diff options
Diffstat (limited to 'uploader/templates')
17 files changed, 1853 insertions, 25 deletions
diff --git a/uploader/templates/background-jobs/sui-default-success-page.html b/uploader/templates/background-jobs/sui-default-success-page.html new file mode 100644 index 0000000..5732456 --- /dev/null +++ b/uploader/templates/background-jobs/sui-default-success-page.html @@ -0,0 +1,17 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Background Jobs: Success{%endblock%} + +{%block pagetitle%}Background Jobs: Success{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>Job <strong>{{job.job_id}}</strong>, + {%if job.get("metadata", {}).get("job-type")%} + of type '<em>{{job.metadata["job-type"]}}</em> + {%endif%}' completed successfully.</p> +</div> +{%endblock%} diff --git a/uploader/templates/jobs/sui-job-error.html b/uploader/templates/jobs/sui-job-error.html new file mode 100644 index 0000000..1a839a6 --- /dev/null +++ b/uploader/templates/jobs/sui-job-error.html @@ -0,0 +1,17 @@ +{%extends "sui-base.html"%} + +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Background Jobs: Error{%endblock%} + +{%block pagetitle%}Background Jobs: Error{%endblock%} + +{%block contents%} + +<h1>Background Jobs: Error</h1> +<p>Job <strong>{{job["job_id"]}}</strong> failed!</p> +<p>The error details are in the "STDERR" section below.</p> + +<h2>STDERR</h2> +<pre>{{job["stderr"]}}</pre> +{%endblock%} diff --git a/uploader/templates/jobs/sui-job-not-found.html b/uploader/templates/jobs/sui-job-not-found.html new file mode 100644 index 0000000..96c8586 --- /dev/null +++ b/uploader/templates/jobs/sui-job-not-found.html @@ -0,0 +1,11 @@ +{%extends "sui-base.html"%} + +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block contents%} +<p>Could not find job with ID: {{job_id}}</p> +{%endblock%} diff --git a/uploader/templates/jobs/sui-job-status.html b/uploader/templates/jobs/sui-job-status.html new file mode 100644 index 0000000..fc5e532 --- /dev/null +++ b/uploader/templates/jobs/sui-job-status.html @@ -0,0 +1,24 @@ +{%extends "sui-base.html"%} + +{%from "flash_messages.html" import flash_all_messages%} + +{%block extrameta%} +<meta http-equiv="refresh" content="5" /> +{%endblock%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block contents%} + +<p>Status: {{job["metadata"]["status"]}}</p> +<p>Job Type: {{job["metadata"]["job-type"]}}</p> + +<h2>STDOUT</h2> +<pre>{{job["stdout"]}}</pre> + +<h2>STDERR</h2> +<pre>{{job["stderr"]}}</pre> + +{%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/sui-add-phenotypes-base.html b/uploader/templates/phenotypes/sui-add-phenotypes-base.html new file mode 100644 index 0000000..1e71267 --- /dev/null +++ b/uploader/templates/phenotypes/sui-add-phenotypes-base.html @@ -0,0 +1,155 @@ +{%extends "phenotypes/sui-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block contents%} +{{super()}} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-add-phenotypes" + method="POST" + enctype="multipart/form-data" + action="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + use_bundle=use_bundle)}}" + data-resumable-target="{{url_for('files.resumable_upload_post')}}"> + <legend>Add New Phenotypes</legend> + + <div class="form-text help-block"> + {%block frm_add_phenotypes_documentation%}{%endblock%} + <p><strong class="text-warning">This will not update any existing phenotypes!</strong></p> + </div> + + {%block frm_add_phenotypes_elements%}{%endblock%} + + <fieldset id="fldset-publication-info"> + <legend>Publication Information</legend> + <input type="hidden" name="publication-id" id="txt-publication-id" /> + <span class="form-text text-muted"> + Select a publication for your data. <br /> + Can't find a publication you can use? Go ahead and + <a href="{{url_for( + 'publications.create_publication', + return_to='species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">create a new publication</a>.</span> + <table id="tbl-select-publication" class="table compact stripe"> + <thead> + <tr> + <th>#</th> + <th>PubMed ID</th> + <th>Title</th> + <th>Authors</th> + </tr> + </thead> + + <tbody></tbody> + </table> + </fieldset> + + <div class="form-group"> + <input type="submit" + value="upload phenotypes" + class="btn btn-primary" /> + </div> + </form> +</div> + +<div class="row"> + {%block page_documentation%}{%endblock%} +</div> + +{%endblock%} + + + + +{%block javascript%} +<script type="text/javascript"> + $(function() { + var publicationsDataTable = buildDataTable( + "#tbl-select-publication", + [], + [ + {data: "index"}, + { + searchable: true, + data: (pub) => { + if(pub.PubMed_ID) { + return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + + `${pub.PubMed_ID}/" target="_blank" ` + + `title="Link to publication on NCBI.">` + + `${pub.PubMed_ID}</a>`; + } + return ""; + } + }, + { + searchable: true, + data: (pub) => { + var title = "⸻"; + if(pub.Title) { + title = pub.Title + } + return `<a href="/publications/view/${pub.Id}" ` + + `target="_blank" ` + + `title="Link to view publication details">` + + `${title}</a>`; + } + }, + { + searchable: true, + data: (pub) => { + authors = pub.Authors.split(",").map( + (item) => {return item.trim();}); + if(authors.length > 1) { + return authors[0] + ", et. al."; + } + return authors[0]; + } + } + ], + { + serverSide: true, + ajax: { + url: "/publications/list", + dataSrc: "publications" + }, + select: "single", + paging: true, + scrollY: 700, + deferRender: true, + scroller: true, + scrollCollapse: true, + layout: { + topStart: "info", + topEnd: "search" + } + }); + publicationsDataTable.on("select", (event, datatable, type, indexes) => { + indexes.forEach((element, index, thearray) => { + let row = datatable.row(element).node(); + console.debug(datatable.row(element).data()); + $("#frm-add-phenotypes #txt-publication-id").val( + datatable.row(element).data().Id); + }); + }); + publicationsDataTable.on("deselect", (event, datatable, type, indexes) => { + indexes.forEach((element, index, thearray) => { + let row = datatable.row(element).node(); + $("#frm-add-phenotypes #txt-publication-id").val(null); + }); + }); + }); +</script> + +{%block more_javascript%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/phenotypes/sui-add-phenotypes-raw-files.html b/uploader/templates/phenotypes/sui-add-phenotypes-raw-files.html new file mode 100644 index 0000000..6038617 --- /dev/null +++ b/uploader/templates/phenotypes/sui-add-phenotypes-raw-files.html @@ -0,0 +1,829 @@ +{%extends "phenotypes/sui-add-phenotypes-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-preview-table.html" import display_preview_table%} +{%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%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 + you want instead to upload all your files as a single ZIP file, + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + use_bundle=true)}}" + title="">click here</a>.