diff options
Diffstat (limited to 'uploader/templates')
29 files changed, 2080 insertions, 287 deletions
diff --git a/uploader/templates/base.html b/uploader/templates/base.html index 019aa39..90652bf 100644 --- a/uploader/templates/base.html +++ b/uploader/templates/base.html @@ -8,7 +8,7 @@ <meta name="viewport" content="width=device-width, initial-scale=1.0" /> {%block extrameta%}{%endblock%} - <title>GN Uploader: {%block title%}{%endblock%}</title> + <title>Data Upload and Quality Control: {%block title%}{%endblock%}</title> <link rel="stylesheet" type="text/css" href="{{url_for('base.bootstrap', @@ -23,25 +23,26 @@ </head> <body> - <header id="header" class="container-fluid"> - <div class="row"> - <span class="header col-lg-9">GeneNetwork Data Quality Control and Upload</span> - <nav class="header-nav col-lg-3"> - <ul class="nav justify-content-end"> - <li> - {%if user_logged_in()%} - <a href="{{url_for('oauth2.logout')}}" - title="Log out of the system">{{user_email()}} — Log Out</a> - {%else%} - <a href="{{authserver_authorise_uri()}}" - title="Log in to the system">Log In</a> - {%endif%} - </li> - </ul> - </nav> + <header id="header"> + <span id="header-text">GeneNetwork</span> + <nav id="header-nav"> + <ul class="nav justify-content-end"> + <li> + {%if user_logged_in()%} + <a href="{{url_for('oauth2.logout')}}" + title="Log out of the system"> + <span class="glyphicon glyphicon-user"></span> + Sign Out</a> + {%else%} + <a href="{{authserver_authorise_uri()}}" + title="Log in to the system">Sign In</a> + {%endif%} + </li> + </ul> + </nav> </header> - <aside id="nav-sidebar" class="container-fluid"> + <aside id="nav-sidebar"> <ul class="nav flex-column"> <li {%if activemenu=="home"%}class="activemenu"{%endif%}> <a href="/" >Home</a></li> @@ -70,9 +71,11 @@ <li {%if activemenu=="phenotypes"%}class="activemenu"{%endif%}> <a href="{{url_for('species.populations.phenotypes.index')}}" title="Upload phenotype data.">Phenotype Data</a></li> + <!-- <li {%if activemenu=="expression-data"%}class="activemenu"{%endif%}> <a href="{{url_for('species.populations.expression-data.index')}}" - title="Upload expression data.">Expression Data</a></li> + title="Upload expression data." + class="not-implemented">Expression Data</a></li> <li {%if activemenu=="individuals"%}class="activemenu"{%endif%}> <a href="#" class="not-implemented" @@ -86,35 +89,36 @@ class="not-implemented" title="View and manage the backgroud jobs you have running"> Background Jobs</a></li> + --> </ul> </aside> - <main id="main" class="main container-fluid"> + <main id="main" class="main"> - <div class="pagetitle row"> - <h1>GN Uploader: {%block pagetitle%}{%endblock%}</h1> - <nav> - <ol class="breadcrumb"> - <li {%if activelink is not defined or activelink=="home"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('base.index')}}">Home</a> - </li> - {%block lvl1_breadcrumbs%}{%endblock%} - </ol> - </nav> + <div id="pagetitle" class="pagetitle"> + <span class="title">Data Upload and Quality Control: {%block pagetitle%}{%endblock%}</span> + <!-- + <nav> + <ol class="breadcrumb"> + <li {%if activelink is not defined or activelink=="home"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('base.index')}}">Home</a> + </li> + {%block lvl1_breadcrumbs%}{%endblock%} + </ol> + </nav> + --> </div> - <div class="row"> - <div class="container-fluid"> - <div class="col-md-8 main-content"> - {%block contents%}{%endblock%} - </div> - <div class="sidebar-content col-md-4"> - {%block sidebarcontents%}{%endblock%} - </div> + <div id="all-content"> + <div id="main-content"> + {%block contents%}{%endblock%} + </div> + <div id="sidebar-content"> + {%block sidebarcontents%}{%endblock%} </div> </div> </main> @@ -126,7 +130,5 @@ filename='js/bootstrap.min.js')}}"></script> <script type="text/javascript" src="/static/js/misc.js"></script> {%block javascript%}{%endblock%} - </body> - </html> diff --git a/uploader/templates/cli-output.html b/uploader/templates/cli-output.html index 33fb73b..64b1a9a 100644 --- a/uploader/templates/cli-output.html +++ b/uploader/templates/cli-output.html @@ -1,7 +1,7 @@ {%macro cli_output(job, stream)%} -<h4>{{stream | upper}} Output</h4> -<div class="cli-output"> +<h4 class="subheading">{{stream | upper}} Output</h4> +<div class="cli-output" style="max-height: 10em; overflow: auto;"> <pre>{{job.get(stream, "")}}</pre> </div> diff --git a/uploader/templates/genotypes/base.html b/uploader/templates/genotypes/base.html index 1b274bf..7d61312 100644 --- a/uploader/templates/genotypes/base.html +++ b/uploader/templates/genotypes/base.html @@ -6,7 +6,18 @@ {%else%} class="breadcrumb-item" {%endif%}> + {%if population is mapping%} + <a href="{{url_for('species.populations.genotypes.list_genotypes', + species_id=species.SpeciesId, + population_id=population.Id)}}"> + {%if dataset is defined and dataset is mapping%} + {{dataset.Name}} + {%else%} + Genotypes + {%endif%}</a> + {%else%} <a href="{{url_for('species.populations.genotypes.index')}}">Genotypes</a> + {%endif%} </li> {%block lvl4_breadcrumbs%}{%endblock%} {%endblock%} diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html index e4c39eb..0f074fd 100644 --- a/uploader/templates/genotypes/list-genotypes.html +++ b/uploader/templates/genotypes/list-genotypes.html @@ -26,7 +26,8 @@ <p>There are a total of {{total_markers}} currently registered genetic markers for the "{{species.FullName}}" species. You can click <a href="{{url_for('species.populations.genotypes.list_markers', - species_id=species.SpeciesId)}}" + species_id=species.SpeciesId, + population_id=population.Id)}}" title="View genetic markers for species '{{species.FullName}}"> this link to view the genetic markers </a>. @@ -70,7 +71,7 @@ {%if genocode | length < 1%} <a href="#add-genotype-encoding" title="Add a genotype encoding system for this population" - class="btn btn-primary"> + class="btn btn-primary not-implemented"> add genotype encoding </a> {%endif%} diff --git a/uploader/templates/genotypes/list-markers.html b/uploader/templates/genotypes/list-markers.html index 9198b44..a705ae3 100644 --- a/uploader/templates/genotypes/list-markers.html +++ b/uploader/templates/genotypes/list-markers.html @@ -13,7 +13,8 @@ class="breadcrumb-item" {%endif%}> <a href="{{url_for('species.populations.genotypes.list_markers', - species_id=species.SpeciesId)}}">List markers</a> + species_id=species.SpeciesId, + population_id=population.Id)}}">List markers</a> </li> {%endblock%} @@ -30,6 +31,7 @@ {%if start_from > 0%} <a href="{{url_for('species.populations.genotypes.list_markers', species_id=species.SpeciesId, + population_id=population.Id, start_from=start_from-count, count=count)}}"> <span class="glyphicon glyphicon-backward"></span> @@ -45,6 +47,7 @@ {%if start_from + count < total_markers%} <a href="{{url_for('species.populations.genotypes.list_markers', species_id=species.SpeciesId, + population_id=population.Id, start_from=start_from+count, count=count)}}"> Next diff --git a/uploader/templates/index.html b/uploader/templates/index.html index d6f57eb..aa1414e 100644 --- a/uploader/templates/index.html +++ b/uploader/templates/index.html @@ -10,90 +10,98 @@ <div class="row"> {{flash_all_messages()}} <div class="explainer"> - <p>Welcome to the <strong>GeneNetwork Data Quality Control and Upload System</strong>. This system is provided to help in uploading your data onto GeneNetwork where you can do analysis on it.