.js"),g=require("../Data.String.NonEmpty.Internal/index.js"),f=n.toBase(10),b=function(e){return function(r){return o.fromJust()(g.fromString(n.toBase(e)(r)))}},c=b(10),q=new m.Show(function(n){return'fromString "'+f(n)+'"'}),B=new d.Semiring(n.biAdd,n.biMul,n.fromInt(1),n.fromInt(0)),l=new s.Ring(function(){return B},n.biSub),v=n.biMod,I=n.biDiv,x=n["fromNumber'"](o.Just.create)(o.Nothing.value),D=n["fromBase'"](o.Just.create)(o.Nothing.value),j=D(10),w=new r.Eq(n.biEquals),S=new u.Ord(function(){return w},function(e){return function(r){var i=n.biCompare(e)(r);return 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n=require("../Control.Alt/index.js"),e=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),t=require("../Control.Category/index.js"),u=require("../Control.Plus/index.js"),o=require("../Data.Eq/index.js"),i=require("../Data.Foldable/index.js"),a=require("../Data.FoldableWithIndex/index.js"),l=require("../Data.Functor/index.js"),c=require("../Data.FunctorWithIndex/index.js"),f=require("../Data.Maybe/index.js"),d=require("../Data.Ord/index.js"),p=require("../Data.Ordering/index.js"),v=require("../Data.Semigroup/index.js"),s=require("../Data.Semigroup.Foldable/index.js"),x=require("../Data.Show/index.js"),q=require("../Data.Traversable/index.js"),m=require("../Data.TraversableWithIndex/index.js"),y=require("../Data.Tuple/index.js"),h=require("../Data.Unfoldable/index.js"),b=require("../Data.Unfoldable1/index.js"),w=function(){function n(n,e){this.value0=n,this.value1=e}return n.create=function(e){return function(r){return new n(e,r)}},n}(),j=function(n){return 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n=require("../Control.Alt/index.js"),e=require("../Control.Alternative/index.js"),t=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),i=require("../Control.Category/index.js"),o=require("../Control.Comonad/index.js"),a=require("../Control.Extend/index.js"),l=require("../Control.Monad/index.js"),c=require("../Control.MonadPlus/index.js"),f=require("../Control.MonadZero/index.js"),v=require("../Control.Plus/index.js"),s=require("../Data.Eq/index.js"),d=require("../Data.Foldable/index.js"),p=require("../Data.FoldableWithIndex/index.js"),m=require("../Data.Function/index.js"),w=require("../Data.Functor/index.js"),y=require("../Data.FunctorWithIndex/index.js"),x=require("../Data.Maybe/index.js"),E=require("../Data.Monoid/index.js"),L=require("../Data.Newtype/index.js"),h=require("../Data.NonEmpty/index.js"),N=require("../Data.Ord/index.js"),b=require("../Data.Ordering/index.js"),q=require("../Data.Semigroup/index.js"),j=require("../Data.Semigroup.Traversable/index.js"),I=require("../Data.Semiring/index.js"),D=require("../Data.Show/index.js"),W=require("../Data.Traversable/index.js"),F=require("../Data.TraversableWithIndex/index.js"),T=require("../Data.Tuple/index.js"),g=require("../Data.Unfoldable/index.js"),C=require("../Data.Unfoldable1/index.js"),A=function(){function 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d.foldl(Q)(m.flip(U))(t.pure(Fn)(n.value0))(n.value1)})}}});module.exports={Nil:A,Cons:M,NonEmptyList:S,toList:P,nelCons:U,showList:Y,eqList:vn,eq1List:fn,ordList:pn,ord1List:dn,semigroupList:R,monoidList:V,functorList:Z,functorWithIndexList:H,foldableList:Q,foldableWithIndexList:k,unfoldable1List:rn,unfoldableList:un,traversableList:_,traversableWithIndexList:en,applyList:yn,applicativeList:hn,bindList:En,monadList:Nn,altList:qn,plusList:jn,alternativeList:In,monadZeroList:Dn,monadPlusList:Wn,extendList:cn,newtypeNonEmptyList:O,eqNonEmptyList:sn,ordNonEmptyList:mn,showNonEmptyList:$,functorNonEmptyList:J,applyNonEmptyList:xn,applicativeNonEmptyList:Fn,bindNonEmptyList:Ln,monadNonEmptyList:Tn,altNonEmptyList:bn,extendNonEmptyList:ln,comonadNonEmptyList:wn,semigroupNonEmptyList:X,foldableNonEmptyList:G,traversableNonEmptyList:nn,foldable1NonEmptyList:an,unfoldable1NonEmptyList:on,functorWithIndexNonEmptyList:K,foldableWithIndexNonEmptyList:z,traversableWithIndexNonEmptyList:tn,traversable1NonEmptyList:gn}; 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T.TraversableWithIndex(function(){return cn},function(){return ln},function(){return vn},function(n){return function(t){return function(e){return w.map(n.Apply0().Functor0())(function(n){return P(x.defer(function(t){return n}))})(T.traverseWithIndex(N.traversableWithIndexNonEmpty(mn))(n)((r=h.maybe(0)(D.add(D.semiringInt)(1)),function(n){return t(r(n))}))(x.force(e)));var r}}}),wn=new A.Unfoldable1(function n(t){return function(e){return c.defer(H)(function(r){var u=t(e);if(u.value1 instanceof h.Just)return tn(u.value0)(n(t)(u.value1.value0));if(u.value1 instanceof h.Nothing)return tn(u.value0)(U);throw new Error("Failed pattern match at Data.List.Lazy.Types (line 146, column 28 - line 148, column 33): "+[u.constructor.name])})}}),Ln=new g.Unfoldable(function(){return wn},function n(t){return function(e){return c.defer(H)(function(r){var u=t(e);if(u instanceof h.Nothing)return U;if(u instanceof h.Just)return tn(u.value0.value0)(n(t)(u.value0.value1));throw new Error("Failed pattern 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{ +"use strict";var 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t.foldr(p.foldableList)(e)(n)(A(u))}}}),ee=new M.Traversable(function(){return _},function(){return R},function(e){return M.traverse(ee)(e)(u.identity(u.categoryFn))},function(u){return function(a){return function(t){if(t instanceof F)return e.pure(u)(F.value);if(t instanceof T)return n.apply(u.Apply0())(n.apply(u.Apply0())(n.apply(u.Apply0())(v.map(u.Apply0().Functor0())(T.create)(M.traverse(ee)(u)(a)(t.value0)))(e.pure(u)(t.value1)))(a(t.value2)))(M.traverse(ee)(u)(a)(t.value3));if(t instanceof b)return n.apply(u.Apply0())(n.apply(u.Apply0())(n.apply(u.Apply0())(n.apply(u.Apply0())(n.apply(u.Apply0())(n.apply(u.Apply0())(v.map(u.Apply0().Functor0())(b.create)(M.traverse(ee)(u)(a)(t.value0)))(e.pure(u)(t.value1)))(a(t.value2)))(M.traverse(ee)(u)(a)(t.value3)))(e.pure(u)(t.value4)))(a(t.value5)))(M.traverse(ee)(u)(a)(t.value6));throw new Error("Failed pattern match at Data.Map.Internal (line 119, column 1 - line 134, column 31): 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t=require("../Control.Alt/index.js"),e=require("../Control.Alternative/index.js"),n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),a=require("../Control.Bind/index.js"),i=require("../Control.Plus/index.js"),u=require("../Data.Array/index.js"),o=require("../Data.Either/index.js"),l=require("../Data.Foldable/index.js"),c=require("../Data.Function/index.js"),f=require("../Data.Functor/index.js"),s=require("../Data.List/index.js"),m=require("../Data.List.Types/index.js"),p=require("../Data.Map.Internal/index.js"),h=require("../Data.Maybe/index.js"),v=require("../Data.Monoid/index.js"),d=require("../Data.Unit/index.js"),w=function(t,e){this.compact=t,this.separate=e},g=function(e){return function(r){return function(a){return l.foldl(r)(function(r){return function(a){if(a instanceof o.Left)return{left:t.alt(e.Plus1().Alt0())(r.left)(n.pure(e.Applicative0())(a.value0)),right:r.right};if(a instanceof 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n=require("../Data.Foldable/index.js"),e=require("../Data.Generic.Rep/index.js"),r=require("../Data.Monoid/index.js"),t=require("../Data.Semigroup/index.js"),o=require("../Data.Show/index.js"),i=require("../Data.Symbol/index.js"),u=function(n){this.genericShowArgs=n},c=function(n){this["genericShow'"]=n},a=new u(function(n){return[]}),s=function(n){return new u(function(e){return[o.show(n)(e)]})},f=function(n){return n.genericShowArgs},g=function(n){return function(e){return new u(function(r){return t.append(t.semigroupArray)(f(n)(r.value0))(f(e)(r.value1))})}},w=function(e){return function(o){return new c(function(u){var c=i.reflectSymbol(o)(i.SProxy.value),a=f(e)(u);return 0===a.length?c:"("+n.intercalate(n.foldableArray)(r.monoidString)(" ")(t.append(t.semigroupArray)([c])(a))+")"})}},h=function(n){return n["genericShow'"]},S=new c(function(n){return h(S)(n)}),l=function(n){return function(r){return new c(function(t){if(t instanceof e.Inl)return h(n)(t.value0);if(t instanceof 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u(n)(r)}}};module.exports={cmap:u,Contravariant:t,cmapFlipped:e,coerce:i,imapC:c}; +},{"../Data.Functor/index.js":"+0AE","../Data.Void/index.js":"bncE"}],"OmNG":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),t=require("../Control.Semigroupoid/index.js"),e=require("../Data.Bifoldable/index.js"),u=require("../Data.Bifunctor/index.js"),i=require("../Data.Bitraversable/index.js"),o=require("../Data.Eq/index.js"),c=require("../Data.Foldable/index.js"),f=require("../Data.FoldableWithIndex/index.js"),a=require("../Data.Functor/index.js"),s=require("../Data.Functor.Contravariant/index.js"),d=require("../Data.Functor.Invariant/index.js"),l=require("../Data.FunctorWithIndex/index.js"),p=require("../Data.Monoid/index.js"),C=require("../Data.Newtype/index.js"),x=require("../Data.Ord/index.js"),q=require("../Data.Semigroup/index.js"),b=require("../Data.Show/index.js"),w=require("../Data.Traversable/index.js"),m=require("../Data.TraversableWithIndex/index.js"),j=function(n){return n},v=function(n){return new b.Show(function(r){return"(Const "+b.show(n)(r)+")"})},D=function(n){return n},h=new 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+},{"../Control.Applicative/index.js":"qYya","../Control.Apply/index.js":"QcLv","../Control.Semigroupoid/index.js":"/riR","../Data.Bifoldable/index.js":"wjQo","../Data.Bifunctor/index.js":"e2Wc","../Data.Bitraversable/index.js":"8nb9","../Data.Eq/index.js":"Pq4F","../Data.Foldable/index.js":"eVDl","../Data.FoldableWithIndex/index.js":"9Efi","../Data.Functor/index.js":"+0AE","../Data.Functor.Contravariant/index.js":"89+t","../Data.Functor.Invariant/index.js":"AXkC","../Data.FunctorWithIndex/index.js":"OHRN","../Data.Monoid/index.js":"TiEB","../Data.Newtype/index.js":"lz8k","../Data.Ord/index.js":"r4Vb","../Data.Semigroup/index.js":"EsAJ","../Data.Show/index.js":"mFY7","../Data.Traversable/index.js":"n7EE","../Data.TraversableWithIndex/index.js":"V4EF"}],"0DaD":[function(require,module,exports) { +"use strict";var n=require("../Control.Category/index.js"),r=require("../Data.Newtype/index.js"),t=function(n){this.dimap=n},u=new t(function(n){return function(r){return function(t){return 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+},{"../Control.Category/index.js":"IAi2","../Control.Semigroupoid/index.js":"/riR","../Data.Either/index.js":"B2JL","../Data.Functor/index.js":"+0AE","../Data.Profunctor/index.js":"0DaD"}],"af4y":[function(require,module,exports) { +"use strict";var o=require("../Control.Semigroupoid/index.js"),e=require("../Data.Profunctor/index.js"),r=function(o,e){this.Profunctor0=o,this.closed=e},n=new r(function(){return e.profunctorFn},o.compose(o.semigroupoidFn)),t=function(o){return o.closed};module.exports={closed:t,Closed:r,closedFunction:n}; +},{"../Control.Semigroupoid/index.js":"/riR","../Data.Profunctor/index.js":"0DaD"}],"w9p6":[function(require,module,exports) { +"use strict";var n=require("../Control.Category/index.js"),r=require("../Control.Semigroupoid/index.js"),t=require("../Data.Functor/index.js"),e=require("../Data.Profunctor/index.js"),u=require("../Data.Tuple/index.js"),o=function(n,r,t){this.Profunctor0=n,this.first=r,this.second=t},i=new o(function(){return 