diff options
Diffstat (limited to 'uploader/templates')
77 files changed, 3612 insertions, 904 deletions
diff --git a/uploader/templates/base.html b/uploader/templates/base.html index 171e8fa..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', @@ -23,72 +23,102 @@ </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><a href="/" >Home</a></li> - <li><a href="{{url_for('species.list_species')}}" - title="View and manage species information.">Species</a></li> - <li><a href="{{url_for('species.populations.index')}}" - title="View and manage species populations.">Populations</a></li> - <li><a href="{{url_for('species.populations.samples.index')}}" - title="Upload population samples.">Samples</a></li> - <li><a href="{{url_for('species.populations.genotypes.index')}}" - title="Upload Genotype data.">Genotype Data</a></li> - <li><a href="{{url_for('expression-data.index.index')}}" - title="Upload expression data.">Expression Data</a></li> - <li><a href="#" - title="Upload phenotype data.">Phenotype Data</a></li> - <li><a href="#" - title="Upload individual data.">Individual Data</a></li> - <li><a href="#" - title="Upload RNA-Seq data.">RNA-Seq Data</a></li> + <li {%if activemenu=="home"%}class="activemenu"{%endif%}> + <a href="/" >Home</a></li> + <li {%if activemenu=="species"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.list_species')}}" + title="View and manage species information.">Species</a></li> + <li {%if activemenu=="platforms"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.platforms.index')}}" + title="View and manage species platforms.">Sequencing Platforms</a></li> + <li {%if activemenu=="populations"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.index')}}" + title="View and manage species populations.">Populations</a></li> + <li {%if activemenu=="samples"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.samples.index')}}" + title="Upload population samples.">Samples</a></li> + <li {%if activemenu=="genotypes"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.genotypes.index')}}" + title="Upload Genotype data.">Genotype Data</a></li> + <!-- + TODO: Maybe include menus here for managing studies and dataset or + maybe have the studies/datasets managed under their respective + sections, e.g. "Publish*" studies/datasets under the "Phenotypes" + section, "ProbeSet*" studies/datasets under the "Expression Data" + sections, etc. + --> + <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." + class="not-implemented">Expression Data</a></li> + <li {%if activemenu=="individuals"%}class="activemenu"{%endif%}> + <a href="#" + class="not-implemented" + title="Upload individual data.">Individual Data</a></li> + <li {%if activemenu=="rna-seq"%}class="activemenu"{%endif%}> + <a href="#" + class="not-implemented" + title="Upload RNA-Seq data.">RNA-Seq Data</a></li> + <li {%if activemenu=="async-jobs"%}class="activemenu"{%endif%}> + <a href="#" + 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> @@ -98,8 +128,7 @@ filename='jquery.min.js')}}"></script> <script src="{{url_for('base.bootstrap', 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/expression-data/base.html b/uploader/templates/expression-data/base.html new file mode 100644 index 0000000..d63fd7e --- /dev/null +++ b/uploader/templates/expression-data/base.html @@ -0,0 +1,13 @@ +{%extends "populations/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="expression-data"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.expression-data.index')}}"> + Expression Data</a> +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/data_review.html b/uploader/templates/expression-data/data-review.html index 4e5c586..c985b03 100644 --- a/uploader/templates/data_review.html +++ b/uploader/templates/expression-data/data-review.html @@ -26,7 +26,7 @@ <small class="text-muted"> If you encounter an error saying your sample(s)/case(s) do not exist in the GeneNetwork database, then you will have to use the - <a href="{{url_for('expression-data.samples.select_species')}}" + <a href="{{url_for('species.populations.samples.index')}}" title="Upload samples/cases feature">Upload Samples/Cases</a> option on this system to upload them. </small> @@ -70,8 +70,8 @@ column</li> <li>The values of each field <strong>ARE NOT</strong> quoted.</li> <li>Here is an - <a href="https://gitlab.com/fredmanglis/gnqc_py/-/blob/main/tests/test_data/no_data_errors.tsv"> - example file</a> with a single data row.</li> + <a href="https://gitlab.com/fredmanglis/gnqc_py/-/blob/main/tests/test_data/no_data_errors.tsv" + target="_blank">example file</a> with a single data row.</li> </ul> </li> <li>.txt files: Content has the same format as .tsv file above</li> diff --git a/uploader/templates/expression-data/index.html b/uploader/templates/expression-data/index.html index ed5d8dd..9ba3582 100644 --- a/uploader/templates/expression-data/index.html +++ b/uploader/templates/expression-data/index.html @@ -1,5 +1,6 @@ -{%extends "base.html"%} +{%extends "expression-data/base.html"%} {%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} {%block title%}Expression Data{%endblock%} @@ -10,86 +11,23 @@ <a href="{{url_for('base.index')}}">Home</a> </li> <li class="breadcrumb-item active"> - <a href="{{url_for('expression-data.index.index')}}">Expression Data</a> + <a href="{{url_for('species.populations.expression-data.index')}}" + title="Upload expression data."> + Expression Data</a> </li> {%endblock%} {%block contents%} <div class="row"> - {{flash_all_messages()}} - - <h1 class="heading">data upload</h1> - - <div class="explainer"> - <p>Each of the sections below gives you a different option for data expression-data. - Please read the documentation for each section carefully to understand what - each section is about.</p> - </div> -</div> - -<div class="row"> - <h2 class="heading">R/qtl2 Bundles</h2> - - <div class="explainer"> - <p>This feature combines and extends the two upload methods below. Instead of - uploading one item at a time, the R/qtl2 bundle you upload can contain both - the genotypes data (samples/individuals/cases and their data) and the - expression data.</p> - <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither - of the methods below can handle.</p> - - <a href="{{url_for('expression-data.rqtl2.select_species')}}" - title="Upload a zip bundle of R/qtl2 files"> - <button class="btn btn-primary">upload R/qtl2 bundle</button></a> - </div> -</div> - - -<div class="row"> <h2 class="heading">Expression Data</h2> + {{flash_all_messages()}} - <div class="explainer"> - <p>This feature enables you to upload expression data. It expects the data to - be in <strong>tab-separated values (TSV)</strong> files. The data should be - a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a - list of the <em>phenotypes</em> and the first row is a list of - <em>samples/cases</em>.</p> - - <p>If you haven't done so please go to this page to learn the requirements for - file formats and helpful suggestions to enter your data in a fast and easy - way.</p> - - <ol> - <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies - with our system requirements. ( - <a href="{{url_for('expression-data.index.data_review')}}#data-concerns" - title="Details for the data expectations.">Help</a> - )</li> - <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept - <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong> - files (<a href="{{url_for('expression-data.index.data_review')}}#file-types" - title="Details for the data expectations.">Help</a>)</li> - </ol> - </div> - - <a href="{{url_for('expression-data.index.upload_file')}}" - title="Upload your expression data" - class="btn btn-primary">upload expression data</a> + <p>This section allows you to enter the expression data for your experiment. + You will need to select the species that your data concerns below.</p> </div> <div class="row"> - <h2 class="heading">samples/cases</h2> - - <div class="explainer"> - <p>For the expression data above, you need the samples/cases in your file to - already exist in the GeneNetwork database. If there are any samples that do - not already exist the upload of the expression data will fail.