</p> + <p>Welcome to the <strong>GeneNetwork Data Upload and Quality Control + System</strong>.</p> + <p>This tool helps you prepare and upload research data to GeneNetwork for + analysis.</p> - <p>The sections below provide an overview of what features the menu items on - the left provide to you. Please peruse the information to get a good - big-picture understanding of what the system provides you and how to get - the most out of it.</p> + <h2 class="heading">Getting Started</h2> + <p>The sections below explain the features of the system. Review this guide + to learn how to use the system.</p> {%block extrapageinfo%}{%endblock%} - <h2>Species</h2> - - <p>The GeneNetwork service provides datasets and tools for doing genetic - studies — from - <a href="{{gn2server_intro}}" - target="_blank" - title="GeneNetwork introduction — opens in a new tab."> - its introduction</a>: - - <blockquote class="blockquote"> - <p>GeneNetwork is a group of linked data sets and tools used to study - complex networks of genes, molecules, and higher order gene function - and phenotypes. …</p> - </blockquote> - </p> - - <p>With this in mind, it follows that the data in the system is centered - aroud a variety of species. The <strong>species section</strong> will - list the currently available species in the system, and give you the - ability to add new ones, if the one you want to work on does not currently - exist on GeneNetwork</p> - - <h2>Populations</h2> - - <p>Your studies will probably focus on a particular subset of the entire - species you are interested in – your population.</p> - <p>Populations are a way to organise the species data so as to link data to - specific know populations for a particular species, e.g. The BXD - population of mice (Mus musculus)</p> - <p>In older GeneNetwork documentation, you might run into the term - <em>InbredSet</em>. Should you run into it, it is a term that we've - deprecated that essentially just means the population.</p> - - <h2>Samples</h2> - - <p>These are the samples or individuals (sometimes cases) that were involved - in the experiment, and from whom the data was derived.</p> - - <h2>Genotype Data</h2> - - <p>This section will allow you to view and upload the genetic markers for - your species, and the genotype encodings used for your particular - population.</p> - <p>While, technically, genetic markers relate to the species in general, and - not to a particular population, the data (allele information) itself - relates to the particular population it was generated from – - specifically, to the actual individuals used in the experiment.</p> - <p>This is the reason why the genotype data information comes under the - population, and will check for the prior existence of the related - samples/individuals before attempting an upload of your data.</p> - - <h2>Expression Data</h2> + <h3 class="subheading">Species</h3> - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>TODO</strong>: Document this …</p> + <p>GeneNetwork supports genetic studies across multiple species (e.g. mice + [Mus musculus], human [homo sapiens], rats [Rattus norvegicus], etc.) . + Here you can:</p> + <ul> + <li>View all species that are currently supported</li> + <li>Add new species not yet in the system</li> + </ul> + + <h3 class="subheading">Populations</h3> + + <p>A "population" refers to a specific subgroup within a species that you’re + studying (e.g., BXD mice). Here you can:</p> + <ul> + <li>View the populations that exist for a selected species</li> + <li>Add new populations of study for a selected species</li> + </ul> + + <h3 class="subheading">Samples</h3> + + <p>Manage individual specimens or cases used in your experiments. These + include:</p> + + <ul> + <li>Experimental subjects</li> + <li>Data sources (e.g., tissue samples, clinical cases)</li> + <li>Strain means (instead of entering multiple BXD1 individuals, for + example, the mean would be entered for a single BXD1 strain)</li> + </ul> + + + <h3 class="subheading">Genotype Data</h3> + + <p>Upload and review genetic markers and allele encodings for your + population. Key details:</p> + + <ul> + <li>Markers are species-level (e.g., mouse SNP databases).</li> + <li>Allele data is population-specific (tied to your experimental + samples).</li> + </ul> + + <p><strong>Requirement</strong>: Samples must already have been registered + in the system before uploading genotype data.</p> + + <h3 class="subheading">Phenotype Data</h3> + + <p>Phenotypes are the visible traits or features of a living thing. For + example, phenotypes include:</p> + + <ul> + <li>Weight</li> + <li>Height</li> + <li>Color (such as the color of fur or eyes)</li> + </ul> + + <p>This part of the system will allow you to upload and manage the values + for different phenotypes from various samples in your studies.</p> + + <!-- - <h2>Phenotype Data</h2> + <h3 class="subheading">Expression Data</h3> <p class="text-danger"> <span class="glyphicon glyphicon-exclamation-sign"></span> <strong>TODO</strong>: Document this …</p> - <h2>Individual Data</h2> + <h3 class="subheading">Individual Data</h3> <p class="text-danger"> <span class="glyphicon glyphicon-exclamation-sign"></span> <strong>TODO</strong>: Document this …</p> - <h2>RNA-Seq Data</h2> + <h3 class="subheading">RNA-Seq Data</h3> <p class="text-danger"> <span class="glyphicon glyphicon-exclamation-sign"></span> <strong>TODO</strong>: Document this …</p> </div> + --> </div> {%endblock%} diff --git a/uploader/templates/login.html b/uploader/templates/login.html index 1f71416..e76c644 100644 --- a/uploader/templates/login.html +++ b/uploader/templates/login.html @@ -5,7 +5,8 @@ {%block pagetitle%}log in{%endblock%} {%block extrapageinfo%} -<p class="text-dark text-primary"> - You <strong>do need to be logged in</strong> to upload data onto this system. - Please do that by clicking the "Log In" button at the top of the page.</p> +<p class="text-dark"> + You <strong>need to + <a href="{{authserver_authorise_uri()}}" + title="Sign in to the system">sign in</a></strong> to use this system.