diff options
| -rw-r--r-- | api_readme.md | 155 | ||||
| -rw-r--r-- | wqflask/wqflask/db_info.py | 127 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/css/marker_regression.css | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/search_results.js | 22 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/base.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gsearch_gene.html | 16 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gsearch_pheno.html | 17 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/info_page.html | 92 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/mapping_results.html | 139 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/tutorials.html | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/user_login.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 13 |
14 files changed, 491 insertions, 128 deletions
diff --git a/api_readme.md b/api_readme.md new file mode 100644 index 00000000..96e8b246 --- /dev/null +++ b/api_readme.md @@ -0,0 +1,155 @@ +# API Query Documentation # +--- +# Fetching Dataset/Trait info/data # +--- +## Fetch Species List ## + +To get a list of species with data available in GN (and their associated names and ids): +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species +[ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ] +``` + +Or to get a single species info: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse.json +``` + +*For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later* + +## Fetch Groups/RISets ## + +This query can optionally filter by species: + +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/groups (for all species) +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mouse/groups (for just mouse groups/RISets) +[ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ] +``` + +## Fetch Genotypes for Group/RISet ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/genotypes/BXD +``` +Returns a CSV file with metadata in the first few rows, sample/strain names as columns, and markers as rows. Currently only works for genotypes we have stored in .geno files; I'll add the option to download BIMBAM files soon. + +## Fetch Datasets ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/bxd +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd +[ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ] +``` +(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" ### + +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` +{ "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 } +``` +(This also has the option to specify group/riset) + +### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ### +For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example: +``` +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 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 Info (Name, Description, Location, etc) ## +### For mRNA Expression/"ProbeSet" ### +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at +{ "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" } +``` + +### For "Phenotypes" ### +For phenotypes this just gets the max LRS, its location, and additive effect (as calculated by qtlreaper) + +Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001 +{ "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } +``` + +--- + +# Analyses # +--- +## Mapping ## +Currently two mapping tools can be used - GEMMA and R/qtl. qtlreaper will be added later with Christian Fischer's RUST implementation - https://github.com/chfi/rust-qtlreaper + +Each method's query takes the following parameters respectively (more will be added): +### GEMMA ### +* trait_id (*required*) - ID for trait being mapped +* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) +* use_loco - Whether to use LOCO (leave one chromosome out) method (default = false) +* maf - minor allele frequency (default = 0.01) + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true +``` + +### R/qtl ### +(See the R/qtl guide for information on some of these options - http://www.rqtl.org/manual/qtl-manual.pdf) +* trait_id (*required*) - ID for trait being mapped +* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) +* rqtl_method - hk (default) | ehk | em | imp | mr | mr-imp | mr-argmax ; Corresponds to the "method" option for the R/qtl scanone function. +* rqtl_model - normal (default) | binary | 2-part | np ; corresponds to the "model" option for the R/qtl scanone function +* num_perm - number of permutations; 0 by default +* control_marker - Name of marker to use as control; this relies on the user knowing the name of the marker they want to use as a covariate +* interval_mapping - Whether to use interval mapping; "false" by default +* pair_scan - *NYI* + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 +``` + +Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case) + +## Calculate Correlation ## +Currently only Sample and Tissue correlations are implemented + +This query currently takes the following parameters (though more will be added): +* trait_id (*required*) - ID for trait used for correlation +* db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets) +* target_db (*required*) - Target DB name to be correlated against +* type - sample (default) | tissue +* method - pearson (default) | spearman +* return - Number of results to return (default = 500) + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100 +[ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ] +``` diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py new file mode 100644 index 00000000..f04e38bf --- /dev/null +++ b/wqflask/wqflask/db_info.py @@ -0,0 +1,127 @@ +import httplib, urllib2 +import re + +from flask import Flask, g + +from utility.logger import getLogger +logger = getLogger(__name__ ) + +class InfoPage(object): + def __init__(self, start_vars): + self.info = None + self.gn_accession_id = None + if 'gn_accession_id' in start_vars: + self.gn_accession_id = start_vars['gn_accession_id'] + self.info_page_name = start_vars['info_page_name'] + + self.get_info() + self.get_datasets_list() + + def get_info(self, create=False): + query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " + + "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " + + "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " + + "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " + + "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " + + "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " + + "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " + + "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " + + "FROM InfoFiles " + + "LEFT JOIN Species USING (SpeciesId) " + + "LEFT JOIN Tissue USING (TissueId) " + + "LEFT JOIN InbredSet USING (InbredSetId) " + + "LEFT JOIN GeneChip USING (GeneChipId) " + + "LEFT JOIN AvgMethod USING (AvgMethodId) " + + "LEFT JOIN Datasets USING (DatasetId) " + + "LEFT JOIN Investigators USING (InvestigatorId) " + + "LEFT JOIN Organizations USING (OrganizationId) " + + "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ") + + if self.gn_accession_id: + final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id) + results = g.db.execute(final_query).fetchone() + if self.info_page_name and not results: + final_query = query_base + "InfoPageName={}".format(self.info_page_name) + elif self.info_page_name: + final_query = query_base + "InfoPageName={}".format(self.info_page_name) + results = g.db.execute(final_query).fetchone() + else: + raise 'No correct parameter found' + + if results: + self.info = process_query_results(results) + + if (not results or len(results) < 1) and self.info_page_name and create: + insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name) + return self.get_info() + + if not self.gn_accession_id and self.info: + self.gn_accession_id = self.info['accession_id'] + if not self.info_page_name and self.info: + self.info_page_name = self.info['info_page_name'] + + def get_datasets_list(self): + self.filelist = [] + try: + response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id) + data = response.read() + + matches = re.findall(r"<tr>.+?</tr>", data, re.DOTALL) + for i, match in enumerate(matches): + if i == 0: + continue + cells = re.findall(r"<td.+?>.+?</td>", match, re.DOTALL) + full_filename = re.search(r"<a href=\"(.+?)\"", cells[1], re.DOTALL).group(1).strip() + filename = full_filename.split("/")[-1] + filesize = re.search(r">(.+?)<", cells[2]).group(1).strip() + filedate = "N/A" #ZS: Since we can't get it for now + + self.filelist.append([filename, filedate, filesize]) + except Exception, e: + pass + +def process_query_results(results): + info_ob = { + 'info_page_name': results[0], + 'accession_id': results[1], + 'menu_name': results[2], + 'taxonomy_id': results[3], + 'tissue_name': results[4], + 'group_name': results[5], + 'gene_chip_name': results[6], + 'geo_platform': results[7], + 'avg_method_name': results[8], + 'dataset_name': results[9], + 'geo_series': results[10], + 'publication_title': results[11], + 'dataset_status_name': results[12], + 'dataset_summary': results[13], + 'about_cases': results[14], + 'about_tissue': results[15], + 'about_data_processing': results[16], + 'acknowledgement': results[17], + 'experiment_design': results[18], + 'contributors': results[19], + 'citation': results[20], + 'notes': results[21], + 'investigator_firstname': results[22], + 'investigator_lastname': results[23], + 'investigator_address': results[24], + 'investigator_city': results[25], + 'investigator_state': results[26], + 'investigator_zipcode': results[27], + 'investigator_country': results[28], + 'investigator_phone': results[29], + 'investigator_email': results[30], + 'investigator_url': results[31], + 'organization_name': results[32], + 'investigator_id': results[33], + 'dataset_id': results[34], + 'dataset_status_is': results[35], + 'about_platform': results[36], + 'info_file_title': results[37], + 'specifics': results[38] + } + + return info_ob + \ No newline at end of file diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 9bde343c..8a44b3fd 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -401,9 +401,7 @@ class RunMapping(object): rs = marker['name'], pos = this_ps ) - #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: @@ -417,6 +415,12 @@ class RunMapping(object): 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()): + if 'Mb' in marker.keys(): + marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['Mb']) + elif 