diff options
Diffstat (limited to 'uploader/templates/phenotypes')
14 files changed, 512 insertions, 237 deletions
diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html index 9909c20..3207129 100644 --- a/uploader/templates/phenotypes/add-phenotypes-base.html +++ b/uploader/templates/phenotypes/add-phenotypes-base.html @@ -1,26 +1,13 @@ {%extends "phenotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%block title%}Phenotypes{%endblock%} {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="add-phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">Add Phenotypes</a> -</li> -{%endblock%} - {%block contents%} +{{super()}} {{flash_all_messages()}} <div class="row"> @@ -42,8 +29,7 @@ {%block frm_add_phenotypes_elements%}{%endblock%} - <fieldset id="fldset-publication-info"> - <legend>Publication Information</legend> + <h4>Publication Information</h4> <input type="hidden" name="publication-id" id="txt-publication-id" /> <span class="form-text text-muted"> Select a publication for your data. <br /> @@ -57,7 +43,7 @@ <table id="tbl-select-publication" class="table compact stripe"> <thead> <tr> - <th>#</th> + <th>Index</th> <th>PubMed ID</th> <th>Title</th> <th>Authors</th> @@ -66,7 +52,6 @@ <tbody></tbody> </table> - </fieldset> <div class="form-group"> <input type="submit" @@ -83,6 +68,8 @@ {%endblock%} + + {%block javascript%} <script type="text/javascript"> $(function() { @@ -97,7 +84,8 @@ if(pub.PubMed_ID) { return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + `${pub.PubMed_ID}/" target="_blank" ` + - `title="Link to publication on NCBI.">` + + `title="Link to publication on NCBI. This will ` + + `open in a new tab.">` + `${pub.PubMed_ID}</a>`; } return ""; @@ -110,10 +98,7 @@ if(pub.Title) { title = pub.Title } - return `<a href="/publications/view/${pub.Id}" ` + - `target="_blank" ` + - `title="Link to view publication details">` + - `${title}</a>`; + return title; } }, { diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html index 67b56e3..b1322b2 100644 --- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html +++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html @@ -1,7 +1,6 @@ {%extends "phenotypes/add-phenotypes-base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%from "phenotypes/macro-display-preview-table.html" import display_preview_table%} {%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%} @@ -9,19 +8,6 @@ {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="add-phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">Add Phenotypes</a> -</li> -{%endblock%} - {%block frm_add_phenotypes_documentation%} <p>This page will allow you to upload all the separate files that make up your phenotypes. Here, you will have to upload each separate file individually. If @@ -35,8 +21,7 @@ {%endblock%} {%block frm_add_phenotypes_elements%} -<fieldset id="fldset-file-metadata"> - <legend>File(s) Metadata</legend> + <h4>File(s) Metadata</h4> <div class="form-group"> <label for="txt-file-separator" class="form-label">File Separator</label> <div class="input-group"> @@ -103,12 +88,9 @@ <a href="#docs-file-na" title="Documentation for no-value fields"> documentation for more information</a>.</span> </div> -</fieldset> -<fieldset id="fldset-files"> <legend>Data File(s)</legend> - <fieldset id="fldset-descriptions-file"> <div class="form-group"> <div class="form-check"> <input id="chk-phenotype-descriptions-transposed" @@ -159,10 +141,8 @@ {{display_preview_table( "tbl-preview-pheno-desc", "phenotype descriptions")}} </div> - </fieldset> - - <fieldset id="fldset-data-file"> + <div class="form-group"> <div class="form-check"> <input id="chk-phenotype-data-transposed" @@ -210,11 +190,9 @@ on the expected format for the file provided here.