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-rw-r--r--qc_app/static/css/custom-bootstrap.css4
-rw-r--r--qc_app/static/css/styles.css7
-rw-r--r--qc_app/templates/base.html3
-rw-r--r--qc_app/templates/continue_from_create_dataset.html18
-rw-r--r--qc_app/templates/continue_from_create_study.html18
-rw-r--r--qc_app/templates/errors_display.html2
-rw-r--r--qc_app/templates/index.html214
-rw-r--r--qc_app/templates/insert_error.html32
-rw-r--r--qc_app/templates/insert_progress.html21
-rw-r--r--qc_app/templates/insert_success.html6
-rw-r--r--qc_app/templates/job_progress.html29
-rw-r--r--qc_app/templates/rqtl2/create-geno-dataset-success.html42
-rw-r--r--qc_app/templates/rqtl2/create-probe-dataset-success.html46
-rw-r--r--qc_app/templates/rqtl2/create-probe-study-success.html42
-rw-r--r--qc_app/templates/rqtl2/create-tissue-success.html116
-rw-r--r--qc_app/templates/rqtl2/index.html20
-rw-r--r--qc_app/templates/rqtl2/rqtl2-qc-job-results.html78
-rw-r--r--qc_app/templates/rqtl2/rqtl2-qc-job-success.html34
-rw-r--r--qc_app/templates/rqtl2/select-geno-dataset.html248
-rw-r--r--qc_app/templates/rqtl2/select-population.html148
-rw-r--r--qc_app/templates/rqtl2/select-probeset-dataset.html323
-rw-r--r--qc_app/templates/rqtl2/select-probeset-study-id.html242
-rw-r--r--qc_app/templates/rqtl2/select-tissue.html181
-rw-r--r--qc_app/templates/rqtl2/summary-info.html86
-rw-r--r--qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html20
-rw-r--r--qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html34
-rw-r--r--qc_app/templates/samples/select-population.html54
-rw-r--r--qc_app/templates/samples/select-species.html15
-rw-r--r--qc_app/templates/samples/upload-samples.html132
-rw-r--r--qc_app/templates/select_dataset.html102
-rw-r--r--qc_app/templates/select_platform.html96
-rw-r--r--qc_app/templates/select_study.html61
-rw-r--r--qc_app/templates/stdout_output.html4
33 files changed, 1268 insertions, 1210 deletions
diff --git a/qc_app/static/css/custom-bootstrap.css b/qc_app/static/css/custom-bootstrap.css
new file mode 100644
index 0000000..e5f6594
--- /dev/null
+++ b/qc_app/static/css/custom-bootstrap.css
@@ -0,0 +1,4 @@
+/** Customize some bootstrap selectors **/
+.btn {
+ text-transform: capitalize;
+}
diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
new file mode 100644
index 0000000..a88c229
--- /dev/null
+++ b/qc_app/static/css/styles.css
@@ -0,0 +1,7 @@
+.heading {
+ text-transform: capitalize;
+}
+
+label {
+ text-transform: capitalize;
+}
diff --git a/qc_app/templates/base.html b/qc_app/templates/base.html
index 00ff2d7..91faee8 100644
--- a/qc_app/templates/base.html
+++ b/qc_app/templates/base.html
@@ -14,6 +14,9 @@
<link rel="shortcut icon" type="image/png" sizes="64x64"
href="{{url_for('static', filename='images/CITGLogo.png')}}" />
+ <link rel="stylesheet" type="text/css" href="/static/css/custom-bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="/static/css/styles.css" />
+
{%block css%}{%endblock%}
</head>
diff --git a/qc_app/templates/continue_from_create_dataset.html b/qc_app/templates/continue_from_create_dataset.html
index f95f96f..03bb49c 100644
--- a/qc_app/templates/continue_from_create_dataset.html
+++ b/qc_app/templates/continue_from_create_dataset.html
@@ -20,7 +20,7 @@
{%endif%}
{%endwith%}
-<div class="two-column-with-separator">
+<div class="row">
<form method="POST" action="{{url_for('dbinsert.final_confirmation')}}"
id="select-platform-form" data-genechips="{{genechips_data}}"
class="two-col-sep-col1">
@@ -29,15 +29,15 @@
filename, filetype, species=species, genechipid=genechipid,
studyid=studyid, datasetid=datasetid, totallines=totallines)}}
- <fieldset>
- <input type="submit"
- value="continue"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit" class="btn btn-primary">continue</button>
</form>
+</div>
+<div class="row">
<p class="two-col-sep-separator">OR</p>
+</div>
+<div class="row">
<form method="POST" action="{{url_for('dbinsert.select_dataset')}}"
id="select-platform-form" data-genechips="{{genechips_data}}"
class="two-col-sep-col2">
@@ -46,11 +46,7 @@
filename, filetype, species=species, genechipid=genechipid,
studyid=studyid, datasetid=datasetid, totallines=totallines)}}
- <fieldset>
- <input type="submit"
- value="go back"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit" class="btn btn-primary">go back</button>
</form>
</div>
{%endblock%}
diff --git a/qc_app/templates/continue_from_create_study.html b/qc_app/templates/continue_from_create_study.html
index 7455fbc..34e6e5e 100644
--- a/qc_app/templates/continue_from_create_study.html
+++ b/qc_app/templates/continue_from_create_study.html
@@ -20,7 +20,7 @@
{%endif%}
{%endwith%}
-<div class="two-column-with-separator">
+<div class="row">
<form method="POST" action="{{url_for('dbinsert.select_dataset')}}"
id="select-platform-form" data-genechips="{{genechips_data}}"
class="two-col-sep-col1">
@@ -29,15 +29,15 @@
filename, filetype, species=species, genechipid=genechipid,
studyid=studyid, totallines=totallines)}}
- <fieldset>
- <input type="submit"
- value="continue"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit" class="btn btn-primary">continue</button>
</form>
+</div>
+<div class="row">
<p class="two-col-sep-separator">OR</p>
+</div>
+<div class="row">
<form method="POST" action="{{url_for('dbinsert.select_study')}}"
id="select-platform-form" data-genechips="{{genechips_data}}"
class="two-col-sep-col2">
@@ -46,11 +46,7 @@
filename, filetype, species=species, genechipid=genechipid,
studyid=studyid, totallines=totallines)}}
- <fieldset>
- <input type="submit"
- value="go back"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit" class="btn btn-primary">go back</button>
</form>
</div>
{%endblock%}
diff --git a/qc_app/templates/errors_display.html b/qc_app/templates/errors_display.html
index 0ee5e85..715cfcf 100644
--- a/qc_app/templates/errors_display.html
+++ b/qc_app/templates/errors_display.html
@@ -5,7 +5,7 @@
{%else %}
<p class="alert-danger">{{error_message}}</p>
-<table class="reports-table">
+<table class="table reports-table">
<thead>
<tr>
<th>line number</th>
diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html
index 06d1e87..0d301f5 100644
--- a/qc_app/templates/index.html
+++ b/qc_app/templates/index.html
@@ -5,118 +5,130 @@
{%block title%}Data Upload{%endblock%}
{%block contents%}
-<h1 class="heading">data upload</h1>
-
-<div class="explainer">
- <p>Each of the sections below gives you a different option for data upload.
- Please read the documentation for each section carefully to understand what
- each section is about.</p>
+<div class="row">
+ <h1 class="heading">data upload</h1>
+
+ <div class="explainer">
+ <p>Each of the sections below gives you a different option for data upload.
+ Please read the documentation for each section carefully to understand what
+ each section is about.</p>
+ </div>
</div>
-<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("upload.rqtl2.select_species")}}
- title="Upload a zip bundle of R/qtl2 files">
- <button class="btn btn-primary">upload R/qtl2 bundle</button></a>
+<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("upload.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>
-<h2 class="heading">Expression Data</h2>
-
-<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('entry.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('entry.data_review')}}#file-types"
- title="Details for the data expectations.">Help</a>)</li>
- </ol>
-</div>
-<form action="{{url_for('entry.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")}}
-
- <fieldset>
- <label for="select_species01">Species</label>
- <select id="select_species01"
- name="speciesid"
- required="required">
- <option value="">Select species</option>
- {%for aspecies in species%}
- <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
- {%endfor%}
- </select>
- </fieldset>
-
- <fieldset>
- <legend>file type</legend>
-
- <input type="radio" name="filetype" value="average" id="filetype_average"
- required="required" class="form-col-1" />
- <label for="filetype_average" class="form-col-2">average</label>
-
- <input type="radio" name="filetype" value="standard-error"
- id="filetype_standard_error" required="required"
- class="form-col-1" />
- <label for="filetype_standard_error" class="form-col-2">
- standard error
- </label>
- </fieldset>
-
- <fieldset>
- <span id="no-file-error" class="alert-danger" style="display: none;">
- No file selected
- </span>
- <label for="file_upload" class="form-col-1">select file</label>
- <input type="file" name="qc_text_file" id="file_upload"
- accept="text/plain, text/tab-separated-values, application/zip"
- class="form-col-2"/>
- </fieldset>
-
- <fieldset>
- <input type="submit" value="upload file" class="btn btn-primary form-col-2" />
- </fieldset>
+<div class="row">
+ <h2 class="heading">Expression Data</h2>
+
+ <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('entry.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('entry.data_review')}}#file-types"
+ title="Details for the data expectations.">Help</a>)</li>
+ </ol>
+ </div>
+
+ <form action="{{url_for('entry.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" />upload file</button>
</form>
{{upload_progress_indicator()}}
+</div>
-<h2 class="heading">samples/cases</h2>
+<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>
+ <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("samples.select_species")}}
- title="Upload samples/cases/individuals for your data">
- upload Samples/Cases</a>
+ <a href={{url_for("samples.select_species")}}
+ title="Upload samples/cases/individuals for your data"
+ class="btn btn-primary">upload Samples/Cases</a>
+</div>
{%endblock%}
diff --git a/qc_app/templates/insert_error.html b/qc_app/templates/insert_error.html
index 56dd195..5301288 100644
--- a/qc_app/templates/insert_error.html
+++ b/qc_app/templates/insert_error.html
@@ -5,24 +5,28 @@
{%block contents%}
<h1 class="heading">Insertion Failure</h1>
-<p>
- There was an error inserting data into the database
-</p>
+<div class="row">
+ <p>
+ There was an error inserting data into the database
+ </p>
-<p>
- Please notify the developers of this issue when you encounter it,
- providing the information below.