</p> {%endblock%} diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html new file mode 100644 index 0000000..97b55f2 --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-base.html @@ -0,0 +1,331 @@ +{%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%} +{{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%} + + <div class="checkbox"> + <label> + <input id="chk-published" type="checkbox" name="published?" /> + These phenotypes are published</label> + </div> + + <fieldset id="fldset-publication-info" class="hidden"> + <legend>Publication Information</legend> + <div class="form-group"> + <label for="txt-pubmed-id" class="form-label">Pubmed ID</label> + <div class="input-group"> + <input id="txt-pubmed-id" name="pubmed-id" type="text" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-search-pubmed-id" class="btn btn-info">Search</button> + </span> + </div> + <span id="search-pubmed-id-error" + class="form-text text-muted text-danger hidden"> + </span><br /> + <span class="form-text text-muted"> + Enter your publication's PubMed ID above and click "Search" to search + for some (or all) of the publication details requested below. + </span> + </div> + + <div class="form-group"> + <label for="txt-publication-authors" class="form-label">Authors</label> + <input id="txt-publication-authors" name="publication-authors" + type="text" class="form-control" /> + <span class="form-text text-muted"> + Enter the authors in the following format …</span> + </div> + + <div class="form-group"> + <label for="txt-publication-title" class="form-label"> + Publication Title</label> + <input id="txt-publication-title" name="publication-title" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter your publication's title.</span> + </div> + + <div class="form-group"> + <label for="txt-publication-abstract" class="form-label"> + Publication Abstract</label> + <textarea id="txt-publication-abstract" name="publication-abstract" + class="form-control" rows="10"></textarea> + <span class="form-text text-muted"> + Enter the abstract for your publication.</span> + </div> + + <div class="form-group"> + <label for="txt-publication-journal" class="form-label">Journal</label> + <input id="txt-publication-journal" name="journal" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the name of the journal where your work was published.</span> + </div> + + <div class="form-group"> + <label for="txt-publication-volume" class="form-label">Volume</label> + <input id="txt-publication-volume" name="publication-volume" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the volume in the following format …</span> + </div> + + <div class="form-group"> + <label for="txt-publication-pages" class="form-label">Pages</label> + <input id="txt-publication-pages" name="publication-pages" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the journal volume where your work was published.</span> + </div> + + <div class="form-group"> + <label for="select-publication-month" class="form-label"> + Publication Month</label> + <select id="select-publication-month" name="publication-month" + class="form-control"> + {%for month in monthnames%} + <option value="{{month | lower}}" + {%if current_month | lower == month | lower%} + selected="selected" + {%endif%}>{{month | capitalize}}</option> + {%endfor%} + </select> + <span class="form-text text-muted"> + Select the month when the work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span></span> + </div> + + <div class="form-group"> + <label for="txt-publication-year" class="form-label">Publication Year</label> + <input id="txt-publication-year" name="publication-year" type="text" + class="form-control" value="{{current_year}}" /> + <span class="form-text text-muted"> + Enter the year your work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span> + </span> + </div> + </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"> + var remove_class = (element, classvalue) => { + new_classes = (element.attr("class") || "").split(" ").map((val) => { + return val.trim(); + }).filter((val) => { + return ((val !== classvalue) && + (val !== "")) + }).join(" "); + + if(new_classes === "") { + element.removeAttr("class"); + } else { + element.attr("class", new_classes); + } + }; + + var add_class = (element, classvalue) => { + remove_class(element, classvalue); + element.attr("class", (element.attr("class") || "") + " " + classvalue); + }; + + $("#chk-published").on("click", (event) => { + pub_details = $("#fldset-publication-info") + if(event.target.checked) { + // display the publication details + remove_class(pub_details, "hidden"); + } else { + // hide the publication details + add_class(pub_details, "hidden"); + } + }); + + var extract_details = (pubmed_id, details) => { + var months = { + "jan": "January", + "feb": "February", + "mar": "March", + "apr": "April", + "may": "May", + "jun": "June", + "jul": "July", + "aug": "August", + "sep": "September", + "oct": "October", + "nov": "November", + "dec": "December" + }; + var _date = details[pubmed_id].pubdate.split(" "); + return { + "authors": details[pubmed_id].authors.map((authobj) => { + return authobj.name; + }), + "title": details[pubmed_id].title, + "journal": details[pubmed_id].fulljournalname, + "volume": details[pubmed_id].volume, + "pages": details[pubmed_id].pages, + "month": _date.length > 1 ? months[_date[1].toLowerCase()] : "jan", + "year": _date[0], + }; + }; + + var update_publication_details = (details) => { + Object.entries(details).forEach((entry) => {; + switch(entry[0]) { + case "authors": + $("#txt-publication-authors").val(entry[1].join(", ")); + break; + case "month": + $("#select-publication-month") + .children("option") + .each((index, child) => { + child.selected = child.value == entry[1].toLowerCase(); + }); + default: + $("#txt-publication-" + entry[0]).val(entry[1]); + break; + } + }); + }; + + var fetch_publication_abstract = (pubmed_id, pub_details) => { + $.ajax("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi", + { + "method": "GET", + "data": { + "db": "pubmed", + "id": pubmed_id, + "rettype": "abstract", + "retmode": "xml" + }, + "success": (data, textStatus, jqXHR) => { + update_publication_details({ + ...pub_details, + ...