</p>')}} {{display_preview_table("tbl-preview-pheno-data", "phenotype data")}} </div> - </fieldset> {%if population.Family in families_with_se_and_n%} - <fieldset id="fldset-se-file"> <div class="form-group"> <div class="form-check"> <input id="chk-phenotype-se-transposed" @@ -261,10 +239,8 @@ {{display_preview_table("tbl-preview-pheno-se", "standard errors")}} </div> - </fieldset> - <fieldset id="fldset-n-file"> <div class="form-group"> <div class="form-check"> <input id="chk-phenotype-n-transposed" @@ -311,8 +287,6 @@ {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}} </div> - </fieldset> -</fieldset> {%endif%} {%endblock%} @@ -447,10 +421,6 @@ {%endblock%} -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} - {%block more_javascript%} <script src="{{url_for('base.node_modules', @@ -495,7 +465,7 @@ .map((field) => { var value = field.trim(); if(navalues.includes(value)) { - return "⋘NUL⋙"; + return "[NO-VALUE]"; } return value; }) diff --git a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html index 898fc0c..4afd6ab 100644 --- a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html +++ b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html @@ -1,25 +1,11 @@ {%extends "phenotypes/add-phenotypes-base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%block title%}Phenotypes{%endblock%} {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="add-phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">Add Phenotypes</a> -</li> -{%endblock%} - {%block frm_add_phenotypes_documentation%} <p>Select the zip file bundle containing information on the phenotypes you wish to upload, then click the "Upload Phenotypes" button below to @@ -201,7 +187,3 @@ <em>phenotypes × individuals</em>.</p> </div> {%endblock%} - -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} diff --git a/uploader/templates/phenotypes/base.html b/uploader/templates/phenotypes/base.html index adbc012..5959422 100644 --- a/uploader/templates/phenotypes/base.html +++ b/uploader/templates/phenotypes/base.html @@ -1,19 +1,27 @@ {%extends "populations/base.html"%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_sui_pheno_dataset_card%} -{%block lvl3_breadcrumbs%} -<li {%if activelink=="phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - {%if dataset is mapping%} +{%block breadcrumbs%} +{{super()}} +{%if dataset%} +<li class="breadcrumb-item"> <a href="{{url_for('species.populations.phenotypes.view_dataset', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">{{dataset.Name}}</a> - {%else%} - <a href="{{url_for('species.populations.phenotypes.index')}}">Phenotypes</a> - {%endif%} + species_id=species['SpeciesId'], + population_id=population['Id'], + dataset_id=dataset['Id'])}}"> + {{dataset["Name"]}} + </a> </li> -{%block lvl4_breadcrumbs%}{%endblock%} +{%endif%} +{%endblock%} + +{%block contents%} +<div class="row"> + <h2 class="heading">{{dataset.FullName}} ({{dataset.Name}})</h2> +</div> +{%endblock%} + + +{%block sidebarcontents%} +{{display_sui_pheno_dataset_card(species, population, dataset)}} {%endblock%} diff --git a/uploader/templates/phenotypes/confirm-delete-phenotypes.html b/uploader/templates/phenotypes/confirm-delete-phenotypes.html new file mode 100644 index 0000000..3cf6e65 --- /dev/null +++ b/uploader/templates/phenotypes/confirm-delete-phenotypes.html @@ -0,0 +1,196 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Delete Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">View</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"><h2>Delete Phenotypes</h2></div> + +{%if phenotypes | length > 0%} +<div class="row"> + <p>You have requested to delete the following phenotypes:</p> +</div> + +<div class="row"> + <div class="col"> + <a id="btn-select-all-phenotypes" + href="#" + class="btn btn-info" + title="Select all phenotypes">select all</a> + </div> + <div class="col"> + <a id="btn-deselect-all-phenotypes" + href="#" + class="btn btn-warning" + title="Deselect all phenotypes">deselect all</a> + </div> +</div> + +<div class="row"> + <table id="tbl-delete-phenotypes" class="table"> + <thead> + <tr> + <th>Index</th> + <th>Record ID</th> + <th>Description</th> + </tr> + </thead> + <tbody> + {%for phenotype in