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n=require("../Control.Alt/index.js"),r=require("../Control.Alternative/index.js"),t=require("../Control.Applicative/index.js"),e=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),i=require("../Control.Category/index.js"),o=require("../Control.Monad/index.js"),c=require("../Control.MonadPlus/index.js"),a=require("../Control.MonadZero/index.js"),f=require("../Control.Plus/index.js"),l=require("../Control.Semigroupoid/index.js"),p=require("../Data.Distributive/index.js"),d=require("../Data.Either/index.js"),s=require("../Data.Functor/index.js"),v=require("../Data.Functor.Invariant/index.js"),S=require("../Data.Newtype/index.js"),w=require("../Data.Profunctor/index.js"),x=require("../Data.Profunctor.Choice/index.js"),j=require("../Data.Profunctor.Closed/index.js"),q=require("../Data.Profunctor.Strong/index.js"),A=require("../Data.Tuple/index.js"),C=function(n){return n},m=function(n){return new l.Semigroupoid(function(r){return function(t){return function(e){return 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u(i(n))}}},function(n){return function(t){return function(e){return p.collect(r)(n)(function(n){return n(e)})(t)}}})},M=function(n){return new j.Closed(function(){return y(n.Functor0())},function(r){return function(t){return p.distribute(n)(s.functorFn)(function(n){return r(t(n))})}})},B=function(n){return new x.Choice(function(){return y(n.Apply0().Functor0())},function(r){return C(d.either((u=s.map(n.Apply0().Functor0())(d.Left.create),function(n){return u(r(n))}))((e=t.pure(n),function(n){return e(d.Right.create(n))})));var e,u},function(r){return C(d.either((u=t.pure(n),function(n){return u(d.Left.create(n))}))((e=s.map(n.Apply0().Functor0())(d.Right.create),function(n){return e(r(n))})));var e,u})},Z=function(n){return new i.Category(function(){return m(n.Bind1())},t.pure(n.Applicative0()))},T=function(n){return new e.Apply(function(){return h(n.Functor0())},function(r){return function(t){return function(u){return e.apply(n)(r(u))(t(u))}}})},I=function(n){return new u.Bind(function(){return T(n.Apply0())},function(r){return function(t){return function(e){return u.bind(n)(r(e))(function(n){return t(n)(e)})}}})},L=function(n){return new t.Applicative(function(){return T(n.Apply0())},function(r){return function(e){return t.pure(n)(r)}})},N=function(n){return new o.Monad(function(){return L(n.Applicative0())},function(){return I(n.Bind1())})},R=function(r){return new n.Alt(function(){return h(r.Functor0())},function(t){return function(e){return function(u){return n.alt(r)(t(u))(e(u))}}})},E=function(n){return new f.Plus(function(){return R(n.Alt0())},function(r){return f.empty(n)})},k=function(n){return new r.Alternative(function(){return L(n.Applicative0())},function(){return E(n.Plus1())})},z=function(n){return new a.MonadZero(function(){return k(n.Alternative1())},function(){return N(n.Monad0())})},G=function(n){return new c.MonadPlus(function(){return 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n=require("../Data.Functor/index.js"),t=require("../Data.Identity/index.js"),r=require("../Data.Newtype/index.js"),e=require("../Data.Profunctor.Choice/index.js"),i=require("../Data.Profunctor.Star/index.js"),u=require("../Data.Profunctor.Strong/index.js"),o=function(n,t,r){this.Choice1=n,this.Strong0=t,this.wander=r},a=function(n){return new o(function(){return i.choiceStar(n)},function(){return i.strongStar(n.Apply0().Functor0())},function(t){return function(r){return t(n)(r)}})},c=new o(function(){return e.choiceFn},function(){return u.strongFn},function(e){return r.alaF(n.functorFn)(n.functorFn)(t.newtypeIdentity)(t.newtypeIdentity)(t.Identity)(e(t.applicativeIdentity))}),d=function(n){return n.wander};module.exports={wander:d,Wander:o,wanderFunction:c,wanderStar:a}; 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n=require("../Data.Const/index.js"),r=require("../Data.Either/index.js"),e=require("../Data.Functor/index.js"),t=require("../Data.Lens.Internal.Wander/index.js"),o=require("../Data.Monoid/index.js"),u=require("../Data.Newtype/index.js"),i=require("../Data.Profunctor/index.js"),c=require("../Data.Profunctor.Choice/index.js"),f=require("../Data.Profunctor.Cochoice/index.js"),a=require("../Data.Profunctor.Strong/index.js"),s=require("../Data.Semigroup/index.js"),d=require("../Data.Tuple/index.js"),F=function(n){return n},g=function(n){return s.semigroupFn(n)},p=new i.Profunctor(function(n){return function(r){return function(r){return function(e){return r(n(e))}}}}),x=new a.Strong(function(){return p},function(n){return function(r){return n(d.fst(r))}},function(n){return function(r){return n(d.snd(r))}}),j=new u.Newtype(function(n){return n},F),m=function(n){return o.monoidFn(n)},q=new f.Cochoice(function(){return p},function(n){return function(e){return 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+},{"../Data.Const/index.js":"OmNG","../Data.Either/index.js":"B2JL","../Data.Functor/index.js":"+0AE","../Data.Lens.Internal.Wander/index.js":"i7fd","../Data.Monoid/index.js":"TiEB","../Data.Newtype/index.js":"lz8k","../Data.Profunctor/index.js":"0DaD","../Data.Profunctor.Choice/index.js":"nkqb","../Data.Profunctor.Cochoice/index.js":"FnLc","../Data.Profunctor.Strong/index.js":"w9p6","../Data.Semigroup/index.js":"EsAJ","../Data.Tuple/index.js":"II/O"}],"V4/H":[function(require,module,exports) { +"use strict";var e=require("../Data.Either/index.js"),n=require("../Data.Lens.Internal.Wander/index.js"),r=require("../Data.Newtype/index.js"),t=require("../Data.Profunctor/index.js"),u=require("../Data.Profunctor.Choice/index.js"),o=require("../Data.Profunctor.Strong/index.js"),c=require("../Data.Tuple/index.js"),i=function(e){return e},a=function(e){return new t.Profunctor(function(n){return function(r){return function(u){return 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n=require("../Control.Category/index.js"),e=require("../Control.Monad.State.Class/index.js"),t=require("../Data.Lens.Internal.Forget/index.js"),r=require("../Data.Lens.Internal.Indexed/index.js"),u=require("../Data.Newtype/index.js"),o=require("../Data.Profunctor.Strong/index.js"),i=function(e){return u.unwrap(t.newtypeForget)(e(n.identity(n.categoryFn)))},a=function(n){return function(e){return i(e)(n)}},c=function(n){return function(t){return e.gets(n)(function(n){return a(n)(t)})}},s=function(n){return function(e){var r=u.unwrap(t.newtypeForget)(e);return function(e){return r(n(e))}}},f=function(e){return function(t){return s(o.fanout(n.categoryFn)(o.strongFn)(i(e))(i(t)))}},d=function(e){return u.unwrap(t.newtypeForget)(e(r.Indexed(n.identity(n.categoryFn))))},g=function(n){return function(t){return e.gets(n)(d(t))}},w=function(n){return s(i(n))};module.exports={viewOn:a,view:i,to:s,takeBoth:f,use:c,iview:d,iuse:g,cloneGetter:w}; +},{"../Control.Category/index.js":"IAi2","../Control.Monad.State.Class/index.js":"u1pL","../Data.Lens.Internal.Forget/index.js":"mj9z","../Data.Lens.Internal.Indexed/index.js":"V4/H","../Data.Newtype/index.js":"lz8k","../Data.Profunctor.Strong/index.js":"w9p6"}],"eUa0":[function(require,module,exports) { +"use strict";var n=require("../Data.Functor/index.js"),r=require("../Data.Profunctor/index.js"),u=function(){function n(n,r){this.value0=n,this.value1=r}return n.create=function(r){return function(u){return new n(r,u)}},n}(),t=new r.Profunctor(function(n){return function(r){return function(t){return new u(function(r){return t.value0(n(r))},function(n){return r(t.value1(n))})}}}),e=new n.Functor(function(n){return function(r){return new u(r.value0,function(u){return n(r.value1(u))})}});module.exports={Exchange:u,functorExchange:e,profunctorExchange:t}; +},{"../Data.Functor/index.js":"+0AE","../Data.Profunctor/index.js":"0DaD"}],"NfU6":[function(require,module,exports) { +"use strict";var n=function(n,t,u){this.Profunctor0=n,this.unfirst=t,this.unsecond=u},t=function(n){return n.unsecond},u=function(n){return n.unfirst};module.exports={unfirst:u,unsecond:t,Costrong:n}; +},{}],"IZDD":[function(require,module,exports) { +"use strict";var n=require("../Data.Newtype/index.js"),r=require("../Data.Profunctor/index.js"),t=require("../Data.Profunctor.Choice/index.js"),u=require("../Data.Profunctor.Cochoice/index.js"),e=require("../Data.Profunctor.Costrong/index.js"),o=require("../Data.Profunctor.Strong/index.js"),c=function(n){return n},i=function(n){return new r.Profunctor(function(t){return function(u){return function(e){var o=r.dimap(n)(u)(t);return function(n){return e(o(n))}}}})},f=function(n){return new e.Costrong(function(){return i(n.Profunctor0())},function(r){var t=o.first(n);return function(n){return r(t(n))}},function(r){var t=o.second(n);return function(n){return r(t(n))}})},a=new n.Newtype(function(n){return n},c),s=function(n){return new 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strict";var n=require("../Control.Category/index.js"),r=require("../Data.Boolean/index.js"),t=require("../Data.Eq/index.js"),u=require("../Data.Function/index.js"),e=require("../Data.Functor/index.js"),i=require("../Data.Lens.Internal.Exchange/index.js"),o=require("../Data.Lens.Internal.Re/index.js"),c=require("../Data.Maybe/index.js"),f=require("../Data.Newtype/index.js"),a=require("../Data.Profunctor/index.js"),d=require("../Data.Tuple/index.js"),s=function(r){return function(t){var u=r(new i.Exchange(n.identity(n.categoryFn),n.identity(n.categoryFn)));return t(u.value0)(u.value1)}},p=function(n){return s(n)(function(n){return function(r){return function(t){return function(u){return n(t(r(u)))}}}})},l=function(r){return f.unwrap(o.newtypeRe)(r(n.identity(n.categoryFn)))},y=function(n){return function(r){return function(t){return function(u){return a.dimap(t)(n)(r)(u)}}}},m=function(n){return function(r){return function(t){return function(u){return s(t)(function(t){return function(i){return y(e.map(n)(t))(e.map(r)(i))(u)}})}}}},x=function(n){return function(u){return function(e){return y(c.fromMaybe(u))(function(e){if(t.eq(n)(e)(u))return c.Nothing.value;if(r.otherwise)return new c.Just(e);throw new Error("Failed pattern match at Data.Lens.Iso (line 45, column 9 - line 46, column 33): "+[e.constructor.name])})(e)}}},q=function(n){return y(d.uncurry)(d.curry)(n)},j=function(n){return y(u.flip)(u.flip)(n)},D=function(n){return function(r){return function(t){return function(u){return function(e){return s(t)(function(t){return function(i){return s(u)(function(u){return function(o){return y(a.dimap(n)(t)(u))(a.dimap(r)(i)(o))(e)}})}})}}}}},g=function(n){return y(d.curry)(d.uncurry)(n)},w=function(n){return function(r){return s(n)(function(n){return function(t){return function(u){return y(n)(t)(r)(u)}}})}},h=function(n){return function(r){return s(r)(function(r){return function(t){return function(u){return function(e){return function(i){return 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+},{"../Data.Lens.Iso/index.js":"fFCp","../Data.Newtype/index.js":"lz8k"}],"ONWB":[function(require,module,exports) { +"use strict";var o=function(o,e,t,s,n,i){this.Monad0=o,this.chooseBool=e,this.chooseFloat=t,this.chooseInt=s,this.resize=n,this.sized=i},e=function(o){return o.sized},t=function(o){return o.resize},s=function(o){return o.chooseInt},n=function(o){return o.chooseFloat},i=function(o){return o.chooseBool};module.exports={chooseBool:i,chooseFloat:n,chooseInt:s,resize:t,sized:e,MonadGen:o}; +},{}],"s7H0":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),e=require("../Control.Bind/index.js"),t=require("../Control.Monad.Gen.Class/index.js"),r=require("../Control.Monad.Rec.Class/index.js"),u=require("../Data.Boolean/index.js"),i=require("../Data.Foldable/index.js"),o=require("../Data.Function/index.js"),a=require("../Data.Functor/index.js"),c=require("../Data.Maybe/index.js"),l=require("../Data.Monoid.Additive/index.js"),d=require("../Data.Newtype/index.js"),f=require("../Data.Semigroup/index.js"),s=require("../Data.Semigroup.Foldable/index.js"),p=require("../Data.Semiring/index.js"),v=require("../Data.Tuple/index.js"),m=require("../Data.Unfoldable/index.js"),w=require("../Data.Unit/index.js"),M=function(){function