-</p>
+ <p>
+ Please notify the developers of this issue when you encounter it,
+ providing the information below.
+ </p>
-<h4>Debugging Information</h4>
+ <h4>Debugging Information</h4>
-<ul>
- <li><strong>job id</strong>: {{job["job_id"]}}</li>
-</ul>
+ <ul>
+ <li><strong>job id</strong>: {{job["jobid"]}}</li>
+ </ul>
+</div>
-<h4>STDERR Output</h4>
-<div class="cli-output">
- {{job["stderr"]}}
+<div class="row">
+ <h4>STDERR Output</h4>
+ <pre class="cli-output">
+ {{job["stderr"]}}
+ </pre>
</div>
{%endblock%}
diff --git a/qc_app/templates/insert_progress.html b/qc_app/templates/insert_progress.html
index 0e1a9e0..52177d6 100644
--- a/qc_app/templates/insert_progress.html
+++ b/qc_app/templates/insert_progress.html
@@ -10,8 +10,12 @@
{%block contents%}
<h1 class="heading">{{job_name}}</h1>
-<label for="job_status">status:</label>
-<span>{{job_status}}: {{message}}</span><br />
+<div class="row">
+ <form>
+ <div class="form-group">
+ <label for="job_status" class="form-label">status:</label>
+ <span class="form-text">{{job_status}}: {{message}}</span>
+ </div>
{%if job.get("stdout", "").split("\n\n") | length < 3 %}
{%set lines = 0%}
@@ -25,9 +29,16 @@
{%set fraction = (lines/totallines)%}
{%endif%}
-<label for="job_{{job_id}}">inserting: </label>
-<progress id="jobs_{{job_id}}" value="{{(fraction)}}">{{fraction*100}}</progress>
-<span>{{"%.2f" | format(fraction * 100 | float)}}%</span><br />
+ <div class="form-group">
+ <label for="job_{{job_id}}" class="form-label">inserting: </label>
+ <progress id="jobs_{{job_id}}"
+ value="{{(fraction)}}"
+ class="form-control">{{fraction*100}}</progress>
+ <span class="form-text text-muted">
+ {{"%.2f" | format(fraction * 100 | float)}}%</span>
+ </div>
+ </form>
+</div>
{{stdout_output(job)}}
diff --git a/qc_app/templates/insert_success.html b/qc_app/templates/insert_success.html
index 4406c66..7e1fa8d 100644
--- a/qc_app/templates/insert_success.html
+++ b/qc_app/templates/insert_success.html
@@ -6,10 +6,14 @@
{%block contents%}
<h1 class="heading">Insertion Success</h1>
+<div class="row">
<p>Data inserted successfully!</p>
<p>The following queries were run:</p>
+</div>
-{{stdout_output(job)}}
+<div class="row">
+ {{stdout_output(job)}}
+</div>
{%endblock%}
diff --git a/qc_app/templates/job_progress.html b/qc_app/templates/job_progress.html
index 1b08814..1af0763 100644
--- a/qc_app/templates/job_progress.html
+++ b/qc_app/templates/job_progress.html
@@ -10,21 +10,30 @@
{%block contents%}
<h1 class="heading">{{job_name}}</h2>
-<label for="job_status">status:</label>
-<span>{{job_status}}: {{message}}</span><br />
-
-<label for="job_{{job_id}}">parsing: </label>
-<progress id="job_{{job_id}}" value="{{progress/100}}">{{progress}}</progress>
-<span>{{"%.2f" | format(progress)}}%</span>
-
-<div>
+<div class="row">
<form action="{{url_for('parse.abort')}}" method="POST">
+ <legend class="heading">Status</legend>
+ <div class="form-group">
+ <label for="job_status" class="form-label">status:</label>
+ <span class="form-text">{{job_status}}: {{message}}</span><br />
+ </div>
+
+ <div class="form-group">
+ <label for="job_{{job_id}}" class="form-label">parsing: </label>
+ <progress id="job_{{job_id}}"
+ value="{{progress/100}}"
+ class="form-control">
+ {{progress}}</progress>
+ <span class="form-text text-muted">{{"%.2f" | format(progress)}}%</span>
+ </div>
+
<input type="hidden" name="job_id" value="{{job_id}}" />
- <input type="submit" value="Abort" class="btn btn-danger" />
+
+ <button type="submit" class="btn btn-danger">Abort</button>
</form>
</div>
-<div>
+<div class="row">
{{errors_display(errors, "No errors found so far", "We have found the following errors so far", False)}}
</div>
diff --git a/qc_app/templates/rqtl2/create-geno-dataset-success.html b/qc_app/templates/rqtl2/create-geno-dataset-success.html
index 4333612..1b50221 100644
--- a/qc_app/templates/rqtl2/create-geno-dataset-success.html
+++ b/qc_app/templates/rqtl2/create-geno-dataset-success.html
@@ -31,27 +31,25 @@
</p>
</div>
-<form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.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}}" />
-
- <fieldset>
- <input type="submit"
- value="continue"
- class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+<div class="row">
+ <form id="frm-upload-rqtl2-bundle"
+ action="{{url_for('upload.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/qc_app/templates/rqtl2/create-probe-dataset-success.html b/qc_app/templates/rqtl2/create-probe-dataset-success.html
index 57df449..790d174 100644
--- a/qc_app/templates/rqtl2/create-probe-dataset-success.html
+++ b/qc_app/templates/rqtl2/create-probe-dataset-success.html
@@ -6,7 +6,7 @@
{%block contents%}
<h2 class="heading">Create ProbeSet Dataset</h2>
-<div class="explainer">
+<div class="row">
<p>You successfully created the ProbeSet dataset with the following
information.
<dl>
@@ -34,28 +34,26 @@
</p>
</div>
-<form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.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}}" />
-
- <fieldset>
- <input type="submit"
- value="continue"
- class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+<div class="row">
+ <form id="frm-upload-rqtl2-bundle"
+ action="{{url_for('upload.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/qc_app/templates/rqtl2/create-probe-study-success.html b/qc_app/templates/rqtl2/create-probe-study-success.html
index 5d3d123..d0ee508 100644
--- a/qc_app/templates/rqtl2/create-probe-study-success.html
+++ b/qc_app/templates/rqtl2/create-probe-study-success.html
@@ -6,7 +6,7 @@
{%block contents%}
<h2 class="heading">Create ProbeSet Study</h2>
-<div class="explainer">
+<div class="row">
<p>You successfully created the ProbeSet study with the following
information.
<dl>
@@ -26,28 +26,24 @@
<dd>{{study.today}}</dd>
</dl>
</p>
-</div>
-<form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.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}}" />
-
- <fieldset>
- <input type="submit"
- value="continue"
- class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+ <form id="frm-upload-rqtl2-bundle"
+ action="{{url_for('upload.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/qc_app/templates/rqtl2/create-tissue-success.html b/qc_app/templates/rqtl2/create-tissue-success.html
index 7ea0c65..5f2c5a0 100644
--- a/qc_app/templates/rqtl2/create-tissue-success.html
+++ b/qc_app/templates/rqtl2/create-tissue-success.html
@@ -6,61 +6,18 @@
{%block contents%}
<h2 class="heading">Select Tissue</h2>
-<div class="explainer">
+<div class="row">
<p>You have successfully added a new tissue, organ or biological material with
the following details:</p>
</div>
-{{flash_all_messages()}}
-
-<form id="frm-create-tissue-display"
- method="POST"
- action="#">
- <legend class="heading">Create Tissue</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}}" />
-
- <fieldset>
- <label>Name</label>
- <label>{{tissue.TissueName}}</label>
- </fieldset>
-
- <fieldset>
- <label>Short Name</label>
- <label>{{tissue.Short_Name}}</label>
- </fieldset>
-
- {%if tissue.BIRN_lex_ID%}
- <fieldset>
- <label>BIRN Lex ID</label>
- <label>{{tissue.BIRN_lex_ID}}</label>
- </fieldset>
- {%endif%}
-
- {%if tissue.BIRN_lex_Name%}
- <fieldset>
- <label>BIRN Lex Name</label>
- <label>{{tissue.BIRN_lex_Name}}</label>
- </fieldset>
- {%endif%}
-</form>
-
-<div id="action-buttons"
- style="width:65ch;display:inline-grid;column-gap:5px;">
-
- <form id="frm-create-tissue-success-continue"
+<div class="row">
+ {{flash_all_messages()}}
+
+ <form id="frm-create-tissue-display"
method="POST"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- style="display: inline; width: 100%; grid-column: 1 / 2;
- padding-top: 0.5em; text-align: center; border: none;
- background-color: inherit;">
+ action="#">
+ <legend class="heading">Create Tissue</legend>
<input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
<input type="hidden" name="population_id"
@@ -69,16 +26,63 @@
<input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
<input type="hidden" name="tissueid" value="{{tissue.Id}}" />
- <input type="submit"
- value="continue"
- class="btn btn-primary form-col-2" />
+ <div class="form-group">
+ <label>Name</label>
+ <label>{{tissue.TissueName}}</label>
+ </div>
+
+ <div class="form-group">
+ <label>Short Name</label>
+ <label>{{tissue.Short_Name}}</label>
+ </div>
+
+ {%if tissue.BIRN_lex_ID%}
+ <div class="form-group">
+ <label>BIRN Lex ID</label>
+ <label>{{tissue.BIRN_lex_ID}}</label>
+ </div>
+ {%endif%}
+
+ {%if tissue.BIRN_lex_Name%}
+ <div class="form-group">
+ <label>BIRN Lex Name</label>
+ <label>{{tissue.BIRN_lex_Name}}</label>
+ </div>
+ {%endif%}
</form>
+ <div id="action-buttons"
+ style="width:65ch;display:inline-grid;column-gap:5px;">
+
+ <form id="frm-create-tissue-success-continue"
+ method="POST"
+ action="{{url_for('upload.rqtl2.select_dataset_info',
+ species_id=species.SpeciesId,
+ population_id=population.InbredSetId)}}"
+ style="display: inline; width: 100%; grid-column: 1 / 2;
+ padding-top: 0.5em; text-align: center; border: none;
+ background-color: inherit;">
+
+ <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}}" />
+
+ <button type="submit" class="btn btn-primary">continue</button>
+ </form>
+ </div>
+</div>
+
+<div class="row">
<p style="display:inline;width:100%;grid-column:2/3;text-align:center;
color:#336699;font-weight:bold;">
OR
</p>
+</div>
+<div class="row">
<form id="frm-create-tissue-success-select-existing"
method="POST"
action="{{url_for('upload.rqtl2.select_tissue',
@@ -94,11 +98,9 @@
<input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
<input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="submit"
- value="select from existing tissues"
- class="btn btn-primary form-col-2" />
+ <button type="submit" class="btn btn-primary">
+ select from existing tissues</button>
</form>
-
</div>
{%endblock%}
diff --git a/qc_app/templates/rqtl2/index.html b/qc_app/templates/rqtl2/index.html
index 45018e7..f3329c2 100644
--- a/qc_app/templates/rqtl2/index.html
+++ b/qc_app/templates/rqtl2/index.html
@@ -12,23 +12,25 @@
id="frm-rqtl2-upload">
<legend class="heading">upload R/qtl2 bundle</legend>
{{flash_messages("error-rqtl2")}}
- <fieldset>
- <label for="select:species">Species</label>
- <select id="select:species" name="species_id" required="required">
+
+ <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>
- <span class="form-input-help">
+ <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.