phenotypes%} + <tr> + <td> + <input id="chk-xref-id-{{phenotype.xref_id}}" + name="xref_ids" + type="checkbox" + value="{{phenotype.xref_id}}" + class="chk-row-select" /> + </td> + <td>{{phenotype.xref_id}}</td> + <td>{{phenotype.Post_publication_description or + phenotype.Pre_publication_description or + phenotype.original_description}}</td> + </tr> + {%endfor%} + </tbody> + </table> +</div> + +<div class="row"> + <form id="frm-delete-phenotypes-selected" + method="POST" + action="{{url_for('species.populations.phenotypes.delete_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}"> + <div class="row"> + <div class="col"> + <input class="btn btn-info" + type="submit" + title="Cancel delete and return to dataset page." + name="action" + value="cancel" /></div> + <div class="col"> + <input id="btn-delete-phenotypes-selected" + class="btn btn-danger" + type="submit" + title="Delete the selected phenotypes from this dataset." + name="action" + value="delete" /> + </div> + </div> + </form> +</div> +{%else%} +<div class="row"> + <p>You did not select any phenotypes to delete. Delete everything?</p> +</div> + +<div class="row"> + <form id="frm-delete-phenotypes-all" + method="POST" + action="{{url_for('species.populations.phenotypes.delete_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}"> + <div class="form-check"> + <input class="form-check-input" + type="checkbox" + name="confirm_delete_all_phenotypes" + id="chk-confirm-delete-all-phenotypes" /> + <label class="form-check-label" + for="chk-confirm-delete-all-phenotypes"> + delete all phenotypes?</label> + </div> + + <div class="row"> + <div class="col"> + <input class="btn btn-info" + type="submit" + title="Cancel delete and return to dataset page." + name="action" + value="cancel" /></div> + <div class="col"> + <input class="btn btn-danger" + type="submit" + title="Delete all phenotypes in this dataset." + name="action" + value="delete" /> + </div> + </div> + </form> +</div> +{%endif%} + +{%endblock%} + +{%block javascript%} +<script type="text/javascript"> + $(function() { + var dt = buildDataTable( + "#tbl-delete-phenotypes", + data=[], + columns=[], + userSettings={ + responsive: true, + select: { + style: "os", + info: false + }, + initComplete: function(setting, json) { + var api = this.api(); + api.rows().select(); + api.rows({selected: true}).nodes().each((node, index) => { + setRowChecked(node); + }); + } + }); + + $("#btn-select-all-phenotypes").on("click", function(event) { + dt.selectAll(); + }); + + $("#btn-deselect-all-phenotypes").on("click", function(event) { + dt.deselectAll(); + }); + + $("#btn-delete-phenotypes-selected").on("click", function(event) { + event.preventDefault(); + form = $("#frm-delete-phenotypes-selected"); + form.find(".dynamically-added-element").remove(); + dt.rows({selected: true}).nodes().each(function(node, index) { + var xref_id = $(node) + .find('input[type="checkbox"]:checked') + .val(); + var chk = $('<input type="checkbox">'); + chk.attr("class", "dynamically-added-element"); + chk.attr("value", xref_id); + chk.attr("name", "xref_ids"); + chk.attr("style", "display: none"); + chk.prop("checked", true); + form.append(chk); + }); + form.append( + $('<input type="hidden" name="action" value="delete" />')); + form.submit(); + }) + }); +</script> +{%endblock%} + diff --git a/uploader/templates/phenotypes/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html index 19a2b34..9963953 100644 --- a/uploader/templates/phenotypes/create-dataset.html +++ b/uploader/templates/phenotypes/create-dataset.html @@ -48,7 +48,8 @@ {%else%} class="form-control" {%endif%} - required="required" /> + required="required" + readonly="readonly" /> <small class="form-text text-muted"> <p>A short representative name for the dataset.