n(n,e){this.value0=n,this.value1=e}return n.create=function(e){return function(t){return new n(e,t)}},n}(),h=function(){function n(){}return n.value=new n,n}(),F=function(n){return n},q=function(n){return n},x=function(i){return function(o){return function(l){return function(d){var 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function(t){return t<=0?n(t):e(t-1|0)}}}),b=function(n){return function(e){return v.snd(n(e))}},g=function(n){return n},A=function(n){return function(e){return e>=n.value0?new v.Tuple(new c.Just(e-n.value0),n.value1):new v.Tuple(c.Nothing.value,n.value1)}},B=function(n){return function(r){return function(u){var o=d.alaF(a.functorFn)(a.functorFn)(d.newtypeAdditive)(d.newtypeAdditive)(l.Additive)(i.foldMap(r.Foldable0())(l.monoidAdditive(p.semiringNumber)))(v.fst)(u);return e.bind(n.Monad0().Bind1())(t.chooseFloat(n)(0)(o))(b(s.foldMap1(r)(j)(A)(u)))}}},C=function(n){return function(e){return function(t){return r.tailRecM(n)(function(n){return a.mapFlipped(e.Monad0().Bind1().Apply0().Functor0())(t)(function(n){if(n instanceof c.Nothing)return new r.Loop(w.unit);if(n instanceof c.Just)return new r.Done(n.value0);throw new Error("Failed pattern match at Control.Monad.Gen (line 117, column 24 - line 119, column 23): "+[n.constructor.name])})})(w.unit)}}},y=function(n){return function(e){return function(t){return function(r){return C(n)(e)(a.mapFlipped(e.Monad0().Bind1().Apply0().Functor0())(t)(function(n){return r(n)?new c.Just(n):c.Nothing.value}))}}}},T=function(n){return function(r){return function(u){return e.bind(n.Monad0().Bind1())(t.chooseBool(n))(function(n){return n?r:u})}}},N=function(n){return q(o.const(n))},J=function(n){return function(e){return function(t){return g(s.foldMap1(n)(D)(N)(t))(e)}}},S=function(r){return function(u){return function(o){return e.bind(r.Monad0().Bind1())(t.chooseInt(r)(0)(i.length(u.Foldable0())(p.semiringInt)(o)-1|0))(function(e){return n.pure(r.Monad0().Applicative0())(J(u)(e)(o))})}}},G=function(n){return function(r){return function(u){return e.bind(n.Monad0().Bind1())(t.chooseInt(n)(0)(i.length(r.Foldable0())(p.semiringInt)(u)-1|0))(function(n){return J(r)(n)(u)})}}};module.exports={choose:T,oneOf:G,frequency:B,elements:S,unfoldable:x,suchThat:y,filtered:C}; 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n=require("../Control.Applicative/index.js"),e=require("../Control.Apply/index.js"),r=require("../Control.Bind/index.js"),t=require("../Control.Monad.Gen/index.js"),i=require("../Control.Monad.Gen.Class/index.js"),u=require("../Data.Either/index.js"),o=require("../Data.Functor/index.js"),a=require("../Data.Identity/index.js"),d=require("../Data.Maybe/index.js"),c=require("../Data.NonEmpty/index.js"),p=require("../Data.Ord/index.js"),l=require("../Data.Tuple/index.js"),f=function(n){return e.lift2(n)(l.Tuple.create)},s=function(n){return function(r){return function(u){return function(a){return e.apply(r.Monad0().Bind1().Apply0())(o.map(r.Monad0().Bind1().Apply0().Functor0())(c.NonEmpty.create)(a))(i.resize(r)((d=p.max(p.ordInt)(0),function(n){return d(n-1|0)}))(t.unfoldable(n)(r)(u)(a)));var d}}}},y=function(e){return function(t){return function(u){return r.bind(e.Monad0().Bind1())(i.chooseFloat(e)(0)(1))(function(r){return r0)return new f.Just(x(n));if(u.otherwise)return 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n=require("../Data.Array.NonEmpty/index.js"),r=require("../Data.Maybe/index.js"),t=require("../Data.Semigroup.Foldable/index.js"),e=require("../Data.String.CodeUnits/index.js"),u=require("../Data.String.NonEmpty.Internal/index.js"),o=require("../Data.String.Unsafe/index.js"),i=require("../Unsafe.Coerce/index.js"),a=i.unsafeCoerce,f=function(n){return function(r){return a(r+e.singleton(n))}},c=function(n){return a(e.singleton(n))},s=i.unsafeCoerce,l=function(n){var r=s(e.takeWhile(n));return function(n){return u.fromString(r(n))}},h=function(n){var r=e["lastIndexOf'"](n);return function(n){return s(r(n))}},g=function(n){return s(e.lastIndexOf(n))},d=function(n){var r=e["indexOf'"](n);return function(n){return s(r(n))}},m=function(n){return s(e.indexOf(n))},v=i.unsafeCoerce,x=function(n){return e.length(v(n))},p=function(n){return function(r){var t=e.splitAt(n)(v(r));return{before:u.fromString(t.before),after:u.fromString(t.after)}}},y=function(n){return function(t){var u=v(t);return 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n)({}).hasOwnProperty.call(n,o)&&(a[o]=n[o]);for(var t in r)({}).hasOwnProperty.call(r,t)&&(a[t]=r[t]);return a}; +},{}],"cB+g":[function(require,module,exports) { +"use strict";exports.mkFn0=function(n){return function(){return n({})}},exports.mkFn2=function(n){return function(r,t){return n(r)(t)}},exports.mkFn3=function(n){return function(r,t,u){return n(r)(t)(u)}},exports.mkFn4=function(n){return function(r,t,u,e){return n(r)(t)(u)(e)}},exports.mkFn5=function(n){return function(r,t,u,e,o){return n(r)(t)(u)(e)(o)}},exports.mkFn6=function(n){return function(r,t,u,e,o,c){return n(r)(t)(u)(e)(o)(c)}},exports.mkFn7=function(n){return function(r,t,u,e,o,c,i){return n(r)(t)(u)(e)(o)(c)(i)}},exports.mkFn8=function(n){return function(r,t,u,e,o,c,i,f){return n(r)(t)(u)(e)(o)(c)(i)(f)}},exports.mkFn9=function(n){return function(r,t,u,e,o,c,i,f,s){return n(r)(t)(u)(e)(o)(c)(i)(f)(s)}},exports.mkFn10=function(n){return function(r,t,u,e,o,c,i,f,s,p){return 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n=require("../Data.Eq/index.js"),r=require("../Data.Symbol/index.js"),u=require("../Record.Unsafe/index.js"),t=require("../Record.Unsafe.Union/index.js"),e=require("../Type.Data.RowList/index.js"),i=require("../Unsafe.Coerce/index.js"),o=function(n){this.equalFields=n},f=function(n){return function(n){return function(r){return t.unsafeUnionFn(n,r)}}},c=function(n){return function(t){return function(t){return function(t){return function(e){return function(i){return u.unsafeSet(r.reflectSymbol(n)(t))(e)(i)}}}}}},s=function(n){return i.unsafeCoerce},a=function(n){return function(n){return function(n){return function(r){return t.unsafeUnionFn(n,r)}}}},l=function(n){return function(t){return function(t){return function(t){return function(e){return function(i){return u.unsafeSet(r.reflectSymbol(n)(t))(e)(i)}}}}}},d=function(n){return function(t){return function(t){return function(e){return u.unsafeGet(r.reflectSymbol(n)(t))(e)}}}},q=function(n){return function(r){return function(u){return 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Error(r)},exports.message=function(r){return r.message},exports.name=function(r){return r.name||"Error"},exports.stackImpl=function(r){return function(t){return function(n){return n.stack?r(n.stack):t}}},exports.throwException=function(r){return function(){throw r}},exports.catchException=function(r){return function(t){return function(){try{return t()}catch(n){return n instanceof Error||"[object Error]"===Object.prototype.toString.call(n)?r(n)():r(new Error(n.toString()))()}}}}; +},{}],"0OCW":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),r=require("../Control.Applicative/index.js"),t=require("../Data.Either/index.js"),i=require("../Data.Functor/index.js"),o=require("../Data.Maybe/index.js"),n=require("../Data.Show/index.js"),a=require("../Effect/index.js"),c=function(o){return e.catchException((n=r.pure(a.applicativeEffect),function(e){return n(t.Left.create(e))}))(i.map(a.functorEffect)(t.Right.create)(o));var n},u=function(r){return e.throwException(e.error(r))},s=e.stackImpl(o.Just.create)(o.Nothing.value),p=new n.Show(e.showErrorImpl);module.exports={stack:s,throw:u,try:c,showError:p,error:e.error,message:e.message,name:e.name,throwException:e.throwException,catchException:e.catchException}; +},{"./foreign.js":"OvLS","../Control.Applicative/index.js":"qYya","../Data.Either/index.js":"B2JL","../Data.Functor/index.js":"+0AE","../Data.Maybe/index.js":"5mN7","../Data.Show/index.js":"mFY7","../Effect/index.js":"oTWB"}],"L8Lk":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Bind/index.js"),t=require("../Data.Either/index.js"),o=require("../Data.Function/index.js"),e=require("../Data.Functor/index.js"),i=require("../Data.Maybe/index.js"),u=require("../Data.Unit/index.js"),a=require("../Effect/index.js"),c=require("../Effect.Exception/index.js"),f=function(n,r){this.Monad0=n,this.throwError=r},d=function(n,r){this.MonadThrow0=n,this.catchError=r},h=function(n){return n.throwError},s=new f(function(){return i.monadMaybe},o.const(i.Nothing.value)),l=new f(function(){return t.monadEither},t.Left.create),w=new f(function(){return a.monadEffect},c.throwException),E=new d(function(){return s},function(n){return function(r){if(n instanceof i.Nothing)return r(u.unit);if(n instanceof i.Just)return new i.Just(n.value0);throw new Error("Failed pattern match at Control.Monad.Error.Class (line 79, column 1 - line 81, column 33): "+[n.constructor.name,r.constructor.name])}}),m=new d(function(){return l},function(n){return function(r){if(n instanceof t.Left)return r(n.value0);if(n instanceof t.Right)return new t.Right(n.value0);throw new Error("Failed pattern match at Control.Monad.Error.Class (line 72, column 1 - line 74, column 35): "+[n.constructor.name,r.constructor.name])}}),M=new d(function(){return w},o.flip(c.catchException)),p=function(n){return n.catchError},x=function(n){return function(r){return function(t){return function(o){return p(n)(t)(function(t){var e=r(t);if(e instanceof i.Nothing)return h(n.MonadThrow0())(t);if(e instanceof i.Just)return o(e.value0);throw new Error("Failed pattern match at Control.Monad.Error.Class (line 57, column 5 - line 59, column 26): "+[e.constructor.name])})}}}},T=function(r){return function(o){return p(r)(e.map(r.MonadThrow0().Monad0().Bind1().Apply0().Functor0())(t.Right.create)(o))((i=n.pure(r.MonadThrow0().Monad0().Applicative0()),function(n){return i(t.Left.create(n))}));var i}},v=function(o){return function(e){return function(i){return function(u){return r.bind(o.MonadThrow0().Monad0().Bind1())(e)(function(e){return r.bind(o.MonadThrow0().Monad0().Bind1())(T(o)(u(e)))(function(u){return r.discard(r.discardUnit)(o.MonadThrow0().Monad0().Bind1())(i(e))(function(){return t.either(h(o.MonadThrow0()))(n.pure(o.MonadThrow0().Monad0().Applicative0()))(u)})})})}}}};module.exports={catchError:p,throwError:h,MonadThrow:f,MonadError:d,catchJust:x,try:T,withResource:v,monadThrowEither:l,monadErrorEither:m,monadThrowMaybe:s,monadErrorMaybe:E,monadThrowEffect:w,monadErrorEffect:M}; +},{"../Control.Applicative/index.js":"qYya","../Control.Bind/index.js":"7VcT","../Data.Either/index.js":"B2JL","../Data.Function/index.js":"ImXJ","../Data.Functor/index.js":"+0AE","../Data.Maybe/index.js":"5mN7","../Data.Unit/index.js":"NhVk","../Effect/index.js":"oTWB","../Effect.Exception/index.js":"0OCW"}],"c2ZJ":[function(require,module,exports) { +"use strict";var n=require("../Control.Category/index.js"),o=require("../Control.Monad/index.js"),e=require("../Control.Semigroupoid/index.js"),r=require("../Data.Functor/index.js"),t=function(n,o){this.Monad0=n,this.ask=o},i=function(n,o){this.MonadAsk0=n,this.local=o},u=new t(function(){return o.monadFn},n.identity(n.categoryFn)),a=new i(function(){return u},e.composeFlipped(e.semigroupoidFn)),d=function(n){return