</p> - <p>This section gives you the opportunity to upload any missing samples</p> - </div> - - <a href="{{url_for('expression-data.samples.select_species')}}" - title="Upload samples/cases/individuals for your data" - class="btn btn-primary">upload Samples/Cases</a> + {{select_species_form(url_for("species.populations.expression-data.index"), + species)}} </div> - {%endblock%} diff --git a/uploader/templates/job_progress.html b/uploader/templates/expression-data/job-progress.html index 2feaa89..ef264e1 100644 --- a/uploader/templates/job_progress.html +++ b/uploader/templates/expression-data/job-progress.html @@ -1,5 +1,6 @@ {%extends "base.html"%} {%from "errors_display.html" import errors_display%} +{%from "populations/macro-display-population-card.html" import display_population_card%} {%block extrameta%} <meta http-equiv="refresh" content="5"> @@ -11,7 +12,9 @@ <h1 class="heading">{{job_name}}</h2> <div class="row"> - <form action="{{url_for('expression-data.parse.abort')}}" method="POST"> + <form action="{{url_for('species.populations.expression-data.abort', + species_id=species.SpeciesId, + population_id=population.Id)}}" method="POST"> <legend class="heading">Status</legend> <div class="form-group"> <label for="job_status" class="form-label">status:</label> @@ -38,3 +41,7 @@ </div> {%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/no_such_job.html b/uploader/templates/expression-data/no-such-job.html index 874d047..d22c429 100644 --- a/uploader/templates/no_such_job.html +++ b/uploader/templates/expression-data/no-such-job.html @@ -1,7 +1,8 @@ {%extends "base.html"%} {%block extrameta%} -<meta http-equiv="refresh" content="5;url={{url_for('expression-data.index.upload_file')}}"> +<meta http-equiv="refresh" + content="5;url={{url_for('species.populations.expression-data.index.upload_file')}}"> {%endblock%} {%block title%}No Such Job{%endblock%} diff --git a/uploader/templates/parse_failure.html b/uploader/templates/expression-data/parse-failure.html index 31f6be8..31f6be8 100644 --- a/uploader/templates/parse_failure.html +++ b/uploader/templates/expression-data/parse-failure.html diff --git a/uploader/templates/expression-data/parse-results.html b/uploader/templates/expression-data/parse-results.html new file mode 100644 index 0000000..03a23e2 --- /dev/null +++ b/uploader/templates/expression-data/parse-results.html @@ -0,0 +1,39 @@ +{%extends "base.html"%} +{%from "errors_display.html" import errors_display%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Parse Results{%endblock%} + +{%block contents%} + +<div class="row"> + <h2 class="heading">{{job_name}}: parse results</h2> + + {%if user_aborted%} + <span class="alert-warning">Job aborted by the user</span> + {%endif%} + + {{errors_display(errors, "No errors found in the file", "We found the following errors", True)}} + + {%if errors | length == 0 and not user_aborted %} + <form method="post" action="{{url_for('dbinsert.select_platform')}}"> + <input type="hidden" name="job_id" value="{{job_id}}" /> + <input type="submit" value="update database" class="btn btn-primary" /> + </form> + {%endif%} + + {%if errors | length > 0 or user_aborted %} + <br /> + <a href="{{url_for('species.populations.expression-data.upload_file', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Back to index page." + class="btn btn-primary">Go back</a> + + {%endif%} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/expression-data/select-file.html b/uploader/templates/expression-data/select-file.html new file mode 100644 index 0000000..4ca461e --- /dev/null +++ b/uploader/templates/expression-data/select-file.html @@ -0,0 +1,115 @@ +{%extends "expression-data/base.html"%} +{%from "flash_messages.html" import flash_messages%} +{%from "upload_progress_indicator.html" import upload_progress_indicator%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Expression Data — Upload Data{%endblock%} + +{%block pagetitle%}Expression Data — Upload Data{%endblock%} + +{%block contents%} +{{upload_progress_indicator()}} + +<div class="row"> + <h2 class="heading">Upload Expression Data</h2> + + <p>This feature enables you to upload expression data. It expects the data to + be in <strong>tab-separated values (TSV)</strong> files. The data should be + a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a + list of the <em>phenotypes</em> and the first row is a list of + <em>samples/cases</em>.</p> + + <p>If you haven't done so please go to this page to learn the requirements for + file formats and helpful suggestions to enter your data in a fast and easy + way.</p> + + <ol> + <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies + with our system requirements. ( + <a href="{{url_for('species.populations.expression-data.data_review')}}#data-concerns" + title="Details for the data expectations.">Help</a> + )</li> + <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept + <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong> + files (<a href="{{url_for('species.populations.expression-data.data_review')}}#file-types" + title="Details for the data expectations.">Help</a>)</li> + </ol> +</div> + +<div class="row"> + <form action="{{url_for( + 'species.populations.expression-data.upload_file', + species_id=species.SpeciesId, + population_id=population.Id)}}" + method="POST" + enctype="multipart/form-data" + id="frm-upload-expression-data"> + {{flash_messages("error-expr-data")}} + + <div class="form-group"> + <legend class="heading">File Type</legend> + + <div class="radio"> + <label for="filetype_average" class="form-check-label"> + <input type="radio" name="filetype" value="average" id="filetype_average" + required="required" class="form-check-input" /> + Average</label> + <p class="form-text text-muted"> + <small>The averages data …</small></p> + </div> + + <div class="radio"> + <label for="filetype_standard_error" class="form-check-label"> + <input type="radio" name="filetype" value="standard-error" + id="filetype_standard_error" required="required" + class="form-check-input" /> + Standard Error + </label> + <p class="form-text text-muted"> + <small>The standard errors computed from the averages …</small></p> + </div> + </div> + + <div class="form-group"> + <span id="no-file-error" class="alert-danger" style="display: none;"> + No file selected + </span> + <label for="file_upload" class="form-label">Select File</label> + <input type="file" name="qc_text_file" id="file_upload" + accept="text/plain, text/tab-separated-values, application/zip" + class="form-control"/> + <p class="form-text text-muted"> + <small>Select the file to upload.</small></p> + </div> + + <button type="submit" + class="btn btn-primary" + data-toggle="modal" + data-target="#upload-progress-indicator">upload file</button> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/upload_progress.js"></script> +<script type="text/javascript"> + function setup_formdata(form) { + var formdata = new FormData(); + formdata.append( + "qc_text_file", + form.querySelector("input[type='file']").files[0]); + formdata.append( + "filetype", + selected_filetype( + Array.from(form.querySelectorAll("input[type='radio']")))); + return formdata; + } + + setup_upload_handlers( + "frm-upload-expression-data", make_data_uploader(setup_formdata)); +</script> +{%endblock%} diff --git a/uploader/templates/expression-data/select-population.html b/uploader/templates/expression-data/select-population.html new file mode 100644 index 0000000..8555e27 --- /dev/null +++ b/uploader/templates/expression-data/select-population.html @@ -0,0 +1,29 @@ +{%extends "expression-data/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} +{%from "populations/macro-select-population.html" import select_population_form%} + +{%block title%}Expression Data{%endblock%} + +{%block pagetitle%}Expression Data{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>You have selected the species. Now you need to select the population that + the expression data belongs to.</p> +</div> + +<div class="row"> + {{select_population_form(url_for( + "species.populations.expression-data.select_population", + species_id=species.SpeciesId), + populations)}} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} 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/create-dataset.html b/uploader/templates/genotypes/create-dataset.html new file mode 100644 index 0000000..10331c1 --- /dev/null +++ b/uploader/templates/genotypes/create-dataset.html @@ -0,0 +1,82 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes — Create Dataset{%endblock%} + +{%block pagetitle%}Genotypes — Create Dataset{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="create-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}">Create Dataset</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-geno-create-dataset" + method="POST" + action="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}"> + <legend>Create a new Genotype Dataset</legend> + + <div class="form-group"> + <label for="txt-geno-dataset-name" class="form-label">Name</label> + <input type="text" + id="txt-geno-dataset-name" + name="geno-dataset-name" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a short representative, but constrained name for the genotype + dataset.