</p> <p>Recommended: Use the population name and append "Publish" at the end. @@ -66,7 +67,7 @@ <input id="txt-dataset-fullname" name="dataset-fullname" type="text" - value="{{original_formdata.get('dataset-fullname', '')}}" + value="{{original_formdata.get('dataset-fullname', '') or population.Name + ' Phenotypes'}}" {%if errors["dataset-fullname"] is defined%} class="form-control danger" {%else%} diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html index 115d6af..1b3ee9d 100644 --- a/uploader/templates/phenotypes/edit-phenotype.html +++ b/uploader/templates/phenotypes/edit-phenotype.html @@ -142,7 +142,7 @@ <table class="table table-striped table-responsive table-form-table"> <thead style="position: sticky; top: 0;"> <tr> - <th>#</th> + <th>Index</th> <th>Sample</th> <th>Value</th> {%if population.Family in families_with_se_and_n%} diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html index 257f726..951907f 100644 --- a/uploader/templates/phenotypes/job-status.html +++ b/uploader/templates/phenotypes/job-status.html @@ -2,7 +2,6 @@ {%from "cli-output.html" import cli_output%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%block extrameta%} {%if job and job.status not in ("success", "completed:success", "error", "completed:error")%} @@ -14,23 +13,13 @@ {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="add-phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">View Datasets</a> -</li> -{%endblock%} - {%block contents%} {%if job%} -<h4 class="subheading">Progress</h4> +<div class="row"> + <h2 class="heading">{{dataset.FullName}} ({{dataset.Name}})</h2> + <h3 class="subheading">upload progress</h3> +</div> <div class="row" style="overflow:scroll;"> <p><strong>Process Status:</strong> {{job.status}}</p> {%if metadata%} @@ -63,10 +52,10 @@ <p> {%if errors | length == 0%} <a href="{{url_for('species.populations.phenotypes.review_job_data', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id, - job_id=job_id)}}" + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + job_id=job_id)}}" class="btn btn-primary" title="Continue to process data">Continue</a> {%else%} @@ -80,14 +69,29 @@ {%endif%} </div> -<h4 class="subheading">Errors</h4> +<h3 class="subheading">upload errors</h3> +{%if errors | length == 0 %} <div class="row" style="max-height: 20em; overflow: scroll;"> - {%if errors | length == 0 %} <p class="text-info"> <span class="glyphicon glyphicon-info-sign"></span> No errors found so far </p> - {%else%} +</div> +{%else%} +{%if errors | length > 0%} +<div class="row"> + <div class="col"> + <a href="{{url_for('species.populations.phenotypes.download_errors', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + job_id=job_id)}}" + class="btn btn-info" + title="Download the errors as a CSV file.">download errors CSV</a> + </div> +</div> +{%endif%} +<div class="row" style="max-height: 20em; overflow: scroll;"> <table class="table table-responsive"> <thead style="position: sticky; top: 0; background: white;"> <tr> @@ -122,7 +126,8 @@ {%endfor%} </tbody> </table> - {%endif%} +</div> +{%endif%} </div> <div class="row"> @@ -149,7 +154,3 @@ </div> {%endif%} {%endblock%} - -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} diff --git a/uploader/templates/phenotypes/load-phenotypes-success.html b/uploader/templates/phenotypes/load-phenotypes-success.html index 645be16..1fb0e61 100644 --- a/uploader/templates/phenotypes/load-phenotypes-success.html +++ b/uploader/templates/phenotypes/load-phenotypes-success.html @@ -1,26 +1,14 @@ {%extends "phenotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%block title%}Phenotypes{%endblock%} {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="load-phenotypes-success"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">Add Phenotypes</a> -</li> -{%endblock%} - {%block contents%} +{{super()}} + <div class="row"> <p>You have successfully loaded <!