</p> +{%endblock%} + +{%block frm_add_phenotypes_elements%} +<fieldset id="fldset-file-metadata"> + <legend>File(s) Metadata</legend> + <div class="form-group"> + <label for="txt-file-separator" class="form-label">File Separator</label> + <div class="input-group"> + <input id="txt-file-separator" + name="file-separator" + type="text" + value="	" + class="form-control" + maxlength="1" /> + <span class="input-group-btn"> + <button id="btn-reset-file-separator" class="btn btn-info">Reset Default</button> + </span> + </div> + <span class="form-text text-muted"> + Provide the character that separates the fields in your file(s). It should + be the same character for all files (if more than one is provided).<br /> + A tab character will be assumed if you leave this field blank. See + <a href="#docs-file-separator" + title="Documentation for file-separator characters"> + documentation for more information</a>. + </span> + </div> + + <div class="form-group"> + <label for="txt-file-comment-character" class="form-label">File Comment-Character</label> + <div class="input-group"> + <input id="txt-file-comment-character" + name="file-comment-character" + type="text" + value="#" + class="form-control" + maxlength="1" /> + <span class="input-group-btn"> + <button id="btn-reset-file-comment-character" class="btn btn-info"> + Reset Default</button> + </span> + </div> + <span class="form-text text-muted"> + This specifies that lines that begin with the character provided will be + considered comment lines and ignored in their entirety. See + <a href="#docs-file-comment-character" + title="Documentation for comment characters"> + documentation for more information</a>. + </span> + </div> + + <div class="form-group"> + <label for="txt-file-na" class="form-label">File "No-Value" Indicators</label> + <div class="input-group"> + <input id="txt-file-na" + name="file-na" + type="text" + value="- NA N/A" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-reset-file-na" class="btn btn-info">Reset Default</button> + </span> + </div> + <span class="form-text text-muted"> + This specifies strings in your file indicate that there is no value for a + particular cell (a cell is where a column and row intersect). Provide a + space-separated list of strings if you have more than one way of + indicating no values. See + <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" + name="phenotype-descriptions-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-descriptions-transposed" + class="form-check-label"> + Description file transposed?</label> + </div> + + <div class="non-resumable-elements"> + <label for="finput-phenotype-descriptions" class="form-label"> + Phenotype Descriptions</label> + <input id="finput-phenotype-descriptions" + name="phenotype-descriptions" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-desc" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the phenotype descriptions, + <a href="#docs-file-phenotype-description" + title="Documentation of the phenotype data file format."> + the documentation for the expected format of the file</a>.</span> + </div> + {{display_resumable_elements( + "resumable-phenotype-descriptions", + "phenotype descriptions", + '<p>Drag and drop the CSV file that contains the descriptions of your + phenotypes here.</p> + + <p>The CSV file should be a matrix of + <strong>phenotypes × descriptions</strong> i.e. The first column + contains the phenotype names/identifiers whereas the first row is a list + of metadata fields like, "description", "units", etc.</p> + + <p>If the format is transposed (i.e. + <strong>descriptions × phenotypes</strong>) select the checkbox above. + </p> + + <p>Please see the + <a href="#docs-file-phenotype-description" + title="Documentation of the phenotype data file format."> + "Phenotypes Descriptions" documentation</a> section below for more + information on the expected format of the file provided here.</p>')}} + {{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" + name="phenotype-data-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-data-transposed" class="form-check-label"> + Data file transposed?</label> + </div> + + <div class="non-resumable-elements"> + <label for="finput-phenotype-data" class="form-label">Phenotype Data</label> + <input id="finput-phenotype-data" + name="phenotype-data" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-data" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the phenotype data. See + <a href="#docs-file-phenotype-data" + title="Documentation of the phenotype data file format."> + the documentation for the expected format of the file</a>.</span> + </div> + + {{display_resumable_elements( + "resumable-phenotype-data", + "phenotype data", + '<p>Drag and drop a CSV file that contains the phenotypes numerical data + here. You can click the "Browse" button (below and to the right) to + select the file from your computer.</p> + + <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, + i.e. The first column contains the samples identifiers while the first + row is the list of phenotypes identifiers occurring in the phenotypes + descriptions file.</p> + + <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) + select the checkbox above.</p> + <p>Please see the + <a href="#docs-file-phenotype-data" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below for more information + 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" + name="phenotype-se-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-se-transposed" class="form-check-label"> + Standard-Errors file transposed?</label> + </div> + <div class="group non-resumable-elements"> + <label for="finput-phenotype-se" class="form-label">Phenotype: Standard Errors</label> + <input id="finput-phenotype-se" + name="phenotype-se" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-se" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the standard errors for the phenotypes, + computed from the data above.</span> + </div> + + {{display_resumable_elements( + "resumable-phenotype-se", + "standard errors", + '<p>Drag and drop a CSV file that contains the phenotypes standard-errors + data here. You can click the "Browse" button (below and to the right) to + select the file from your computer.</p> + + <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, + i.e. The first column contains the samples identifiers while the first + row is the list of phenotypes identifiers occurring in the phenotypes + descriptions file.</p> + + <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) + select the checkbox above.</p> + + <p>Please see the + <a href="#docs-file-phenotype-se" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below for more information + on the expected format of the file provided here.</p>')}} + + {{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" + name="phenotype-n-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-n-transposed" class="form-check-label"> + Counts file transposed?</label> + </div> + <div class="non-resumable-elements"> + <label for="finput-phenotype-n" class="form-label">Phenotype: Number of Samples/Individuals</label> + <input id="finput-phenotype-n" + name="phenotype-n" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-n" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the number of samples/individuals used in + the computation of the standard errors above.