<br /> + The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens + and underscores. Any other character will cause the name to be + rejected.</p></small> + </div> + + <div class="form-group"> + <label for="txt-geno-dataset-fullname" class="form-label">Full Name</label> + <input type="text" + id="txt-geno-dataset-fullname" + name="geno-dataset-fullname" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a longer, more descriptive name for your dataset.</p></small> + </div> + + <div class="form-group"> + <label for="txt-geno-dataset-shortname" + class="form-label">Short Name</label> + <input type="text" + id="txt-geno-dataset-shortname" + name="geno-dataset-shortname" + class="form-control" /> + <small class="form-text text-muted"> + <p>A short name for your dataset. If you leave this field blank, the + short name will be set to the same value as the + "<strong>Name</strong>" field above.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + class="btn btn-primary" + value="create dataset" /> + </div> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html index 8afd591..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%} @@ -95,14 +96,8 @@ <p>The genotype data is organised under various genotype datasets. You can click on the link for the relevant dataset to view a little more information about it.</p> - <p>You can also create a new genotype dataset by clicking the button below. - <br /> - <a href="#create-new-genotype-dataset" - title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species." - class="btn btn-primary"> - create new genotype dataset</a></p> - {%if datasets | length > 0%} + {%if dataset is not none%} <table class="table"> <thead> <tr> @@ -112,7 +107,6 @@ </thead> <tbody> - {%for dataset in datasets%} <tr> <td>{{dataset.Name}}</td> <td><a href="{{url_for('species.populations.genotypes.view_dataset', @@ -122,16 +116,32 @@ title="View details regarding and manage dataset '{{dataset.FullName}}'"> {{dataset.FullName}}</a></td> </tr> - {%endfor%} </tbody> </table> {%else%} - <p class="text-warning"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - There are no genotype datasets to display, yet! - </p> + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There is no genotype dataset defined for this population. + </p> + <p> + <a href="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species." + class="btn btn-primary"> + create new genotype dataset</a></p> {%endif%} </div> +<div class="row text-warning"> + <p> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a + single genotype dataset. If there is more than one, the system apparently + fails in unpredictable ways. + </p> + <p>Fix this to allow multiple datasets, each with a different assembly from + all the rest.</p> +</div> {%endblock%} {%block sidebarcontents%} 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/genotypes/view-dataset.html b/uploader/templates/genotypes/view-dataset.html new file mode 100644 index 0000000..e7ceb36 --- /dev/null +++ b/uploader/templates/genotypes/view-dataset.html @@ -0,0 +1,61 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes: View Dataset{%endblock%} + +{%block pagetitle%}Genotypes: View Dataset{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">view dataset</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Genotype Dataset Details</h2> + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td>{{dataset.FullName}}</td> + </tr> + </tbody> + </table> +</div> + +<div class="row text-warning"> + <h2>Assembly Details</h2> + + <p>Maybe include the assembly details here if found to be necessary.</p> +</div> + +<div class="row"> + <h2>Genotype Data</h2> + + <p class="text-danger"> + Provide link to enable uploading of genotype data here.</p> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/index.html b/uploader/templates/index.html index 48848a3..aa1414e 100644 --- a/uploader/templates/index.html +++ b/uploader/templates/index.html @@ -5,101 +5,103 @@ {%block pagetitle%}Home{%endblock%} -{%block breadcrumb%} -<li class="breadcrumb-item active"> - <a href="{{url_for('base.index')}}">Home</a> -</li> -{%endblock%} - {%block contents%} <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/macro-table-pagination.html b/uploader/templates/macro-table-pagination.html new file mode 100644 index 0000000..292c531 --- /dev/null +++ b/uploader/templates/macro-table-pagination.html @@ -0,0 +1,26 @@ +{%macro table_pagination(start_at, page_count, total_count, base_uri, name)%} +{%set ns = namespace(forward_uri=base_uri, back_uri=base_uri)%} +{%set ns.forward_uri="brr"%} + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%if start_at > 0%} + <a href="{{base_uri + + '?start_at='+((start_at-page_count)|string) + + '&count='+(page_count|string)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + <div class="col-md-8" style="text-align: center;"> + Displaying {{name}} {{start_at+1}} to {{start_at+page_count if start_at+page_count < total_count else total_count}} of {{total_count}}</div> + <div class="col-md-2" style="text-align: end;"> + {%if start_at + page_count < total_count%} + <a href="{{base_uri + + '?start_at='+((start_at+page_count)|string) + + '&count='+(page_count|string)}}"> + Next<span class="glyphicon glyphicon-forward"></span></a> + {%endif%} + </div> + </div> +{%endmacro%} diff --git a/uploader/templates/parse_results.html b/uploader/templates/parse_results.html deleted file mode 100644 index 46fbaaf..0000000 --- a/uploader/templates/parse_results.html +++ /dev/null @@ -1,30 +0,0 @@ -{%extends "base.html"%} -{%from "errors_display.html" import errors_display%} - -{%block title%}Parse Results{%endblock%} - -{%block contents%} -<h1 class="heading">{{job_name}}: parse results</h2> - -{%if user_aborted%} -<span class="alert-warning">Job aborted by the user</span> -{%endif%} - -{{errors_display(errors, "No errors found in the file", "We found the following errors", True)}} - -{%if errors | length == 0 and not user_aborted %} -<form method="post" action="{{url_for('dbinsert.select_platform')}}"> - <input type="hidden" name="job_id" value="{{job_id}}" /> - <input type="submit" value="update database" class="btn btn-primary" /> -</form> -{%endif%} - -{%if errors | length > 0 or user_aborted %} -<br /> -<a href="{{url_for('expression-data.index.upload_file')}}" title="Back to index page." - class="btn btn-primary"> - Go back -</a> -{%endif%} - -{%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-with-rqtl2-bundle.html b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html new file mode 100644 index 0000000..898fc0c --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html @@ -0,0 +1,207 @@ +{%extends "phenotypes/add-phenotypes-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">Add Phenotypes</a> +</li> +{%endblock%} + +{%block frm_add_phenotypes_documentation%} +<p>Select the zip file bundle containing information on the phenotypes you + wish to upload, then click the "Upload Phenotypes" button below to + 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%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/base.html b/uploader/templates/phenotypes/base.html new file mode 100644 index 0000000..adbc012 --- /dev/null +++ b/uploader/templates/phenotypes/base.html @@ -0,0 +1,19 @@ +{%extends "populations/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="phenotypes"%} + class="breadcrumb-item active" + {%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/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html new file mode 100644 index 0000000..93de92f --- /dev/null +++ b/uploader/templates/phenotypes/create-dataset.html @@ -0,0 +1,106 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="create-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}">Create Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>Create a new phenotype dataset.</p> +</div> + +<div class="row"> + <form id="frm-create-pheno-dataset" + action="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + method="POST"> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-name">Name</label> + {%if errors["dataset-name"] is defined%} + <small class="form-text text-muted danger"> + <p>{{errors["dataset-name"]}}</p></small> + {%endif%} + <input type="text" + name="dataset-name" + id="txt-dataset-name" + value="{{original_formdata.get('dataset-name') or (population.InbredSetCode + 'Publish')}}" + {%if errors["dataset-name"] is defined%} + class="form-control danger" + {%else%} + class="form-control" + {%endif%} + required="required" /> + <small class="form-text text-muted"> + <p>A short representative name for the dataset.</p> + <p>Recommended: Use the population code and append "Publish" at the end. + <br />This field will only accept names composed of + letters ('A-Za-z'), numbers (0-9), hyphens and underscores.