- </span>
- </fieldset>
+ </small>
+ </div>
- <fieldset>
- <input type="submit" value="submit" class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit" class="btn btn-primary" />submit</button>
</form>
{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html
index 35dc95a..59bc8cd 100644
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html
@@ -6,61 +6,61 @@
{%block contents%}
<h1 class="heading">R/qtl2 bundle: QC job results</h1>
-<div class="explainer">
+<div class="row">
<p>The R/qtl2 bundle you uploaded has passed all automated quality-control
checks successfully.</p>
<p>You may now continue to load the data into GeneNetwork for the bundle, with
the following details:</p>
</div>
-<form id="form-qc-job-results"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.Id)}}"
- method="POST">
- <fieldset>
- <legend>Species</legend>
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+<div class="row">
+ <form id="form-qc-job-results"
+ action="{{url_for('upload.rqtl2.select_dataset_info',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}"
+ method="POST">
+ <div class="form-group">
+ <legend>Species</legend>
+ <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <span class="form-col-1">Name</span>
- <span class="form-col-2">{{species.Name | capitalize}}</span>
+ <span class="form-label">Name</span>
+ <span class="form-text">{{species.Name | capitalize}}</span>
- <span class="form-col-1">Scientific</span>
- <span class="form-col-2">{{species.FullName | capitalize}}</span>
- </fieldset>
+ <span class="form-label">Scientific</span>
+ <span class="form-text">{{species.FullName | capitalize}}</span>
+ </div>
- <fieldset>
- <legend>population</legend>
- <input type="hidden" name="population_id" value="{{population.Id}}" />
+ <div class="form-group">
+ <legend>population</legend>
+ <input type="hidden" name="population_id" value="{{population.Id}}" />
- <span class="form-col-1">Name</span>
- <span class="form-col-2">{{population.InbredSetName}}</span>
+ <span class="form-label">Name</span>
+ <span class="form-text">{{population.InbredSetName}}</span>
- <span class="form-col-1">Full Name</span>
- <span class="form-col-2">{{population.FullName}}</span>
+ <span class="form-label">Full Name</span>
+ <span class="form-text">{{population.FullName}}</span>
- <span class="form-col-1">Genetic Type</span>
- <span class="form-col-2">{{population.GeneticType}}</span>
+ <span class="form-label">Genetic Type</span>
+ <span class="form-text">{{population.GeneticType}}</span>
- <span class="form-col-1">Description</span>
- <span class="form-col-2">{{population.Description or "-"}}</span>
- </fieldset>
+ <span class="form-label">Description</span>
+ <span class="form-text">{{population.Description or "-"}}</span>
+ </div>
- <fieldset>
- <legend>R/qtl2 Bundle File</legend>
- <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2bundle}}" />
- <input type="hidden" name="original-filename" value="{{rqtl2bundleorig}}" />
+ <div class="form-group">
+ <legend>R/qtl2 Bundle File</legend>
+ <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2bundle}}" />
+ <input type="hidden" name="original-filename" value="{{rqtl2bundleorig}}" />
- <span class="form-col-1">Original Name</span>
- <span class="form-col-2">{{rqtl2bundleorig}}</span>
+ <span class="form-label">Original Name</span>
+ <span class="form-text">{{rqtl2bundleorig}}</span>
- <span class="form-col-1">Internal Name</span>
- <span class="form-col-2">{{rqtl2bundle[0:25]}}&hellip;</span>
- </fieldset>
+ <span class="form-label">Internal Name</span>
+ <span class="form-text">{{rqtl2bundle[0:25]}}&hellip;</span>
+ </div>
- <fieldset>
- <input type="submit" value="continue" class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+ <button type="submit" class="btn btn-primary">continue</button>
+ </form>
+</div>
{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html b/qc_app/templates/rqtl2/rqtl2-qc-job-success.html
index d492898..2861a04 100644
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-success.html
@@ -6,7 +6,7 @@
{%block contents%}
<h2 class="heading">R/qtl2 Bundle: Quality Control Successful</h2>
-<div class="explainer">
+<div class="row">
<p>The R/qtl2 bundle you uploaded has passed <emph>all</emph> quality control
checks successfully, and is now ready for uploading into the database.</p>
<p>Click "Continue" below to proceed.</p>
@@ -16,22 +16,22 @@
The "action" on this form takes us to the next step, where we can
select all the other data necessary to enter the data into the database.
-->
-<form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- {{flash_all_messages()}}
- <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}}" />
+<div class="row">
+ <form id="frm-upload-rqtl2-bundle"
+ action="{{url_for('upload.rqtl2.select_dataset_info',
+ species_id=species.SpeciesId,
+ population_id=population.InbredSetId)}}"
+ method="POST"
+ enctype="multipart/form-data">
+ {{flash_all_messages()}}
+ <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}}" />
- <fieldset>
- <input type="submit" value="continue" class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+ <button type="submit" class="btn btn-primary">continue</button>
+ </form>
+</div>
{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/qc_app/templates/rqtl2/select-geno-dataset.html
index f092dbc..873f9c3 100644
--- a/qc_app/templates/rqtl2/select-geno-dataset.html
+++ b/qc_app/templates/rqtl2/select-geno-dataset.html
@@ -6,131 +6,139 @@
{%block contents%}
<h2 class="heading">Select Genotypes Dataset</h2>
-<div class="explainer">
+<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>
-<form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.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")}}
-
- <fieldset>
- <legend>Datasets</legend>
- <label for="select:geno-datasets">Dataset</label>
- <select id="select:geno-datasets"
- name="geno-dataset-id"
- required="required"
- {%if datasets | length == 0%}
- disabled="disabled"
- {%endif%}>
- <option value="">Select dataset</option>
- {%for dset in datasets%}
- <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option>
- {%endfor%}
- </select>
- <span class="form-col-2">
- Select from the existing genotype datasets for species
- {{species.SpeciesName}} ({{species.FullName}}).
- </span>
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="select dataset"
- class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
-
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-
-<form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.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")}}
-
- <fieldset>
- <label for="txt:dataset-name">Name</label>
- <input type="text"
- id="txt:dataset-name"
- name="dataset-name"
- maxlength="100"
- required="required" />
- <span class="form-col-2">
- Provide the new name for the genotype dataset, e.g. "BXDGeno"
- </span>
- </fieldset>
-
- <fieldset>
- <label for="txt:dataset-fullname">Full Name</label>
- <input type="text"
- id="txt:dataset-fullname"
- name="dataset-fullname"
- required="required"
- maxlength="100" />
-
- <span class="form-col-2">
- Provide a longer name that better describes the genotype dataset, e.g.