-- maybe indicate the number of phenotypes here? -->your @@ -34,9 +22,5 @@ </div> {%endblock%} -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} - {%block more_javascript%}{%endblock%} diff --git a/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html index 11b108b..641421d 100644 --- a/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html +++ b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html @@ -1,4 +1,4 @@ -{%from "populations/macro-display-population-card.html" import display_population_card%} +{%from "populations/macro-display-population-card.html" import display_population_card, display_sui_population_card%} {%macro display_pheno_dataset_card(species, population, dataset)%} {{display_population_card(species, population)}} @@ -29,3 +29,29 @@ </div> </div> {%endmacro%} + +{%macro display_sui_pheno_dataset_card(species, population, dataset)%} +{{display_sui_population_card(species, population)}} + +<div class="row"> + <table class="table"> + <caption>Current dataset</caption> + <tbody> + <tr> + <th>Name</th> + <td>{{dataset.Name}}</td> + </tr> + + <tr> + <th>Full Name</th> + <td>{{dataset.FullName}}</td> + </tr> + + <tr> + <th>Short Name</th> + <td>{{dataset.ShortName}}</td> + </tr> + </tbody> + </table> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/macro-display-preview-table.html b/uploader/templates/phenotypes/macro-display-preview-table.html index 5a4c422..6dffe9f 100644 --- a/uploader/templates/phenotypes/macro-display-preview-table.html +++ b/uploader/templates/phenotypes/macro-display-preview-table.html @@ -1,19 +1,11 @@ {%macro display_preview_table(tableid, filetype)%} -<div class="card"> - <div class="card-body"> - <h5 class="card-title">{{filetype | title}}: File Preview</h5> - <div class="card-text" style="overflow: scroll;"> - <table id="{{tableid}}" class="table table-condensed table-responsive"> - <thead> - <tr> - </tr> - <tbody> - <tr> - <td class="data-row-template text-info"></td> - </tr> - </tbody> - </table> - </div> - </div> +<div class="table-responsive" + style="max-width:39.2em;border-radius:5px;border: solid 1px;overflow-x: scroll;"> + <h5>{{filetype | title}}: File Preview</h5> + <table id="{{tableid}}" class="table"> + <thead><tr></tr></thead> + + <tbody></tbody> + </table> </div> {%endmacro%} diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html index 859df74..0e8f119 100644 --- a/uploader/templates/phenotypes/review-job-data.html +++ b/uploader/templates/phenotypes/review-job-data.html @@ -70,6 +70,9 @@ {%endif%} {%endfor%} </ul> +</div> + +<div class="row"> <form id="frm-review-phenotype-data" method="POST" @@ -78,10 +81,38 @@ population_id=population.Id, dataset_id=dataset.Id)}}"> <input type="hidden" name="data-qc-job-id" value="{{job.jobid}}" /> - <input type="submit" - value="continue" - class="btn btn-primary" /> + <div class="form-group"> + <label for="txt-data-name">data name</label> + <input type="text" + id="txt-data-name" + class="form-control" + name="data_name" + title="A short, descriptive name for this data." + placeholder="{{user.email}} - {{dataset.Name}} - {{timestamp}}" + value="{{user.email}} - {{dataset.Name}} - {{timestamp}}" + required="required"> + <span class="form-text text-muted"> + This is a short, descriptive name for the data. It is useful to humans, + enabling them identify what traits each data "resource" wraps around. + </span> + </div> + + {%if view_under_construction%} + <div class="form-group"> + <label for="txt-data-description">data description</label> + <textarea id="txt-data-description" + class="form-control" + name="data_description" + title="A longer description for this data." + rows="5"></textarea> + <span class="form-text text-muted"> + </span> + </div> + {%endif%} + + <button type="submit" class="btn btn-primary">continue</button> </form> + </div> {%else%} <div class="row"> @@ -104,10 +135,6 @@ {%endif%} {%endblock%} -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} - {%block javascript%} <script type="text/javascript"> diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index 306dcce..fc84757 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -1,7 +1,6 @@ {%extends "phenotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Phenotypes{%endblock%} @@ -24,37 +23,6 @@ {{flash_all_messages()}} <div