{ + "abstract": Array.from(data + .getElementsByTagName( + "Abstract")[0] + .children) + .map((elt) => {return elt.textContent.trim();}) + .join("\r\n") + }}); + }, + "error": (jqXHR, textStatus, errorThrown) => {}, + "complete": (jqXHR, textStatus) => {}, + "dataType": "xml" + }); + }; + + var fetch_publication_details = (pubmed_id, complete_thunks) => { + error_display = $("#search-pubmed-id-error"); + error_display.text(""); + add_class(error_display, "hidden"); + $.ajax("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi", + { + "method": "GET", + "data": {"db": "pubmed", "id": pubmed_id, "format": "json"}, + "success": (data, textStatus, jqXHR) => { + // process and update publication details + hasError = ( + Object.hasOwn(data, "error") || + Object.hasOwn(data.result[pubmed_id], "error")); + if(hasError) { + error_display.text( + "There was an error fetching a publication with " + + "the given PubMed ID! The error received " + + "was: '" + ( + data.error || + data.result[pubmed_id].error) + + "'. Please check ID you provided and try " + + "again."); + remove_class(error_display, "hidden"); + } else { + fetch_publication_abstract( + pubmed_id, + extract_details(pubmed_id, data.result)); + } + }, + "error": (jqXHR, textStatus, errorThrown) => {}, + "complete": () => { + complete_thunks.forEach((thunk) => {thunk()}); + }, + "dataType": "json" + }); + }; + + $("#btn-search-pubmed-id").on("click", (event) => { + event.preventDefault(); + var search_button = event.target; + var pubmed_id = $("#txt-pubmed-id").val().trim(); + remove_class($("#txt-pubmed-id").parent(), "has-error"); + if(pubmed_id == "") { + add_class($("#txt-pubmed-id").parent(), "has-error"); + return false; + } + + search_button.disabled = true; + // Fetch publication details + fetch_publication_details(pubmed_id, + [() => {search_button.disabled = false;}]); + return false; + }); +</script> + +{%block more_javascript%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html new file mode 100644 index 0000000..7f8d8b0 --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html @@ -0,0 +1,732 @@ +{%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%} + +{%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>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-data-files"> + <legend>Data File(s)</legend> + + <div class="form-group 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>You can drop a CSV file that contains the phenotype descriptions here, + or you can click the "Browse" button (below and to the right) to select it + from your computer.</p> + <p>The CSV file must conform to some standards, as documented in the + <a href="#docs-file-phenotype-description" + title="Documentation of the phenotype data file format."> + "Phenotypes Descriptions" documentation</a> section below.</p>')}} + + + <div class="form-group 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>You can drop a CSV file that contains the phenotype data here, + or you can click the "Browse" button (below and to the right) to select it + from your computer.</p> + <p>The CSV file must conform to some standards, as documented in the + <a href="#docs-file-phenotype-data" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below.</p>')}} + + {%if population.Family in families_with_se_and_n%} + <div class="form-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>You can drop a CSV file that contains the computed standard-errors data + here, or you can click the "Browse" button (below and to the right) to + select it from your computer.</p> + <p>The CSV file must conform to some standards, as documented in the + <a href="#docs-file-phenotype-se" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below.</p>')}} + + + <div class="form-group 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>You can drop a CSV file that contains the number of samples/individuals + used in computation of the standard-errors here, or you can click the + "Browse" button (below and to the right) to select it from your computer. + </p> + <p>The CSV file must conform to some standards, as documented in the + <a href="#docs-file-phenotype-n" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below.</p>')}} +</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>phenotypes × individuals</em>, e.g.</p> + <code> + # num-cases: 2549 + # num-phenos: 13 + id,IND001,IND002,IND003,IND004,…<br /> + pheno10001,61.400002,54.099998,483,49.799999,…<br /> + pheno10002,49,50.099998,403,45.5,…<br /> + pheno10003,62.5,53.299999,501,62.900002,…<br /> + pheno10004,53.099998,55.099998,403,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 sidebarcontents%} +{{display_preview_table("tbl-preview-pheno-desc", "descriptions")}} +{{display_preview_table("tbl-preview-pheno-data", "data")}} +{%if population.Family in families_with_se_and_n%} +{{display_preview_table("tbl-preview-pheno-se", "standard errors")}} +{{display_preview_table("tbl-preview-pheno-n", "number of samples")}} +{%endif%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%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"), "hidden"); + } else { + remove_class(table.find(".data-row-template"), "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.length === 1) { + readFirstNLines( + file_input[0].files[0], + 10, + [makePreviewUpdater(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, "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, "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, "hidden"); + remove_class(cancel_button, "hidden"); + add_class(browse_button, "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, "hidden"); + remove_class(retry_button, "hidden"); + remove_class(browse_button, "hidden"); + }); + }; + + + var startUpload = (browse_button, retry_button, cancel_button) => { + return (event) => { + remove_class(cancel_button, "hidden"); + add_class(retry_button, "hidden"); + add_class(browse_button, "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"); + 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"]), + 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) => { + return makeResumableObject(row[0], row[1], row[2], row[3]); + }).filter((val) => { + return Boolean(val); + }); + + $("#frm-add-phenotypes input[type=submit]").on("click", (event) => { + event.preventDefault(); + // 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/add-phenotypes.html b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html index 196bc69..898fc0c 100644 --- a/uploader/templates/phenotypes/add-phenotypes.html +++ b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html @@ -1,4 +1,4 @@ -{%extends "phenotypes/base.html"%} +{%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%} @@ -16,52 +16,39 @@ <a href="{{url_for('species.populations.phenotypes.add_phenotypes', species_id=species.SpeciesId, population_id=population.Id, - dataset_id=dataset.Id)}}">View Datasets</a> + dataset_id=dataset.Id)}}">Add Phenotypes</a> </li> {%endblock%} -{%block contents%} -{{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)}}"> - <legend>Add New Phenotypes</legend> - - <div class="form-text help-block"> - <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>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> - <p><strong>This will not update any existing phenotypes!</strong></p> - </div> - - <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> +{%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%} - <div class="form-group"> - <input type="submit" - value="upload phenotypes" - class="btn btn-primary" /> - </div> - </form> +{%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 @@ -213,17 +200,6 @@ <code>pheno_transposed: True</code>, then the file will be a matrix of <em>phenotypes × individuals</em>.</p> </div> - -<div class="row text-warning"> - <h3 class="subheading">Notes for Devs (well… Fred, really.)