- "BXD Genotypes"
- </span>
- </fieldset>
-
- <fieldset>
- <label for="txt:dataset-shortname">Short Name</label>
- <input type="text"
- id="txt:dataset-shortname"
- name="dataset-shortname"
- maxlength="100" />
-
- <span class="form-col-2">
- 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>
- </fieldset>
-
- <fieldset>
- <input type="checkbox"
- id="chk:dataset-public"
- name="dataset-public"
- checked="checked" />
- <label for="chk:dataset-public">Public?</label>
-
- <span class="form-col-2">
- 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>
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="create new dataset"
- class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+<div class="row">
+ <form id="frm-upload-rqtl2-bundle"
+ action="{{url_for('upload.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('upload.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/qc_app/templates/rqtl2/select-population.html b/qc_app/templates/rqtl2/select-population.html
index 1102805..37731f0 100644
--- a/qc_app/templates/rqtl2/select-population.html
+++ b/qc_app/templates/rqtl2/select-population.html
@@ -22,29 +22,26 @@
{{flash_messages("error-select-population")}}
<input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <fieldset>
- <label for="select:inbredset" class="form-col-1">population</label>
+
+ <div class="form-group">
+ <label for="select:inbredset" class="form-label">population</label>
<select id="select:inbredset"
name="inbredset_id"
required="required"
- class="form-col-2">
+ 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-input-help">If you are adding data to an already existing
+ <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>
- </fieldset>
+ </div>
- <fieldset>
- <input type="submit"
- value="select population"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit" class="btn btn-primary" />select population</button>
</form>
<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
@@ -55,70 +52,81 @@
{{flash_messages("error-create-population")}}
<input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <fieldset>
- <legend>mandatory</legend>
- <label for="txt:inbredset-name" class="form-col-1">name</label>
- <input id="txt:inbredset-name"
- name="inbredset_name"
- type="text"
- required="required"
- maxlength="30"
- placeholder="Enter grouping/population name"
- class="form-col-2" />
- <span class="form-input-help">This is a short name that identifies the
- population. Useful for menus, and quick scanning.</span>
-
- <label for="txt:" class="form-col-1">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-col-2" />
- <span class="form-input-help">This can be the same as the name above, or can
- be longer. Useful for documentation, and human communication.</span>
- </fieldset>
- <fieldset>
- <legend>Optional</legend>
-
- <label for="num:public" class="form-col-1">public?</label>
- <select id="num:public"
- name="public"
- class="form-col-2">
- <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-input-help">This determines whether the
- population/grouping will appear on the menus for users.</span>
-
- <label for="txt:inbredset-family" class="form-col-1">family</label>
- <input id="txt:inbredset-family"
- name="inbredset_family"
- type="text"
- placeholder="I am not sure what this is about."
- class="form-col-2" />
- <span class="form-input-help">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>
-
- <label for="txtarea:" class="form-col-1">Description</label>
+
+ <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-col-2"></textarea>
- <span class="form-input-help">A long-form description of what the population
- consists of. Useful for humans.</span>
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="create grouping/population"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ 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%}
diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html
index c5acb72..26f52ed 100644
--- a/qc_app/templates/rqtl2/select-probeset-dataset.html
+++ b/qc_app/templates/rqtl2/select-probeset-dataset.html
@@ -6,173 +6,186 @@
{%block contents%}
<h2 class="heading">Phenotype(ProbeSet) Dataset</h2>
-<div class="explainer">
+<div class="row">
<p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
file(s). This data needs to be organised under a dataset.</p>
<p>This page gives you the ability to do that.</p>
</div>
{%if datasets | length > 0%}
-<form method="POST"
- action="{{url_for('upload.rqtl2.select_probeset_dataset',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:select-probeset-dataset">
- <legend class="heading">Select from existing ProbeSet datasets</legend>
- {{flash_messages("error-rqtl2")}}
-
- <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="{{probe_study.Id}}" />
-
- <fieldset>
- <label for="select:probe-dataset">Dataset</label>
- <select id="select:probe-dataset"
- name="probe-dataset-id"
- required="required"
- {%if datasets | length == 0%}disabled="disabled"{%endif%}>
- <option value="">Select a dataset</option>
- {%for dataset in datasets%}
- <option value={{dataset.Id}}>
- {{dataset.Name}}
- {%if dataset.FullName%}
- -- ({{dataset.FullName}})
- {%endif%}
- </option>
- {%endfor%}
- </select>
-
- <span class="form-col-2">Select from existing ProbeSet datasets.</span>
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="select dataset"
- class="btn btn-primary form-col-2" />
- </fieldset>
+<div class="row">
+ <form method="POST"
+ action="{{url_for('upload.rqtl2.select_probeset_dataset',
+ species_id=species.SpeciesId, population_id=population.Id)}}"
+ id="frm:select-probeset-dataset">
+ <legend class="heading">Select from existing ProbeSet datasets</legend>
+ {{flash_messages("error-rqtl2")}}
+
+ <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="{{probe_study.Id}}" />
+
+ <div class="form-group">
+ <label class="form-label" for="select:probe-dataset">Dataset</label>
+ <select id="select:probe-dataset"
+ name="probe-dataset-id"
+ required="required"
+ {%if datasets | length == 0%}disabled="disabled"{%endif%}
+ class="form-control"
+ aria-describedby="help-probe-dataset">
+ <option value="">Select a dataset</option>
+ {%for dataset in datasets%}
+ <option value={{dataset.Id}}>
+ {{dataset.Name}}
+ {%if dataset.FullName%}
+ -- ({{dataset.FullName}})
+ {%endif%}
+ </option>
+ {%endfor%}
+ </select>
+
+ <span id="help-probe-dataset" class="form-text text-muted">
+ Select from existing ProbeSet datasets.</span>
+ </div>
+
+ <button type="submit" class="btn btn-primary" />select dataset</button>
</form>
+</div>
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+<div class="row">
+ <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+</div>
{%endif%}
-<div class="explainer">
+<div class="row">
<p>Create an entirely new ProbeSet dataset for your data.</p>
</div>
-<form method="POST"
- action="{{url_for('upload.rqtl2.create_probeset_dataset',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:create-probeset-dataset">
- <legend class="heading">Create a new ProbeSet dataset</legend>
- {{flash_messages("error-rqtl2-create-probeset-dataset")}}
-
- <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="{{probe_study.Id}}" />
-
- <fieldset>
- <label for="select:average">averaging method</label>
- <select id="select:average"
- name="averageid"
- required="required">
- <option value="">Select averaging method</option>
- {%for avgmethod in avgmethods%}
- <option value="{{avgmethod.Id}}">
- {{avgmethod.Name}}
- {%if avgmethod.Normalization%}
- ({{avgmethod.Normalization}})
- {%endif%}
- </option>
- {%endfor%}
- </select>
-
- <span class="form-col-2">
- Select the averaging method used for your data.
- </span>
- </fieldset>
-
- <fieldset>
- <label for="txt:datasetname">Name</label>
- <input type="text" id="txt:datasetname" name="datasetname"
- required="required"
- maxlength="40"
- title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)" />
-
- <span class="form-col-2">
- Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This
- is mandatory <strong>MUST</strong> be provided.
- </span>
- </fieldset>
-
- <fieldset>
- <label for="txt:datasetfullname">Full Name</label>
- <input type="text" id="txt:datasetfullname" name="datasetfullname"
- required="required"
- maxlength="100"
- title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)" />
-
- <span class="form-col-2">
- Provide a longer, more descriptive name for the dataset e.g.
- "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and
- <strong>MUST</strong> be provided.
- </span>
- </fieldset>
-
- <fieldset>
- <label for="txt:datasetshortname">Short Name</label>
- <input type="text" id="txt:datasetshortname" name="datasetshortname"
- maxlength="100"
- title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)" />
-
- <span class="form-col-2">
- Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M".
- This is optional.
- </span>
- </fieldset>
-
- <fieldset>
- <input type="checkbox" id="chk:public" name="datasetpublic"
- checked="checked"
- title="Whether or not the dataset is accessible by the general public." />
- <label for="chk:datasetpublic">Public?</label>
-
- <span class="form-col-2">
- Check to specify that the dataset will be publicly available. Uncheck to
- limit access to the dataset.
- </span>
- </fieldset>
-
- <fieldset>
- <label for="select:datasetdatascale">Data Scale</label>
- <select id="select:datasetdatascale"
- name="datasetdatascale"
- required="required">
- <option value="log2" selected="selected">log2</option>
- <option value="z_score">z_score</option>
- <option value="log2_ratio">log2_ratio</option>
- <option value="linear">linear</option>
- <option value="linear_positive">linear_positive</option>
- </select>
-
- <span class="form-col-2">
- Select from a list of scaling methods.
- </span>
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="create dataset"
- class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+<div class="row">
+ <form method="POST"
+ action="{{url_for('upload.rqtl2.create_probeset_dataset',
+ species_id=species.SpeciesId, population_id=population.Id)}}"
+ id="frm:create-probeset-dataset">
+ <legend class="heading">Create a new ProbeSet dataset</legend>
+ {{flash_messages("error-rqtl2-create-probeset-dataset")}}
+
+ <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="{{probe_study.Id}}" />
+
+ <div class="form-group">
+ <label class="form-label" for="select:average">averaging method</label>
+ <select id="select:average"
+ name="averageid"
+ required="required"
+ class="form-control"
+ aria-describedby="help-average">
+ <option value="">Select averaging method</option>
+ {%for avgmethod in avgmethods%}
+ <option value="{{avgmethod.Id}}">
+ {{avgmethod.Name}}
+ {%if avgmethod.Normalization%}
+ ({{avgmethod.Normalization}})
+ {%endif%}
+ </option>
+ {%endfor%}
+ </select>
+
+ <span id="help-average" class="form-text text-muted">
+ Select the averaging method used for your data.
+ </span>
+ </div>
+
+ <div class="form-group">
+ <label class="form-label" for="txt:datasetname">Name</label>
+ <input type="text" id="txt:datasetname" name="datasetname"
+ required="required"
+ maxlength="40"
+ title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)"
+ class="form-control"
+ aria-describedby="help-dataset-name" />
+
+ <span id="help-dataset-name" class="form-text text-muted">
+ Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This
+ is mandatory <strong>MUST</strong> be provided.
+ </span>
+ </div>
+
+ <div class="form-group">
+ <label class="form-label" for="txt:datasetfullname">Full Name</label>
+ <input type="text" id="txt:datasetfullname" name="datasetfullname"
+ required="required"
+ maxlength="100"
+ title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)"
+ class="form-control"
+ aria-describedby="help-dataset-fullname" />
+
+ <span id="help-dataset-fullname" class="form-text text-muted">
+ Provide a longer, more descriptive name for the dataset e.g.
+ "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and
+ <strong>MUST</strong> be provided.
+ </span>
+ </div>
+
+ <div class="form-group">
+ <label class="form-label" for="txt:datasetshortname">Short Name</label>
+ <input type="text" id="txt:datasetshortname" name="datasetshortname"
+ maxlength="100"
+ title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)"
+ class="form-control"
+ aria-describedby="help-dataset-shortname" />
+
+ <span id="help-dataset-shortname" class="form-text text-muted">
+ Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M".
+ This is optional.