class="row"> - <p>The basic dataset details are:</p> - - <table class="table"> - <thead> - <tr> - <th>Name</th> - <th>Full Name</th> - <th>Short Name</th> - </tr> - </thead> - - <tbody> - <tr> - <td>{{dataset.Name}}</td> - <td>{{dataset.FullName}}</td> - <td>{{dataset.ShortName}}</td> - </tr> - </tbody> - </table> -</div> - -<div class="row"> - <p><a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}" - title="Add a bunch of phenotypes" - class="btn btn-primary">Add phenotypes</a></p> -</div> - -<div class="row"> <h2>Phenotype Data</h2> <p>Click on any of the phenotypes in the table below to view and edit that @@ -63,9 +31,70 @@ phenotypes of interest.</p> </div> - <div class="row"> + <div class="col"> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="Add a bunch of phenotypes" + class="btn btn-primary">Add phenotypes</a> + </div> + + <div class="col"> + <form id="frm-recompute-phenotype-means" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.recompute_means', + species_id=species['SpeciesId'], + population_id=population['Id'], + dataset_id=dataset['Id'])}}" + class="d-flex flex-row align-items-center flex-wrap" + style="display: inline;"> + <input type="submit" + title="Compute/Recompute the means for all phenotypes." + class="btn btn-info" + value="compute means" + id="submit-frm-recompute-phenotype-means" /> + </form> + </div> + + <div class="col"> + <form id="frm-run-qtlreaper" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.rerun_qtlreaper', + species_id=species['SpeciesId'], + population_id=population['Id'], + dataset_id=dataset['Id'])}}" + class="d-flex flex-row align-items-center flex-wrap" + style="display: inline;"> + <input type="submit" + title="Run/Rerun QTLReaper." + class="btn btn-info" + value="run QTLReaper" + id="submit-frm-rerun-qtlreaper" /> + </form> + </div> + + <div class="col"> + <form id="frm-delete-phenotypes" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.delete_phenotypes', + species_id=species['SpeciesId'], + population_id=population['Id'], + dataset_id=dataset['Id'])}}"> + <input type="submit" + class="btn btn-danger" + id="btn-delete-phenotypes" + title="Delete phenotypes from this dataset. If no phenotypes are selected in the table, this will delete ALL the phenotypes." + value="delete phenotypes" /> + </form> + </div> +</div> +<div class="row" style="margin-top: 0.5em;"> <table id="tbl-phenotypes-list" class="table compact stripe cell-border"> <thead> <tr> @@ -81,12 +110,10 @@ </div> {%endblock%} -{%block sidebarcontents%} -{{display_population_card(species, population)}} -{%endblock%} - {%block javascript%} +<script type="text/javascript" src="/static/js/urls.js"></script> + <script type="text/javascript"> $(function() { var species_id = {{species.SpeciesId}}; @@ -113,21 +140,44 @@ var spcs_id = {{species.SpeciesId}}; var pop_id = {{population.Id}}; var dtst_id = {{dataset.Id}}; - return `<a href="/species/${spcs_id}` + + var url = buildURLFromCurrentURL( + (`/species/${spcs_id}` + `/populations/${pop_id}` + `/phenotypes/datasets/${dtst_id}` + - `/phenotype/${pheno.xref_id}` + - `" target="_blank">` + + `/phenotype/${pheno.xref_id}`)); + return `<a href="${url.toString()}" target="_blank">` + `${pheno.InbredSetCode}_${pheno.xref_id}` + `</a>`; - } + }, + title: "Record", + visible: true, + searchable: true }, { data: function(pheno) { return (pheno.Post_publication_description || pheno.Original_description || pheno.Pre_publication_description); - } + }, + title: "Description", + visible: true, + searchable: true + }, + { + data: function(pheno) { + return pheno.publication.Title; + }, + title: "Publication Title", + visible: false, + searchable: true + }, + { + data: function(pheno) { + return pheno.publication.Authors; + }, + title: "Authors", + visible: false, + searchable: true } ], { @@ -145,6 +195,54 @@ return `${pheno.InbredSetCode}_${pheno.xref_id}`; } }); + + + $("#submit-frm-rerun-qtlreaper").on( + "click", + function(event) { + // (Re)run