</span> + </div> + + {{display_resumable_elements( + "resumable-phenotype-n", + "number of samples/individuals", + '<p>Drag and drop a CSV file that contains the samples\' phenotypes counts + data here. You can click the "Browse" button (below and to the right) to + select the file from your computer.</p> + + <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, + i.e. The first column contains the samples identifiers while the first + row is the list of phenotypes identifiers occurring in the phenotypes + descriptions file.</p> + + <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) + select the checkbox above.</p> + + <p>Please see the + <a href="#docs-file-phenotype-se" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below for more information + on the expected format of the file provided here.</p>')}} + + {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}} + </div> + </fieldset> +</fieldset> +{%endif%} +{%endblock%} + + +{%block page_documentation%} +<div class="row"> + <h2 class="heading" id="docs-help">Help</h2> + <h3 class="subheading">Common Features</h3> + <p>The following are the common expectations for <strong>ALL</strong> the + files provided in the form above: + <ul> + <li>The file <strong>MUST</strong> be character-separated values (CSV) + text file</li> + <li>The first row in the file <strong>MUST</strong> be a heading row, and + will be composed of the list identifiers for all of + samples/individuals/cases involved in your study.</li> + <li>The first column of data in the file <strong>MUST</strong> be the + identifiers for all of the phenotypes you wish to upload.</li> + </ul> + </p> + + <p>If you do not specify the separator character, then we will assume a + <strong>TAB</strong> character was used as your separator.</p> + + <p>We also assume you might include comments lines in your files. In that + case, if you do not specify what character denotes that a line in your files + is a comment line, we will assume the <strong>#</strong> character.<br /> + A comment <strong>MUST ALWAYS</strong> begin at the start of the line marked + with the comment character specified.</p> + + <h3 class="subheading" id="docs-file-metadata">File Metadata</h3> + <p>We request some details about your files to help us parse and process the + files correctly. The details we collect are:</p> + <dl> + <dt id="docs-file-separator">File separator</dt> + <dd>The files you provide should be character-separated value (CSV) files. + We need to know what character you used to separate the values in your + file. Some common ones are the Tab character, the comma, etc.<br /> + Providing that information makes it possible for the system to parse and + process your files correctly.<br> + <strong>NOTE:</strong> All the files you upload MUST use the same + separator.</dd> + + <dt id="docs-file-comment-character">Comment character</dt> + <dd>We support use of comment lines in your files. We only support one type + of comment style, the <em>line comment</em>.<br /> + This mean the comment begins at the start of the line, and the end of that + line indicates the end of that comment. If you have a really long comment, + then you need to break it across multiple lines, marking each line a + comment line.<br /> + The "comment character" is the character at the start of the line that + indicates that the line is a line comment.</dd> + + <dt id="docs-file-na">No-Value indicator(s)</dt> + <dd>Data in the real world is messy, and in some cases, entirely absent. You + need to indicate, in your files, that a particular field did not have a + value, and once you do that, you then need to let the system know how you + mark such fields. Common ways of indicating "empty values" are, leaving + the field blank, using a character such as '-', or using strings like + "NA", "N/A", "NULL", etc.<br /> + Providing this information will help with parsing and processing such + no-value fields the correct way.</dd> + </dl> + + <h3 class="subheading" id="docs-file-phenotype-description"> + file: Phenotypes Descriptions</h3> + <p>The data in this file is a matrix of <em>phenotypes × metadata-fields</em>. + Please note we use the term "metadata-fields" above loosely, due to lack of + a good word for this.</p> + <p>The file <strong>MUST</strong> have columns in this order: + <dl> + <dt>Phenotype Identifiers</dt> + <dd>These are the names/identifiers for your phenotypes. These + names/identifiers are the same ones you will have in all the other files you are + uploading.</dd> + + <dt>Descriptions</dt> + <dd>Each phenotype will need a description. Good description are necessary + to inform other people of what the data is about. Good description are + hard to construct, so we provide + <a href="https://info.genenetwork.org/faq.php#q-22" + title="How to write phenotype descriptions"> + advice on describing your phenotypes.</a></dd> + + <dt>Units</dt> + <dd>Each phenotype will need units for the measurements taken. If there are + none, then indicate the field is a no-value field.</dd> + </dl></p> + <p>You can add more columns after those three if you want to, but these 3 + <strong>MUST</strong> be present.</p> + <p>The file would, for example, look like the following:</p> + <code>id,description,units,…<br /> + pheno10001|Central nervous system, behavior, cognition; …|mg|…<br /> + pheno10002|Aging, metabolism, central nervous system: …|mg|…<br /> + ⋮<br /></code> + + <p><strong>Note 01</strong>: The first usable row is the heading row.</p> + <p><strong>Note 02: </strong>This example demonstrates a subtle issue that + could make your CSV file invalid — the choice of your field separator + character.<br > + In the example above, we use the pipe character (<code>|</code>) as our + field separator. This is because, if we follow the advice on how to write + good descriptions, then we cannot use the comma as our separator – if + we did, then our CSV file would be invalid because the system would have no + way to tell the difference between the comma as a field separator, and the + comma as a way to separate the "general category and ontology terms".</p> + + <h3 class="subheading">file: Phenotype Data, Standard Errors and/or Sample Counts</h3> + <span id="docs-file-phenotype-data"></span> + <span id="docs-file-phenotype-se"></span> + <span id="docs-file-phenotype-n"></span> + <p>The data is a matrix of <em>samples(or individuals) × phenotypes</em>, e.g.</p> + <code> + # num-cases: 2549 + # num-phenos: 13 + id,pheno10001,pheno10002,pheno10003,pheno10004,53.099998,…<br /> + IND001,61.400002,49,62.5,55.099998,…<br /> + IND002,54.099998,50.099998,53.299999,55.099998,…<br /> + IND003,483,403,501,403,…<br /> + IND004,49.799999,45.5,62.900002,NA,…<br /> + ⋮<br /></code> + + <p>where <code>IND001,IND002,IND003,IND004,…</code> are the + samples/individuals/cases in your study, and + <code>pheno10001,pheno10002,pheno10004,pheno10004,…</code> are the + identifiers for your phenotypes.