+ </span>
+ </div>
+
+ <div class="form-check">
+ <input type="checkbox" id="chk:public" name="datasetpublic"
+ checked="checked"
+ title="Whether or not the dataset is accessible by the general public."
+ class="form-check-input"
+ aria-describedby="help-public" />
+ <label class="form-check-label" for="chk:datasetpublic">Public?</label>
+
+ <span id="help-public" class="form-text text-muted">
+ Check to specify that the dataset will be publicly available. Uncheck to
+ limit access to the dataset.
+ </span>
+ </div>
+
+ <div class="form-group">
+ <label class="form-label" for="select:datasetdatascale">Data Scale</label>
+ <select id="select:datasetdatascale"
+ name="datasetdatascale"
+ required="required"
+ class="form-control"
+ aria-describedby="help-dataset-datascale">
+ <option value="log2" selected="selected">log2</option>
+ <option value="z_score">z_score</option>
+ <option value="log2_ratio">log2_ratio</option>
+ <option value="linear">linear</option>
+ <option value="linear_positive">linear_positive</option>
+ </select>
+
+ <span id="help-dataset-datascale" class="form-text text-muted">
+ Select from a list of scaling methods.
+ </span>
+ </div>
+
+ <button type="submit" class="btn btn-primary">create dataset</button>
+ </form>
+</div>
{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-probeset-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html
index c387514..b9bf52e 100644
--- a/qc_app/templates/rqtl2/select-probeset-study-id.html
+++ b/qc_app/templates/rqtl2/select-probeset-study-id.html
@@ -6,128 +6,138 @@
{%block contents%}
<h2 class="heading">Phenotype(ProbeSet) Study</h2>
-<div class="explainer">
+<div class="row">
<p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
file(s). This data needs to be organised under a study.</p>
<p>In this page, you can either select from a existing dataset:</p>
+
+ <form method="POST"
+ action="{{url_for('upload.rqtl2.select_probeset_study',
+ species_id=species.SpeciesId, population_id=population.Id)}}"
+ id="frm:select-probeset-study">
+ <legend class="heading">Select from existing ProbeSet studies</legend>
+ {{flash_messages("error-rqtl2-select-probeset-study")}}
+
+ <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}}" />
+
+ <div>
+ <label for="select:probe-study" class="form-label">Study</label>
+ <select id="select:probe-study"
+ name="probe-study-id"
+ required="required"
+ aria-describedby="help-select-probeset-study"
+ {%if studies | length == 0%}disabled="disabled"{%endif%}
+ class="form-control">
+ <option value="">Select a study</option>
+ {%for study in studies%}
+ <option value={{study.Id}}>
+ {{study.Name}}
+ {%if study.FullName%}
+ -- ({{study.FullName}})
+ {%endif%}
+ </option>
+ {%endfor%}
+ </select>
+ <small id="help-select-probeset-study" class="form-text text-muted">
+ Select from existing ProbeSet studies.
+ </small>
+ </div>
+
+ <button type="submit" class="btn btn-primary">select study</button>
+ </form>
</div>
-<form method="POST"
- action="{{url_for('upload.rqtl2.select_probeset_study',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:select-probeset-study">
- <legend class="heading">Select from existing ProbeSet studies</legend>
- {{flash_messages("error-rqtl2-select-probeset-study")}}
-
- <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}}" />
-
- <fieldset>
- <label for="select:probe-study">Study</label>
- <select id="select:probe-study"
- name="probe-study-id"
- required="required"
- {%if studies | length == 0%}disabled="disabled"{%endif%}>
- <option value="">Select a study</option>
- {%for study in studies%}
- <option value={{study.Id}}>
- {{study.Name}}
- {%if study.FullName%}
- -- ({{study.FullName}})
- {%endif%}
- </option>
- {%endfor%}
- </select>
- <span class="form-col-2">Select from existing ProbeSet studies.</span>
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="select study"
- class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
-
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-
-<div class="explainer">
- <p>Create a new ProbeSet dataset below:</p>
+<div class="row">
+ <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
</div>
-<form method="POST"
- action="{{url_for('upload.rqtl2.create_probeset_study',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:create-probeset-study">
- <legend class="heading">Create new ProbeSet study</legend>
-
- {{flash_messages("error-rqtl2-create-probeset-study")}}
-
- <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}}" />
-
- <fieldset>
- <label for="select:platform">Platform</label>
- <select id="select:platform"
- name="platformid"
- required="required"
- {%if platforms | length == 0%}disabled="disabled"{%endif%}>
- <option value="">Select a platform</option>
- {%for platform in platforms%}
- <option value="{{platform.GeneChipId}}">
- {{platform.GeneChipName}} ({{platform.Name}})
- </option>
- {%endfor%}
- </select>
- <span class="form-col-2">Select from a list of known genomics platforms.
- </span>
- </fieldset>
-
- <fieldset>
- <label for="txt:studyname">Study name</label>
- <input type="text" id="txt:studyname" name="studyname"
- placeholder="Name of the study. (Required)"
- required="required"
- maxlength="100" />
- <span class="form-col-2">Provide a name for the study.</span>
- </fieldset>
-
- <fieldset>
- <label for="txt:studyfullname">Full Study Name</label>
- <input type="text" id="txt:studyfullname" name="studyfullname"
- placeholder="Longer name of the study. (Optional)"
- maxlength="100" />
- <span class="form-col-2">
- Provide a longer, more descriptive name for the study. This is optional
- and you can leave it blank.
- </span>
- </fieldset>
-
- <fieldset>
- <label for="txt:studyshortname">Short Study Name</label>
- <input type="text" id="txt:studyshortname" name="studyshortname"
- placeholder="Shorter name of the study. (Optional)"
- maxlength="100" />
- <span class="form-col-2">
- Provide a shorter name for the study. This is optional and you can leave
- it blank.
- </span>
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="create study"
- class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+<div class="row">
+
+ <p>Create a new ProbeSet dataset below:</p>
+
+ <form method="POST"
+ action="{{url_for('upload.rqtl2.create_probeset_study',
+ species_id=species.SpeciesId, population_id=population.Id)}}"
+ id="frm:create-probeset-study">
+ <legend class="heading">Create new ProbeSet study</legend>
+
+ {{flash_messages("error-rqtl2-create-probeset-study")}}
+
+ <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}}" />
+
+ <div>
+ <label for="select:platform" class="form-label">Platform</label>
+ <select id="select:platform"
+ name="platformid"
+ required="required"
+ aria-describedby="help-select-platform"
+ {%if platforms | length == 0%}disabled="disabled"{%endif%}
+ class="form-control">
+ <option value="">Select a platform</option>
+ {%for platform in platforms%}
+ <option value="{{platform.GeneChipId}}">
+ {{platform.GeneChipName}} ({{platform.Name}})
+ </option>
+ {%endfor%}
+ </select>
+ <small id="help-select-platform" class="form-text text-muted">
+ Select from a list of known genomics platforms.
+ </small>
+ </div>
+
+ <div class="form-group">
+ <label for="txt:studyname" class="form-label">Study name</label>
+ <input type="text" id="txt:studyname" name="studyname"
+ placeholder="Name of the study. (Required)"
+ required="required"
+ maxlength="100"
+ class="form-control" />
+ <span class="form-text text-muted" id="help-study-name">
+ Provide a name for the study.</span>
+ </div>
+
+ <div class="form-group">
+ <label for="txt:studyfullname" class="form-label">Full Study Name</label>
+ <input type="text"
+ id="txt:studyfullname"
+ name="studyfullname"
+ placeholder="Longer name of the study. (Optional)"
+ maxlength="100"
+ class="form-control" />
+ <span class="form-text text-muted" id="help-study-full-name">
+ Provide a longer, more descriptive name for the study. This is optional
+ and you can leave it blank.
+ </span>
+ </div>
+
+ <div class="form-group">
+ <label for="txt:studyshortname" class="form-label">Short Study Name</label>
+ <input type="text"
+ id="txt:studyshortname"
+ name="studyshortname"
+ placeholder="Shorter name of the study. (Optional)"
+ maxlength="100"
+ class="form-control" />
+ <span class="form-text text-muted" id="help-study-short-name">
+ Provide a shorter name for the study. This is optional and you can leave
+ it blank.