the QTLReaper script for selected phenotypes. + event.preventDefault(); + var form = $("#frm-run-qtlreaper"); + form.find(".dynamically-added-element").remove(); + dtPhenotypesList.rows({selected: true}).nodes().each((node, index) => { + _cloned = $(node).find(".chk-row-select").clone(); + _cloned.removeAttr("id"); + _cloned.removeAttr("class"); + _cloned.attr("style", "display: none;"); + _cloned.attr("data-type", "dynamically-added-element"); + _cloned.attr("class", "dynamically-added-element checkbox"); + _cloned.prop("checked", true); + form.append(_cloned); + }); + form.submit(); + }); + + $("#btn-delete-phenotypes").on( + "click", + function(event) { + // Collect selected phenotypes for deletion, if any. + event.preventDefault(); + form = $("#frm-delete-phenotypes"); + form.find(".dynamically-added-element").remove(); + $("#tbl-phenotypes-list") + .DataTable() + .rows({selected: true}). + nodes().each(function(node, index) { + var parts = $(node) + .find(".chk-row-select") + .val() + .split("_"); + var xref_id = parts[parts.length - 1].trim(); + var chk = $('<input type="checkbox">'); + chk.attr("class", "dynamically-added-element"); + chk.attr("value", xref_id); + chk.attr("name", "xref_ids"); + chk.attr("style", "display: none"); + chk.prop("checked", true); + form.append(chk); + }); + form.submit(); + }); }); </script> {%endblock%} diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html index 21ac501..a59949e 100644 --- a/uploader/templates/phenotypes/view-phenotype.html +++ b/uploader/templates/phenotypes/view-phenotype.html @@ -1,31 +1,18 @@ {%extends "phenotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Phenotypes{%endblock%} {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="view-phenotype"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.view_phenotype', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id, - xref_id=xref_id)}}">View Phenotype</a> -</li> -{%endblock%} - {%block contents%} {{flash_all_messages()}} <div class="row"> - <div class="panel panel-default"> - <div class="panel-heading"><strong>Basic Phenotype Details</strong></div> + <div class="card"> + <div class="card-header"> + <h5 class="card-title">Basic Phenotype Details</h5> + </div> <table class="table"> <tbody> @@ -41,24 +28,46 @@ <td><strong>Units</strong></td> <td>{{phenotype.Units}}</td> </tr> - {%for key,value in publish_data.items()%} - <tr> - <td><strong>{{key}}</strong></td> - <td>{{value}}</td> - </tr> - {%else%} - <tr> - <td colspan="2" class="text-muted"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - No publication data found. - </td> - </tr> - {%endfor%} </tbody> </table> </div> </div> +<div class="row" style="margin-top:5px;"> + <div class="card"> + <div class="card-header"> + <h5 class="card-title">Publication Details</h5> + </div> + + <div class="card-body"> + <table class="table"> + <tbody> + <tr> + {%for key in ("PubMed_ID", "Authors", "Title", "Journal"):%} + <tr> + <td><strong>{{key}}</strong></td> + <td>{{publication.get(key, "")}}</td> + </tr> + {%else%} + <tr> + <td colspan="2" class="text-muted"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + No publication data found. + </td> + </tr> + {%endfor%} + </tr> + </tbody> + </table> + <div style="text-align: right;"> + <a href="{{url_for('publications.edit_publication', publication_id=publication.Id, next=next)}}" + class="btn btn-info">edit</a> + <a href="#" class="btn btn-danger not-implemented">change</a> + </div> + </div> + </div> +</div> + {%if "group:resource:edit-resource" in privileges or "group:resource:delete-resource" in privileges%} <div class="row"> @@ -94,7 +103,7 @@ or "group:resource:delete-resource" in privileges%} <table class="table"> <thead> <tr> - <th>#</th> + <th>Index</th> <th>Sample</th> <th>Value</th> {%if has_se%} @@ -129,7 +138,3 @@ or "group:resource:delete-resource" in privileges%} </div> {%endblock%} - -{%block sidebarcontents%} -{{display_population_card(species, population)}} -{%endblock%} |