diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/gsearch.py | 115 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gsearch_gene.html | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gsearch_pheno.html | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/loading.html | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/mapping_results.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 13 |
9 files changed, 127 insertions, 55 deletions
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index fb8bdc55..8f66f7e9 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -121,16 +121,14 @@ class GSearch: continue max_lrs_text = "N/A" - if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None: - max_lrs_text = "Chr" + \ - str(this_trait['locus_chr']) + \ - ": " + str(this_trait['locus_mb']) + if this_trait['locus_chr'] and this_trait['locus_mb']: + max_lrs_text = f"Chr{str(this_trait['locus_chr'])}: {str(this_trait['locus_mb'])}" this_trait['max_lrs_text'] = max_lrs_text trait_list.append(this_trait) self.trait_count = len(trait_list) - self.trait_list = json.dumps(trait_list) + self.trait_list = trait_list self.header_fields = ['Index', 'Record', @@ -146,6 +144,22 @@ class GSearch: 'Max LRS Location', 'Additive Effect'] + self.header_data_names = [ + 'index', + 'name', + 'species', + 'group', + 'tissue', + 'dataset_fullname', + 'symbol', + 'description', + 'location_repr', + 'mean', + 'LRS_score_repr', + 'max_lrs_text', + 'additive', + ] + elif self.type == "phenotype": search_term = self.terms group_clause = "" @@ -169,24 +183,23 @@ class GSearch: PublishXRef.`LRS`, PublishXRef.`additive`, InbredSet.`InbredSetCode`, - PublishXRef.`mean` - FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication - WHERE PublishXRef.`InbredSetId`=InbredSet.`Id` - AND PublishFreeze.`InbredSetId`=InbredSet.`Id` - AND InbredSet.`SpeciesId`=Species.`Id` + PublishXRef.`mean`, + PublishFreeze.Id, + Geno.Chr as geno_chr, + Geno.Mb as geno_mb + FROM Species + INNER JOIN InbredSet ON InbredSet.`SpeciesId`=Species.`Id` + INNER JOIN PublishFreeze ON PublishFreeze.`InbredSetId`=InbredSet.`Id` + INNER JOIN PublishXRef ON PublishXRef.`InbredSetId`=InbredSet.`Id` + INNER JOIN Phenotype ON PublishXRef.`PhenotypeId`=Phenotype.`Id` + INNER JOIN Publication ON PublishXRef.`PublicationId`=Publication.`Id` + LEFT JOIN Geno ON PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id + WHERE + ( + (MATCH (Phenotype.Post_publication_description, Phenotype.Pre_publication_description, Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code) AGAINST ('{1}' IN BOOLEAN MODE) ) + OR (MATCH (Publication.Abstract, Publication.Title, Publication.Authors) AGAINST ('{1}' IN BOOLEAN MODE) ) + ) {0} - AND PublishXRef.`PhenotypeId`=Phenotype.`Id` - AND PublishXRef.`PublicationId`=Publication.`Id` - AND (Phenotype.Post_publication_description REGEXP "[[:<:]]{1}[[:>:]]" - OR Phenotype.Pre_publication_description REGEXP "[[:<:]]{1}[[:>:]]" - OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]{1}[[:>:]]" - OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]{1}[[:>:]]" - OR Phenotype.Lab_code REGEXP "[[:<:]]{1}[[:>:]]" - OR Publication.PubMed_ID REGEXP "[[:<:]]{1}[[:>:]]" - OR Publication.Abstract REGEXP "[[:<:]]{1}[[:>:]]" - OR Publication.Title REGEXP "[[:<:]]{1}[[:>:]]" - OR Publication.Authors REGEXP "[[:<:]]{1}[[:>:]]" - OR PublishXRef.Id REGEXP "[[:<:]]{1}[[:>:]]") ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id` LIMIT 6000 """.format(group_clause, search_term) @@ -221,6 +234,9 @@ class GSearch: this_trait['mean'] = f"{line[13]:.3f}" else: this_trait['mean'] = "N/A" + this_trait['dataset_id'] = line[14] + this_trait['locus_chr'] = line[15] + this_trait['locus_mb'] = line[16] this_trait['authors'] = line[7] this_trait['year'] = line[8] if this_trait['year'].isdigit(): @@ -241,32 +257,51 @@ class GSearch: if line[11] != "" and line[11] != None: this_trait['additive'] = '%.3f' % line[11] + dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="Publish", species=this_trait["species"]) + permissions = check_resource_availability(dataset_ob, this_trait['name']) + if type(permissions['data']) is list: + if "view" not in permissions['data']: + continue + else: + if permissions['data'] == 'no-access': + continue + this_trait['max_lrs_text'] = "N/A" - trait_ob = create_trait( - dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) - if not trait_ob: - continue if this_trait['dataset'] == this_trait['group'] + "Publish": try: - if trait_ob.locus_chr != "" and trait_ob.locus_mb != "": - this_trait['max_lrs_text'] = "Chr" + \ - str(trait_ob.locus_chr) + \ - ": " + str(trait_ob.locus_mb) + if this_trait['locus_chr'] and this_trait['locus_mb']: + this_trait['max_lrs_text'] = f"Chr{str(this_trait['locus_chr'])}: {str(this_trait['locus_mb'])}" except: this_trait['max_lrs_text'] = "N/A" trait_list.append(this_trait) self.trait_count = len(trait_list) - self.trait_list = json.dumps(trait_list) + self.trait_list = trait_list self.header_fields = ['Index', - 'Species', - 'Group', - 'Record', - 'Description', - 'Authors', - 'Year', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] + 'Species', + 'Group', + 'Record', + 'Description', + 'Authors', + 'Year', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] + + self.header_data_names = [ + 'index', + 'name', + 'species', + 'group', + 'tissue', + 'dataset_fullname', + 'symbol', + 'description', + 'location_repr', + 'mean', + 'LRS_score_repr', + 'max_lrs_text', + 'additive', + ] diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index a9a3e1a0..4cad2749 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -4,7 +4,7 @@ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" /> <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}"> - <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/css/all.min.css"> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/all.min.css') }}"/> <link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} @@ -141,7 +141,7 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> - <script language="javascript" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/js/all.