</p> + </small> + </div> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-fullname">Full Name</label> + {%if errors["dataset-fullname"] is defined%} + <small class="form-text text-muted danger"> + <p>{{errors["dataset-fullname"]}}</p></small> + {%endif%} + <input id="txt-dataset-fullname" + name="dataset-fullname" + type="text" + value="{{original_formdata.get('dataset-fullname', '')}}" + {%if errors["dataset-fullname"] is defined%} + class="form-control danger" + {%else%} + class="form-control" + {%endif%} + required="required" /> + <small class="form-text text-muted"> + <p>A longer, descriptive name for the dataset — useful for humans. + </p></small> + </div> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-shortname">Short Name</label> + <input id="txt-dataset-shortname" + name="dataset-shortname" + type="text" + class="form-control" + value="{{original_formdata.get('dataset-shortname') or (population.InbredSetCode + ' Publish')}}" /> + <small class="form-text text-muted"> + <p>An optional, short name for the dataset. <br /> + If this is not provided, it will default to the value provided for the + <strong>Name</strong> field above.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + class="btn btn-primary" + value="create phenotype dataset" /> + </div> + + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%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/index.html b/uploader/templates/phenotypes/index.html new file mode 100644 index 0000000..0c691e6 --- /dev/null +++ b/uploader/templates/phenotypes/index.html @@ -0,0 +1,26 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>This section deals with phenotypes that + <span class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + … what are the characteristics of these phenotypes? …</span></p> + <p>Select the species to begin the process of viewing/uploading data about + your phenotypes</p> +</div> + +<div class="row"> + {{select_species_form(url_for("species.populations.phenotypes.index"), + species)}} +</div> +{%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/list-datasets.html b/uploader/templates/phenotypes/list-datasets.html new file mode 100644 index 0000000..2eaf43a --- /dev/null +++ b/uploader/templates/phenotypes/list-datasets.html @@ -0,0 +1,65 @@ +{%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=="list-datasets"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.list_datasets', + species_id=species.SpeciesId, + population_id=population.Id)}}">List Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + {%if datasets | length > 0%} + <p>The dataset(s) available for this population is/are:</p> + + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + <th>Short Name</th> + </tr> + </thead> + + <tbody> + {%for dataset in datasets%} + <tr> + <td><a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">{{dataset.Name}}</a></td> + <td>{{dataset.FullName}}</td> + <td>{{dataset.ShortName}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There is no dataset for this population!</p> + <p><a href="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + class="btn btn-primary" + title="Create a new phenotype dataset.">create dataset</a></p> + {%endif%} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html new file mode 100644 index 0000000..11b108b --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html @@ -0,0 +1,31 @@ +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%macro display_pheno_dataset_card(species, population, dataset)%} +{{display_population_card(species, population)}} + +<div class="card"> + <div class="card-body"> + <h5 class="card-title">Phenotypes' Dataset</h5> + <div class="card-text"> + <table class="table"> + <tbody> + <tr> + <td>Name</td> + <td>{{dataset.Name}}</td> + </tr> + + <tr> + <td>Full Name</td> + <td>{{dataset.FullName}}</td> + </tr> + + <tr> + <td>Short Name</td> + <td>{{dataset.ShortName}}</td> + </tr> + </tbody> + </table> + </div> + </div> +</div> +{%endmacro%} 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/select-population.html b/uploader/templates/phenotypes/select-population.html new file mode 100644 index 0000000..eafd4a7 --- /dev/null +++ b/uploader/templates/phenotypes/select-population.html @@ -0,0 +1,28 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} +{%from "populations/macro-select-population.html" import select_population_form%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>Select the population for your phenotypes to view and manage the phenotype + datasets that relate to it.</p> +</div> + +<div class="row"> + {{select_population_form(url_for("species.populations.phenotypes.select_population", + species_id=species.SpeciesId), + populations)}} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html new file mode 100644 index 0000000..4f2b79b --- /dev/null +++ b/uploader/templates/phenotypes/view-dataset.html @@ -0,0 +1,116 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block css%} +<link rel="stylesheet" + href="{{url_for('base.datatables', filename='css/jquery.dataTables.css')}}" /> +{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">View</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>The basic dataset details are:</p> + + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + <th>Short Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td>{{dataset.FullName}}</td> + <td>{{dataset.ShortName}}</td> + </tr> + </tbody> + </table> +</div> + +<div class="row"> + <p><a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="Add a bunch of phenotypes" + class="btn btn-primary">Add phenotypes</a></p> +</div> + +<div class="row"> + <h2>Phenotype Data</h2> + <table id="tbl-phenotypes-list" class="table"> + <thead> + <tr> + <th></th> + <th>Record</th> + <th>Description</th> + </tr> + </thead> + + <tbody></tbody> + </table> +</div> +{%endblock%} + +{%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 new file mode 100644 index 0000000..21ac501 --- /dev/null +++ b/uploader/templates/phenotypes/view-phenotype.html @@ -0,0 +1,135 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-phenotype"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.view_phenotype', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}">View Phenotype</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <div class="panel panel-default"> + <div class="panel-heading"><strong>Basic Phenotype Details</strong></div> + + <table class="table"> + <tbody> + <tr> + <td><strong>Phenotype</strong></td> + <td>{{phenotype.Post_publication_description or phenotype.Pre_publication_abbreviation or phenotype.Original_description}} + </tr> + <tr> + <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> + +{%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"> + <div class="panel-heading"><strong>Phenotype Data</strong></div> + {%if "group:resource:view-resource" in privileges%} + <table class="table"> + <thead> + <tr> + <th>#</th> + <th>Sample</th> + <th>Value</th> + {%if has_se%} + <th>SE</th> + <th>N</th> + {%endif%} + </tr> + </thead> + + <tbody> + {%for item in phenotype.data%} + <tr> + <td>{{loop.index}}</td> + <td>{{item.StrainName}}</td> + <td>{{item.value}}</td> + {%if has_se%} + <td>{{item.error or "-"}}</td> + <td>{{item.count or "-"}}</td> + {%endif%} + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + You do not currently have privileges to view this phenotype in greater + detail. + </p> + {%endif%} + </div> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/platforms/base.html b/uploader/templates/platforms/base.html new file mode 100644 index 0000000..dac965f --- /dev/null +++ b/uploader/templates/platforms/base.html @@ -0,0 +1,13 @@ +{%extends "species/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="platforms"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.platforms.index')}}"> + Sequencing Platforms</a> +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/platforms/create-platform.html b/uploader/templates/platforms/create-platform.html new file mode 100644 index 0000000..0866d5e --- /dev/null +++ b/uploader/templates/platforms/create-platform.html @@ -0,0 +1,124 @@ +{%extends "platforms/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Platforms — Create Platforms{%endblock%} + +{%block pagetitle%}Platforms — Create Platforms{%endblock%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="create-platform"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}">create platform</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Create New Platform</h2> + + <p>You can create a new genetic sequencing platform below.