+ </span>
+ </div>
+
+ <button type="submit" class="btn btn-primary">create study</button>
+ </form>
+</div>
{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-tissue.html b/qc_app/templates/rqtl2/select-tissue.html
index 78d5afe..34e1758 100644
--- a/qc_app/templates/rqtl2/select-tissue.html
+++ b/qc_app/templates/rqtl2/select-tissue.html
@@ -6,107 +6,110 @@
{%block contents%}
<h2 class="heading">Tissue</h2>
-<div class="explainer">
+<div class="row">
<p>The data you are uploading concerns a tissue, cell, organ, or other
biological material used in an experiment.</p>
<p>Select the appropriate biological material below</p>
</div>
{%if tissues | length > 0%}
-<form method="POST"
- action="{{url_for('upload.rqtl2.select_tissue',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:select-probeset-dataset">
- <legend class="heading">Select from existing ProbeSet datasets</legend>
- {{flash_messages("error-select-tissue")}}
-
- <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}}" />
-
- <fieldset>
- <label for="select-tissue">Tissue</label>
- <select id="select-tissue"
- name="tissueid"
- required="required"
- {%if tissues | length == 0%}disabled="disabled"{%endif%}>
- <option value="">Select a tissue</option>
- {%for tissue in tissues%}
- <option value={{tissue.Id}}>
- {{tissue.Name}}
- {%if tissue.Short_Name%}
- -- ({{tissue.Short_Name}})
- {%endif%}
- </option>
- {%endfor%}
- </select>
-
- <span class="form-col-2">Select from existing biological material.</span>
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="use selected"
- class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+<div class="row">
+ <form method="POST"
+ action="{{url_for('upload.rqtl2.select_tissue',
+ species_id=species.SpeciesId, population_id=population.Id)}}"
+ id="frm:select-probeset-dataset">
+ <legend class="heading">Select from existing ProbeSet datasets</legend>
+ {{flash_messages("error-select-tissue")}}
+
+ <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}}" />
+
+ <div class="form-group">
+ <label class="form-label" for="select-tissue">Tissue</label>
+ <select id="select-tissue"
+ name="tissueid"
+ required="required"
+ {%if tissues | length == 0%}disabled="disabled"{%endif%}
+ class="form-control"
+ aria-describedby="help-select-tissue">
+ <option value="">Select a tissue</option>
+ {%for tissue in tissues%}
+ <option value={{tissue.Id}}>
+ {{tissue.Name}}
+ {%if tissue.Short_Name%}
+ -- ({{tissue.Short_Name}})
+ {%endif%}
+ </option>
+ {%endfor%}
+ </select>
+
+ <span id="help-select-tissue" class="form-text text-muted">
+ Select from existing biological material.</span>
+ </div>
+
+ <button type="submit" class="btn btn-primary">use selected</button>
+ </form>
+</div>
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+<div class="row">
+ <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+</div>
{%endif%}
-<div class="explainer">
+<div class="row">
<p>If you cannot find the biological material in the drop-down above, add it
to the system below.</p>
-</div>
-<form method="POST"
- action="{{url_for('upload.rqtl2.create_tissue',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:create-probeset-dataset">
- <legend class="heading">Add new tissue, organ or biological material</legend>
- {{flash_messages("error-create-tissue")}}
-
- <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}}" />
-
- <fieldset>
- <label for="tissue-name">name</label>
- <input type="text"
- id="txt-tissuename"
- name="tissuename"
- required="required"
- title = "A name to identify the tissue, organ or biological material." />
-
- <span class="form-col-2">
- A name to identify the tissue, organ or biological material.
- </span>
- </fieldset>
-
- <fieldset>
- <label for="txt-shortname">short name</label>
- <input type="text" id="txt-tissueshortname" name="tissueshortname"
- required="required"
- maxlength="7"
- title="A short name (e.g. 'Mam') for the biological material." />
-
- <span class="form-col-2">
- Provide a short name for the tissue, organ or biological material used in
- the experiment.
- </span>
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="add new material"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ <form method="POST"
+ action="{{url_for('upload.rqtl2.create_tissue',
+ species_id=species.SpeciesId, population_id=population.Id)}}"
+ id="frm:create-probeset-dataset">
+ <legend class="heading">Add new tissue, organ or biological material</legend>
+ {{flash_messages("error-create-tissue")}}
+
+ <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}}" />
+
+ <div class="form-group">
+ <label class="form-label" for="tissue-name">name</label>
+ <input type="text"
+ id="txt-tissuename"
+ name="tissuename"
+ required="required"
+ title = "A name to identify the tissue, organ or biological material."
+ class="form-control"
+ aria-describedby="help-tissue-name" />
+
+ <span class="form-text text-muted" id="help-tissue-name">
+ A name to identify the tissue, organ or biological material.
+ </span>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-shortname" class="form-label">short name</label>
+ <input type="text" id="txt-tissueshortname" name="tissueshortname"
+ required="required"
+ maxlength="7"
+ title="A short name (e.g. 'Mam') for the biological material."
+ class="form-control"
+ aria-describedby="help-tissue-short-name" />
+
+ <span class="form-text text-muted" id="help-tissue-short-name">
+ Provide a short name for the tissue, organ or biological material used in
+ the experiment.
+ </span>
+ </div>
+
+ <button type="submit" class="btn btn-primary" />add new material</button>
</form>
+</div>
{%endblock%}
diff --git a/qc_app/templates/rqtl2/summary-info.html b/qc_app/templates/rqtl2/summary-info.html
index 8b05578..1be87fa 100644
--- a/qc_app/templates/rqtl2/summary-info.html
+++ b/qc_app/templates/rqtl2/summary-info.html
@@ -6,60 +6,60 @@
{%block contents%}
<h2 class="heading">Summary</h2>
-<div class="explainer">
+<div class="row">
<p>This is the information you have provided to accompany the R/qtl2 bundle
you have uploaded. Please verify the information is correct before
proceeding.</p>
</div>
-<dl>
- <dt>Species</dt>
- <dd>{{species.SpeciesName}} ({{species.FullName}})</dd>
+<div class="row">
+ <dl>
+ <dt>Species</dt>
+ <dd>{{species.SpeciesName}} ({{species.FullName}})</dd>
- <dt>Population</dt>
- <dd>{{population.InbredSetName}}</dd>
+ <dt>Population</dt>
+ <dd>{{population.InbredSetName}}</dd>
- {%if geno_dataset%}
- <dt>Genotype Dataset</dt>
- <dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd>
- {%endif%}
+ {%if geno_dataset%}
+ <dt>Genotype Dataset</dt>
+ <dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd>
+ {%endif%}
- {%if tissue%}
- <dt>Tissue</dt>
- <dd>{{tissue.TissueName}} ({{tissue.Name}}, {{tissue.Short_Name}})</dd>
- {%endif%}
+ {%if tissue%}
+ <dt>Tissue</dt>
+ <dd>{{tissue.TissueName}} ({{tissue.Name}}, {{tissue.Short_Name}})</dd>
+ {%endif%}
- {%if probe_study%}
- <dt>ProbeSet Study</dt>
- <dd>{{probe_study.Name}} ({{probe_study.FullName}})</dd>
- {%endif%}
+ {%if probe_study%}
+ <dt>ProbeSet Study</dt>
+ <dd>{{probe_study.Name}} ({{probe_study.FullName}})</dd>
+ {%endif%}
- {%if probe_dataset%}
- <dt>ProbeSet Dataset</dt>
- <dd>{{probe_dataset.Name2}} ({{probe_dataset.FullName}})</dd>
- {%endif%}
-</dl>
+ {%if probe_dataset%}
+ <dt>ProbeSet Dataset</dt>
+ <dd>{{probe_dataset.Name2}} ({{probe_dataset.FullName}})</dd>
+ {%endif%}
+ </dl>
+</div>
-<form id="frm:confirm-rqtl2bundle-details"
- action="{{url_for('upload.rqtl2.confirm_bundle_details',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">Create ProbeSet dataset</legend>
+<div class="row">
+ <form id="frm:confirm-rqtl2bundle-details"
+ action="{{url_for('upload.rqtl2.confirm_bundle_details',
+ 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="probe-study-id" value="{{probe_study.Id}}" />
- <input type="hidden" name="probe-dataset-id" value="{{probe_dataset.Id}}" />
+ <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="{{probe_study.Id}}" />
+ <input type="hidden" name="probe-dataset-id" value="{{probe_dataset.Id}}" />
- <fieldset>
- <input type="submit"
- value="continue"
- class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+ <button type="submit" class="btn btn-primary">continue</button>
+ </form>
+</div>
{%endblock%}
diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
index cc7c92e..5cf9dfd 100644
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
+++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
@@ -21,13 +21,14 @@
{{flash_all_messages()}}
- <fieldset>
- <legend>file upload</legend>
- <label for="file-rqtl2-bundle">R/qtl2 bundle</label>
+ <div form-group>
+ <legend class="heading">file upload</legend>
+ <label for="file-rqtl2-bundle" class="form-label">R/qtl2 bundle</label>
<input type="file" id="file-rqtl2-bundle" name="rqtl2_bundle_file"
accept="application/zip, .zip"
- required="required" />
- <span class="form-input-help"><p>Provide a valid R/qtl2 zip file here. In
+ required="required"
+ class="form-control" />
+ <span class="form-text text-muted"><p>Provide a valid R/qtl2 zip file here. In
particular, ensure your zip bundle contains exactly one control file and
the corresponding files mentioned in the control file.</p>
<p>The control file can be either a YAML or JSON file. <em>ALL</em> other
@@ -36,12 +37,9 @@
<a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html"
target="_blank">
R/qtl2 file format specifications</a> for more details.</p></span>
- </fieldset>
- <fieldset>
- <input type="submit"
- value="upload R/qtl2 bundle"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ </div>
+
+ <button type="submit" class="btn btn-primary">upload R/qtl2 bundle</button>
</form>
{%endblock%}
diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
index 75f4a96..93b1dc9 100644
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