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='fontawesome/js/all.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script> diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 6fd0abe8..48953d98 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -55,7 +55,15 @@ <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script type='text/javascript'> - var the_rows = {{ trait_list|safe }}; + var getParams = function(url) { + let parser = document.createElement('a'); + parser.href = url; + let params = parser.search.substring(1); + if(params.length > 0) { + return ('?'+params); + } + return params; + }; </script> <script type="text/javascript" charset="utf-8"> @@ -142,7 +150,6 @@ $('td', row).eq(12).attr('data-export', $('td', row).eq(12).text()); $('td', row).eq(13).attr('data-export', $('td', row).eq(13).text()); }, - 'data': the_rows, 'columns': [ { 'data': null, @@ -237,11 +244,13 @@ 'order': [[1, "asc" ]], 'sDom': "pitirp", 'autoWidth': true, - 'iDisplayLength': 500, 'deferRender': false, 'paging': true, 'orderClasses': true, 'processing': true, + 'iDisplayLength': 100, + 'bServerSide': true, + 'sAjaxSource': '/gsearch_table'+getParams(window.location.href), 'language': { 'loadingRecords': ' ', 'processing': 'Loading...' diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index 987b51a7..af9740ae 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -55,7 +55,15 @@ <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script type='text/javascript'> - var the_rows = {{ trait_list|safe }}; + var getParams = function(url) { + let parser = document.createElement('a'); + parser.href = url; + let params = parser.search.substring(1); + if(params.length > 0) { + return ('?'+params); + } + return params; + }; </script> <script type="text/javascript" charset="utf-8"> @@ -130,7 +138,6 @@ $('td', row).eq(9).attr('data-export', $('td', row).eq(9).text()); $('td', row).eq(10).attr('data-export', $('td', row).eq(10).text()); }, - 'data': the_rows, 'columns': [ { 'data': null, @@ -241,10 +248,12 @@ 'sDom': "pitirp", 'autoWidth': false, 'deferRender': false, - 'iDisplayLength': 500, 'paging': true, 'orderClasses': true, 'processing': true, + 'iDisplayLength': 100, + 'bServerSide': true, + 'sAjaxSource': '/gsearch_table'+getParams(window.location.href), 'language': { 'loadingRecords': ' ', 'processing': 'Loading...' diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 1adeb2bd..6d6136ac 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -33,18 +33,24 @@ <br> minor allele frequency lower limit = <b><i>{{ start_vars.maf }}</i></b> {% endif %} - {% if start_vars.covariates != "" and start_vars.method != "reaper" %} <br> + {% if start_vars.covariates != "" and start_vars.method != "reaper" %} {% set covariate_list = start_vars.covariates.split(",") %} cofactors = <b><i>{% for covariate in covariate_list %}{% set this_covariate = covariate.split(":")[0] %}{{ this_covariate }}{% if not loop.last %}, {% endif %}{% endfor %}</i></b> + {% else %} + cofactors = <b><i>None</i></b> {% endif %} {% if start_vars.control_marker != "" and start_vars.do_control == "true" and start_vars.method != "gemma" %} <br> marker covariate = <b><i>{{ start_vars.control_marker }}</i></b> {% endif %} - {% set genofile_desc = start_vars.genofile.split(":")[1] %} <br> - Genotype File = <b><i>{{ genofile_desc }}</i></b> + {% if start_vars.genofile != "" %} + {% set genofile_desc = start_vars.genofile.split(":")[1] %} + genotype file = <b><i>{{ genofile_desc }}</i></b> + {% else %} + genotype file = <b><i>{{ start_vars.group[0] | upper }}{{ start_vars.group[1:] }}.geno</i></b> + {% endif %} {% if start_vars.num_perm | int > 0 and start_vars.method != "gemma" %} <br> n of permutations = <b><i>{{ start_vars.num_perm }}</i></b> diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 73d7501b..d6fc6e37 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -357,7 +357,7 @@ {% endif %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='purescript-genome-browser/js/purescript-genetics-browser.js') }}"></script> diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index e7a7bc51..827bad98 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -4,7 +4,7 @@ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/font-awesome.min.css') }}" /> <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}"> - <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/css/all.min.css"> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/all.min.css') }}"/> <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> <link rel="stylesheet" type="text/css" href="static/new/css/trait_list.css" /> {% endblock %} @@ -150,7 +150,7 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/js/all.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='fontawesome/js/all.min.js') }}"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 09ecb7b6..fc14822c 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -148,7 +148,7 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> - <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.3/js/dataTables.scroller.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='nouislider/nouislider.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script> <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index f3b0257c..3c875163 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -280,6 +280,19 @@ def gsearchact(): elif type == "phenotype": return render_template("gsearch_pheno.html", **result) +@app.route("/gsearch_table", methods=('GET',)) +def gsearchtable(): + logger.info(request.url) + + gsearch_table_data = GSearch(request.args) + current_page = server_side.ServerSideTable( + gsearch_table_data.trait_count, + gsearch_table_data.trait_list, + gsearch_table_data.header_data_names, + request.args, + ).get_page() + + return flask.jsonify(current_page) @app.route("/gsearch_updating", methods=('POST',)) def gsearch_updating(): |