</p> +</div> + +<div class="row"> + <form id="frm-create-platform" + method="POST" + action="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}"> + + <div class="form-group"> + <label for="txt-geo-platform" class="form-label">GEO Platform</label> + <input type="text" + id="txt-geo-platform" + name="geo-platform" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is the platform's + <a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}" + title="Platforms for '{{species.FullName}}' on NCBI"> + accession value on NCBI</a>. If you do not know the value, click the + link and search on NCBI for species '{{species.FullName}}'.</p></small> + </div> + + <div class="form-group"> + <label for="txt-platform-name" class="form-label">Platform Name</label> + <input type="text" + id="txt-platform-name" + name="platform-name" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is name of the genetic sequencing platform.</p></small> + </div> + + <div class="form-group"> + <label for="txt-platform-shortname" class="form-label"> + Platform Short Name</label> + <input type="text" + id="txt-platform-shortname" + name="platform-shortname" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>Use the following conventions for this field: + <ol> + <li>Start with a 4-letter vendor code, e.g. "Affy" for "Affymetrix", "Illu" for "Illumina", etc.</li> + <li>Append an underscore to the 4-letter vendor code</li> + <li>Use the name of the array given by the vendor, e.g. U74AV2, MOE430A, etc.</li> + </ol> + </p> + </small> + </div> + + <div class="form-group"> + <label for="txt-platform-title" class="form-label">Platform Title</label> + <input type="text" + id="txt-platform-title" + name="platform-title" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>The full platform title. Sometimes, this is the same as the Platform + Name above.</p></small> + </div> + + <div class="form-group"> + <label for="txt-go-tree-value" class="form-label">GO Tree Value</label> + <input type="text" + id="txt-go-tree-value" + name="go-tree-value" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a Chip identification value useful for analysis with the + <strong> + <a href="https://www.geneweaver.org/" + title="Go to the GeneWeaver site." + target="_blank">GeneWeaver</a></strong> + and + <strong> + <a href="https://www.webgestalt.org/" + title="Go to the WEB-based GEne SeT AnaLysis Toolkit site." + target="_blank">WebGestalt</a></strong> + tools.<br /> + This can be left blank for custom platforms.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + value="create new platform" + class="btn btn-primary" /> + </div> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/platforms/index.html b/uploader/templates/platforms/index.html new file mode 100644 index 0000000..35b6464 --- /dev/null +++ b/uploader/templates/platforms/index.html @@ -0,0 +1,21 @@ +{%extends "platforms/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Platforms{%endblock%} + +{%block pagetitle%}Platforms{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>In this section, you will be able to view and manage the sequencing + platforms that are currently supported by GeneNetwork.</p> +</div> + +<div class="row"> + {{select_species_form(url_for("species.platforms.index"), species)}} +</div> +{%endblock%} diff --git a/uploader/templates/platforms/list-platforms.html b/uploader/templates/platforms/list-platforms.html new file mode 100644 index 0000000..a6bcfdc --- /dev/null +++ b/uploader/templates/platforms/list-platforms.html @@ -0,0 +1,93 @@ +{%extends "platforms/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Platforms — List Platforms{%endblock%} + +{%block pagetitle%}Platforms — List Platforms{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>View the list of the genetic sequencing platforms that are currently + supported by GeneNetwork.</p> + <p>If you cannot find the platform you wish to use, you can add it by clicking + the "New Platform" button below.</p> + <p><a href="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}" + title="Create a new genetic sequencing platform for species {{species.FullName}}" + class="btn btn-primary">Create Platform</a></p> +</div> + +<div class="row"> + <h2>Supported Platforms</h2> + {%if platforms is defined and platforms | length > 0%} + <p>There are {{total_platforms}} platforms supported by GeneNetwork</p> + + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%if start_from > 0%} + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId, + start_from=start_from-count, + count=count)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + <div class="col-md-8" style="text-align: center;"> + Displaying platforms {{start_from+1}} to {{start_from+count if start_from+count < total_platforms else total_platforms}} of + {{total_platforms}} + </div> + <div class="col-md-2" style="text-align: end;"> + {%if start_from + count < total_platforms%} + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId, + start_from=start_from+count, + count=count)}}"> + Next + <span class="glyphicon glyphicon-forward"></span> + </a> + {%endif%} + </div> + </div> + + <table class="table"> + <thead> + <tr> + <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" + target="_blank">GEO Platform</a></th> + <th>Title</th> + </tr> + </thead> + + <tbody> + {%for platform in platforms%} + <tr> + <td>{{platform.sequence_number}}</td> + <td>{{platform.GeneChipName}}</td> + <td><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{platform.GeoPlatform}}" + title="View platform on the Gene Expression Omnibus" + target="_blank">{{platform.GeoPlatform}}</a></td> + <td>{{platform.Title}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There are no platforms supported at this time!</p> + {%endif%} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} 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/create-population.html b/uploader/templates/populations/create-population.html index b05ce37..86aebda 100644 --- a/uploader/templates/populations/create-population.html +++ b/uploader/templates/populations/create-population.html @@ -107,9 +107,12 @@ value="{{error_values.population_code or ''}}" class="form-control" /> <small class="form-text text-muted"> - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - What is this field is for? Confirm with Arthur and the rest. + <p class="form-text text-muted"> + This is a 3-character code for your population, that is prepended to + the phenotype identifiers. e.g. For the "BXD Family" population, the + code is "BXD" and therefore, the phenotype identifiers for the + population look like the following examples: <em>BXD_10148</em>, + <em>BXD_10180</em>, <em>BXD_10197</em>, etc. </p> </small> </div> 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 e68f8e3..16b477f 100644 --- a/uploader/templates/populations/macro-display-population-card.html +++ b/uploader/templates/populations/macro-display-population-card.html @@ -7,25 +7,34 @@ <div class="card-body"> <h5 class="card-title">Population</h5> <div class="card-text"> - <dl> - <dt>Name</dt> - <dd>{{population.Name}}</dd> + <table class="table"> + <tbody> + <tr> + <td>Name</td> + <td>{{population.Name}}</td> + </tr> - <dt>Full Name</dt> - <dd>{{population.FullName}}</dd> + <tr> + <td>Full Name</td> + <td>{{population.FullName}}</td> + </tr> - <dt>Code</dt> - <dd>{{population.InbredSetCode}}</dd> + <tr> + <td>Code</td> + <td>{{population.InbredSetCode}}</td> + </tr> - <dt>Genetic Type</dt> - <dd>{{population.GeneticType}}</dd> + <tr> + <td>Genetic Type</td> + <td>{{population.GeneticType}}</td> + </tr> - <dt>Family</dt> - <dd>{{population.Family}}</dd> - - <dt>Description</dt> - <dd>{{population.Description or "-"}}</dd> - </dl> + <tr> + <td>Family</td> + <td>{{population.Family}}</td> + </tr> + </tbody> + </table> </div> </div> </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/rqtl2/create-tissue-success.html b/uploader/templates/populations/rqtl2/create-tissue-success.html index d6fe154..d6fe154 100644 --- a/uploader/templates/rqtl2/create-tissue-success.html +++ b/uploader/templates/populations/rqtl2/create-tissue-success.html diff --git a/uploader/templates/populations/rqtl2/index.html b/uploader/templates/populations/rqtl2/index.html new file mode 100644 index 0000000..ec6ffb8 --- /dev/null +++ b/uploader/templates/populations/rqtl2/index.html @@ -0,0 +1,54 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Data Upload{%endblock%} + +{%block contents%} +<h1 class="heading">R/qtl2 data upload</h1> + +<h2>R/qtl2 Upload</h2> + +<div class="row"> + <form method="POST" action="{{url_for('expression-data.rqtl2.select_species')}}" + id="frm-rqtl2-upload"> + <legend class="heading">upload R/qtl2 bundle</legend> + {{flash_messages("error-rqtl2")}} + + <div class="form-group"> + <label for="select:species" class="form-label">Species</label> + <select id="select:species" + name="species_id" + required="required" + class="form-control"> + <option value="">Select species</option> + {%for spec in species%} + <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option> + {%endfor%} + </select> + <small class="form-text text-muted"> + Data that you upload to the system should belong to a know species. + Here you can select the species that you wish to upload data for. + </small> + </div> + + <input type="submit" class="btn btn-primary" value="submit" /> + </form> +</div> + +<div class="row"> + <h2 class="heading">R/qtl2 Bundles</h2> + + <div class="explainer"> + <p>This feature combines and extends the two upload methods below. Instead of + uploading one item at a time, the R/qtl2 bundle you upload can contain both + the genotypes data (samples/individuals/cases and their data) and the + expression data.