</h3> - <p>Use the following resources for automated retrieval of certain data</p> - <ul> - <li><a href="https://www.ncbi.nlm.nih.gov/pmc/tools/developers/" - title="NCBI APIs: Retrieve articles' metadata etc."> - NCBI APIS</a></li> - </ul> -</div> - {%endblock%} {%block sidebarcontents%} diff --git a/uploader/templates/phenotypes/base.html b/uploader/templates/phenotypes/base.html index 3bc5dea..adbc012 100644 --- a/uploader/templates/phenotypes/base.html +++ b/uploader/templates/phenotypes/base.html @@ -6,7 +6,14 @@ {%else%} class="breadcrumb-item" {%endif%}> + {%if dataset is mapping%} + <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%} </li> {%block lvl4_breadcrumbs%}{%endblock%} {%endblock%} diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html new file mode 100644 index 0000000..32c903f --- /dev/null +++ b/uploader/templates/phenotypes/edit-phenotype.html @@ -0,0 +1,332 @@ +{%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=="edit-phenotype"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2 class="heading">edit phenotype data</h2> + <p>The forms provided in this page help you update the data for the + phenotypes, and the publication information for the phenotype, + respectively.</p> +</div> + +<div class="row"> + <h3 class="subheading">Basic metadata</h3> + <form name="frm-phenotype-basic-metadata" + class="form-horizontal" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}"> + <input type="hidden" name="phenotype-id" value="{{phenotype.Id}}" /> + <div class="form-group"> + <label for="txt-pre-publication-description" + class="control-label col-sm-2">Pre-Publication Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-pre-publication-description" + name="pre-publication-description" + class="form-control" + value="{{phenotype['Pre_publication_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-pre-publication-abbreviation" + class="control-label col-sm-2">Pre-Publication Abbreviation</label> + <div class="col-sm-10"> + <input type="text" + id="txt-pre-publication-abbreviation" + name="pre-publication-abbreviation" + class="form-control" + value="{{phenotype['Pre_publication_abbreviation'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-post-publication-description" + class="control-label col-sm-2">Post-Publication Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-post-publication-description" + name="post-publication-description" + class="form-control" + value="{{phenotype['Post_publication_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-post-publication-abbreviation" + class="control-label col-sm-2">Post-Publication Abbreviation</label> + <div class="col-sm-10"> + <input type="text" + id="txt-post-publication-abbreviation" + name="post-publication-abbreviation" + class="form-control" + value="{{phenotype['Post_publication_abbreviation'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-original-description" + class="control-label col-sm-2">Original Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-original-description" + name="original-description" + class="form-control" + value="{{phenotype['Original_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-units" + class="control-label col-sm-2">units</label> + <div class="col-sm-10"> + <input type="text" + id="txt-units" + name="units" + class="form-control" + required="required" + value="{{phenotype['Units']}}" /> + </div> + </div> + + <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary" + value="update basic metadata"> + </div> + </div> + </form> +</div> + + +<div class="row"> + <h3 class="subheading">phenotype data</h3> + <form id="frm-edit-phenotype-data" + class="form-horizontal" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}"> + <div style="max-height: 23.37em;overflow-y: scroll;"> + <table class="table table-striped table-responsive table-form-table"> + <thead style="position: sticky; top: 0;"> + <tr> + <th>#</th> + <th>Sample</th> + <th>Value</th> + {%if population.Family in families_with_se_and_n%} + <th>Standard-Error</th> + <th>Number of Samples</th> + {%endif%} + </tr> + </thead> + + <tbody> + {%for item in phenotype.data%} + <tr> + <td>{{loop.index}}</td> + <td>{{item.StrainName}}</td> + <td> + <input type="text" + name="value-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.value}}" + class="form-control" /> + <input type="hidden" + name="value-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.value}}" /></td> + {%if population.Family in families_with_se_and_n%} + <td> + <input type="text" + name="se-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.error or ''}}" + data-original-value="{{item.error or ''}}" + class="form-control" /> + <input type="hidden" + name="se-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.error or ''}}" /></td> + <td> + <input type="text" + name="n-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.count or ''}}" + data-original-value="{{item.count or "-"}}" + class="form-control" /> + <input type="hidden" + name="n-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.count or ''}}" /></td> + {%endif%} + </tr> + {%endfor%} + </tbody> + </table> + </div> + <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary" + value="update data" /> + </div> + </div> + </form> +</div> + + +<div class="row"> + <h3 class="subheading">publication information</h3> + <p>Use the form below to update the publication information for this + phenotype.</p> + <form id="frm-edit-phenotype-pub-data" + class="form-horizontal" + method="POST" + action="#"> + <div class="form-group"> + <label for="txt-pubmed-id" class="control-label col-sm-2">Pubmed ID</label> + <div class="col-sm-10"> + <input id="txt-pubmed-id" name="pubmed-id" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter your publication's PubMed ID.</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-authors" class="control-label col-sm-2">Authors</label> + <div class="col-sm-10"> + <input id="txt-publication-authors" name="publication-authors" + type="text" class="form-control" /> + <span class="form-text text-muted"> + Enter the authors.</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-title" class="control-label col-sm-2"> + Publication Title</label> + <div class="col-sm-10"> + <input id="txt-publication-title" name="publication-title" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter your publication's title.</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-abstract" class="control-label col-sm-2"> + Publication Abstract</label> + <div class="col-sm-10"> + <textarea id="txt-publication-abstract" name="publication-abstract" + class="form-control" rows="10"></textarea> + <span class="form-text text-muted"> + Enter the abstract for your publication.