</p> + <p>The lines beginning with the "<em>#</em>" symbol (i.e. + <code># num-cases: 2549</code> and <code># num-phenos: 13</code> are comment + lines and will be ignored</p> + <p>In this example, the comma (,) is used as the file separator.</p> +</div> + +{%endblock%} + + +{%block more_javascript%} +<script src="{{url_for('base.node_modules', + filename='resumablejs/resumable.js')}}"></script> +<script type="text/javascript" src="/static/js/files.js"></script> + +<script type="text/javascript"> + $("#btn-reset-file-separator").on("click", (event) => { + event.preventDefault(); + $("#txt-file-separator").val("\t"); + $("#txt-file-separator").trigger("change"); + }); + $("#btn-reset-file-comment-character").on("click", (event) => { + event.preventDefault(); + $("#txt-file-comment-character").val("#"); + $("#txt-file-comment-character").trigger("change"); + }); + $("#btn-reset-file-na").on("click", (event) => { + event.preventDefault(); + $("#txt-file-na").val("- NA N/A"); + $("#txt-file-na").trigger("change"); + }); + + var update_preview = (table, filedata, formdata, numrows) => { + table.find("thead tr").remove() + table.find(".data-row").remove(); + var linenum = 0; + var tableheader = table.find("thead"); + var tablebody = table.find("tbody"); + var numheadings = 0; + var navalues = formdata + .na_strings + .split(" ") + .map((v) => {return v.trim();}) + .filter((v) => {return Boolean(v);}); + filedata.forEach((line) => { + if(line.startsWith(formdata.comment_char) || linenum >= numrows) { + return false; + } + var row = $("<tr></tr>"); + line.split(formdata.separator) + .map((field) => { + var value = field.trim(); + if(navalues.includes(value)) { + return "⋘NUL⋙"; + } + return value; + }) + .filter((field) => { + return (field !== "" && field != undefined && field != null); + }) + .forEach((field) => { + if(linenum == 0) { + numheadings += 1; + var tablefield = $("<th></th>"); + tablefield.text(field); + row.append(tablefield); + } else { + add_class(row, "data-row"); + var tablefield = $("<td></td>"); + tablefield.text(field); + row.append(tablefield); + } + }); + + if(linenum == 0) { + tableheader.append(row); + } else { + tablebody.append(row); + } + linenum += 1; + }); + + if(table.find("tbody tr.data-row").length > 0) { + add_class(table.find(".data-row-template"), "visually-hidden"); + } else { + remove_class(table.find(".data-row-template"), "visually-hidden"); + } + }; + + var makePreviewUpdater = (preview_table) => { + return (data) => { + update_preview( + preview_table, + data, + filesMetadata(), + PREVIEW_ROWS); + }; + }; + + var preview_tables_to_elements_map = { + "#tbl-preview-pheno-desc": "#finput-phenotype-descriptions", + "#tbl-preview-pheno-data": "#finput-phenotype-data", + "#tbl-preview-pheno-se": "#finput-phenotype-se", + "#tbl-preview-pheno-n": "#finput-phenotype-n" + }; + + var filesMetadata = () => { + return { + "separator": $("#txt-file-separator").val(), + "comment_char": $( + "#txt-file-comment-character").val(), + "na_strings": $("#txt-file-na").val() + } + }; + + var PREVIEW_ROWS = 5; + + var handler_update_previews = (event) => { + Object.entries(preview_tables_to_elements_map).forEach((mapentry) => { + var preview_table = $(mapentry[0]); + var file_input = $(mapentry[1]); + if(file_input[0].files.length > 0) { + readFirstNLines( + file_input[0].files[0], + 10, + [makePreviewUpdater(preview_table)]); + } + }); + + if(typeof(resumables) !== "undefined") { + resumables.forEach((resumable) => { + if(resumable.files.length > 0) { + readFirstNLines( + resumable.files[0].file, + 10, + [makePreviewUpdater(resumable.preview_table)]); + } + }); + } + }; + + [ + "#txt-file-separator", + "#txt-file-comment-character", + "#txt-file-na" + ].forEach((elementid) => { + $(elementid).on("change", handler_update_previews); + }); + + [ + "#finput-phenotype-descriptions", + "#finput-phenotype-data", + "#finput-phenotype-se", + "#finput-phenotype-n" + ].forEach((elementid) => { + $(elementid).on("change", (event) => { + readFirstNLines( + event.target.files[0], + 10, + [makePreviewUpdater( + $("#" + event.target.getAttribute("data-preview-table")))]); + }); + }); + + + var resumableDisplayFiles = (display_area, files) => { + files.forEach((file) => { + display_area.find(".file-display").remove(); + var display_element = display_area + .find(".file-display-template") + .clone(); + remove_class(display_element, "visually-hidden"); + remove_class(display_element, "file-display-template"); + add_class(display_element, "file-display"); + display_element.find(".filename").text(file.name + || file.fileName + || file.relativePath + || file.webkitRelativePath); + display_element.find(".filesize").text( + (file.size / (1024*1024)).toFixed(2) + "MB"); + display_element.find(".fileuniqueid").text(file.uniqueIdentifier); + display_element.find(".filemimetype").text(file.file.type); + display_area.append(display_element); + }); + }; + + + var indicateProgress = (resumable, progress_bar) => { + return () => {/*Has no event!*/ + var progress = (resumable.progress() * 100).toFixed(2); + var pbar = progress_bar.find(".progress-bar"); + remove_class(progress_bar, "visually-hidden"); + pbar.css("width", progress+"%"); + pbar.attr("aria-valuenow", progress); + pbar.text("Uploading: " + progress + "%"); + }; + }; + + var retryUpload = (retry_button, cancel_button) => { + retry_button.on("click", (event) => { + resumable.files.forEach((file) => {file.retry();}); + add_class(retry_button, "visually-hidden"); + remove_class(cancel_button, "visually-hidden"); + add_class(browse_button, "visually-hidden"); + }); + }; + + var cancelUpload = (cancel_button, retry_button) => { + cancel_button.on("click", (event) => { + resumable.files.forEach((file) => { + if(file.isUploading()) { + file.abort(); + } + }); + add_class(cancel_button, "visually-hidden"); + remove_class(retry_button, "visually-hidden"); + remove_class(browse_button, "visually-hidden"); + }); + }; + + + var startUpload = (browse_button, retry_button, cancel_button) => { + return (event) => { + remove_class(cancel_button, "visually-hidden"); + add_class(retry_button, "visually-hidden"); + add_class(browse_button, "visually-hidden"); + }; + }; + + var processForm = (form) => { + var formdata = new FormData(form); + uploaded_files.forEach((msg) => { + formdata.delete(msg["file-input-name"]); + formdata.append(msg["file-input-name"], JSON.stringify({ + "uploaded-file": msg["uploaded-file"], + "original-name": msg["original-name"] + })); + }); + formdata.append("resumable-upload", "true"); + formdata.append("publication-id", $("#txt-publication-id").val()); + return formdata; + } + + var uploaded_files = new Set(); + var submitForm = (new_file) => { + uploaded_files.add(new_file); + if(uploaded_files.size === resumables.length) { + var form = $("#frm-add-phenotypes"); + if(form.length !