+++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
@@ -6,30 +6,28 @@
{%block contents%}
<h2 class="heading">Upload R/qtl2 Bundle</h2>
-<div class="explainer">
+<div class="row">
<p>You have successfully uploaded the zipped bundle of R/qtl2 files.</p>
<p>The next step is to select the various extra information we need to figure
out what to do with the data. You will select/create the relevant studies
and/or datasets to organise the data in the steps that follow.</p>
<p>Click "Continue" below to proceed.</p>
-</div>
-<form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- {{flash_all_messages()}}
- <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}}" />
+ <form id="frm-upload-rqtl2-bundle"
+ action="{{url_for('upload.rqtl2.select_dataset_info',
+ species_id=species.SpeciesId,
+ population_id=population.InbredSetId)}}"
+ method="POST"
+ enctype="multipart/form-data">
+ {{flash_all_messages()}}
+ <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}}" />
- <fieldset>
- <input type="submit" value="continue" class="btn btn-primary form-col-2" />
- </fieldset>
-</form>
+ <button type="submit" class="btn btn-primary">continue</button>
+ </form>
+</div>
{%endblock%}
diff --git a/qc_app/templates/samples/select-population.html b/qc_app/templates/samples/select-population.html
index 5d78826..da19ddc 100644
--- a/qc_app/templates/samples/select-population.html
+++ b/qc_app/templates/samples/select-population.html
@@ -13,33 +13,28 @@
(e.g. Inbred populations, cell tissue, etc.)</p>
</div>
-<hr />
-
<form method="POST" action="{{url_for('samples.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}}" />
- <fieldset>
- <label for="select:inbredset" class="form-col-1">grouping/population</label>
+
+ <div class="form-group">
+ <label for="select:inbredset" class="form-label">grouping/population</label>
<select id="select:inbredset"
name="inbredset_id"
required="required"
- class="form-col-2">
+ 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>
- </fieldset>
+ </div>
- <fieldset>
- <input type="submit"
- value="select population"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit" class="btn btn-primary">select population</button>
</form>
<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
@@ -50,54 +45,51 @@
{{flash_messages("error-create-population")}}
<input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <fieldset>
+ <div class="form-group">
<legend>mandatory</legend>
- <label for="txt:inbredset-name" class="form-col-1">name</label>
+
+ <label for="txt:inbredset-name" class="form-label">name</label>
<input id="txt:inbredset-name"
name="inbredset_name"
type="text"
required="required"
placeholder="Enter grouping/population name"
- class="form-col-2" />
+ class="form-control" />
- <label for="txt:" class="form-col-1">full name</label>
+ <label for="txt:" class="form-label">full name</label>
<input id="txt:inbredset-fullname"
name="inbredset_fullname"
type="text"
required = "required"
placeholder="Enter the grouping/population's full name"
- class="form-col-2" />
- </fieldset>
- <fieldset>
+ class="form-control" />
+ </div>
+ <div class="form-group">
<legend>Optional</legend>
- <label for="num:public" class="form-col-1">public?</label>
+ <label for="num:public" class="form-label">public?</label>
<input id="num:public"
name="public"
type="number"
min="0" max="2" value="2"
- class="form-col-2" />
+ class="form-control" />
- <label for="txt:inbredset-family" class="form-col-1">family</label>
+ <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-col-2" />
+ class="form-control" />
- <label for="txtarea:" class="form-col-1">Description</label>
+ <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-col-2"></textarea>
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="create grouping/population"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ class="form-control"></textarea>
+ </div>
+
+ <button type="submit" class="btn btn-primary">create grouping/population</button>
</form>
{%endblock%}
diff --git a/qc_app/templates/samples/select-species.html b/qc_app/templates/samples/select-species.html
index 44c0d4f..edadc61 100644
--- a/qc_app/templates/samples/select-species.html
+++ b/qc_app/templates/samples/select-species.html
@@ -12,18 +12,19 @@
<form method="POST" action="{{url_for('samples.select_species')}}">
<legend class="heading">upload samples</legend>
- <fieldset>
- <label for="select_species02">Species</label>
- <select id="select_species02" name="species_id" required="required">
+ <div class="form-group">
+ <label for="select_species02" class="form-label">Species</label>
+ <select id="select_species02"
+ 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>
- </fieldset>
+ </div>
- <fieldset>
- <input type="submit" value="submit" class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit" class="btn btn-primary">submit</button>
</form>
{%endblock%}
diff --git a/qc_app/templates/samples/upload-samples.html b/qc_app/templates/samples/upload-samples.html
index 29b08f6..e62de57 100644
--- a/qc_app/templates/samples/upload-samples.html
+++ b/qc_app/templates/samples/upload-samples.html
@@ -3,16 +3,7 @@
{%block title%}Upload Samples{%endblock%}
-{%block css%}
-<style type="text/css">
- #form-samples {
- background-color: #D1D1D1;
- }
- #form-samples fieldset:nth-child(odd){
- background-color: white;
- }
-</style>
-{%endblock%}
+{%block css%}{%endblock%}
{%block contents%}
<h1 class="heading">upload samples</h1>
@@ -20,23 +11,23 @@
{{flash_messages("alert-success")}}
<p>You can now upload a character-separated value (CSV) file that contains
- details about your samples. The CSV file should have the following fields:
- <dl>
- <dt>Name</dt>
- <dd>The primary name for the sample</dd>
+ details about your samples. The CSV file should have the following fields:
+ <dl>
+ <dt>Name</dt>
+ <dd>The primary name for the sample</dd>
- <dt>Name2</dt>
- <dd>A secondary name for the sample. This can simply be the same as
- <strong>Name</strong> above. This field <strong>MUST</strong> contain a
- value.</dd>
+ <dt>Name2</dt>
+ <dd>A secondary name for the sample. This can simply be the same as
+ <strong>Name</strong> above. This field <strong>MUST</strong> contain a
+ value.</dd>
- <dt>Symbol</dt>
- <dd>A symbol for the sample. Can be an empty field.</dd>
+ <dt>Symbol</dt>
+ <dd>A symbol for the sample. Can be an empty field.</dd>
- <dt>Alias</dt>
- <dd>An alias for the sample. Can be an empty field.</dd>
- </dl>
- </p>
+ <dt>Alias</dt>
+ <dd>An alias for the sample. Can be an empty field.</dd>
+ </dl>
+</p>
<form id="form-samples"
method="POST"
@@ -45,32 +36,32 @@
population_id=population.InbredSetId)}}"
enctype="multipart/form-data">
<legend class="heading">upload samples</legend>
- <fieldset>
+
+ <div class="form-group">
<input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <label class="form-col-1">species:</label>
- <span class="form-col-2">{{species.SpeciesName}} [{{species.MenuName}}]</span>
- </fieldset>
+ <label class="form-label">species:</label>
+ <span class="form-text">{{species.SpeciesName}} [{{species.MenuName}}]</span>
+ </div>
- <fieldset>
+ <div class="form-group">
<input type="hidden" name="inbredset_id" value="{{population.InbredSetId}}" />
- <label class="form-col-1">grouping/population:</label>
- <span class="form-col-2">{{population.Name}} [{{population.FullName}}]</span>
- </fieldset>
+ <label class="form-label">grouping/population:</label>
+ <span class="form-text">{{population.Name}} [{{population.FullName}}]</span>
+ </div>
- <fieldset>
- <input id="chk:heading"
- type="checkbox"
- name="first_line_heading"
- class="form-col-1" />
- <label for="chk:heading" class="form-col-2">first line is a heading?</label>
- </fieldset>
+ <div class="form-group">
+ <label for="file-samples" class="form-label">select file</label>
+ <input type="file" name="samples_file" id="file:samples"
+ accept="text/csv, text/tab-separated-values"
+ class="form-control" />
+ </div>
- <fieldset>
- <label for="select:separator" class="form-col-1">field separator</label>
+ <div class="form-group">
+ <label for="select:separator" class="form-label">field separator</label>
<select id="select:separator"
name="separator"
required="required"
- class="form-col-2">
+ class="form-control">
<option value="">Select separator for your file: (default is comma)</option>
<option value="&#x0009;">TAB</option>
<option value="&#x0020;">Space</option>
@@ -81,43 +72,46 @@
<input id="txt:separator"
type="text"
name="other_separator"
- class="form-col-2" />
- <span class="form-col-2">
- This is the character that separates the fields in your CSV file. If you
- select "<strong>Other</strong>", then you must provide the separator in
- the text field provided.
- </span>
- </fieldset>
-
- <fieldset>
- <label for="txt:delimiter" class="form-col-1">field delimiter</label>
+ class="form-control" />
+ <small class="form-text text-muted">
+ If you select '<strong>Other</strong>' for the field separator value,
+ enter the character that separates the fields in your CSV file in the form
+ field below.
+ </small>
+ </div>
+
+ <div class="form-group form-check">
+ <input id="chk:heading"
+ type="checkbox"
+ name="first_line_heading"
+ class="form-check-input" />
+ <label for="chk:heading" class="form-check-label">
+ first line is a heading?</label>
+ <small class="form-text text-muted">
+ Select this if the first line in your file contains headings for the
+ columns.
+ </small>
+ </div>
+
+ <div class="form-group">
+ <label for="txt:delimiter" class="form-label">field delimiter</label>
<input id="txt:delimiter"
type="text"
name="field_delimiter"
maxlength="1"
- class="form-col-2" />
- <span class="form-col-2">
+ class="form-control" />
+ <small class="form-text text-muted">
If there is a character delimiting the string texts within particular
fields in your CSV, provide the character here. This can be left blank if
no such delimiters exist in your file.