</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-journal" class="control-label col-sm-2">Journal</label> + <div class="col-sm-10"> + <input id="txt-publication-journal" name="journal" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the name of the journal where your work was published.</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-volume" class="control-label col-sm-2">Volume</label> + <div class="col-sm-10"> + <input id="txt-publication-volume" name="publication-volume" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the volume in the following format …</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-pages" class="control-label col-sm-2">Pages</label> + <div class="col-sm-10"> + <input id="txt-publication-pages" name="publication-pages" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the journal volume where your work was published.</span> + </div> + </div> + + <div class="form-group"> + <label for="select-publication-month" class="control-label col-sm-2"> + Publication Month</label> + <div class="col-sm-10"> + <select id="select-publication-month" name="publication-month" + class="form-control"> + {%for month in monthnames%} + <option value="{{month | lower}}" + {%if current_month | lower == month | lower%} + selected="selected" + {%endif%}>{{month | capitalize}}</option> + {%endfor%} + </select> + <span class="form-text text-muted"> + Select the month when the work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span></span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-year" class="control-label col-sm-2">Publication Year</label> + <div class="col-sm-10"> + <input id="txt-publication-year" name="publication-year" type="text" + class="form-control" value="{{current_year}}" /> + <span class="form-text text-muted"> + Enter the year your work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span> + </span> + </div> + </div> + <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary not-implemented" + value="update publication" /> + </div> + </div> + </form> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html new file mode 100644 index 0000000..12963c1 --- /dev/null +++ b/uploader/templates/phenotypes/job-status.html @@ -0,0 +1,155 @@ +{%extends "phenotypes/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 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 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" 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> + +<h4 class="subheading">Errors</h4> +<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 | 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%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/macro-display-preview-table.html b/uploader/templates/phenotypes/macro-display-preview-table.html new file mode 100644 index 0000000..f54c53e --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-preview-table.html @@ -0,0 +1,21 @@ +{%macro display_preview_table(tableid, filetype)%} +<div class="card" style="max-width: 676px;"> + <div class="card-body"> + <h5 class="card-title">Phenotypes '{{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"> + Provide a phenotype '{{filetype | lower}}' file to preview. + </td> + </tr> + </tbody> + </table> + </div> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/macro-display-resumable-elements.html b/uploader/templates/phenotypes/macro-display-resumable-elements.html new file mode 100644 index 0000000..b0bf1b5 --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-resumable-elements.html @@ -0,0 +1,60 @@ +{%macro display_resumable_elements(id, title, help)%} +<div id="{{id}}" + class="resumable-elements hidden" + style="background:#D4D4EE;border-radius: 5px;;padding: 1em;border-left: solid #B2B2CC 1px;border-bottom: solid #B2B2CC 2px;margin-top:0.3em;"> + <strong style="line-height: 1.2em;">{{title | title}}</strong> + + <span class="form-text text-muted">{{help | safe}}</span> + + <div id="{{id}}-selected-files" + class="resumable-selected-files" + style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;"> + <div class="panel panel-info file-display-template hidden"> + <div class="panel-heading filename">The Filename Goes Here!</div> + <div class="panel-body"> + <ul> + <li> + <strong>Name</strong>: + <span class="filename">the file's name</span></li> + + <li><strong>Size</strong>: <span class="filesize">0 MB</span></li> + + <li> + <strong>Unique Identifier</strong>: + <span class="fileuniqueid">brrr</span></li> + + <li> + <strong>Mime</strong>: + <span class="filemimetype">text/csv</span></li> + </ul> + </div> + </div> + </div> + + <a id="{{id}}-browse-button" + class="resumable-browse-button btn btn-info" + href="#" + style="margin-left: 80%;">Browse</a> + + <div id="{{id}}-progress-bar" class="progress hidden"> + <div class="progress-bar" + role="progress-bar" + aria-valuenow="60" + aria-valuemin="0" + aria-valuemax="100" + style="width: 0%;"> + Uploading: 60% + </div> + </div> + + <div id="{{id}}-cancel-resume-buttons"> + <a id="{{id}}-resume-button" + class="resumable-resume-button btn btn-info hidden" + href="#">resume upload</a> + + <a id="{{id}}-cancel-button" + class="resumable-cancel-button btn btn-danger hidden" + href="#">cancel upload</a> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html new file mode 100644 index 0000000..7bc8c62 --- /dev/null +++ b/uploader/templates/phenotypes/review-job-data.html @@ -0,0 +1,101 @@ +{%extends "phenotypes/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>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> + + {%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%} + {%if summary.get(ftype, False)%} + <ul> + <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> + </ul> + {%endif%} + {%endfor%} + + <a href="#" class="not-implemented btn btn-primary">continue</a> +</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 sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%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/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index b136bb6..4f2b79b 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -5,6 +5,11 @@ {%block title%}Phenotypes{%endblock%} +{%block css%} +<link rel="stylesheet" + href="{{url_for('base.datatables', filename='css/jquery.dataTables.css')}}" /> +{%endblock%} + {%block pagetitle%}Phenotypes{%endblock%} {%block lvl4_breadcrumbs%} @@ -16,7 +21,7 @@ <a href="{{url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId, population_id=population.Id, - dataset_id=dataset.Id)}}">View Datasets</a> + dataset_id=dataset.Id)}}">View</a> </li> {%endblock%} @@ -56,37 +61,16 @@ <div class="row"> <h2>Phenotype Data</h2> - - <p>This dataset has a total of {{phenotype_count}} phenotypes.