</p> + <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither + of the methods below can handle.</p> + + <a href="{{url_for('expression-data.rqtl2.select_species')}}" + title="Upload a zip bundle of R/qtl2 files"> + <button class="btn btn-primary">upload R/qtl2 bundle</button></a> + </div> +</div> +{%endblock%} diff --git a/uploader/templates/rqtl2/no-such-job.html b/uploader/templates/populations/rqtl2/no-such-job.html index b17004f..b17004f 100644 --- a/uploader/templates/rqtl2/no-such-job.html +++ b/uploader/templates/populations/rqtl2/no-such-job.html diff --git a/uploader/templates/rqtl2/rqtl2-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-job-error.html index 9817518..9817518 100644 --- a/uploader/templates/rqtl2/rqtl2-job-error.html +++ b/uploader/templates/populations/rqtl2/rqtl2-job-error.html diff --git a/uploader/templates/rqtl2/rqtl2-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-job-results.html index 4ecd415..4ecd415 100644 --- a/uploader/templates/rqtl2/rqtl2-job-results.html +++ b/uploader/templates/populations/rqtl2/rqtl2-job-results.html diff --git a/uploader/templates/rqtl2/rqtl2-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-job-status.html index e896f88..e896f88 100644 --- a/uploader/templates/rqtl2/rqtl2-job-status.html +++ b/uploader/templates/populations/rqtl2/rqtl2-job-status.html diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html index 90e8887..90e8887 100644 --- a/uploader/templates/rqtl2/rqtl2-qc-job-error.html +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html index b3c3a8f..b3c3a8f 100644 --- a/uploader/templates/rqtl2/rqtl2-qc-job-results.html +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html index f4a6266..f4a6266 100644 --- a/uploader/templates/rqtl2/rqtl2-qc-job-status.html +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html index f126835..f126835 100644 --- a/uploader/templates/rqtl2/rqtl2-qc-job-success.html +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html diff --git a/uploader/templates/populations/rqtl2/select-geno-dataset.html b/uploader/templates/populations/rqtl2/select-geno-dataset.html new file mode 100644 index 0000000..3233abc --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-geno-dataset.html @@ -0,0 +1,69 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Select Genotypes Dataset</h2> + +<div class="row"> + <p>Your R/qtl2 files bundle could contain a "geno" specification. You will + therefore need to select from one of the existing Genotype datasets or + create a new one.</p> + <p>This is the dataset where your data will be organised under.</p> +</div> + +<div class="row"> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('expression-data.rqtl2.select_geno_dataset', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + <legend class="heading">select from existing genotype datasets</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + + {{flash_messages("error-rqtl2-select-geno-dataset")}} + + <div class="form-group"> + <legend>Datasets</legend> + <label for="select:geno-datasets" class="form-label">Dataset</label> + <select id="select:geno-datasets" + name="geno-dataset-id" + required="required" + {%if datasets | length == 0%} + disabled="disabled" + {%endif%} + class="form-control" + aria-describedby="help-geno-dataset-select-dataset"> + <option value="">Select dataset</option> + {%for dset in datasets%} + <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option> + {%endfor%} + </select> + <span id="help-geno-dataset-select-dataset" class="form-text text-muted"> + Select from the existing genotype datasets for species + {{species.SpeciesName}} ({{species.FullName}}). + </span> + </div> + + <button type="submit" class="btn btn-primary">select dataset</button> + </form> +</div> + +<div class="row"> + <p>If the genotype dataset you need does not currently exist for your dataset, + go the <a href="{{url_for( + 'species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Create a new genotypes dataset for {{species.FullName}}"> + genotypes page to create the genotype dataset</a></p> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-population.html b/uploader/templates/populations/rqtl2/select-population.html new file mode 100644 index 0000000..ded425f --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-population.html @@ -0,0 +1,57 @@ +{%extends "expression-data/index.html"%} +{%from "flash_messages.html" import flash_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Select Grouping/Population{%endblock%} + +{%block contents%} +<h1 class="heading">Select grouping/population</h1> + +<div class="row"> + <p>The data is organised in a hierarchical form, beginning with + <em>species</em> at the very top. Under <em>species</em> the data is + organised by <em>population</em>, sometimes referred to as <em>grouping</em>. + (In some really old documents/systems, you might see this referred to as + <em>InbredSet</em>.)</p> + <p>In this section, you get to define what population your data is to be + organised by.</p> +</div> + +<div class="row"> + <form method="POST" + action="{{url_for('expression-data.rqtl2.select_population', + species_id=species.SpeciesId)}}"> + <legend class="heading">select grouping/population</legend> + {{flash_messages("error-select-population")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + + <div class="form-group"> + <label for="select:inbredset" class="form-label">population</label> + <select id="select:inbredset" + name="inbredset_id" + required="required" + class="form-control"> + <option value="">Select a grouping/population</option> + {%for pop in populations%} + <option value="{{pop.InbredSetId}}"> + {{pop.InbredSetName}} ({{pop.FullName}})</option> + {%endfor%} + </select> + <span class="form-text text-muted">Select the population for your data from + the list below.</span> + </div> + + <button type="submit" class="btn btn-primary" />select population</button> +</form> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} + + +{%block javascript%} +{%endblock%} diff --git a/uploader/templates/rqtl2/select-probeset-dataset.html b/uploader/templates/populations/rqtl2/select-probeset-dataset.html index 74f8f69..74f8f69 100644 --- a/uploader/templates/rqtl2/select-probeset-dataset.html +++ b/uploader/templates/populations/rqtl2/select-probeset-dataset.html diff --git a/uploader/templates/rqtl2/select-probeset-study-id.html b/uploader/templates/populations/rqtl2/select-probeset-study-id.html index e3fd9cc..e3fd9cc 100644 --- a/uploader/templates/rqtl2/select-probeset-study-id.html +++ b/uploader/templates/populations/rqtl2/select-probeset-study-id.html diff --git a/uploader/templates/rqtl2/select-tissue.html b/uploader/templates/populations/rqtl2/select-tissue.html index fe3080a..fe3080a 100644 --- a/uploader/templates/rqtl2/select-tissue.html +++ b/uploader/templates/populations/rqtl2/select-tissue.html diff --git a/uploader/templates/rqtl2/summary-info.html b/uploader/templates/populations/rqtl2/summary-info.html index 0adba2e..0adba2e 100644 --- a/uploader/templates/rqtl2/summary-info.html +++ b/uploader/templates/populations/rqtl2/summary-info.html diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html index 9d45c5f..9d45c5f 100644 --- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html +++ b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html index 8210ed0..8210ed0 100644 --- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html +++ b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html 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/rqtl2/create-geno-dataset-success.html b/uploader/templates/rqtl2/create-geno-dataset-success.html deleted file mode 100644 index bb6d63d..0000000 --- a/uploader/templates/rqtl2/create-geno-dataset-success.html +++ /dev/null @@ -1,55 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -<h2 class="heading">Select Genotypes Dataset</h2> - -<div class="explainer"> - <p>You successfully created the genotype dataset with the following - information. - <dl> - <dt>ID</dt> - <dd>{{geno_dataset.id}}</dd> - - <dt>Name</dt> - <dd>{{geno_dataset.name}}</dd> - - <dt>Full Name</dt> - <dd>{{geno_dataset.fname}}</dd> - - <dt>Short Name</dt> - <dd>{{geno_dataset.sname}}</dd> - - <dt>Created On</dt> - <dd>{{geno_dataset.today}}</dd> - - <dt>Public?