'cM' in marker.keys(): + marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['cM']) + else: + marker['display_pos'] = "N/A" self.qtl_results.append(marker) with Bench("Exporting Results"): diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css index f1a26a83..e0a5ceea 100644 --- a/wqflask/wqflask/static/new/css/marker_regression.css +++ b/wqflask/wqflask/static/new/css/marker_regression.css @@ -62,6 +62,10 @@ table.dataTable tbody td { padding: 4px 20px 2px 10px; } +table.dataTable tbody tr.selected { + background-color: #ffee99; +} + table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td { border-top: 1px solid #ccc; border-right: 1px solid #ccc; diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js index 4e87d67a..685d6291 100644 --- a/wqflask/wqflask/static/new/javascript/search_results.js +++ b/wqflask/wqflask/static/new/javascript/search_results.js @@ -259,14 +259,16 @@ $(function() { let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"] let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"] + let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A + function sort_NAs(a, b, sort_function){ - if (a === "N/A" && b === "N/A") { + if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) { return 0; } - if (a === "N/A"){ + if (na_equivalent_vals.includes(a)){ return 1 } - if (b === "N/A") { + if (na_equivalent_vals.includes(b)) { return -1; } return sort_function(a, b) @@ -281,4 +283,18 @@ $(function() { } }); + $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) + { + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $('input', td).prop('checked') ? '1' : '0'; + } ); + }; + + $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) + { + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $(td).text(); + } ); + } + }); \ No newline at end of file diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 50562200..e6802cc4 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -4,7 +4,9 @@ <head> <meta charset="utf-8"> - <title>{% block title %}{% endblock %}</title> + + <title>{% block title %}{% endblock %} GeneNetwork 2</title> + <meta name="description" content=""> <meta name="author" content=""> <link rel="icon" type="image/png" sizes="64x64" href="/static/new/images/CITGLogo.png"> diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 478d6f5f..d2c78d65 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -59,20 +59,6 @@ </script> <script type="text/javascript" charset="utf-8"> - $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $('input', td).prop('checked') ? '1' : '0'; - } ); - }; - - $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $(td).text(); - } ); - } - $(document).ready( function () { $('#trait_table tr').click(function(event) { @@ -252,7 +238,7 @@ 'sDom': "pitirp", 'autoWidth': true, 'iDisplayLength': 500, - 'deferRender': true, + 'deferRender': false, 'paging': true, 'orderClasses': true, 'processing': true, diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index eb998d15..c44231f3 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -59,20 +59,6 @@ </script> <script type="text/javascript" charset="utf-8"> - $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $('input', td).prop('checked') ? '1' : '0'; - } ); - }; - - $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $(td).text(); - } ); - } - $(document).ready( function () { $('#trait_table tr').click(function(event) { @@ -172,6 +158,7 @@ 'title': "Record", 'type': "natural", 'data': null, + 'orderDataType': "dom-inner-text", 'render': function(data, type, row, meta) { return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>' } @@ -252,7 +239,7 @@ 'order': [[1, "asc" ]], 'sDom': "pitirp", 'autoWidth': false, - 'deferRender': true, + 'deferRender': false, 'iDisplayLength': 500, 'paging': true, 'orderClasses': true, diff --git a/wqflask/wqflask/templates/info_page.html b/wqflask/wqflask/templates/info_page.html new file mode 100644 index 00000000..d8b7d74c --- /dev/null +++ b/wqflask/wqflask/templates/info_page.html @@ -0,0 +1,92 @@ +{% extends "base.html" %} +{% block title %}Policies{% endblock %} +{% block content %} + +<h1 id="parent-fieldname-title">Data Set Group: {{ info.dataset_name }} +<!--<a href="/infoshare/manager/member-studies-edit.html?DatasetId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>--> +<span style="color:red;">{{ info.info_page_name }}</span> +</h1> +<table border="0" width="100%"> +<tr> +<td valign="top" width="50%"> +<table name="info_table" cellSpacing=0 cellPadding=5 width=100% border=0> + <tr><td><b>Data Set:</b> {{ info.info_file_title }} <!