</p> - - {{table_pagination(start_from, count, phenotype_count, url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id), "phenotypes")}} - - <table class="table"> + <table id="tbl-phenotypes-list" class="table"> <thead> <tr> - <th>#</th> + <th></th> <th>Record</th> <th>Description</th> </tr> </thead> - <tbody> - {%for pheno in phenotypes%} - <tr> - <td>{{pheno.sequence_number}}</td> - <td><a href="{{url_for('species.populations.phenotypes.view_phenotype', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id, - xref_id=pheno['pxr.Id'])}}" - title="View phenotype details"> - {{pheno.InbredSetCode}}_{{pheno["pxr.Id"]}}</a></td> - <td>{{pheno.Post_publication_description or pheno.Pre_publication_abbreviation or pheno.Original_description}}</td> - </tr> - {%else%} - <tr><td colspan="5"></td></tr> - {%endfor%} - </tbody> + <tbody></tbody> </table> </div> {%endblock%} @@ -94,3 +78,39 @@ {%block sidebarcontents%} {{display_population_card(species, population)}} {%endblock%} + + +{%block javascript%} +<script src="{{url_for('base.datatables', + filename='js/jquery.dataTables.js')}}"></script> +<script type="text/javascript"> + $(function() { + $("#tbl-phenotypes-list").DataTable({ + responsive: true, + data: {{phenotypes | tojson}}, + columns: [ + {data: "sequence_number"}, + { + data: function(pheno) { + var spcs_id = {{species.SpeciesId}}; + var pop_id = {{population.Id}}; + var dtst_id = {{dataset.Id}}; + return `<a href="/species/${spcs_id}` + + `/populations/${pop_id}` + + `/phenotypes/datasets/${dtst_id}` + + `/phenotype/${pheno.xref_id}` + + `" target="_blank">` + + `${pheno.InbredSetCode}_${pheno.xref_id}` + + `</a>`; + } + }, + {data: function(pheno) { + return (pheno.Post_publication_description || + pheno.Original_description || + pheno.Pre_publication_description); + }} + ] + }); + }); +</script> +{%endblock%} diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html index 99bb8e5..21ac501 100644 --- a/uploader/templates/phenotypes/view-phenotype.html +++ b/uploader/templates/phenotypes/view-phenotype.html @@ -16,7 +16,7 @@ species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id, - xref_id=xref_id)}}">View Datasets</a> + xref_id=xref_id)}}">View Phenotype</a> </li> {%endblock%} @@ -34,51 +34,58 @@ <td>{{phenotype.Post_publication_description or phenotype.Pre_publication_abbreviation or phenotype.Original_description}} </tr> <tr> - <td><strong>Cross-Reference ID</strong></td> - <td>{{phenotype.xref_id}}</td> - </tr> - <tr> - <td><strong>Collation</strong></td> + <td><strong>Database</strong></td> <td>{{dataset.FullName}}</td> </tr> <tr> <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> - <form action="#edit-delete-phenotype" - method="POST" - id="frm-delete-phenotype"> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" value="{{population.Id}}" /> - <input type="hidden" name="dataset_id" value="{{dataset.Id}}" /> - <input type="hidden" name="phenotype_id" value="{{phenotype.Id}}" /> - - <div class="btn-group btn-group-justified"> - <div class="btn-group"> - {%if "group:resource:edit-resource" in privileges%} - <input type="submit" - title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values." - class="btn btn-primary not-implemented" - value="edit" /> - {%endif%} - </div> - <div class="btn-group"></div> - <div class="btn-group"> - {%if "group:resource:delete-resource" in privileges%} - <input type="submit" - title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype." - class="btn btn-danger not-implemented" - value="delete" /> - {%endif%} - </div> - </div> - </form> +{%if "group:resource:edit-resource" in privileges +or "group:resource:delete-resource" in privileges%} +<div class="row"> + <div class="btn-group btn-group-justified"> + <div class="btn-group"> + {%if "group:resource:edit-resource" in privileges%} + <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}" + title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values." + class="btn btn-primary">Edit</a> + {%endif%} + </div> + <div class="btn-group"></div> + <div class="btn-group"> + {%if "group:resource:delete-resource" in privileges%} + <a href="#" + title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype." + class="btn btn-danger not-implemented" + disabled="disabled">delete</a> + {%endif%} + </div> </div> </div> +{%endif%} <div class="row"> <div class="panel panel-default"> @@ -90,9 +97,10 @@ <th>#</th> <th>Sample</th> <th>Value</th> - <th>Symbol</th> + {%if has_se%} <th>SE</th> <th>N</th> + {%endif%} </tr> </thead> @@ -102,9 +110,10 @@ <td>{{loop.index}}</td> <td>{{item.StrainName}}</td> <td>{{item.value}}</td> - <td>{{item.Symbol or "-"}}</td> + {%if has_se%} <td>{{item.error or "-"}}</td> <td>{{item.count or "-"}}</td> + {%endif%} </tr> {%endfor%} </tbody> diff --git a/uploader/templates/platforms/list-platforms.html b/uploader/templates/platforms/list-platforms.html index 718dd1d..a6bcfdc 100644 --- a/uploader/templates/platforms/list-platforms.html +++ b/uploader/templates/platforms/list-platforms.html @@ -58,7 +58,7 @@ <table class="table"> <thead> <tr> - <th>#</th> + <th></th> <th>Platform Name</th> <th><a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}" title="Gene Expression Omnibus: Platforms section" diff --git a/uploader/templates/populations/base.html b/uploader/templates/populations/base.html index d763fc1..9db8083 100644 --- a/uploader/templates/populations/base.html +++ b/uploader/templates/populations/base.html @@ -6,7 +6,13 @@ {%else%} class="breadcrumb-item" {%endif%}> + {%if population is mapping%} + <a href="{{url_for('species.populations.view_population', + species_id=species.SpeciesId, + population_id=population.Id)}}">{{population.Name}}</a> + {%else%} <a href="{{url_for('species.populations.index')}}">Populations</a> + {%endif%} </li> {%block lvl3_breadcrumbs%}{%endblock%} {%endblock%} diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html index 7c7145f..f780e94 100644 --- a/uploader/templates/populations/list-populations.html +++ b/uploader/templates/populations/list-populations.html @@ -51,7 +51,7 @@ <caption>Populations for {{species.FullName}}</caption> <thead> <tr> - <th>#</th> + <th></th> <th>Name</th> <th>Full Name</th> <th>Description</th> diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html index 79f7925..16b477f 100644 --- a/uploader/templates/populations/macro-display-population-card.html +++ b/uploader/templates/populations/macro-display-population-card.html @@ -33,11 +33,6 @@ <td>Family</td> <td>{{population.Family}}</td> </tr> - - <tr> - <td>Description</td> - <td>{{(population.Description or "")[0:500]}}…</td> - </tr> </tbody> </table> </div> diff --git a/uploader/templates/populations/macro-select-population.html b/uploader/templates/populations/macro-select-population.html index af4fd3a..ef74ac3 100644 --- a/uploader/templates/populations/macro-select-population.html +++ b/uploader/templates/populations/macro-select-population.html @@ -1,29 +1,32 @@ {%macro select_population_form(form_action, populations)%} -<form method="GET" action="{{form_action}}"> +<form method="GET" action="{{form_action}}" class="form-horizontal"> <legend>Select Population</legend> <div class="form-group"> - <label