== 1) { + // TODO: Handle error somehow? + alert("Could not find form!!!"); + return false; + } + + $.ajax({ + "url": form.attr("action"), + "type": "POST", + "data": processForm(form[0]), + "processData": false, + "contentType": false, + "success": (data, textstatus, jqxhr) => { + // TODO: Redirect to endpoint that should come as part of the + // success/error message. + console.log("SUCCESS DATA: ", data); + console.log("SUCCESS STATUS: ", textstatus); + console.log("SUCCESS jqXHR: ", jqxhr); + window.location.assign(window.location.origin + data["redirect-to"]); + }, + }); + return false; + } + return false; + }; + + var uploadSuccess = (file_input_name) => { + return (file, message) => { + submitForm({...JSON.parse(message), "file-input-name": file_input_name}); + }; + }; + + + var uploadError = () => { + return (message, file) => { + $("#frm-add-phenotypes input[type=submit]").removeAttr("disabled"); + console.log("THE FILE:", file); + console.log("THE ERROR MESSAGE:", message); + }; + }; + + + + var makeResumableObject = (form_id, file_input_id, resumable_element_id, preview_table_id) => { + var the_form = $("#" + form_id); + var file_input = $("#" + file_input_id); + var submit_button = the_form.find("input[type=submit]"); + if(file_input.length != 1) { + return false; + } + var r = errorHandler( + fileSuccessHandler( + uploadStartHandler( + filesAddedHandler( + markResumableDragAndDropElement( + makeResumableElement( + the_form.attr("data-resumable-target"), + file_input.parent(), + $("#" + resumable_element_id), + submit_button, + ["csv", "tsv", "txt"]), + file_input.parent(), + $("#" + resumable_element_id), + $("#" + resumable_element_id + "-browse-button")), + (files) => { + // TODO: Also trigger preview! + resumableDisplayFiles( + $("#" + resumable_element_id + "-selected-files"), files); + files.forEach((file) => { + readFirstNLines( + file.file, + 10, + [makePreviewUpdater( + $("#" + preview_table_id))]) + }); + }), + startUpload($("#" + resumable_element_id + "-browse-button"), + $("#" + resumable_element_id + "-retry-button"), + $("#" + resumable_element_id + "-cancel-button"))), + uploadSuccess(file_input.attr("name"))), + uploadError()); + + /** Setup progress indicator **/ + progressHandler( + r, + indicateProgress(r, $("#" + resumable_element_id + "-progress-bar"))); + + return r; + }; + + var resumables = [ + ["frm-add-phenotypes", "finput-phenotype-descriptions", "resumable-phenotype-descriptions", "tbl-preview-pheno-desc"], + ["frm-add-phenotypes", "finput-phenotype-data", "resumable-phenotype-data", "tbl-preview-pheno-data"], + ["frm-add-phenotypes", "finput-phenotype-se", "resumable-phenotype-se", "tbl-preview-pheno-se"], + ["frm-add-phenotypes", "finput-phenotype-n", "resumable-phenotype-n", "tbl-preview-pheno-n"], + ].map((row) => { + r = makeResumableObject(row[0], row[1], row[2], row[3]); + r.preview_table = $("#" + row[3]); + return r; + }).filter((val) => { + return Boolean(val); + }); + + $("#frm-add-phenotypes input[type=submit]").on("click", (event) => { + event.preventDefault(); + console.debug(); + if ($("#txt-publication-id").val() == "") { + alert("You MUST provide a publication for the phenotypes."); + return false; + } + // TODO: Check all the relevant files exist + // TODO: Verify that files are not duplicated + var filenames = []; + var nondupfiles = []; + resumables.forEach((r) => { + var fname = r.files[0].file.name; + filenames.push(fname); + if(!nondupfiles.includes(fname)) { + nondupfiles.push(fname); + } + }); + + // Check that all files were provided + if(resumables.length !== filenames.length) { + window.alert("You MUST provide all the files requested."); + event.target.removeAttribute("disabled"); + return false; + } + + // Check that there are no duplicate files + var duplicates = Object.entries(filenames.reduce( + (acc, curr, idx, arr) => { + acc[curr] = (acc[curr] || 0) + 1; + return acc; + }, + {})).filter((entry) => {return entry[1] !== 1;}); + if(duplicates.length > 0) { + var msg = "The file(s):\r\n"; + msg = msg + duplicates.reduce( + (msgstr, afile) => { + return msgstr + " • " + afile[0] + "\r\n"; + }, + ""); + msg = msg + "is(are) duplicated. Please fix and try again."; + window.alert(msg); + event.target.removeAttribute("disabled"); + return false; + } + // TODO: Check all fields + // Start the uploads. + event.target.setAttribute("disabled", "disabled"); + resumables.forEach((r) => {r.upload();}); + }); +</script> +{%endblock%} diff --git a/uploader/templates/phenotypes/sui-add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/sui-add-phenotypes-with-rqtl2-bundle.html new file mode 100644 index 0000000..29a8dea --- /dev/null +++ b/uploader/templates/phenotypes/sui-add-phenotypes-with-rqtl2-bundle.html @@ -0,0 +1,189 @@ +{%extends "phenotypes/sui-add-phenotypes-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%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 + upload the data.</p> +<p>If you wish to upload the files individually instead, + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="">click here</a>.</p> +<p>See the <a href="#section-file-formats">File Formats</a> section below + to get an understanding of what is expected of the bundle files you + upload.</p> +{%endblock%} + +{%block frm_add_phenotypes_elements%} +<div class="form-group"> + <label for="finput-phenotypes-bundle" class="form-label"> + Phenotypes Bundle</label> + <input type="file" + id="finput-phenotypes-bundle" + name="phenotypes-bundle" + accept="application/zip, .zip" + required="required" + class="form-control" /> +</div> +{%endblock%} + +{%block page_documentation%} +<div class="row"> + <h2 class="heading" id="section-file-formats">File Formats</h2> + <p>We accept an extended form of the + <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html#format-of-the-data-files" + title="R/qtl2 software input file format documentation"> + input files' format used with the R/qtl2 software</a> as a single ZIP + file</p> + <p>The files that are used for this feature are: + <ul> + <li>the <em>control</em> file</li> + <li><em>pheno</em> file(s)</li> + <li><em>phenocovar</em> file(s)</li> + <li><em>phenose</em> files(s)</li> + </ul> + </p> + <p>Other files within the bundle will be ignored, for this feature.</p> + <p>The following section will detail the expectations for each of the + different file types within the uploaded ZIP file bundle for phenotypes:</p> + + <h3 class="subheading">Control File</h3> + <p>There <strong>MUST be <em>one, and only one</em></strong> file that acts + as the control file. This file can be: + <ul> + <li>a <em>JSON</em> file, or</li> + <li>a <em>YAML</em> file.</li> + </ul> + </p> + + <p>The control file is useful for defining things about the bundle such as:</p> + <ul> + <li>The field separator value (default: <code>sep: ','</code>). There can + only ever be one field separator and it <strong>MUST</strong> be the same + one for <strong>ALL</strong> files in the bundle.</li> + <li>The comment character (default: <code>comment.char: '#'</code>). Any + line that starts with this character will be considered a comment line and + be ignored in its entirety.