n.local},s=function(n){return n.ask},c=function(n){return function(o){return r.map(n.Monad0().Bind1().Apply0().Functor0())(o)(s(n))}};module.exports={ask:s,local:d,MonadAsk:t,asks:c,MonadReader:i,monadAskFun:u,monadReaderFun:a}; +},{"../Control.Category/index.js":"IAi2","../Control.Monad/index.js":"U/Ix","../Control.Semigroupoid/index.js":"/riR","../Data.Functor/index.js":"+0AE"}],"5tIR":[function(require,module,exports) { +"use strict";var t=function(t){this.lift=t},i=function(t){return t.lift};module.exports={lift:i,MonadTrans:t}; +},{}],"gxgA":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),e=require("../Control.Bind/index.js"),t=require("../Data.Tuple/index.js"),i=function(n,e){this.Monad0=n,this.tell=e},r=function(n,e,t){this.MonadTell0=n,this.listen=e,this.pass=t},u=function(n){return n.tell},l=function(n){return n.pass},o=function(n){return n.listen},a=function(i){return function(r){return function(u){return e.bind(i.MonadTell0().Monad0().Bind1())(o(i)(u))(function(e){return n.pure(i.MonadTell0().Monad0().Applicative0())(new t.Tuple(e.value0,r(e.value1)))})}}},s=function(i){return function(r){return function(u){return l(i)(e.bind(i.MonadTell0().Monad0().Bind1())(u)(function(e){return n.pure(i.MonadTell0().Monad0().Applicative0())(new t.Tuple(e,r))}))}}};module.exports={listen:o,pass:l,tell:u,MonadTell:i,MonadWriter:r,listens:a,censor:s}; +},{"../Control.Applicative/index.js":"qYya","../Control.Bind/index.js":"7VcT","../Data.Tuple/index.js":"II/O"}],"dWtH":[function(require,module,exports) { +"use strict";var t=require("../Control.Category/index.js"),e=require("../Effect/index.js"),f=function(t,e){this.Monad0=t,this.liftEffect=e},n=new f(function(){return e.monadEffect},t.identity(t.categoryFn)),i=function(t){return t.liftEffect};module.exports={liftEffect:i,MonadEffect:f,monadEffectEffect:n}; +},{"../Control.Category/index.js":"IAi2","../Effect/index.js":"oTWB"}],"34Kp":[function(require,module,exports) { +"use strict";var n=require("../Control.Alt/index.js"),t=require("../Control.Alternative/index.js"),e=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),u=require("../Control.Bind/index.js"),o=require("../Control.Lazy/index.js"),i=require("../Control.Monad/index.js"),a=require("../Control.Monad.Cont.Class/index.js"),c=require("../Control.Monad.Error.Class/index.js"),l=require("../Control.Monad.Reader.Class/index.js"),f=require("../Control.Monad.Rec.Class/index.js"),d=require("../Control.Monad.State.Class/index.js"),s=require("../Control.Monad.Trans.Class/index.js"),p=require("../Control.Monad.Writer.Class/index.js"),T=require("../Control.MonadPlus/index.js"),M=require("../Control.MonadZero/index.js"),v=require("../Control.Plus/index.js"),w=require("../Data.Functor/index.js"),S=require("../Data.Newtype/index.js"),C=require("../Data.Tuple/index.js"),m=require("../Data.Unit/index.js"),x=require("../Effect.Class/index.js"),j=function(n){return n},q=function(n){return function(t){return function(e){return t(n(e))}}},A=function(n){return n},y=new S.Newtype(function(n){return n},j),E=new s.MonadTrans(function(n){return function(t){return function(r){return u.bind(n.Bind1())(t)(function(t){return e.pure(n.Applicative0())(new C.Tuple(t,r))})}}}),h=function(n){return function(t){return function(e){return n(t(e))}}},B=new o.Lazy(function(n){return function(t){return n(m.unit)(t)}}),R=function(n){return new w.Functor(function(t){return function(e){return function(r){return w.map(n)(function(n){return new C.Tuple(t(n.value0),n.value1)})(e(r))}}})},b=function(n){return function(t){return function(e){return w.map(n)(C.snd)(t(e))}}},D=function(n){return function(t){return function(e){return w.map(n)(C.fst)(t(e))}}},P=function(n){return new i.Monad(function(){return L(n)},function(){return F(n)})},F=function(n){return new u.Bind(function(){return k(n)},function(t){return function(e){return function(r){return u.bind(n.Bind1())(t(r))(function(n){return e(n.value0)(n.value1)})}}})},k=function(n){return new r.Apply(function(){return R(n.Bind1().Apply0().Functor0())},i.ap(P(n)))},L=function(n){return new e.Applicative(function(){return k(n)},function(t){return function(r){return e.pure(n.Applicative0())(new C.Tuple(t,r))}})},Z=function(n){return new l.MonadAsk(function(){return P(n.Monad0())},s.lift(E)(n.Monad0())(l.ask(n)))},z=function(n){return new l.MonadReader(function(){return Z(n.MonadAsk0())},(t=l.local(n),function(n){return h(t(n))}));var t},W=function(n){return new a.MonadCont(function(){return P(n.Monad0())},function(t){return function(e){return a.callCC(n)(function(n){return t(function(t){return function(e){return n(new C.Tuple(t,e))}})(e)})}})},N=function(n){return new x.MonadEffect(function(){return P(n.Monad0())},(t=s.lift(E)(n.Monad0()),e=x.liftEffect(n),function(n){return t(e(n))}));var t,e},U=function(n){return new f.MonadRec(function(){return P(n.Monad0())},function(t){return function(r){var o=function(r){var o=t(r.value0);return u.bind(n.Monad0().Bind1())(o(r.value1))(function(t){return e.pure(n.Monad0().Applicative0())(function(){if(t.value0 instanceof f.Loop)return new f.Loop(new C.Tuple(t.value0.value0,t.value1));if(t.value0 instanceof f.Done)return new f.Done(new C.Tuple(t.value0.value0,t.value1));throw new Error("Failed pattern match at Control.Monad.State.Trans (line 87, column 16 - line 89, column 40): "+[t.value0.constructor.name])}())})};return function(t){return f.tailRecM(n)(o)(new C.Tuple(r,t))}}})},g=function(n){return new d.MonadState(function(){return P(n)},function(t){return j((r=e.pure(n.Applicative0()),function(n){return r(t(n))}));var r})},G=function(n){return new p.MonadTell(function(){return P(n.Monad0())},(t=s.lift(E)(n.Monad0()),e=p.tell(n),function(n){return t(e(n))}));var t,e},H=function(n){return new p.MonadWriter(function(){return G(n.MonadTell0())},function(t){return function(r){return u.bind(n.MonadTell0().Monad0().Bind1())(p.listen(n)(t(r)))(function(t){return e.pure(n.MonadTell0().Monad0().Applicative0())(new C.Tuple(new C.Tuple(t.value0.value0,t.value1),t.value0.value1))})}},function(t){return function(r){return p.pass(n)(u.bind(n.MonadTell0().Monad0().Bind1())(t(r))(function(t){return e.pure(n.MonadTell0().Monad0().Applicative0())(new C.Tuple(new C.Tuple(t.value0.value0,t.value1),t.value0.value1))}))}})},I=function(n){return new c.MonadThrow(function(){return P(n.Monad0())},function(t){return s.lift(E)(n.Monad0())(c.throwError(n)(t))})},J=function(n){return new c.MonadError(function(){return I(n.MonadThrow0())},function(t){return function(e){return function(r){return c.catchError(n)(t(r))(function(n){return e(n)(r)})}}})},K=function(t){return function(t){return new n.Alt(function(){return R(t.Functor0())},function(e){return function(r){return function(u){return n.alt(t)(e(u))(r(u))}}})}},O=function(n){return function(t){return new v.Plus(function(){return K(n)(t.Alt0())},function(n){return v.empty(t)})}},Q=function(n){return function(e){return new t.Alternative(function(){return L(n)},function(){return O(n)(e.Plus1())})}},V=function(n){return new M.MonadZero(function(){return Q(n.Monad0())(n.Alternative1())},function(){return P(n.Monad0())})},X=function(n){return new T.MonadPlus(function(){return V(n.MonadZero0())})};module.exports={StateT:j,runStateT:A,evalStateT:D,execStateT:b,mapStateT:h,withStateT:q,newtypeStateT:y,functorStateT:R,applyStateT:k,applicativeStateT:L,altStateT:K,plusStateT:O,alternativeStateT:Q,bindStateT:F,monadStateT:P,monadRecStateT:U,monadZeroStateT:V,monadPlusStateT:X,monadTransStateT:E,lazyStateT:B,monadEffectState:N,monadContStateT:W,monadThrowStateT:I,monadErrorStateT:J,monadAskStateT:Z,monadReaderStateT:z,monadStateStateT:g,monadTellStateT:G,monadWriterStateT:H}; 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t=require("../Control.Monad.State.Trans/index.js"),e=require("../Data.Identity/index.js"),n=require("../Data.Newtype/index.js"),r=t.withStateT,u=function(t){var r=n.unwrap(e.newtypeIdentity);return function(e){return r(t(e))}},a=function(r){return t.mapStateT((u=n.unwrap(e.newtypeIdentity),function(t){return e.Identity(r(u(t)))}));var u},i=function(t){return function(e){return t(e).value1}},o=function(t){return function(e){return t(e).value0}};module.exports={runState:u,evalState:o,execState:i,mapState:a,withState:r}; +},{"../Control.Monad.State.Trans/index.js":"34Kp","../Data.Identity/index.js":"2OKT","../Data.Newtype/index.js":"lz8k"}],"7S1u":[function(require,module,exports) { +"use strict";exports.random=Math.random; +},{}],"V+tx":[function(require,module,exports) { +"use strict";var r=require("./foreign.js"),n=require("../Data.Functor/index.js"),e=require("../Data.Int/index.js"),t=require("../Effect/index.js"),o=function(n){return function(e){return function(){return 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function(r){return function(t){var e,u,o,i,a=n,f=r,c=!1;for(;!c;)u=a,o=t,i=void 0,e=(i=q(f))instanceof d.Just&&u(i.value0.head)?(a=u,f=i.value0.tail,void(t=o+1|0)):(c=!0,o);return e}}},G=function(n){return function(r){return z(n)(r)(0)}},H=n._countPrefix(G)(j),K=function(n){return function(r){return W(H(n)(r))(r)}},L=function(n){return function(r){return N(H(n)(r))(r)}},Q=function(){var n=u.fromEnum(u.boundedEnumChar);return function(r){return E(n(r))}}(),V=function(n){return function(r){var t,e,u,o=n,i=!1;for(;!i;)e=o,u=void 0,t=(u=q(r))instanceof d.Just?0===e?(i=!0,new d.Just(u.value0.head)):(o=e-1|0,void(r=u.value0.tail)):(i=!0,d.Nothing.value);return t}},X=function(r){return function(t){return r<0?d.Nothing.value:0===r&&""===t?d.Nothing.value:0===r?new d.Just(j(t)):n._codePointAt(V)(d.Just.create)(d.Nothing.value)(j)(r)(t)}},Y=new e.Bounded(function(){return R},0,1114111),Z=new u.BoundedEnum(function(){return Y},function(){return $},1114112,function(n){return n},function(n){if(n>=0&&n<=1114111)return new d.Just(n);if(t.otherwise)return d.Nothing.value;throw new Error("Failed pattern match at Data.String.CodePoints (line 63, column 1 - line 68, column 26): "+[n.constructor.name])}),$=new u.Enum(function(){return R},u.defaultPred(u.toEnum(Z))(u.fromEnum(Z)),u.defaultSucc(u.toEnum(Z))(u.fromEnum(Z)));module.exports={codePointFromChar:Q,singleton:_,fromCodePointArray:k,toCodePointArray:A,codePointAt:X,uncons:q,length:y,countPrefix:H,indexOf:O,"indexOf'":T,lastIndexOf:J,"lastIndexOf'":B,take:N,takeWhile:L,drop:W,dropWhile:K,splitAt:U,eqCodePoint:F,ordCodePoint:R,showCodePoint:C,boundedCodePoint:Y,enumCodePoint:$,boundedEnumCodePoint:Z}; 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n.source},exports["flags'"]=function(n){return{multiline:n.multiline,ignoreCase:n.ignoreCase,global:n.global,sticky:!!n.sticky,unicode:!!n.unicode}},exports.test=function(n){return function(r){var t=n.lastIndex,e=n.test(r);return n.lastIndex=t,e}},exports._match=function(n){return function(r){return function(t){return function(e){var u=e.match(t);if(null==u||0===u.length)return r;for(var o=0;o ")(o)+")"}),d=new a.Semigroup(function(e){return function(i){return new l({global:e.value0.global||i.value0.global,ignoreCase:e.value0.ignoreCase||i.value0.ignoreCase,multiline:e.value0.multiline||i.value0.multiline,sticky:e.value0.sticky||i.value0.sticky,unicode:e.value0.unicode||i.value0.unicode})}}),c=new l({global:!1,ignoreCase:!1,multiline:!1,sticky:!1,unicode:!1}),v=new l({global:!1,ignoreCase:!1,multiline:!0,sticky:!1,unicode:!1}),m=new r.Monoid(function(){return d},c),y=new l({global:!1,ignoreCase:!0,multiline:!1,sticky:!1,unicode:!1}),f=new l({global:!0,ignoreCase:!1,multiline:!1,sticky:!1,unicode:!1}),p=new i.Eq(function(e){return function(i){return