</dt> - <dd>{%if geno_dataset.public == 0%}No{%else%}Yes{%endif%}</dd> - </dl> - </p> -</div> - -<div class="row"> - <form id="frm-upload-rqtl2-bundle" - action="{{url_for('expression-data.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">select from existing genotype datasets</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" - value="{{geno_dataset.id}}" /> - - <button type="submit" class="btn btn-primary">continue</button> - </form> -</div> - -{%endblock%} diff --git a/uploader/templates/rqtl2/create-probe-dataset-success.html b/uploader/templates/rqtl2/create-probe-dataset-success.html deleted file mode 100644 index 03b75c7..0000000 --- a/uploader/templates/rqtl2/create-probe-dataset-success.html +++ /dev/null @@ -1,59 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -<h2 class="heading">Create ProbeSet Dataset</h2> - -<div class="row"> - <p>You successfully created the ProbeSet dataset with the following - information. - <dl> - <dt>Averaging Method</dt> - <dd>{{avgmethod.Name}}</dd> - - <dt>ID</dt> - <dd>{{dataset.datasetid}}</dd> - - <dt>Name</dt> - <dd>{{dataset.name2}}</dd> - - <dt>Full Name</dt> - <dd>{{dataset.fname}}</dd> - - <dt>Short Name</dt> - <dd>{{dataset.sname}}</dd> - - <dt>Created On</dt> - <dd>{{dataset.today}}</dd> - - <dt>DataScale</dt> - <dd>{{dataset.datascale}}</dd> - </dl> - </p> -</div> - -<div class="row"> - <form id="frm-upload-rqtl2-bundle" - action="{{url_for('expression-data.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">Create ProbeSet dataset</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> - <input type="hidden" name="probe-study-id" value="{{study.Id}}" /> - <input type="hidden" name="probe-dataset-id" value="{{dataset.datasetid}}" /> - - <button type="submit" class="btn btn-primary">continue</button> - </form> -</div> - -{%endblock%} diff --git a/uploader/templates/rqtl2/create-probe-study-success.html b/uploader/templates/rqtl2/create-probe-study-success.html deleted file mode 100644 index e293f6f..0000000 --- a/uploader/templates/rqtl2/create-probe-study-success.html +++ /dev/null @@ -1,49 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -<h2 class="heading">Create ProbeSet Study</h2> - -<div class="row"> - <p>You successfully created the ProbeSet study with the following - information. - <dl> - <dt>ID</dt> - <dd>{{study.id}}</dd> - - <dt>Name</dt> - <dd>{{study.name}}</dd> - - <dt>Full Name</dt> - <dd>{{study.fname}}</dd> - - <dt>Short Name</dt> - <dd>{{study.sname}}</dd> - - <dt>Created On</dt> - <dd>{{study.today}}</dd> - </dl> - </p> - - <form id="frm-upload-rqtl2-bundle" - action="{{url_for('expression-data.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">Create ProbeSet study</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="probe-study-id" value="{{study.studyid}}" /> - - <button type="submit" class="btn btn-primary">continue</button> - </form> -</div> - -{%endblock%} diff --git a/uploader/templates/rqtl2/index.html b/uploader/templates/rqtl2/index.html deleted file mode 100644 index 8ce13bf..0000000 --- a/uploader/templates/rqtl2/index.html +++ /dev/null @@ -1,36 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Data Upload{%endblock%} - -{%block contents%} -<h1 class="heading">R/qtl2 data upload</h1> - -<h2>R/qtl2 Upload</h2> - -<form method="POST" action="{{url_for('expression-data.rqtl2.select_species')}}" - id="frm-rqtl2-upload"> - <legend class="heading">upload R/qtl2 bundle</legend> - {{flash_messages("error-rqtl2")}} - - <div class="form-group"> - <label for="select:species" class="form-label">Species</label> - <select id="select:species" - name="species_id" - required="required" - class="form-control"> - <option value="">Select species</option> - {%for spec in species%} - <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option> - {%endfor%} - </select> - <small class="form-text text-muted"> - Data that you upload to the system should belong to a know species. - Here you can select the species that you wish to upload data for. - </small> - </div> - - <button type="submit" class="btn btn-primary" />submit</button> -</form> - -{%endblock%} diff --git a/uploader/templates/rqtl2/select-geno-dataset.html b/uploader/templates/rqtl2/select-geno-dataset.html deleted file mode 100644 index 1db51e0..0000000 --- a/uploader/templates/rqtl2/select-geno-dataset.html +++ /dev/null @@ -1,144 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -<h2 class="heading">Select Genotypes Dataset</h2> - -<div class="row"> - <p>Your R/qtl2 files bundle contains a "geno" specification. You will - therefore need to select from one of the existing Genotype datasets or - create a new one.</p> - <p>This is the dataset where your data will be organised under.</p> -</div> - -<div class="row"> - <form id="frm-upload-rqtl2-bundle" - action="{{url_for('expression-data.rqtl2.select_geno_dataset', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">select from existing genotype datasets</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - - {{flash_messages("error-rqtl2-select-geno-dataset")}} - - <div class="form-group"> - <legend>Datasets</legend> - <label for="select:geno-datasets" class="form-label">Dataset</label> - <select id="select:geno-datasets" - name="geno-dataset-id" - required="required" - {%if datasets | length == 0%} - disabled="disabled" - {%endif%} - class="form-control" - aria-describedby="help-geno-dataset-select-dataset"> - <option value="">Select dataset</option> - {%for dset in datasets%} - <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option> - {%endfor%} - </select> - <span id="help-geno-dataset-select-dataset" class="form-text text-muted"> - Select from the existing genotype datasets for species - {{species.SpeciesName}} ({{species.FullName}}). - </span> - </div> - - <button type="submit" class="btn btn-primary">select dataset</button> - </form> -</div> - -<div class="row"> - <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> -</div> - -<div class="row"> - <form id="frm-upload-rqtl2-bundle" - action="{{url_for('expression-data.rqtl2.create_geno_dataset', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">create a new genotype dataset</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - - {{flash_messages("error-rqtl2-create-geno-dataset")}} - - <div class="form-group"> - <label for="txt:dataset-name" class="form-label">Name</label> - <input type="text" - id="txt:dataset-name" - name="dataset-name" - maxlength="100" - required="required" - class="form-control" - aria-describedby="help-geno-dataset-name" /> - <span id="help-geno-dataset-name" class="form-text text-muted"> - Provide the new name for the genotype dataset, e.g. "BXDGeno" - </span> - </div> - - <div class="form-group"> - <label for="txt:dataset-fullname" class="form-label">Full Name</label> - <input type="text" - id="txt:dataset-fullname" - name="dataset-fullname" - required="required" - maxlength="100" - class="form-control" - aria-describedby="help-geno-dataset-fullname" /> - - <span id="help-geno-dataset-fullname" class="form-text text-muted"> - Provide a longer name that better describes the genotype dataset, e.g. - "BXD Genotypes" - </span> - </div> - - <div class="form-group"> - <label for="txt:dataset-shortname" class="form-label">Short Name</label> - <input type="text" - id="txt:dataset-shortname" - name="dataset-shortname" - maxlength="100" - class="form-control" - aria-describedby="help-geno-dataset-shortname" /> - - <span id="help-geno-dataset-shortname" class="form-text text-muted"> - Provide a short name for the genotype dataset. This is optional. If not - provided, we'll default to the same value as the "Name" above. - </span> - </div> - - <div class="form-group"> - <input type="checkbox" - id="chk:dataset-public" - name="dataset-public" - checked="checked" - class="form-check" - aria-describedby="help-geno-datasent-public" /> - <label for="chk:dataset-public" class="form-check-label">Public?