</li> + <li>Code for missing values (default: <code>na.strings: 'NA'</code>). You + can specify more than one code to indicate missing values, e.g. + <code>{…, "na.strings": ["NA", "N/A", "-"], …}</code></li> + </ul> + + <h3 class="subheading"><em>pheno</em> File(s)</h3> + <p>These files are the main data files. You must have at least one of these + files in your bundle for it to be valid for this step.</p> + <p>The data is a matrix of <em>individuals × phenotypes</em> by default, as + below:<br /> + <code> + id,10001,10002,10003,10004,…<br /> + BXD1,61.400002,54.099998,483,49.799999,…<br /> + BXD2,49,50.099998,403,45.5,…<br /> + BXD5,62.5,53.299999,501,62.900002,…<br /> + BXD6,53.099998,55.099998,403,NA,…<br /> + ⋮<br /></code> + </p> + <p>If the <code>pheno_transposed</code> value is set to <code>True</code>, + then the data will be a <em>phenotypes × individuals</em> matrix as in the + example below:<br /> + <code> + id,BXD1,BXD2,BXD5,BXD6,…<br /> + 10001,61.400002,49,62.5,53.099998,…<br /> + 10002,54.099998,50.099998,53.299999,55.099998,…<br /> + 10003,483,403,501,403,…<br /> + 10004,49.799999,45.5,62.900002,NA,…<br /> + ⋮ + </code> + </p> + + + <h3 class="subheading"><em>phenocovar</em> File(s)</h3> + <p>At least one phenotypes metadata file with the metadata values such as + descriptions, PubMed Identifier, publication titles (if present), etc.</p> + <p>The data in this/these file(s) is a matrix of + <em>phenotypes × phenotypes-covariates</em>. The first column is always the + phenotype names/identifiers — same as in the R/qtl2 format.</p> + <p><em>phenocovar</em> files <strong>should never be transposed</strong>!</p> + <p>This file <strong>MUST</strong> be present in the bundle, and have data for + the bundle to be considered valid by our system for this step.<br /> + In addition to that, the following are the fields that <strong>must be + present</strong>, and + have values, in the file before the file is considered valid: + <ul> + <li><em>description</em>: A description for each phenotype. Useful + for users to know what the phenotype is about.</li> + <li><em>units</em>: The units of measurement for the phenotype, + e.g. milligrams for brain weight, centimetres/millimetres for + tail-length, etc.</li> + </ul></p> + + <p>The following <em>optional</em> fields can also be provided: + <ul> + <li><em>pubmedid</em>: A PubMed Identifier for the publication where + the phenotype is published. If this field is not provided, the system will + assume your phenotype is not published.</li> + </ul> + </p> + <p>These files will be marked up in the control file with the + <code>phenocovar</code> key, as in the examples below: + <ol> + <li>JSON: single file<br /> + <code>{<br /> + ⋮,<br /> + "phenocovar": "your_covariates_file.csv",<br /> + ⋮<br /> + } + </code> + </li> + <li>JSON: multiple files<br /> + <code>{<br /> + ⋮,<br /> + "phenocovar": [<br /> + "covariates_file_01.csv",<br /> + "covariates_file_01.csv",<br /> + ⋮<br /> + ],<br /> + ⋮<br /> + } + </code> + </li> + <li>YAML: single file or<br /> + <code> + ⋮<br /> + phenocovar: your_covariates_file.csv<br /> + ⋮ + </code> + </li> + <li>YAML: multiple files<br /> + <code> + ⋮<br /> + phenocovar:<br /> + - covariates_file_01.csv<br /> + - covariates_file_02.csv<br /> + - covariates_file_03.csv<br /> + …<br /> + ⋮ + </code> + </li> + </ol> + </p> + + <h3 class="subheading"><em>phenose</em> and <em>phenonum</em> File(s)</h3> + <p>These are extensions to the R/qtl2 standard, i.e. these types ofs file are + not supported by the original R/qtl2 file format</p> + <p>We use these files to upload the standard errors (<em>phenose</em>) when + the data file (<em>pheno</em>) is average data. In that case, the + <em>phenonum</em> file(s) contains the number of individuals that were + involved when computing the averages.</p> + <p>Both types of files are matrices of <em>individuals × phenotypes</em> by + default. Like the related <em>pheno</em> files, if + <code>pheno_transposed: True</code>, then the file will be a matrix of + <em>phenotypes × individuals</em>.</p> +</div> +{%endblock%} diff --git a/uploader/templates/phenotypes/sui-base.html b/uploader/templates/phenotypes/sui-base.html new file mode 100644 index 0000000..d7d980f --- /dev/null +++ b/uploader/templates/phenotypes/sui-base.html @@ -0,0 +1,25 @@ +{%extends "populations/sui-base.html"%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_sui_pheno_dataset_card%} + +{%block breadcrumbs%} +{{super()}} +<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> +</li> +{%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/sui-job-status.html b/uploader/templates/phenotypes/sui-job-status.html new file mode 100644 index 0000000..bca87d5 --- /dev/null +++ b/uploader/templates/phenotypes/sui-job-status.html @@ -0,0 +1,140 @@ +{%extends "phenotypes/sui-base.html"%} +{%from "cli-output.html" import cli_output%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} + +{%block extrameta%} +{%if job and job.status not in ("success", "completed:success", "error", "completed:error")%} +<meta http-equiv="refresh" content="5" /> +{%endif%} +{%endblock%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block contents%} + +{%if job%} +<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%} + <table class="table table-responsive"> + <thead> + <tr> + <th>File</th> + <th>Status</th> + <th>Lines Processed</th> + <th>Total Errors</th> + </tr> + </thead> + + <tbody> + {%for file,meta in metadata.items()%} + <tr> + <td>{{file}}</td> + <td>{{meta.status}}</td> + <td>{{meta.linecount}}</td> + <td>{{meta["total-errors"]}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%endif%} +</div> + +<div class="row"> + {%if job.status in ("completed:success", "success")%} + <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)}}" + class="btn btn-primary" + title="Continue to process data">Continue</a> + {%else%} + <span class="text-muted" + disabled="disabled" + style="border: solid 2px;border-radius: 5px;padding: 0.3em;"> + Cannot continue due to errors. Please fix the errors first. + </span> + {%endif%} + </p> + {%endif%} +</div> + +<h3 class="subheading">upload errors</h3> +<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%} + <table class="table table-responsive"> + <thead style="position: sticky; top: 0; background: white;"> + <tr> + <th>File</th> + <th>Row</th> + <th>Column</th> + <th>Value</th> + <th>Message</th> + </tr> + </thead> + + <tbody style="font-size: 0.9em;"> + {%for error in errors%} + <tr> + <td>{{error.filename}}</td> + <td>{{error.rowtitle}}</td> + <td>{{error.coltitle}}</td> + <td>{%if error.cellvalue is not none and error.cellvalue | length > 25%} + {{error.cellvalue[0:24]}}… + {%else%} + {{error.cellvalue}} + {%endif%} + </td> + <td> + {%if error.message | length > 250 %} + {{error.message[0:249]}}… + {%else%} + {{error.message}} + {%endif%} + </td> + </tr> + {%endfor%} + </tbody> + </table> + {%endif%} +</div> + +<div class="row"> + {{cli_output(job, "stdout")}} +</div> + +<div class="row"> + {{cli_output(job, "stderr")}} +</div> + +{%else%} +<div class="row"> + <h3 class="text-danger">No Such Job</h3> + <p>Could not find a job with the ID: {{job_id}}</p> + <p> + Please go back to + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="'{{dataset.Name}}' dataset page"> + the '{{dataset.Name}}' dataset page</a> + to upload new phenotypes or edit existing ones.