e.value0.global===i.value0.global&&e.value0.ignoreCase===i.value0.ignoreCase&&e.value0.multiline===i.value0.multiline&&e.value0.sticky===i.value0.sticky&&e.value0.unicode===i.value0.unicode}});module.exports={RegexFlags:l,noFlags:c,global:f,ignoreCase:y,multiline:v,sticky:g,unicode:t,semigroupRegexFlags:d,monoidRegexFlags:m,eqRegexFlags:p,showRegexFlags:s}; +},{"../Control.MonadZero/index.js":"lD5R","../Data.Eq/index.js":"Pq4F","../Data.Functor/index.js":"+0AE","../Data.Monoid/index.js":"TiEB","../Data.Semigroup/index.js":"EsAJ","../Data.Show/index.js":"mFY7","../Data.String.Common/index.js":"OSrc"}],"lBFq":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),t=require("../Data.Either/index.js"),a=require("../Data.Maybe/index.js"),r=require("../Data.Show/index.js"),n=require("../Data.String.CodeUnits/index.js"),i=require("../Data.String.Regex.Flags/index.js"),s=new r.Show(e["showRegex'"]),u=e._search(a.Just.create)(a.Nothing.value),c=function(e){return(e.value0.global?"g":"")+(e.value0.ignoreCase?"i":"")+(e.value0.multiline?"m":"")+(e.value0.sticky?"y":"")+(e.value0.unicode?"u":"")},l=function(a){return function(r){return e["regex'"](t.Left.create)(t.Right.create)(a)(c(r))}},o=function(e){return new i.RegexFlags({global:n.contains("g")(e),ignoreCase:n.contains("i")(e),multiline:n.contains("m")(e),sticky:n.contains("y")(e),unicode:n.contains("u")(e)})},g=e._match(a.Just.create)(a.Nothing.value),x=function(t){return i.RegexFlags.create(e["flags'"](t))};module.exports={regex:l,flags:x,renderFlags:c,parseFlags:o,match:g,search:u,showRegex:s,source:e.source,test:e.test,replace:e.replace,"replace'":e["replace'"],split:e.split}; +},{"./foreign.js":"rsyP","../Data.Either/index.js":"B2JL","../Data.Maybe/index.js":"5mN7","../Data.Show/index.js":"mFY7","../Data.String.CodeUnits/index.js":"6c6X","../Data.String.Regex.Flags/index.js":"W1/V"}],"f3ma":[function(require,module,exports) { +"use strict";var n=require("../Control.Applicative/index.js"),r=require("../Control.Bind/index.js"),t=require("../Data.Array.NonEmpty/index.js"),e=require("../Data.Boolean/index.js"),u=require("../Data.Either/index.js"),o=require("../Data.Eq/index.js"),i=require("../Data.Foldable/index.js"),a=require("../Data.Function/index.js"),c=require("../Data.Functor/index.js"),f=require("../Data.Int/index.js"),l=require("../Data.Maybe/index.js"),s=require("../Data.Ord/index.js"),v=require("../Data.Show/index.js"),m=require("../Data.String.CodePoints/index.js"),b=require("../Data.String.Regex/index.js"),h=require("../Math/index.js"),d=function(n){return n},w=function(){function n(){}return n.value=new n,n}(),g=function(){function n(){}return n.value=new n,n}(),p=function(){function n(){}return n.value=new n,n}(),x=function(){function n(){}return n.value=new n,n}(),y=function(){function n(n,r,t,e){this.value0=n,this.value1=r,this.value2=t,this.value3=e}return n.create=function(r){return function(t){return 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function(t){return j(n)(r)(t)(1)}}},I=function(n){return function(r){return function(t){return function(e){return j(f.round(255*n))(f.round(255*r))(f.round(255*t))(e)}}}},M=function(n){return function(r){return function(t){return I(n)(r)(t)(1)}}},N=function(n){return function(r){return function(t){var u=function(n){if(n<=.0031308)return 12.92*n;if(e.otherwise)return 1.055*h.pow(n)(1/2.4)-.055;throw new Error("Failed pattern match at Color (line 224, column 5 - line 225, column 65): "+[n.constructor.name])},o=u(-.9689*n+1.8758*r+.0415*t),i=u(3.2406*n-1.5372*r-.4986*t),a=u(.0557*n-.204*r+1.057*t);return M(i)(o)(a)}}},E=function(n){return function(r){return function(t){return r+n*(t-r)}}},F=function(n){return function(r){return function(t){var e=[{from:r,to:t},{from:r,to:t+360},{from:r+360,to:t}],u=l.fromJust()(i.minimumBy(i.foldableArray)(s.comparing(s.ordNumber)(function(n){return h.abs(n.to-n.from)}))(e));return E(n)(u.from)(u.to)}}},S=function(n){return function(r){return function(t){var e=h.pi/180,u=t.value1-r.value1,o=t.value2-r.value2,i=(r.value0+120)*e,a=(t.value0+120)*e-i;return function(e){var c=h.pow(r.value2+o*e)(n),f=i+a*e,l=(r.value1+u*e)*c*(1-c),s=c+l*(1.97294*h.cos(f)),v=c+l*(-.29227*h.cos(f)-.90649*h.sin(f)),m=c+l*(-.14861*h.cos(f)+1.78277*h.sin(f)),b=E(e)(r.value3)(t.value3);return I(m)(v)(s)(b)}}}},D=function(n){return function(r){return function(t){return function(e){var u=s.clamp(s.ordNumber)(0)(1)(r),o=s.clamp(s.ordNumber)(0)(1)(t),i=s.clamp(s.ordNumber)(0)(1)(e);return new y(n,u,o,i)}}}},A=function(n){return function(r){return function(t){return function(e){var u=r;if(0===t)return D(n)(u/(2-u))(0)(e);if(0===r&&1===t)return D(n)(0)(1)(e);var o=(2-r)*t,i=(u=r*t/(o<1?o:2-o),o/2);return D(n)(u)(i)(e)}}}},L=function(n){return function(r){return function(t){return A(n)(r)(t)(1)}}},B=function(n){return function(r){return D(r.value0)(r.value1)(r.value2+n)(r.value3)}},H=function(n){return function(r){return 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r.bind(l.bindMaybe)(c.map(l.functorMaybe)(s)(r.join(l.bindMaybe)(t.index(e)(3))))(function(r){return v?n.pure(l.applicativeMaybe)(C((16*u|0)+u|0)((16*o|0)+o|0)((16*r|0)+r|0)):n.pure(l.applicativeMaybe)(C(u)(o)(r))})})})})})},P=function(n){return z(-n)},V=function(n){return B(-n)},X={xn:.95047,yn:1,zn:1.08883},Y=function(n){return function(r){return function(t){var u=(n+16)/116,o=function(n){if(n>6/29)return h.pow(n)(3);if(e.otherwise)return 6/29*3*(6/29)*(n-4/29);throw new Error("Failed pattern match at Color (line 249, column 5 - line 250, column 64): "+[n.constructor.name])},i=X.xn*o(u+r/500),a=X.yn*o(u),c=X.zn*o(u-t/200);return N(i)(a)(c)}}},Z=function(n){return function(r){return function(t){var e=h.pi/180,u=r*h.sin(t*e),o=r*h.cos(t*e);return Y(n)(o)(u)}}},$=function(n){var r=function(n){return v.show(v.showNumber)(f.toNumber(f.round(100*n))/100)},t=r(100*n.value1)+"%",e=r(100*n.value2)+"%",u=r(n.value0),o=v.show(v.showNumber)(n.value3);return 1===n.value3?"hsl("+u+", "+t+", 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n/12.92;if(e.otherwise)return h.pow((n+.055)/1.055)(2.4);throw new Error("Failed pattern match at Color (line 604, column 9 - line 605, column 61): "+[n.constructor.name])},u=t(r.g);return.2126*t(r.r)+.7152*u+.0722*t(r.b)},nn=function(n){return function(r){var t=_(r),e=_(n);return e>t?(e+.05)/(t+.05):(t+.05)/(e+.05)}},rn=function(n){return function(r){return nn(n)(r)>4.5}},tn=function(n){var r=W(n),t=f.round(255*r.g);return{r:f.round(255*r.r),g:t,b:f.round(255*r.b),a:r.a}},en=function(n){var r=tn(n),t=v.show(v.showInt)(r.g),e=v.show(v.showInt)(r.r),u=v.show(v.showInt)(r.b),o=v.show(v.showNumber)(r.a);return 1===r.a?"rgb("+e+", "+t+", "+u+")":"rgba("+e+", "+t+", "+u+", "+o+")"},un=new o.Eq(function(n){return function(r){var t=tn(r),e=tn(n);return e.r===t.r&&e.g===t.g&&e.b===t.b&&e.a===t.a}}),on=new v.Show(function(n){var r=tn(n);return"rgba "+v.show(v.showInt)(r.r)+" "+v.show(v.showInt)(r.g)+" "+v.show(v.showInt)(r.b)+" "+v.show(v.showNumber)(r.a)}),an=function(n){var r=function(n){var r=f.toStringAs(f.hexadecimal)(n);return 1===m.length(r)?"0"+r:r},t=tn(n);return"#"+(r(t.r)+(r(t.g)+r(t.b)))},cn=function(n){var r=W(n),t=function(n){if(n<=.04045)return n/12.92;if(e.otherwise)return h.pow((n+.055)/1.055)(2.4);throw new Error("Failed pattern match at Color (line 366, column 5 - line 367, column 63): "+[n.constructor.name])},u=t(r.g),o=t(r.r),i=t(r.b);return{x:.4124*o+.3576*u+.1805*i,y:.2126*o+.7152*u+.0722*i,z:.0193*o+.1192*u+.9505*i}},fn=function(n){var r=cn(n),t=h.pow(6/29)(3),u=function(n){if(n>t)return h.pow(n)(1/3);if(e.otherwise)return 1/3*h.pow(29/6)(2)*n+4/29;throw new Error("Failed pattern match at Color (line 384, column 5 - line 385, column 76): "+[n.constructor.name])},o=u(r.y/X.yn),i=116*o-16,a=200*(o-u(r.z/X.zn));return{l:i,a:500*(u(r.x/X.xn)-o),b:a}},ln=function(n){return function(r){var t=function(n){return h.pow(n)(2)},e=fn(r),u=fn(n);return h.sqrt(t(u.l-e.l)+t(u.a-e.a)+t(u.b-e.b))}},sn=function(n){var r=fn(n),t=180/h.pi,e=h.sqrt(r.a*r.a+r.b*r.b),u=q(h.atan2(r.b)(r.a)*t)(360);return{l:r.l,c:e,h:u}},vn=function(n){return function(r){return function(t){return function(e){if(n instanceof g){var u=T(t),o=T(r);return D(F(e)(o.h)(u.h))(E(e)(o.s)(u.s))(E(e)(o.l)(u.l))(E(e)(o.a)(u.a))}if(n instanceof w){u=W(t),o=W(r);return I(E(e)(o.r)(u.r))(E(e)(o.g)(u.g))(E(e)(o.b)(u.b))(E(e)(o.a)(u.a))}if(n instanceof p){u=sn(t),o=sn(r);return Z(E(e)(o.l)(u.l))(E(e)(o.c)(u.c))(F(e)(o.h)(u.h))}if(n instanceof x){u=fn(t),o=fn(r);return Y(E(e)(o.l)(u.l))(E(e)(o.a)(u.a))(E(e)(o.b)(u.b))}throw new Error("Failed pattern match at Color (line 520, column 1 - line 520, column 34): "+[n.constructor.name,r.constructor.name,t.constructor.name,e.constructor.name])}}}},mn=function(n){var r=sn(n);return P(1)(Z(r.l)(0)(0))},bn=function(n){var r=W(n);return(299*r.r+587*r.g+114*r.b)/1e3},hn=function(n){return bn(n)>.5},dn=R(0)(0)(0),wn=function(n){if(hn(n))return dn;if(e.otherwise)return G;throw new Error("Failed pattern match at Color (line 643, column 1 - line 643, column 28): "+[n.constructor.name])};module.exports={RGB:w,HSL:g,LCh:p,Lab:x,rgba:j,rgb:C,"rgba'":I,"rgb'":M,hsla:D,hsl:R,hsva:A,hsv:L,xyz:N,lab:Y,lch:Z,fromHexString:O,fromInt:J,toHSLA:T,toHSVA:U,toRGBA:tn,"toRGBA'":W,toXYZ:cn,toLab:fn,toLCh:sn,toHexString:an,cssStringHSLA:$,cssStringRGBA:en,black:dn,white:G,graytone:k,rotateHue:H,complementary:K,lighten:B,darken:V,saturate:z,desaturate:P,toGray:mn,mix:vn,mixCubehelix:S,brightness:bn,luminance:_,contrast:nn,isLight:hn,isReadable:rn,textColor:wn,distance:ln,showColor:on,eqColor:un}; 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r=require("../Color/index.js"),o=r.fromInt(16768e3),n=r.fromInt(3787980),t=r.fromInt(14540253),m=r.fromInt(16728374),e=r.fromInt(11603401),f=r.fromInt(16745755),I=r.fromInt(4036976),l=r.fromInt(7999),a=r.fromInt(8721483),i=r.fromInt(130928),u=r.fromInt(3066944),s=r.fromInt(11184810),v=r.fromInt(15733438),c=r.fromInt(29913),d=r.fromInt(1118481),g=r.fromInt(8379391);module.exports={navy:l,blue:c,aqua:g,teal:n,olive:I,green:u,lime:i,yellow:o,orange:f,red:m,maroon:a,fuchsia:v,purple:e,"black'":d,gray:s,silver:t}; +},{"../Color/index.js":"f3ma"}],"BG0s":[function(require,module,exports) { +function t(t){return function(o){return function(e){return t.apply(e,[o])}}}exports.toPrecisionNative=t(Number.prototype.toPrecision),exports.toFixedNative=t(Number.prototype.toFixed),exports.toExponentialNative=t(Number.prototype.toExponential),exports.toString=function(t){return t.toString()}; +},{}],"VX77":[function(require,module,exports) { +"use strict";var n=require("./foreign.js"),t=require("../Data.Ord/index.js"),e=function(){function n(n){this.value0=n}return n.create=function(t){return new n(t)},n}(),r=function(){function n(n){this.value0=n}return n.create=function(t){return new n(t)},n}(),i=function(){function n(n){this.value0=n}return n.create=function(t){return new n(t)},n}(),u=function(t){if(t instanceof e)return n.toPrecisionNative(t.value0);if(t instanceof r)return n.toFixedNative(t.value0);if(t instanceof i)return n.toExponentialNative(t.value0);throw new Error("Failed pattern match at Data.Number.Format (line 59, column 1 - line 59, column 40): "+[t.constructor.name])},o=function(){var n=t.clamp(t.ordInt)(1)(21);return function(t){return e.create(n(t))}}(),a=function(){var n=t.clamp(t.ordInt)(0)(20);return function(t){return r.create(n(t))}}(),c=function(){var n=t.clamp(t.ordInt)(0)(20);return function(t){return i.create(n(t))}}();module.exports={precision:o,fixed:a,exponential:c,toStringWith:u,toString:n.toString}; 