--<a href="/infoshare/manager/member-infofile-edit.html?GN_AccesionId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>--></td></tr> + <tr><td><b>GN Accession:</b> GN{{ gn_accession_id }}</td></tr> + <tr><td><b>GEO Series:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_series }}" target="_blank">{{ info.geo_series }}</a></td></tr> + <tr><td><b>Title:</b> {{ info.publication_title }}</td></tr> + <tr><td><b>Organism:</b> <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id={{ info.taxonomy_id }}" target="_blank">{{ info.menu_name }}</a></td></tr> + <tr><td><b>Group:</b> {{ info.group_name }}</td></tr> + <tr><td><b>Tissue:</b> {{ info.tissue_name }}</td></tr> + <tr><td><b>Dataset Status:</b> {{ info.dataset_status_name }}</td></tr> + <tr><td><b>Platforms:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_platform }}" target="_blank">{{ info.gene_chip_name }}</a></td></tr> + <tr><td><b>Normalization:</b> {{ info.avg_method_name }}</td></tr> +</table> +</td> +<td valign="top" width="50%"> +<table border="0" width="100%"> + <tr> + <td><b>Contact Information</b></td> + </tr> + <tr> + <td> + {{ info.investigator_first_name }} {{ info.inveestigator_last_name }}<br> + {{ info.organization_name }} <br> + {{ info.investigator_address }}<br> + {{ info.investigator_city }}, {{ info.investigator_state }} {{ info.investigator_zipcode }} {{ info.investigator_country }}<br> + Tel. {{ info.investigator_phone }}<br> + {{ info.investigator_email }}<br> + <a href="{{ info.investigator_url }}" target="_blank">Website</a> + </td> + </tr> + +<tr> + <td><b>Download datasets and supplementary data files</b></td> +</tr> +<tr> + <td> + <ul style="line-height: 160%"> + {% for file in filelist %} + <li><a href="http://datafiles.genenetwork.org/download/GN{{ gn_accession_id }}/{{ file[0] }}">{{ file[0] }} ({{ file[2] }})</a></li> + {% endfor %} + </ul> + </td> +</tr> + +<tr><td> +</td></tr> + +</table> +</td> +</tr> +</table> +<HR> +<p> +<table name="info_table" width="100%" border="0" cellpadding="5" cellspacing="0"> +<tr><td><span style="font-size:115%%;font-weight:bold;">Specifics of this Data Set:</span></td></tr> + <tr><td> {{ info.specifics|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%%;font-weight:bold;">Summary:</span></td></tr> + <tr><td> {{ info.dataset_summary|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">About the cases used to generate this set of data:</span></td></tr> + <tr><td> {{ info.about_cases|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">About the tissue used to generate this set of data:</span></td></tr> + <tr><td> {{ info.about_tissue|safe }}<br><br></td></tr> + <tr><td><span style="font-size:115%; font-weight:bold;">About the array platform:</span></td></tr> + <tr><td> {{ info.about_platform|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">About data values and data processing:</span></td></tr> + <tr><td> {{ info.about_data_processing|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Notes:</span></td></tr> + <tr><td> {{ info.notes|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Experiment Type:</span></td></tr> + <tr><td> {{ info.experiment_design|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Contributor:</span></td></tr> + <tr><td> {{ info.contributors|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Citation:</span></td></tr> + <tr><td> {{ info.citation|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Data source acknowledgment:</span></td></tr> + <tr><td> {{ info.acknowledgement|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Study Id:</span></td></tr> + <tr><td> {{ info.dataset_id }}<br><br></td></tr> +</table> +</p> + +{% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 8edda548..41d760c0 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -228,71 +228,61 @@ <button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> <br /> <br /> - <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}500{% else %}470{% endif %}px;"> - <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer"> - <thead> - <tr> - <th></th> - <th>Row</th> - <th>Marker</th> - <th>{{ LRS_LOD }}</th> - <th>Chr</th> - {% if plotScale != "physic" %} - <th>cM</th> - {% else %} - <th align="right">Mb</th> - {% endif %} - {% if 'additive' in trimmed_markers[0] %} - <th>Add Eff</th> - {% endif %} - {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %} - <th>Dom Eff</th> - {% endif %} - </tr> - </thead> - <tbody> - {% for marker in trimmed_markers %} - <tr> - <td align="center" style="padding: 1px 0px 1px 0px;"> - <input type="checkbox" name="selectCheck" - class="checkbox trait_checkbox" - value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}"> - </td> - <td align="right">{{ loop.index }}</td> - <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td> - {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %} - {% if 'lod_score' in marker %} - <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td> - {% else %} - <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td> - {% endif %} - {% else %} - {% if 'lod_score' in marker %} - <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td> - {% else %} - <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td> - {% endif %} - {% endif %} - <td align="right">{{marker.chr}}</td> - {% if plotScale != "physic" %} - {% if 'cM' in marker %} - <td align="right">{{ '%0.3f' | format(marker.cM|float) }}</td> - {% else %} - <td align="right">{{ '%0.3f' | format(marker.Mb|float) }}</td> - {% endif %} - {% else %} - <td align="right">{{ '%0.6f' | format(marker.Mb|float) }}</td> - {% endif %} - {% if 'additive' in marker %} - <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td> - {% endif %} - {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %} - <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td> - {% endif %} - </tr> - {% endfor %} - </tbody> - </table> + <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;"> + <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer"> + <thead> + <tr> + <th></th> + <th>Row</th> + <th>Marker</th> + {% if LRS_LOD == "-log(p)" %} + <th>–log(p)</th> + {% else %} + <th>{{ LRS_LOD }}</th> + {% endif %} + <th>Position ({% if plotScale == "physic" %}Mb{% else %}cM{% endif %})</th> + {% if 'additive' in trimmed_markers[0] %} + <th>Add Eff</th> + {% endif %} + {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %} + <th>Dom Eff</th> + {% endif %} + </tr> + </thead> + <tbody> + {% for marker in trimmed_markers %} + <tr> + <td align="center" style="padding: 1px 0px 1px 0px;"> + <input type="checkbox" name="selectCheck" + class="checkbox trait_checkbox" + value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}"> + </td> + <td align="right">{{ loop.index }}</td> + <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td> + {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %} + {% if 'lod_score' in marker %} + <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td> + {% else %} + <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td> + {% endif %} + {% else %} + {% if 'lod_score' in marker %} + <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td> + {% else %} + <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td> + {% endif %} + {% endif %} + <td align="right">{{ marker.display_pos }}</td> + {% if 'additive' in marker %} + <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td> + {% endif %} + {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %} + <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td> + {% endif %} + </tr> + {% endfor %} + </tbody> + </table> </div> </div> {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %} @@ -362,8 +352,7 @@ "columns": [ { "type": "natural", "width": "5%" }, { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "25%" }, - { "type": "natural" }, + { "type": "natural", "width": "20%" }, { "type": "natural" }, { "type": "natural" }{% if 'additive' in qtlresults[0] %}, { "type": "natural" }{% endif %}{% if 'dominance' in qtlresults[0] and dataset.group.genetic_type != "riset" %}, @@ -395,16 +384,16 @@ $('td', row).eq(9).attr("align", "right"); }, "columns": [ - { "bSortable": false}, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, + { "orderDataType": "dom-checkbox" }, + { "type": "natural"}, + { "type": "natural" , "orderDataType": "dom-inner-text" }, + { "type": "natural" , "orderDataType": "dom-inner-text" }, + { "type": "natural" , "orderDataType": "dom-inner-text" }, { "type": "natural" }, { "type": "natural" }, + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" , "orderDataType": "dom-inner-text" }, { "type": "natural" } ], "columnDefs": [ { diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 53373b41..282e752d 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -174,21 +174,6 @@ </script> <script type="text/javascript" charset="utf-8"> - - $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $('input', td).prop('checked') ? '1' : '0'; - } ); - }; - - $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $(td).text(); - } ); - } - $(document).ready( function () { $('#trait_table tr').click(function(event) { diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html index 3e6ef01c..f9d12ba5 100644 --- a/wqflask/wqflask/templates/tutorials.html +++ b/wqflask/wqflask/templates/tutorials.html @@ -15,3 +15,4 @@ and initial mapping results for Rat GWAS P50 as implemented in GeneNetwork.org</ </TR></TABLE> {% endblock %} + diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index 9331f369..077a799b 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -453,7 +453,9 @@ def register_user(params): user_details['confirmed'] = 1 user_details['registration_info'] = basic_info() - save_user(user_details, user_details['user_id']) + + if len(errors) == 0: + save_user(user_details, user_details['user_id']) return errors diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index fc9949a8..3d623736 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -37,6 +37,7 @@ from wqflask import gsearch from wqflask import update_search_results from wqflask import docs from wqflask import news +from wqflask import db_info from wqflask.submit_bnw import get_bnw_input from base.data_set import create_dataset, DataSet # Used by YAML in marker_regression from wqflask.show_trait import show_trait @@ -908,12 +909,24 @@ def snp_browser_page(): return render_template("snp_browser.html", **template_vars.__dict__) +@app.route("/db_info", methods=('GET',)) +def db_info_page(): + template_vars = db_info.InfoPage(request.args) + + return render_template("info_page.html", **template_vars.__dict__) + @app.route("/tutorial/WebQTLTour", methods=('GET',)) def tutorial_page(): #ZS: Currently just links to GN1 logger.info(request.url) return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/") +@app.route("/tutorial/security", methods=('GET',)) +def security_tutorial_page(): + #ZS: Currently just links to GN1 + logger.info(request.url) + return render_template("admin/security_help.html") + @app.route("/submit_bnw", methods=('POST',)) def submit_bnw(): logger.info(request.url) |