</p> +</div> +{%endif%} +{%endblock%} diff --git a/uploader/templates/phenotypes/sui-load-phenotypes-success.html b/uploader/templates/phenotypes/sui-load-phenotypes-success.html new file mode 100644 index 0000000..dff0682 --- /dev/null +++ b/uploader/templates/phenotypes/sui-load-phenotypes-success.html @@ -0,0 +1,26 @@ +{%extends "phenotypes/sui-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block contents%} +{{super()}} + +<div class="row"> + <p>You have successfully loaded + <!-- maybe indicate the number of phenotypes here? -->your + new phenotypes into the database.</p> + <!-- TODO: Maybe notify user that they have sole access. --> + <!-- TODO: Maybe provide a link to go to GeneNetwork to view the data. --> + <p>View your data + <a href="{{search_page_uri}}" + target="_blank">on GeneNetwork2</a>. + You might need to login to GeneNetwork2 to view specific traits.</p> +</div> +{%endblock%} + + +{%block more_javascript%}{%endblock%} diff --git a/uploader/templates/phenotypes/sui-review-job-data.html b/uploader/templates/phenotypes/sui-review-job-data.html new file mode 100644 index 0000000..ea4183d --- /dev/null +++ b/uploader/templates/phenotypes/sui-review-job-data.html @@ -0,0 +1,121 @@ +{%extends "phenotypes/sui-base.html"%} +{%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 not job%} +<meta http-equiv="refresh" + content="20; url={{url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" /> +{%endif%} +{%endblock%} + +{%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)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} + +{%if job%} +<div class="row"> + <h3 class="heading">Data Review</h3> + <p class="text-info"><strong> + The data has <em>NOT</em> been added/saved yet. Review the details below + and click "Continue" to save the data.</strong></p> + <p>The “<strong>{{dataset.FullName}}</strong>” dataset from the + “<strong>{{population.FullName}}</strong>” population of the + species “<strong>{{species.SpeciesName}} ({{species.FullName}})</strong>” + will be updated as follows:</p> + + <ul> + {%if publication%} + <li>All {{summary.get("pheno", {}).get("total-data-rows", "0")}} phenotypes + are linked to the following publication: + <ul> + <li><strong>Publication Title:</strong> + {{publication.Title or "—"}}</li> + <li><strong>Author(s):</strong> + {{publication.Authors or "—"}}</li> + </ul> + </li> + {%endif%} + {%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%} + {%if summary.get(ftype, False)%} + <li>A total of {{summary[ftype]["number-of-files"]}} files will be processed + adding {%if ftype == "phenocovar"%}(possibly){%endif%} + {{summary[ftype]["total-data-rows"]}} new + {%if ftype == "phenocovar"%} + phenotypes + {%else%} + {{summary[ftype]["description"]}} rows + {%endif%} + to the database. + </li> + {%endif%} + {%endfor%} + </ul> + + <form id="frm-review-phenotype-data" + method="POST" + action="{{url_for('species.populations.phenotypes.load_data_to_database', + species_id=species.SpeciesId, + 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" /> + </form> +</div> +{%else%} +<div class="row"> + <h4 class="subheading">Invalid Job</h3> + <p class="text-danger"> + Could not find a job with the ID: <strong>{{job_id}}.</p> + <p>You will be redirected in + <span id="countdown-element" class="text-info">20</span> second(s)</p> + <p class="text-muted"> + <small> + If you are not redirected, please + <a href="{{url_for( + 'species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">click here</a> to continue + </small> + </p> +</div> +{%endif%} +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(document).ready(function() { + var countdown = 20; + var countdown_element = $("#countdown-element"); + if(countdown_element.length === 1) { + intv = window.setInterval(function() { + countdown = countdown - 1; + countdown_element.html(countdown); + }, 1000); + } + }); +</script> +{%endblock%} diff --git a/uploader/templates/populations/sui-base.html b/uploader/templates/populations/sui-base.html index cc01c9e..0ca5c59 100644 --- a/uploader/templates/populations/sui-base.html +++ b/uploader/templates/populations/sui-base.html @@ -6,7 +6,7 @@ <a href="{{url_for('species.populations.view_population', species_id=species['SpeciesId'], population_id=population['Id'])}}"> - {{population["FullName"]}} + {{population["Name"]}} </a> </li> {%endblock%} diff --git a/uploader/templates/populations/sui-view-population.html b/uploader/templates/populations/sui-view-population.html index 3bf8d0d..6244f4d 100644 --- a/uploader/templates/populations/sui-view-population.html +++ b/uploader/templates/populations/sui-view-population.html @@ -57,55 +57,95 @@ role="tabpanel" aria-labelledby="samples-content-tab"> <p>Think of a <strong>"sample"</strong> as say a single case or individual - in the experiment. It could even be a single strain (where applicable) - under consideration.</p> + in the experiment. It could even be a single strain (where applicable). + </p> <p>This is a convenience feature for when you want to upload phenotypes to the system, but do not have the genotypes data ready yet.</p> - <p>Please click the button below to provide the samples that will be used - in your data.</p> <a href="{{url_for('species.populations.samples.list_samples', species_id=species.SpeciesId, population_id=population.Id)}}" - title="Upload samples for population '{{population['Name']}}'" - class="btn btn-primary">Upload Samples</a> + title="View and upload samples for population '{{population['Name']}}'" + class="btn btn-primary">Manage Samples</a> </div> <div class="tab-pane fade show active" id="phenotypes-content" role="tabpanel" aria-labelledby="phenotypes-content-tab"> - <p>Upload and manage phenotypes and publications for population - "<em>{{population.FullName}} ({{population.Name}})</em>" of species - "<em>{{species.FullName}} ({{species.Name}})</em>".</p> - <p class="text-danger">Tabs will not work nicely here. Maybe present - options e.g.: - </p> - <div class="row"> + <div class="row" style="margin-top: 0.3em;"> <div class="col"> - <a href="{{url_for('species.populations.phenotypes.view_dataset', + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id)}}" title="Upload phenotype data for population '{{population['Name']}}'" class="btn btn-primary">Upload new Phenotypes</a> - <!-- Go straight to upload form(s). --> - </div> - <div class="col"> - <a href="#" - title="List all existing phenotypes for this population." - class="btn btn-info not-implemented">list existing phenotypes</a> - <!-- Means and QTLReaper will be computed in this page. --> </div> <div class="col"> <a href="#" title="List all existing publications for this population." - class="btn btn-info not-implemented">list existing publications</a> + class="btn btn-primary not-implemented">view publications</a> <!