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n=require("../Control.Applicative/index.js"),r=require("../Control.Apply/index.js"),t=require("../Control.Category/index.js"),e=require("../Data.Either/index.js"),u=require("../Data.Eq/index.js"),i=require("../Data.Foldable/index.js"),o=require("../Data.Function/index.js"),f=require("../Data.Functor/index.js"),c=require("../Data.HeytingAlgebra/index.js"),a=require("../Data.Lens.Internal.Forget/index.js"),p=require("../Data.Lens.Internal.Indexed/index.js"),d=require("../Data.List.Types/index.js"),l=require("../Data.Maybe/index.js"),s=require("../Data.Maybe.First/index.js"),y=require("../Data.Maybe.Last/index.js"),w=require("../Data.Monoid/index.js"),v=require("../Data.Monoid.Additive/index.js"),j=require("../Data.Monoid.Conj/index.js"),D=require("../Data.Monoid.Disj/index.js"),q=require("../Data.Monoid.Dual/index.js"),x=require("../Data.Monoid.Endo/index.js"),g=require("../Data.Monoid.Multiplicative/index.js"),O=require("../Data.Newtype/index.js"),m=require("../Data.Ord/index.js"),F=require("../Data.Profunctor/index.js"),h=require("../Data.Profunctor.Choice/index.js"),M=require("../Data.Semigroup/index.js"),A=require("../Data.Tuple/index.js"),E=require("../Data.Unit/index.js"),C=function(n){return 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{ +"use strict";var e=require("../Data.Bifunctor/index.js"),r=require("../Data.Either/index.js"),t=require("../Data.Functor/index.js"),n=require("../Data.Profunctor/index.js"),u=require("../Data.Profunctor.Choice/index.js"),i=function(){function e(e,r){this.value0=e,this.value1=r}return e.create=function(r){return function(t){return new e(r,t)}},e}(),c=new n.Profunctor(function(t){return function(n){return function(u){return new i(function(e){return n(u.value0(e))},(c=e.lmap(r.bifunctorEither)(n),function(e){return c(u.value1(t(e)))}));var c}}}),o=new t.Functor(function(t){return function(n){return new i(function(e){return t(n.value0(e))},(u=e.lmap(r.bifunctorEither)(t),function(e){return u(n.value1(e))}));var u}}),a=new u.Choice(function(){return c},function(t){return new i(function(e){return r.Left.create(t.value0(e))},r.either((n=e.lmap(r.bifunctorEither)(r.Left.create),function(e){return n(t.value1(e))}))(function(e){return r.Left.create(r.Right.create(e))}));var n},function(t){return new i(function(e){return r.Right.create(t.value0(e))},r.either(function(e){return r.Left.create(r.Left.create(e))})((n=e.lmap(r.bifunctorEither)(r.Right.create),function(e){return n(t.value1(e))})));var n});module.exports={Market:i,functorMarket:o,profunctorMarket:c,choiceMarket:a}; +},{"../Data.Bifunctor/index.js":"e2Wc","../Data.Either/index.js":"B2JL","../Data.Functor/index.js":"+0AE","../Data.Profunctor/index.js":"0DaD","../Data.Profunctor.Choice/index.js":"nkqb"}],"h1YV":[function(require,module,exports) { +"use strict";var n=require("../Data.Either/index.js"),r=require("../Data.Eq/index.js"),e=require("../Data.Foldable/index.js"),t=require("../Data.Function/index.js"),u=require("../Data.Functor/index.js"),o=require("../Data.Newtype/index.js"),i=require("../Data.Ord/index.js"),c=require("../Data.Profunctor/index.js"),a=require("../Data.Profunctor.Choice/index.js"),f=require("../Data.Profunctor.Closed/index.js"),d=require("../Data.Profunctor.Costrong/index.js"),g=require("../Data.Traversable/index.js"),s=function(n){return n},q=new c.Profunctor(function(n){return function(n){return function(r){return n(r)}}}),l=new d.Costrong(function(){return q},function(n){return n.value0},function(n){return n.value1}),w=new f.Closed(function(){return q},function(n){return t.const(n)}),x=new a.Choice(function(){return q},function(r){return new n.Left(r)},function(r){return new n.Right(r)}),j=new o.Newtype(function(n){return n},s),p=new u.Functor(function(n){return function(r){return n(r)}}),D=new 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t.bind(o.bindExceptT(m.monadIdentity))(i.mapExcept(d.lmap(a.bifunctorEither)(p.map(E.functorNonEmptyList)(D.ErrorAtProperty.create(c.sumEncoding.value0.contentsFieldName))))(t.bind(o.bindExceptT(m.monadIdentity))(q.index(q.indexString)(f)(c.sumEncoding.value0.contentsFieldName))(y)))(function(n){return e.pure(o.applicativeExceptT(m.monadIdentity))(n)})})}})}}},Yn=new z(D.unsafeToForeign),Zn=new H(D.readChar),$n=new z(D.unsafeToForeign),_n=new H(D.readBoolean),ne=function(n){return new z((e=p.map(p.functorArray)(In(n)),function(n){return D.unsafeToForeign(e(n))}));var e},ee=function(n){return new H((e=function(e){return function(t){return i.mapExcept(d.lmap(a.bifunctorEither)(p.map(E.functorNonEmptyList)(D.ErrorAtIndex.create(e))))(Mn(n)(t))}},t.composeKleisli(o.bindExceptT(m.monadIdentity))(D.readArray)(function(n){return h.sequence(h.traversableArray)(o.applicativeExceptT(m.monadIdentity))(c.zipWith(e)(c.range(0)(c.length(n)))(n))})));var 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{ +"use strict";var e=require("../Data.CommutativeRing/index.js"),n=require("../Data.DivisionRing/index.js"),r=require("../Data.Eq/index.js"),t=require("../Data.EuclideanRing/index.js"),i=require("../Data.Lens.Getter/index.js"),u=require("../Data.Lens.Iso/index.js"),o=require("../Data.Lens.Iso.Newtype/index.js"),a=require("../Data.Maybe/index.js"),c=require("../Data.Newtype/index.js"),d=require("../Data.Number.Format/index.js"),s=require("../Data.Ord/index.js"),p=require("../Data.Ring/index.js"),w=require("../Data.Semiring/index.js"),f=require("../Data.Show/index.js"),g=require("../Data.String.CodeUnits/index.js"),m=require("../Data.String.Common/index.js"),h=require("../Data.String.Pattern/index.js"),x=require("../Foreign.Generic.Class/index.js"),q=require("../Math/index.js"),l=function(e){return e},D=function(e){return e},N=function(e){return e},j=new f.Show(function(e){return e}),B=new f.Show(function(e){return d.toStringWith(d.fixed(0))(e)+" 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U.IsSymbol(function(){return"renderables"}))()()()()(oe.cacherAffNil(be.refl)))(e)("vscale")(we(i)))(function(i){return a.bind(Y.bindAff)(ae.newLayer(Q.monadAffAff)()(oe.cacherAffCons(new U.IsSymbol(function(){return"renderables"}))()()()()(oe.cacherAffNil(be.refl)))(e)("legend")(Me(f)))(function(e){var f,d=(f={rulerColor:T.wrap(ie.newtypeHexColor)(t.red),threshold:n.score},h.traverse_(Y.applicativeAff)(h.foldableArray)(function(e){return a.discard(a.discardUnit)(Y.bindAff)(e.run(f))(function(){return a.bind(Y.bindAff)(e.last.renderables)(e.drawOnCanvas(new P.Pair(0,0)))})})([e,i,r]));return o.pure(Y.applicativeAff)({snps:function(e){return function(r){return a.discard(a.discardUnit)(Y.bindAff)(u.run({snps:{threshold:n.score,render:n.snps},view:r}))(function(){return a.bind(Y.bindAff)(u.last.renderables)(u.drawOnCanvas(e))})}},annotations:function(e){return function(r){return 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e=function(e){return function(t){return function(){return t[e]}}};exports.children=e("children"),exports._firstElementChild=e("firstElementChild"),exports._lastElementChild=e("lastElementChild"),exports.childElementCount=e("childElementCount"),exports._querySelector=function(e){return function(t){return function(){return t.querySelector(e)}}},exports.querySelectorAll=function(e){return function(t){return function(){return t.querySelectorAll(e)}}}; +},{}],"lU5U":[function(require,module,exports) { +"use strict";var e=require("./foreign.js"),r=require("../Data.Eq/index.js"),t=require("../Data.Functor/index.js"),n=require("../Data.Newtype/index.js"),u=require("../Data.Nullable/index.js"),i=require("../Data.Ord/index.js"),l=require("../Effect/index.js"),o=function(e){return e},c=function(r){var n=t.map(l.functorEffect)(u.toMaybe),i=e._querySelector(r);return function(e){return n(i(e))}},a=i.ordString,f=new n.Newtype(function(e){return e},o),d=function(){var 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e=require("./foreign.js"),r=require("../Data.Functor/index.js"),t=require("../Data.Maybe/index.js"),n=require("../Data.Nullable/index.js"),o=require("../Effect/index.js"),a=require("../Unsafe.Coerce/index.js"),u=require("../Web.HTML.HTMLDocument.ReadyState/index.js"),f=require("../Web.Internal.FFI/index.js"),c=a.unsafeCoerce,i=a.unsafeCoerce,d=a.unsafeCoerce,s=a.unsafeCoerce,m=a.unsafeCoerce,T=function(){var n,a=r.map(o.functorEffect)((n=t.fromMaybe(u.Loading.value),function(e){return n(u.parse(e))}));return function(r){return a(e._readyState(r))}}(),g=f.unsafeReadProtoTagged("HTMLDocument"),l=f.unsafeReadProtoTagged("HTMLDocument"),M=f.unsafeReadProtoTagged("HTMLDocument"),D=f.unsafeReadProtoTagged("HTMLDocument"),E=f.unsafeReadProtoTagged("HTMLDocument"),b=function(){var t=r.map(o.functorEffect)(n.toMaybe);return function(r){return t(e._currentScript(r))}}(),v=function(){var t=r.map(o.functorEffect)(n.toMaybe);return function(r){return t(e._body(r))}}(),y=function(){var 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o=r.map(i.functorEffect)(a),u=e._requestIdleCallback(n)(t);return function(e){return o(u(e))}}},m=function(n){var t=r.map(i.functorEffect)(f),o=e._requestAnimationFrame(n);return function(e){return t(o(e))}},d=function(n){return function(t){return function(u){return r.map(i.functorEffect)(o.toMaybe)(e._prompt(n)(t)(u))}}},p=function(n){return function(t){return r.map(i.functorEffect)(o.toMaybe)(e._prompt(n)("")(t))}},q=function(n){return r.map(i.functorEffect)(o.toMaybe)(e._opener(n))},y=function(n){return function(t){return function(u){return function(c){return r.map(i.functorEffect)(o.toMaybe)(e._open(n)(t)(u)(c))}}}},I=new t.Newtype(function(e){return e},a),w=new t.Newtype(function(e){return e},f),b=new n.Eq(function(e){return function(n){return e===n}}),g=new u.Ord(function(){return b},function(e){return function(n){return u.compare(u.ordInt)(e)(n)}}),E=new n.Eq(function(e){return function(n){return e===n}}),h=new u.Ord(function(){return E},function(e){return function(n){return u.compare(u.ordInt)(e)(n)}}),v=function(n){return e._cancelIdleCallback(t.unwrap(I)(n))},C=function(n){return e._cancelAnimationFrame(t.unwrap(w)(n))};module.exports={toEventTarget:l,open:y,prompt:p,promptDefault:d,requestAnimationFrame:m,cancelAnimationFrame:C,requestIdleCallback:s,cancelIdleCallback:v,opener:q,newtypeRequestAnimationFrameId:w,eqRequestAnimationFrameId:E,ordRequestAnimationFrameId:h,newtypeRequestIdleCallbackId:I,eqRequestIdleCallbackId:b,ordRequestIdleCallbackId:g,document:e.document,navigator:e.navigator,location:e.location,history:e.history,innerWidth:e.innerWidth,innerHeight:e.innerHeight,alert:e.alert,confirm:e.confirm,moveBy:e.moveBy,moveTo:e.moveTo,outerHeight:e.outerHeight,outerWidth:e.outerWidth,print:e.print,resizeBy:e.resizeBy,resizeTo:e.resizeTo,screenX:e.screenX,screenY:e.screenY,scroll:e.scroll,scrollBy:e.scrollBy,scrollX:e.scrollX,scrollY:e.scrollY,localStorage:e.localStorage,sessionStorage:e.sessionStorage,parent:e.parent}; 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e=require("./foreign.js"),n=require("../Data.Bounded/index.js"),t=require("../Data.Enum/index.js"),r=require("../Data.Eq/index.js"),o=require("../Data.Maybe/index.js"),u=require("../Data.Ord/index.js"),a=require("../Data.Ordering/index.js"),i=require("../Unsafe.Coerce/index.js"),c=require("../Web.Internal.FFI/index.js"),f=function(){function e(){}return e.value=new e,e}(),s=function(){function e(){}return e.value=new e,e}(),d=function(){function e(){}return e.value=new e,e}(),l=function(){function e(){}return e.value=new e,e}(),v=i.unsafeCoerce,m=i.unsafeCoerce,E=function(e){return 0===e?new o.Just(f.value):1===e?new o.Just(s.value):2===e?new o.Just(d.value):3===e?new