for="select-population" class="form-label">Select Population</label> - <select id="select-population" - name="population_id" - class="form-control" - required="required"> - <option value="">Select Population</option> - {%for family in populations%} - <optgroup {%if family[0][1] is not none%} - label="{{family[0][1]}}" - {%else%} - label="Undefined" - {%endif%}> - {%for population in family[1]%} - <option value="{{population.Id}}">{{population.FullName}}</option> + <label for="select-population" class="control-label col-sm-2"> + Population</label> + <div class="col-sm-10"> + <select id="select-population" + name="population_id" + class="form-control" + required="required"> + <option value="">Select Population</option> + {%for family in populations%} + <optgroup {%if family[0][1] is not none%} + label="{{family[0][1]}}" + {%else%} + label="Undefined" + {%endif%}> + {%for population in family[1]%} + <option value="{{population.Id}}">{{population.FullName}}</option> + {%endfor%} + </optgroup> {%endfor%} - </optgroup> - {%endfor%} - </select> + </select> + </div> </div> - <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> <input type="submit" value="Select" class="btn btn-primary" /> </div> </form> diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html index 1e2964e..b23caeb 100644 --- a/uploader/templates/populations/view-population.html +++ b/uploader/templates/populations/view-population.html @@ -15,7 +15,7 @@ {%endif%}> <a href="{{url_for('species.populations.view_population', species_id=species.SpeciesId, - population_id=population.InbredSetId)}}">view population</a> + population_id=population.InbredSetId)}}">view</a> </li> {%endblock%} @@ -62,29 +62,35 @@ <nav class="nav"> <ul> <li> - <a href="{{url_for('species.populations.genotypes.list_genotypes', + <a href="{{url_for('species.populations.samples.list_samples', species_id=species.SpeciesId, population_id=population.Id)}}" - title="Upload genotypes for {{species.FullName}}">Upload Genotypes</a> + title="Manage samples: Add new or delete existing."> + manage samples</a> </li> <li> - <a href="{{url_for('species.populations.samples.list_samples', + <a href="{{url_for('species.populations.genotypes.list_genotypes', species_id=species.SpeciesId, population_id=population.Id)}}" - title="Manage samples: Add new or delete existing."> - manage samples</a> + title="Manage genotypes for {{species.FullName}}">Manage Genotypes</a> </li> <li> - <a href="#" title="Upload expression data">upload expression data</a> + <a href="{{url_for('species.populations.phenotypes.list_datasets', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Manage phenotype data.">manage phenotype data</a> </li> <li> - <a href="#" title="Upload phenotype data">upload phenotype data</a> + <a href="#" title="Manage expression data" + class="not-implemented">manage expression data</a> </li> <li> - <a href="#" title="Upload individual data">upload individual data</a> + <a href="#" title="Manage individual data" + class="not-implemented">manage individual data</a> </li> <li> - <a href="#" title="Upload RNA-Seq data">upload RNA-Seq data</a> + <a href="#" title="Manage RNA-Seq data" + class="not-implemented">manage RNA-Seq data</a> </li> </ul> </nav> diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html index 13e5cec..185e784 100644 --- a/uploader/templates/samples/list-samples.html +++ b/uploader/templates/samples/list-samples.html @@ -73,7 +73,7 @@ <table class="table"> <thead> <tr> - <th>#</th> + <th></th> <th>Name</th> <th>Auxilliary Name</th> <th>Symbol</th> diff --git a/uploader/templates/species/base.html b/uploader/templates/species/base.html index 04391db..f64f72b 100644 --- a/uploader/templates/species/base.html +++ b/uploader/templates/species/base.html @@ -6,7 +6,12 @@ {%else%} class="breadcrumb-item" {%endif%}> + {%if species is mapping%} + <a href="{{url_for('species.view_species', species_id=species.SpeciesId)}}"> + {{species.Name}}</a> + {%else%} <a href="{{url_for('species.list_species')}}">Species</a> + {%endif%} </li> {%block lvl2_breadcrumbs%}{%endblock%} {%endblock%} diff --git a/uploader/templates/species/list-species.html b/uploader/templates/species/list-species.html index 85c9d40..64084b0 100644 --- a/uploader/templates/species/list-species.html +++ b/uploader/templates/species/list-species.html @@ -29,7 +29,7 @@ <caption>Available Species</caption> <thead> <tr> - <th>#</td> + <th></td> <th title="A common, layman's name for the species.">Common Name</th> <th title="The scientific name for the species">Organism Name</th> <th title="An identifier for the species in the NCBI taxonomy database"> diff --git a/uploader/templates/species/macro-select-species.html b/uploader/templates/species/macro-select-species.html index dd086c0..36ed102 100644 --- a/uploader/templates/species/macro-select-species.html +++ b/uploader/templates/species/macro-select-species.html @@ -1,29 +1,31 @@ {%macro select_species_form(form_action, species)%} {%if species | length > 0%} -<form method="GET" action="{{form_action}}"> +<form method="GET" action="{{form_action}}" class="form-horizontal"> <div class="form-group"> - <label for="select-species" class="form-label">Species</label> - <select id="select-species" - name="species_id" - class="form-control" - required="required"> - <option value="">Select Species</option> - {%for group in species%} - {{group}} - <optgroup {%if group[0][1] is not none%} - label="{{group[0][1].capitalize()}}" - {%else%} - label="Undefined" - {%endif%}> - {%for aspecies in group[1]%} - <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option> + <label for="select-species" class="control-label col-sm-2">Species</label> + <div class="col-sm-10"> + <select id="select-species" + name="species_id" + class="form-control" + required="required"> + <option value="">Select Species</option> + {%for group in species%} + {{group}} + <optgroup {%if group[0][1] is not none%} + label="{{group[0][1].capitalize()}}" + {%else%} + label="Undefined" + {%endif%}> + {%for aspecies in group[1]%} + <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option> + {%endfor%} + </optgroup> {%endfor%} - </optgroup> - {%endfor%} - </select> + </select> + </div> </div> - <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> <input type="submit" value="Select" class="btn btn-primary" /> </div> </form> diff --git a/uploader/templates/species/view-species.html b/uploader/templates/species/view-species.html index b01864d..2d02f7e 100644 --- a/uploader/templates/species/view-species.html +++ b/uploader/templates/species/view-species.html @@ -45,6 +45,12 @@ title="Create/Edit populations for {{species.FullName}}"> Manage populations</a> </li> + <li> + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId)}}" + title="Create/Edit sequencing platforms for {{species.FullName}}"> + Manage sequencing platforms</a> + </li> </ol> |