</label> - - <span id="help-geno-dataset-public" class="form-text text-muted"> - Specify whether the dataset will be available publicly. Check to make the - dataset publicly available and uncheck to limit who can access the dataset. - </span> - </div> - - <button type="submit" class="btn btn-primary">create new dataset</button> - </form> -</div> - -{%endblock%} diff --git a/uploader/templates/rqtl2/select-population.html b/uploader/templates/rqtl2/select-population.html deleted file mode 100644 index 7d27303..0000000 --- a/uploader/templates/rqtl2/select-population.html +++ /dev/null @@ -1,136 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Select Grouping/Population{%endblock%} - -{%block contents%} -<h1 class="heading">Select grouping/population</h1> - -<div class="explainer"> - <p>The data is organised in a hierarchical form, beginning with - <em>species</em> at the very top. Under <em>species</em> the data is - organised by <em>population</em>, sometimes referred to as <em>grouping</em>. - (In some really old documents/systems, you might see this referred to as - <em>InbredSet</em>.)</p> - <p>In this section, you get to define what population your data is to be - organised by.</p> -</div> - -<form method="POST" - action="{{url_for('expression-data.rqtl2.select_population', species_id=species.SpeciesId)}}"> - <legend class="heading">select grouping/population</legend> - {{flash_messages("error-select-population")}} - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - - <div class="form-group"> - <label for="select:inbredset" class="form-label">population</label> - <select id="select:inbredset" - name="inbredset_id" - required="required" - class="form-control"> - <option value="">Select a grouping/population</option> - {%for pop in populations%} - <option value="{{pop.InbredSetId}}"> - {{pop.InbredSetName}} ({{pop.FullName}})</option> - {%endfor%} - </select> - <span class="form-text text-muted">If you are adding data to an already existing - population, simply pick the population from this drop-down selector. If - you cannot find your population from this list, try the form below to - create a new one..</span> - </div> - - <button type="submit" class="btn btn-primary" />select population</button> -</form> - -<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> - -<form method="POST" - action="{{url_for('expression-data.rqtl2.create_population', species_id=species.SpeciesId)}}"> - <legend class="heading">create new grouping/population</legend> - {{flash_messages("error-create-population")}} - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - - <div class="form-group"> - <legend class="heading">mandatory</legend> - - <div class="form-group"> - <label for="txt:inbredset-name" class="form-label">name</label> - <input id="txt:inbredset-name" - name="inbredset_name" - type="text" - required="required" - maxlength="30" - placeholder="Enter grouping/population name" - class="form-control" /> - <span class="form-text text-muted">This is a short name that identifies the - population. Useful for menus, and quick scanning.</span> - </div> - - <div class="form-group"> - <label for="txt:" class="form-label">full name</label> - <input id="txt:inbredset-fullname" - name="inbredset_fullname" - type="text" - required="required" - maxlength="100" - placeholder="Enter the grouping/population's full name" - class="form-control" /> - <span class="form-text text-muted">This can be the same as the name above, or can - be longer. Useful for documentation, and human communication.</span> - </div> - </div> - - <div class="form-group"> - <legend class="heading">optional</legend> - - <div class="form-group"> - <label for="num:public" class="form-label">public?</label> - <select id="num:public" - name="public" - class="form-control"> - <option value="0">0 - Only accessible to authorised users</option> - <option value="1">1 - Publicly accessible to all users</option> - <option value="2" selected> - 2 - Publicly accessible to all users</option> - </select> - <span class="form-text text-muted">This determines whether the - population/grouping will appear on the menus for users.</span> - </div> - - <div class="form-group"> - <label for="txt:inbredset-family" class="form-label">family</label> - <input id="txt:inbredset-family" - name="inbredset_family" - type="text" - placeholder="I am not sure what this is about." - class="form-control" /> - <span class="form-text text-muted">I do not currently know what this is about. - This is a failure on my part to figure out what this is and provide a - useful description. Please feel free to remind me.</span> - </div> - - <div class="form-group"> - <label for="txtarea:" class="form-label">Description</label> - <textarea id="txtarea:description" - name="description" - rows="5" - placeholder="Enter a description of this grouping/population" - class="form-control"></textarea> - <span class="form-text text-muted"> - A long-form description of what the population consists of. Useful for - humans.</span> - </div> - </div> - - <button type="submit" class="btn btn-primary" /> - create grouping/population</button> -</form> - -{%endblock%} - - -{%block javascript%} -{%endblock%} 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/select_species.html b/uploader/templates/select_species.html deleted file mode 100644 index 1642401..0000000 --- a/uploader/templates/select_species.html +++ /dev/null @@ -1,92 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} -{%from "upload_progress_indicator.html" import upload_progress_indicator%} - -{%block title%}expression data: select species{%endblock%} - -{%block contents%} -{{upload_progress_indicator()}} - -<h2 class="heading">expression data: select species</h2> - -<div class="row"> - <form action="{{url_for('expression-data.index.upload_file')}}" - method="POST" - enctype="multipart/form-data" - id="frm-upload-expression-data"> - <legend class="heading">upload expression data</legend> - {{flash_messages("error-expr-data")}} - - <div class="form-group"> - <label for="select_species01" class="form-label">Species</label> - <select id="select_species01" - name="speciesid" - required="required" - class="form-control"> - <option value="">Select species</option> - {%for aspecies in species%} - <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option> - {%endfor%} - </select> - </div> - - <div class="form-group"> - <legend class="heading">file type</legend> - - <div class="form-check"> - <input type="radio" name="filetype" value="average" id="filetype_average" - required="required" class="form-check-input" /> - <label for="filetype_average" class="form-check-label">average</label> - </div> - - <div class="form-check"> - <input type="radio" name="filetype" value="standard-error" - id="filetype_standard_error" required="required" - class="form-check-input" /> - <label for="filetype_standard_error" class="form-check-label"> - standard error - </label> - </div> - </div> - - <div class="form-group"> - <span id="no-file-error" class="alert-danger" style="display: none;"> - No file selected - </span> - <label for="file_upload" class="form-label">select file</label> - <input type="file" name="qc_text_file" id="file_upload" - accept="text/plain, text/tab-separated-values, application/zip" - class="form-control"/> - </div> - - <button type="submit" - class="btn btn-primary" - data-toggle="modal" - data-target="#upload-progress-indicator">upload file</button> - </form> -</div> -{%endblock%} - - -{%block javascript%} -<script type="text/javascript" src="static/js/upload_progress.js"></script> -<script type="text/javascript"> - function setup_formdata(form) { - var formdata = new FormData(); - formdata.append( - "speciesid", - form.querySelector("#select_species01").value) - formdata.append( - "qc_text_file", - form.querySelector("input[type='file']").files[0]); - formdata.append( - "filetype", - selected_filetype( - Array.from(form.querySelectorAll("input[type='radio']")))); - return formdata; - } - - setup_upload_handlers( - "frm-upload-expression-data", make_data_uploader(setup_formdata)); -</script> -{%endblock%} 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-display-species-card.html b/uploader/templates/species/macro-display-species-card.html index 857c0f0..166c7b9 100644 --- a/uploader/templates/species/macro-display-species-card.html +++ b/uploader/templates/species/macro-display-species-card.html @@ -3,13 +3,19 @@ <div class="card-body"> <h5 class="card-title">Species</h5> <div class="card-text"> - <dl> - <dt>Common Name</dt> - <dd>{{species.SpeciesName}}</dd> + <table class="table"> + <tbody> + <tr> + <td>Common Name</td> + <td>{{species.SpeciesName}}</td> + </tr> - <dt>Scientific Name</dt> - <dd>{{species.FullName}}</dd> - </dl> + <tr> + <td>Scientific Name</td> + <td>{{species.FullName}}</td> + </tr> + </tbody> + </table> </div> </div> </div> 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> |