o.Just(l.value):o.Nothing.value},y=c.unsafeReadProtoTagged("KeyboardEvent"),K=c.unsafeReadProtoTagged("KeyboardEvent"),w=function(e){if(e instanceof f)return 0;if(e instanceof s)return 1;if(e instanceof d)return 2;if(e instanceof l)return 3;throw new Error("Failed pattern match at Web.UIEvent.KeyboardEvent (line 107, 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g.Nothing)return G.log(R.monadEffectEffect)("Could not find element '#browser'")();if(a instanceof g.Just){var f=$.read($.readRecord()($.readFieldsCons(new F.IsSymbol(function(){return"chrs"}))($.readRecord()($.readFieldsCons(new F.IsSymbol(function(){return"chrBG1"}))(H.readforeignHexColor)($.readFieldsCons(new F.IsSymbol(function(){return"chrBG2"}))(H.readforeignHexColor)($.readFieldsCons(new F.IsSymbol(function(){return"chrLabels"}))($.readRecord()($.readFieldsCons(new F.IsSymbol(function(){return"fontSize"}))($.readInt)($.readFieldsNil)()()))($.readFieldsNil)()())()())()()))($.readFieldsCons(new F.IsSymbol(function(){return"initialChrs"}))($.readMaybe($.readRecord()($.readFieldsCons(new F.IsSymbol(function(){return"left"}))($.readString)($.readFieldsCons(new F.IsSymbol(function(){return"right"}))($.readString)($.readFieldsNil)()())()())))($.readFieldsCons(new F.IsSymbol(function(){return"score"}))($.readRecord()($.readFieldsCons(new 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line 595, column 33): "+[a.constructor.name])}};module.exports={_render:De,_docResize:Be,initializeTrack:ke,btnUI:Ee,btnUIFixed:xe,keyUI:ge,printSNPInfo:ye,wrapWith:me,snpHTML:pe,peakHTML:Ie,annoPeakHTML:qe,annotationHTML:Ne,annotationHTMLAll:Me,annotationHTMLDefault:je,annotationHTMLShort:Fe,IBoxShow:se,IBoxHide:de,IBoxSetY:ce,IBoxSetX:le,IBoxSetContents:we,updateInfoBox:be,infoBoxId:ve,initInfoBox:he,setHandlers:Te,mkGwas:Ge,mkGene:Re,runBrowser:Le,main:Ue,mouseChrSizes:Se,genericInfoBoxF:Ce,showInfoBoxF:Ae,windowInnerSize:e.windowInnerSize,buttonEvent:e.buttonEvent,keydownEvent:e.keydownEvent,resizeEvent:e.resizeEvent,initDebugDiv:e.initDebugDiv,setDebugDivVisibility:e.setDebugDivVisibility,setDebugDivPoint:e.setDebugDivPoint,setElementContents:e.setElementContents,setWindow:e.setWindow}; +},{"./foreign.js":"DuPX","../Control.Applicative/index.js":"qYya","../Control.Apply/index.js":"QcLv","../Control.Bind/index.js":"7VcT","../Data.Array/index.js":"4t4C","../Data.Bifunctor/index.js":"e2Wc","../Data.BigInt/index.js":"Zx+T","../Data.Either/index.js":"B2JL","../Data.Filterable/index.js":"6hfS","../Data.Foldable/index.js":"eVDl","../Data.Function/index.js":"ImXJ","../Data.Functor/index.js":"+0AE","../Data.Generic.Rep/index.js":"AuzG","../Data.Generic.Rep.Show/index.js":"lpst","../Data.Int/index.js":"xNJb","../Data.Lens.Getter/index.js":"OPOX","../Data.Lens.Internal.Forget/index.js":"mj9z","../Data.Lens.Iso.Newtype/index.js":"CiFJ","../Data.List.Types/index.js":"Xxuc","../Data.Map.Internal/index.js":"RRDs","../Data.Maybe/index.js":"5mN7","../Data.Monoid/index.js":"TiEB","../Data.Newtype/index.js":"lz8k","../Data.Pair/index.js":"PpsX","../Data.Semigroup/index.js":"EsAJ","../Data.Semiring/index.js":"11NF","../Data.Show/index.js":"mFY7","../Data.Symbol/index.js":"4oJQ","../Data.Time.Duration/index.js":"AnkF","../Data.Tuple/index.js":"II/O","../Data.Unit/index.js":"NhVk","../Data.Variant/index.js":"hgdh","../Data.Variant.Internal/index.js":"kYoO","../Effect/index.js":"oTWB","../Effect.Aff/index.js":"I7lu","../Effect.Aff.AVar/index.js":"hACG","../Effect.Class/index.js":"dWtH","../Effect.Class.Console/index.js":"3Dts","../Effect.Exception/index.js":"0OCW","../Effect.Ref/index.js":"/Jaj","../Foreign/index.js":"pu1p","../Genetics.Browser/index.js":"X0te","../Genetics.Browser.Bed/index.js":"UuEA","../Genetics.Browser.Canvas/index.js":"VVkU","../Genetics.Browser.Coordinates/index.js":"7bYH","../Genetics.Browser.Demo/index.js":"mKwt","../Genetics.Browser.Layer/index.js":"YWUW","../Genetics.Browser.Track/index.js":"HH6s","../Genetics.Browser.Types/index.js":"HhmG","../Genetics.Browser.UI.View/index.js":"Tmz+","../Global.Unsafe/index.js":"qSZP","../Math/index.js":"Rpaz","../Record/index.js":"0gG4","../Simple.JSON/index.js":"DqNI","../Type.Equality/index.js":"Uq/R","../Web.DOM.Document/index.js":"0hiR","../Web.DOM.Element/index.js":"S4h2","../Web.DOM.Node/index.js":"P+X4","../Web.DOM.ParentNode/index.js":"lU5U","../Web.HTML/index.js":"UQRJ","../Web.HTML.HTMLDocument/index.js":"EU5r","../Web.HTML.Window/index.js":"o+50","../Web.UIEvent.KeyboardEvent/index.js":"o/+T"}],"Focm":[function(require,module,exports) { +var e=require("./output/Genetics.Browser.UI");window.GenomeBrowser=e; +},{"./output/Genetics.Browser.UI":"JuOH"}]},{},["Focm"], null) \ No newline at end of file -- cgit v1.2.3 From 4e6c8eba35a5ecd9e6b5b1c5faa98021656acb9d Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 12 Aug 2019 16:34:05 -0500 Subject: Fixed some things to update the genome browser and get it running correctly Fixed issue where trait page for genotype traits didn't work Removed bad y axis title on probability plot --- .../marker_regression/display_mapping_results.py | 9 + wqflask/wqflask/marker_regression/run_mapping.py | 49 +- wqflask/wqflask/show_trait/show_trait.py | 4 +- .../static/new/javascript/init_genome_browser.js | 168 +- .../new/javascript/plotly_probability_plot.js | 1 - .../css/purescript-genetics-browser.css | 1 + .../css/purescript_genetics_browser_v01.css | 1 - .../js/purescript-genetics-browser.js | 63016 +++++++++++++++++++ .../js/purescript-genetics-browser_v01.js | 659 - wqflask/wqflask/templates/mapping_results.html | 10 +- wqflask/wqflask/views.py | 4 +- 11 files changed, 63166 insertions(+), 756 deletions(-) create mode 100644 wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css delete mode 100644 wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript_genetics_browser_v01.css create mode 100644 wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js delete mode 100644 wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser_v01.js diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index ea1ca5ed..b1e9dad4 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -31,6 +31,7 @@ import piddle as pid import sys,os import cPickle import httplib +import json from flask import Flask, g @@ -1696,6 +1697,14 @@ class DisplayMappingResults(object): else: LRS_LOD_Max = self.lrsMax + #ZS: Needed to pass to genome browser + js_data = json.loads(self.js_data) + if self.LRS_LOD == "LRS": + js_data['max_score'] = LRS_LOD_Max/4.16 + else: + js_data['max_score'] = LRS_LOD_Max + self.js_data = json.dumps(js_data) + if LRS_LOD_Max > 100: LRSScale = 20.0 elif LRS_LOD_Max > 20: diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 7f6bb0a5..11ad7aa4 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -7,6 +7,7 @@ from pprint import pformat as pf import string import math +from decimal import Decimal import random import sys import datetime @@ -314,30 +315,41 @@ class RunMapping(object): else: self.qtl_results = [] self.qtl_results_for_browser = [] + self.annotations_for_browser = [] highest_chr = 1 #This is needed in order to convert the highest chr to X/Y for marker in results: browser_marker = dict( chr = str(marker['chr']), rs = marker['name'], - ps = marker['Mb']*1000000 + ps = marker['Mb']*1000000, + url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" ) - if 'p_value' in marker: - browser_marker['p_wald'] = marker['p_value'] + annot_marker = dict( + name = str(marker['name']), + chr = str(marker['chr']), + rs = marker['name'], + pos = marker['Mb']*1000000, + url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" + ) + #if 'p_value' in marker: + # logger.debug("P EXISTS:", marker['p_value']) + #else: + if 'lrs_value' in marker and marker['lrs_value'] > 0: + browser_marker['p_wald'] = 10**-(marker['lrs_value']/4.61) + elif 'lod_score' in marker and marker['lod_score'] > 0: + browser_marker['p_wald'] = 10**-(marker['lod_score']) else: - if 'lrs_value' in marker and marker['lrs_value'] > 0: - browser_marker['p_wald'] = -math.log10(marker['lrs_value']/4.16) - elif 'lod_score' in marker and marker['lod_score'] > 0: - browser_marker['p_wald'] = -math.log10(marker['lod_score']) - else: - browser_marker['p_wald'] = 0 + browser_marker['p_wald'] = 0 + self.qtl_results_for_browser.append(browser_marker) + self.annotations_for_browser.append(annot_marker) if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y": if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y": highest_chr = marker['chr'] if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): self.qtl_results.append(marker) - browser_files = write_input_for_browser(self.dataset, self.qtl_results_for_browser) + browser_files = write_input_for_browser(self.dataset, self.qtl_results_for_browser, self.annotations_for_browser) with Bench("Exporting Results"): export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type) @@ -350,6 +362,11 @@ class RunMapping(object): self.trimmed_markers = trim_markers_for_table(results) if self.mapping_method != "gemma": + if self.score_type == "LRS": + significant_for_browser = self.significant / 4.16 + else: + significant_for_browser = self.significant + self.js_data = dict( #result_score_type = self.score_type, #this_trait = self.this_trait.name, @@ -361,7 +378,8 @@ class RunMapping(object): #qtl_results = self.qtl_results, num_perm = self.num_perm, perm_results = self.perm_output, - browser_files = browser_files + browser_files = browser_files, + significant = significant_for_browser ) else: self.js_data = dict( @@ -406,6 +424,7 @@ class RunMapping(object): def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type): with open(results_path, "w+") as output_file: + output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") output_file.write("Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") output_file.write("Data Set: " + dataset.fullname + "\n") if dataset.type == "ProbeSet": @@ -413,6 +432,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("Location: " + str(trait.chr) + " @ " + str(trait.mb) + " Mb\n") output_file.write("\n") output_file.write("Name,Chr,") + if score_type.lower() == "-log(p)": + score_type = "'-log(p)" if mapping_scale == "physic": output_file.write("Mb," + score_type) else: @@ -491,7 +512,7 @@ def trim_markers_for_table(markers): else: return sorted_markers -def write_input_for_browser(this_dataset, markers): +def write_input_for_browser(this_dataset, gwas_results, annotations): file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) gwas_filename = file_base + "_GWAS" annot_filename = file_base + "_ANNOT" @@ -499,8 +520,8 @@ def write_input_for_browser(this_dataset, markers): annot_path = "{}/gn2/".format(TEMPDIR) + annot_filename with open(gwas_path + ".json", "w") as gwas_file, open(annot_path + ".json", "w") as annot_file: - gwas_file.write(json.dumps(markers)) - annot_file.write(json.dumps([])) + gwas_file.write(json.dumps(gwas_results)) + annot_file.write(json.dumps(annotations)) return [gwas_filename, annot_filename] #return [gwas_filename, annot_filename] \ No newline at end of file diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index b0a46b32..02c65d47 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -194,10 +194,10 @@ class ShowTrait(object): trait_symbol = self.this_trait.symbol short_description = trait_symbol - elif self.this_trait.post_publication_abbreviation: + elif hasattr(self.this_trait, 'post_publication_abbreviation'): short_description = self.this_trait.post_publication_abbreviation - elif self.this_trait.pre_publication_abbreviation: + elif hasattr(self.this_trait, 'pre_publication_abbreviation'): short_description = self.this_trait.pre_publication_abbreviation # Todo: Add back in the ones we actually need from below, as we discover we need them diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js index 64a300bc..7dfd6712 100644 --- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js +++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js @@ -1,73 +1,97 @@ -console.log("THE FILES:", js_data.browser_files) - -snps_filename = "/browser_input?filename=" + js_data.browser_files[0] -annot_filename = "/browser_input?filename=" + js_data.browser_files[1] - -localUrls = -{ - snps: snps_filename, - annotations: null -}; - -var vscaleWidth = 90.0; -var legendWidth = 140.0; -var score = { min: 0.0, max: 30.0, sig: 4 }; -var gwasPadding = { top: 35.0, - bottom: 35.0, - left: vscaleWidth, - right: legendWidth }; -var gwasHeight = 420.0; -var genePadding = { top: 10.0, - bottom: 35.0, - left: vscaleWidth, - right: legendWidth }; -var geneHeight = 140.0; - - -var config = -{ trackHeight: 400.0, - padding: gwasPadding, - score: score, - urls: localUrls, - tracks: { - gwas: { - trackHeight: gwasHeight, - padding: gwasPadding, - snps: { - radius: 3.75, - lineWidth: 1.0, - color: { outline: "#FFFFFF", - fill: "#00008B" }, - pixelOffset: {x: 0.0, y: 0.0} - }, - annotations: { - radius: 5.5, - outline: "#000000", - snpColor: "#0074D9", - geneColor: "#FF4136" - }, - score: score, - legend: { - fontSize: 14, - hPad: 0.2, - vPad: 0.2 - }, - vscale: { - color: "#000000", - hPad: 0.125, - numSteps: 3, - fonts: { labelSize: 18, scaleSize: 16 } - }, - } - }, - chrs: { - chrBG1: "#FFFFFF", - chrBG2: "#DDDDDD", - chrLabels: { fontSize: 16 }, - }, - initialChrs: { left: "1", right: "19" } -}; - -GenomeBrowser.main(config)(); - +console.log("THE FILES:", js_data.browser_files) + +snps_filename = "/browser_input?filename=" + js_data.browser_files[0] +annot_filename = "/browser_input?filename=" + js_data.browser_files[1] + +localUrls = +{ + snps: snps_filename, + annotations: annot_filename +}; + +var coordinateSystem = + [ + { chr: "1", size: "195471971" }, + { chr: "2", size: "182113224" }, + { chr: "3", size: "160039680" }, + { chr: "4", size: "156508116" }, + { chr: "5", size: "151834684" }, + { chr: "6", size: "149736546" }, + { chr: "7", size: "145441459" }, + { chr: "8", size: "129401213" }, + { chr: "9", size: "124595110" }, + { chr: "10", size: "130694993" }, + { chr: "11", size: "122082543" }, + { chr: "12", size: "120129022" }, + { chr: "13", size: "120421639" }, + { chr: "14", size: "124902244" }, + { chr: "15", size: "104043685" }, + { chr: "16", size: "98207768" }, + { chr: "17", size: "94987271" }, + { chr: "18", size: "90702639" }, + { chr: "19", size: "61431566" }, + ]; + +var vscaleWidth = 90.0; +var legendWidth = 140.0; + +if ('significant' in js_data) { + var significant_score = parseFloat(js_data.significant) +} else { + var significant_score = 4 +} +var score = { min: 0.0, max: js_data.max_score, sig: significant_score }; +var gwasPadding = { top: 35.0, + bottom: 35.0, + left: vscaleWidth, + right: legendWidth }; +var gwasHeight = 320.0; +var config = +{ score: score, + urls: localUrls, + tracks: { + gwas: { + trackHeight: gwasHeight, + padding: gwasPadding, + snps: { + radius: 3.75, + lineWidth: 1.0, + color: { outline: "#FFFFFF", + fill: "#00008B" }, + pixelOffset: {x: 0.0, y: 0.0} + }, + annotations: { + urls: { + url: "GeneNetwork" + }, + radius: 5.5, + outline: "#000000", + snpColor: "#0074D9", + geneColor: "#FF4136" + }, + score: score, + legend: { + fontSize: 14, + hPad: 0.2, + vPad: 0.2 + }, + vscale: { + color: "#000000", + hPad: 0.125, + numSteps: 3, + fonts: { labelSize: 18, scaleSize: 16 } + }, + }, + }, + chrs: { + chrBG1: "#FFFFFF", + chrBG2: "#EEEEEE", + chrLabels: { fontSize: 16 }, + }, + // initialChrs: { left: "1", right: "5" } + coordinateSystem: coordinateSystem, + }; + +GenomeBrowser.main(config)(); + document.getElementById("controls").style.visibility = "visible"; \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js index cc4195e4..e8b7ab83 100644 --- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js +++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js @@ -195,7 +195,6 @@ } }, yaxis: { - title: "Data Quantiles", zeroline: false, visible: true, linecolor: 'black', diff --git a/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css b/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css new file mode 100644 index 00000000..135292ac --- /dev/null +++ b/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css @@ -0,0 +1 @@ +body,html{max-width:100%;overflow-x:hidden}#browser{position:absolute;margin:0}#info-line{border:1px solid #aaa;padding:2px;position:absolute;right:0;top:1px;min-width:14%;font-size:9pt}#controls{visibility:hidden;position:absolute;top:4px;left:100px;z-index:1000}#controls>button{border:1px solid #aaa;border-radius:2px;padding-left:6px;padding-right:6px;height:23px;min-width:20px}button#scrollRight,button#zoomIn{margin-left:-2px;margin-right:4px}#infoBox{position:absolute;display:inline-block;z-index:10000;visibility:hidden;padding:5px;border:2px solid grey;border-radius:5%;background-color:#fff;min-height:100px;min-width:10px;max-width:80%;margin-top:9.7em;font-family:sans-serif}#infoBox>div{float:left;margin:1em 1.2em}#infoBox>div>p{margin:.1em} \ No newline at end of file diff --git a/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript_genetics_browser_v01.css b/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript_genetics_browser_v01.css deleted file mode 100644 index 135292ac..00000000 --- a/wqflask/wqflask/static/packages/purescript_genome_browser/css/purescript_genetics_browser_v01.css +++ /dev/null @@ -1 +0,0 @@ -body,html{max-width:100%;overflow-x:hidden}#browser{position:absolute;margin:0}#info-line{border:1px solid #aaa;padding:2px;position:absolute;right:0;top:1px;min-width:14%;font-size:9pt}#controls{visibility:hidden;position:absolute;top:4px;left:100px;z-index:1000}#controls>button{border:1px solid #aaa;border-radius:2px;padding-left:6px;padding-right:6px;height:23px;min-width:20px}button#scrollRight,button#zoomIn{margin-left:-2px;margin-right:4px}#infoBox{position:absolute;display:inline-block;z-index:10000;visibility:hidden;padding:5px;border:2px solid grey;border-radius:5%;background-color:#fff;min-height:100px;min-width:10px;max-width:80%;margin-top:9.7em;font-family:sans-serif}#infoBox>div{float:left;margin:1em 1.2em}#infoBox>div>p{margin:.1em} \ No newline at end of file diff --git a/wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js b/wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js new file mode 100644 index 00000000..27bb4b2f --- /dev/null +++ b/wqflask/wqflask/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js @@ -0,0 +1,63016 @@ +// modules are defined as an array +// [ module function, map of requires ] +// +// map of requires is short require name -> numeric require +// +// anything defined in a previous bundle is accessed via the +// orig method which is the require for previous bundles +parcelRequire = (function (modules, cache, entry, globalName) { + // Save the require from previous bundle to this closure if any + var previousRequire = typeof parcelRequire === 'function' && parcelRequire; + var nodeRequire = typeof require === 'function' && require; + + function newRequire(name, jumped) { + if (!cache[name]) { + if (!modules[name]) { + // if we cannot find the module within our internal map or + // cache jump to the current global require ie. the last bundle + // that was added to the page. + var currentRequire = typeof parcelRequire === 'function' && parcelRequire; + if (!jumped && currentRequire) { + return currentRequire(name, true); + } + + // If there are other bundles on this page the require from the + // previous one is saved to 'previousRequire'. Repeat this as + // many times as there are bundles until the module is found or + // we exhaust the require chain. + if (previousRequire) { + return previousRequire(name, true); + } + + // Try the node require function if it exists. + if (nodeRequire && typeof name === 'string') { + return nodeRequire(name); + } + + var err = new Error('Cannot find module \'' + name + '\''); + err.code = 'MODULE_NOT_FOUND'; + throw err; + } + + localRequire.resolve = resolve; + localRequire.cache = {}; + + var module = cache[name] = new newRequire.Module(name); + + modules[name][0].call(module.exports, localRequire, module, module.exports, this); + } + + return cache[name].exports; + + function localRequire(x){ + return newRequire(localRequire.resolve(x)); + } + + function resolve(x){ + return modules[name][1][x] || x; + } + } + + function Module(moduleName) { + this.id = moduleName; + this.bundle = newRequire; + this.exports = {}; + } + + newRequire.isParcelRequire = true; + newRequire.Module = Module; + newRequire.modules = modules; + newRequire.cache = cache; + newRequire.parent = previousRequire; + newRequire.register = function (id, exports) { + modules[id] = [function (require, module) { + module.exports = exports; + }, {}]; + }; + + var error; + for (var i = 0; i < entry.length; i++) { + try { + newRequire(entry[i]); + } catch (e) { + // Save first error but execute all entries + if (!error) { + error = e; + } + } + } + + if (entry.length) { + // Expose entry point to Node, AMD or browser globals + // Based on https://github.com/ForbesLindesay/umd/blob/master/template.js + var mainExports = newRequire(entry[entry.length - 1]); + + // CommonJS + if (typeof exports === "object" && typeof module !== "undefined") { + module.exports = mainExports; + + // RequireJS + } else if (typeof define === "function" && define.amd) { + define(function () { + return mainExports; + }); + + // - + {% endblock %} diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index becb139a..189f8abc 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -19,8 +19,8 @@ - {% if gwa_filename is defined %} - + {% if output_files is defined %} + {% endif %} {% if reaper_version is defined %} @@ -171,7 +171,7 @@ {% endif %} -

    +
    {{header}}Max LRS{{header}}{{header}}{{header}}Additive Effect{{header}}{{header}}{{header}}Sample rNSample p(r)Lit rTissue rTissue p(r)Sample rhoNSample p(rho)Lit rTissue rhoTissue p(rho)Sample r  NSample p(r)Sample rho  NSample p(rho)Sample rNSample p(r)Sample rhoNSample p(rho)
    {{ trait.description_display }} {{ trait.location_repr }} {{ '%0.3f' % trait.mean|float }}{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}{{ trait.LRS_location_repr }}{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %} {{'%0.3f'|format(trait.sample_r)}} {{ trait.num_overlap }} {{'%0.3e'|format(trait.sample_p)}}{{'%0.3f'|format(trait.tissue_corr)}} {{'%0.3e'|format(trait.tissue_pvalue)}}{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}{{ trait.LRS_location_repr }}{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}{{ trait.description_display }} {{ trait.authors }} {{ trait.LRS_score_repr }}{{ trait.LRS_location_repr }}{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %} {{'%0.3f'|format(trait.sample_r)}} {{ trait.num_overlap }} {{'%0.3e'|format(trait.sample_p)}}{{ trait.LRS_score_repr }}{{ trait.LRS_location_repr }}{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}{{ trait.location_repr }} {{'%0.3f'|format(trait.sample_r)}}{{ '%0.2f' | format(marker.lod_score|float) }}{{ '%0.2f' | format(marker.lrs_value|float / 4.16) }}{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}{{ '%0.2f' | format(marker.lod_score|float * 4.16) }}{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}{{ '%0.2f' | format(marker.lrs_value|float) }}