-- Maybe, actually filter publications by population? --> <!-- Provide other features for publications on loaded page. --> </div> </div> + + <div class="row" style="margin-top: 1em;"> + <h3> Phenotypes in Population "{{population.FullName}} ({{population.Name}})"</h3> + + <p>The table below lists the phenotypes that already exist for + population "<em>{{population.FullName}} ({{population.Name}})</em>" of + species "<em>{{species.FullName}} ({{species.Name}})</em>".</p> + + <div class="row phenotypes-list-actions"> + <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'])}}"> + <input id="submit-frm-recompute-phenotype-means" + class="btn btn-info" + type="submit" + title="Compute/Recompute the means for selected phenotypes (or all phenotypes if none selected)." + value="(Rec/C)ompute means" /> + </form> + </div> + <div class="col"> + <form id="frm-rerun-qtlreaper" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.rerun_qtlreaper', + species_id=species['SpeciesId'], + population_id=population['Id'], + dataset_id=dataset['Id'])}}"> + <input id="submit-frm-rerun-qtlreaper" + class="btn btn-info" + type="submit" + title="Run/Rerun QTLReaper for selected phenotypes (or all phenotypes if none selected)." + value="(rer/r)un QTLReaper" /> + </form> + </div> + </div> + + <table id="tbl-phenotypes-list" class="table compact stripe cell-border"> + <thead> + <tr> + <th></th> + <th>Index</th> + <th>Record</th> + <th>Description</th> + </tr> + </thead> + + <tbody></tbody> + </table> + </div> </div> + <div class="tab-pane fade" id="genotypes-content" role="tabpanel" @@ -136,3 +176,92 @@ {%endblock%} + + +{%block javascript%} +<script type="text/javascript" src="/static/js/urls.js"></script> + +<script type="text/javascript"> + $(function() { + /** JS to build list of phenotypes table. **/ + var species_id = {{species.SpeciesId}}; + var population_id = {{population.Id}}; + var dataset_id = {{dataset.Id}}; + var dataset_name = "{{dataset.Name}}"; + var data = {{phenotypes | tojson}}; + + var dtPhenotypesList = buildDataTable( + "#tbl-phenotypes-list", + data, + [ + { + data: function(pheno) { + return `<input type="checkbox" name="selected-phenotypes" ` + + `id="chk-selected-phenotypes-${pheno.InbredSetCode}_${pheno.xref_id}" ` + + `value="${pheno.InbredSetCode}_${pheno.xref_id}" ` + + `class="chk-row-select" />` + } + }, + {data: "sequence_number"}, + { + data: function(pheno, type, set, meta) { + var spcs_id = {{species.SpeciesId}}; + var pop_id = {{population.Id}}; + var dtst_id = {{dataset.Id}}; + var url = buildURLFromCurrentURL( + (`/species/${spcs_id}` + + `/populations/${pop_id}` + + `/phenotypes/datasets/${dtst_id}` + + `/phenotype/${pheno.xref_id}`)); + return `<a href="${url.toString()}" target="_blank">` + + `${pheno.InbredSetCode}_${pheno.xref_id}` + + `</a>`; + } + }, + { + data: function(pheno) { + return (pheno.Post_publication_description || + pheno.Original_description || + pheno.Pre_publication_description); + } + } + ], + { + select: "multi+shift", + layout: { + top1Start: { + pageLength: { + text: "Show _MENU_ of _TOTAL_" + } + }, + topStart: "info", + top1End: null + }, + rowId: function(pheno) { + 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-rerun-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(); + }); + }); +</script> +{%endblock%} diff --git a/uploader/templates/publications/edit-publication.html b/uploader/templates/publications/edit-publication.html index 540ecf1..97fa134 100644 --- a/uploader/templates/publications/edit-publication.html +++ b/uploader/templates/publications/edit-publication.html @@ -12,7 +12,9 @@ <div class="row"> <form id="frm-create-publication" method="POST" - action="{{url_for('publications.edit_publication', publication_id=publication_id, **request.args)}}" + action="{{url_for('publications.edit_publication', + publication_id=publication_id, + next=request.args.get('next', ''))}}" class="form-horizontal"> <div class="row mb-3"> diff --git a/uploader/templates/samples/sui-base.html b/uploader/templates/samples/sui-base.html new file mode 100644 index 0000000..ee08e2e --- /dev/null +++ b/uploader/templates/samples/sui-base.html @@ -0,0 +1,19 @@ +{%extends "populations/sui-base.html"%} +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item">Manage Samples</li> +{%endblock%} + +{%block contents%} +<div class="row"> + <h2 class="heading">{{population.FullName}} ({{population.Name}})</h2> +</div> +{%endblock%} + + + +{%block sidebarcontents%} +{{display_sui_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/samples/sui-list-samples.html b/uploader/templates/samples/sui-list-samples.html new file mode 100644 index 0000000..e9ed71a --- /dev/null +++ b/uploader/templates/samples/sui-list-samples.html @@ -0,0 +1,98 @@ +{%extends "samples/sui-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-select-population.html" import select_population_form%} + +{%block title%}Samples — List Samples{%endblock%} + +{%block contents%} +{{super()}} + +<div class="row"> + <h3 class="subheading">manage samples</h3> + {{flash_all_messages()}} +</div> + +<div class="row"> + <div class="col"> + <a href="{{url_for('species.populations.samples.upload_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Add samples for population '{{population.FullName}}' from species + '{{species.FullName}}'." + class="btn btn-primary">add new samples</a> + </div> +</div> + +{%if samples | length > 0%} +<div class="row"> + <p> + Population "{{population.FullName}} ({{population.Name}})" already has + <strong>{{total_samples}}</strong> samples/individuals entered. You can + explore the list of samples in the table below. + </p> +</div> + +<div class="row"> + <div class="col-md-2"> + {%if offset > 0:%} + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id, + from=offset-count, + count=count)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + + <div class="col-md-8" style="text-align: center;"> + Samples {{offset}} — {{offset+(count if offset + count < total_samples else total_samples - offset)}} / {{total_samples}} + </div> + + <div class="col-md-2"> + {%if offset + count < total_samples:%} + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id, + from=offset+count, + count=count)}}"> + Next + <span class="glyphicon glyphicon-forward"></span> + </a> + {%endif%} + </div> +</div> +<div class="row"> + <table class="table"> + <thead> + <tr> + <th></th> + <th>Name</th> + <th>Auxilliary Name</th> + <th>Symbol</th> + <th>Alias</th> + </tr> + </thead> + + <tbody> + {%for sample in samples%} + <tr> + <td>{{sample.sequence_number}}</td> + <td>{{sample.Name}}</td> + <td>{{sample.Name2}}</td> + <td>{{sample.Symbol or "-"}}</td> + <td>{{sample.Alias or "-"}}</td> + </tr> + {%endfor%} + </tbody> + </table> +</div> +{%else%} +<div class="row"> + <p>There are no samples entered for this population. Click the "Add Samples" + button above, to add some new samples.</p> +</div> +{%endif%} + +{%endblock%} |