- </span>
- </fieldset>
+ </small>
+ </div>
- <fieldset>
- <label for="file:samples" class="form-col-1">select file</label>
- <input type="file" name="samples_file" id="file:samples"
- accept="text/csv, text/tab-separated-values"
- class="form-col-2" />
- </fieldset>
-
- <fieldset>
- <input type="submit"
- value="upload samples file"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit"
+ class="btn btn-primary">upload samples file</button>
</form>
-<table id="tbl:samples-preview">
+<table id="tbl:samples-preview" class="table">
<caption class="heading">preview content</caption>
<thead>
diff --git a/qc_app/templates/select_dataset.html b/qc_app/templates/select_dataset.html
index 3c9bd6b..2f07de8 100644
--- a/qc_app/templates/select_dataset.html
+++ b/qc_app/templates/select_dataset.html
@@ -10,17 +10,17 @@
{%block contents%}
<h2 class="heading">{{filename}}: select dataset</h2>
-<div class="two-column-with-separator">
+<div class="row">
<form method="POST" action="{{url_for('dbinsert.final_confirmation')}}"
id="select-dataset-form" class="two-col-sep-col1">
- <legend>choose existing dataset</legend>
+ <legend class="heading">choose existing dataset</legend>
{{hidden_fields(
filename, filetype, species=species, genechipid=genechipid,
studyid=studyid, totallines=totallines)}}
- <fieldset>
- <label for="datasetid" class="form-col-1">dataset:</label>
- <select id="datasetid" name="datasetid" class="form-col-2"
+ <div class="form-group">
+ <label for="datasetid" class="form-label">dataset:</label>
+ <select id="datasetid" name="datasetid" class="form-control"
{%if datasets | length == 0:%}
disabled="disabled"
{%endif%}>
@@ -30,23 +30,24 @@
</option>
{%endfor%}
</select>
- </fieldset>
+ </div>
- <fieldset>
- <input type="submit" class="btn btn-primary form-col-2"
- value="update database"
- {%if datasets | length == 0:%}
- disabled="disabled"
- {%endif%} />
- </fieldset>
- </form>
+ <button type="submit" class="btn btn-primary"
+ {%if datasets | length == 0:%}
+ disabled="disabled"
+ {%endif%} />update database</button>
+</form>
+</div>
+<div class="row">
<p class="two-col-sep-separator">OR</p>
+</div>
+<div class="row">
<form method="POST" id="create-dataset-form"
action="{{url_for('dbinsert.create_dataset')}}"
class="two-col-sep-col2">
- <legend>create new dataset</legend>
+ <legend class="heading">create new dataset</legend>
{{hidden_fields(
filename, filetype, species=species, genechipid=genechipid,
studyid=studyid, totallines=totallines)}}
@@ -61,9 +62,9 @@
{%endif%}
{%endwith%}
- <fieldset>
- <label for="avgid" class="form-col-1">average:</label>
- <select id="avgid" name="avgid" required="required" class="form-col-2">
+ <div class="form-group">
+ <label for="avgid" class="form-label">average:</label>
+ <select id="avgid" name="avgid" required="required" class="form-control">
<option value="">Select averaging method</option>
{%for method in avgmethods:%}
<option value="{{method['AvgMethodId']}}"
@@ -74,46 +75,46 @@
</option>
{%endfor%}
</select>
- </fieldset>
+ </div>
- <fieldset>
- <label for="datasetname" class="form-col-1">name:</label>
+ <div class="form-group">
+ <label for="datasetname" class="form-label">name:</label>
<input id="datasetname" name="datasetname" type="text"
- class="form-col-2"
+ class="form-control"
{%if datasetname is defined %}
value="{{datasetname}}"
{%endif%} />
- </fieldset>
+ </div>
- <fieldset>
- <label for="datasetname2" class="form-col-1">name 2:</label>
+ <div class="form-group">
+ <label for="datasetname2" class="form-label">name 2:</label>
<input id="datasetname2" name="datasetname2" type="text"
- required="required" class="form-col-2"
+ required="required" class="form-control"
{%if datasetname2 is defined %}
value="{{datasetname2}}"
{%endif%} />
- </fieldset>
+ </div>
- <fieldset>
- <label for="datasetfullname" class="form-col-1">full name:</label>
+ <div class="form-group">
+ <label for="datasetfullname" class="form-label">full name:</label>
<input id="datasetfullname" name="datasetfullname" type="text"
- required="required" class="form-col-2"
+ required="required" class="form-control"
{%if datasetfullname is defined %}
value="{{datasetfullname}}"
{%endif%} />
- </fieldset>
+ </div>
- <fieldset>
- <label for="datasetshortname" class="form-col-1">short name:</label>
+ <div class="form-group">
+ <label for="datasetshortname" class="form-label">short name:</label>
<input id="datasetshortname" name="datasetshortname" type="text"
- required="required" class="form-col-2"
+ required="required" class="form-control"
{%if datasetshortname is defined %}
value="{{datasetshortname}}"
{%endif%} />
- </fieldset>
+ </div>
- <fieldset>
- <label for="datasetpublic" class="form-col-1">public:</label>
+ <div class="form-group">
+ <label for="datasetpublic" class="form-label">public:</label>
<input id="datasetpublic" name="datasetpublic" type="number"
required="required" min="0" max="2"
{%if datasetpublic is defined %}
@@ -121,10 +122,10 @@
{%else%}
value="0"
{%endif%}
- class="form-col-2" />
- </fieldset>
+ class="form-control" />
+ </div>
- <fieldset>
+ <div class="form-group">
<label for="datasetconfidentiality">confidentiality:</label>
<input id="datasetconfidentiality" name="datasetconfidentiality"
type="number" required="required" min="0" max="2"
@@ -133,12 +134,12 @@
{%else%}
value="0"
{%endif%}
- class="form-col-2" />
- </fieldset>
+ class="form-control" />
+ </div>
- <fieldset>
- <label for="datasetdatascale" class="form-col-1">data scale:</label>
- <select id="datasetdatascale" name="datasetdatascale" class="form-col-2">
+ <div class="form-group">
+ <label for="datasetdatascale" class="form-label">data scale:</label>
+ <select id="datasetdatascale" name="datasetdatascale" class="form-control">
<option value="">None</option>
{%for dscale in datascales:%}
<option value="{{dscale}}"
@@ -151,17 +152,10 @@
</option>
{%endfor%}
</select>
- </fieldset>
+ </div>
- <fieldset>
- <input type="submit" value="create new dataset"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit" class="btn btn-primary">create new dataset</button>
</form>
-
</div>
{%endblock%}
-
-{%block javascript%}
-{%endblock%}
diff --git a/qc_app/templates/select_platform.html b/qc_app/templates/select_platform.html
index d69a970..d9bc68f 100644
--- a/qc_app/templates/select_platform.html
+++ b/qc_app/templates/select_platform.html
@@ -5,58 +5,58 @@
{%block contents%}
<h2 class="heading">{{filename}}: select platform</h2>
-<form method="POST" action="{{url_for('dbinsert.select_study')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}">
- <input type="hidden" name="filename" value="{{filename}}" />
- <input type="hidden" name="filetype" value="{{filetype}}" />
- <input type="hidden" name="totallines" value="{{totallines}}" />
+<div class="row">
+ <form method="POST" action="{{url_for('dbinsert.select_study')}}"
+ id="select-platform-form" data-genechips="{{genechips_data}}">
+ <input type="hidden" name="filename" value="{{filename}}" />
+ <input type="hidden" name="filetype" value="{{filetype}}" />
+ <input type="hidden" name="totallines" value="{{totallines}}" />
- <fieldset>
- <label for="species" class="form-col-1">species</label>
- <select id="species" name="species" class="form-col-2">
- {%for row in species:%}
- <option value="{{row['SpeciesId']}}"
- {%if row["Name"] == default_species:%}
- selected="selected"
- {%endif%}>
- {{row["MenuName"]}}
- </option>
- {%endfor%}
- </select>
- </fieldset>
+ <div class="form-group">
+ <label for="species" class="form-label">species</label>
+ <select id="species" name="species" class="form-control">
+ {%for row in species:%}
+ <option value="{{row['SpeciesId']}}"
+ {%if row["Name"] == default_species:%}
+ selected="selected"
+ {%endif%}>
+ {{row["MenuName"]}}
+ </option>
+ {%endfor%}
+ </select>
+ </div>
- <table id="genechips-table">
- <thead>
- <tr>
- <th>Select</th>
- <th>GeneChip ID</th>
- <th>GeneChip Name</th>
- </tr>
- </thead>
+ <table id="genechips-table" class="table">
+ <caption>select platform</caption>
+ <thead>
+ <tr>
+ <th>Select</th>
+ <th>GeneChip ID</th>
+ <th>GeneChip Name</th>
+ </tr>
+ </thead>
- <tbody>
- {%for chip in genechips:%}
- <tr>
- <td>
- <input type="radio" name="genechipid" value="{{chip['GeneChipId']}}"
- required="required" />
- </td>
- <td>{{chip["GeneChipId"]}}</td>
- <td>{{chip["GeneChipName"]}}</td>
- </tr>
- {%else%}
- <tr>
- <td colspan="5">No chips found for selected species</td>
- </tr>
- {%endfor%}
- </tbody>
- </table>
+ <tbody>
+ {%for chip in genechips:%}
+ <tr>
+ <td>
+ <input type="radio" name="genechipid" value="{{chip['GeneChipId']}}"
+ required="required" />
+ </td>
+ <td>{{chip["GeneChipId"]}}</td>
+ <td>{{chip["GeneChipName"]}}</td>
+ </tr>
+ {%else%}
+ <tr>
+ <td colspan="5">No chips found for selected species</td>
+ </tr>
+ {%endfor%}
+ </tbody>
+ </table>
- <fieldset>
- <input type="submit" class="btn btn-primary form-col-2"
- value="submit platform" />
- </fieldset>
-</form>
+ <button type="submit" class="btn btn-primary">submit platform</button>
+ </form>
+</div>
{%endblock%}
{%block javascript%}
diff --git a/qc_app/templates/select_study.html b/qc_app/templates/select_study.html
index e474c50..648ad4c 100644
--- a/qc_app/templates/select_study.html
+++ b/qc_app/templates/select_study.html
@@ -10,34 +10,36 @@
{%block contents%}
<h2 class="heading">{{filename}}: select study</h2>
-<div class="two-column-with-separator">
+<div class="row">
<form method="POST" action="{{url_for('dbinsert.select_dataset')}}"
id="select-platform-form" data-genechips="{{genechips_data}}"
class="two-col-sep-col1">
- <legend>Select from existing study</legend>
+ <legend class="heading">Select from existing study</legend>
{{hidden_fields(filename, filetype, species=species, genechipid=genechipid,
totallines=totallines)}}
- <fieldset>
- <label for="study" class="form-col-1">study:</label>
- <select id="study" name="studyid" class="form-col-2">
+ <div class="form-group">
+ <label class="form-label" for="study">study:</label>
+ <select id="study" name="studyid" class="form-control">
{%for study in studies:%}
<option value="{{study['Id']}}">{{study["Name"]}}</option>
{%endfor%}
</select>
- </fieldset>
+ </div>
- <fieldset>
- <input type="submit" value="submit selected study"
- class="btn btn-primary form-col-2"
- {%if studies | length == 0:%}
- disabled="disabled"
- {%endif%} />
- </fieldset>
- </form>
+ <button type="submit"
+ class="btn btn-primary"
+ {%if studies | length == 0:%}
+ disabled="disabled"
+ {%endif%} />submit selected study</button>
+</form>
+</div>
+<div class="row">
<p class="two-col-sep-separator">OR</p>
+</div>
+<div class="row">
<form method="POST" action="{{url_for('dbinsert.create_study')}}"
id="select-platform-form" data-genechips="{{genechips_data}}"
class="two-col-sep-col2">
@@ -50,22 +52,22 @@
</ul>
{%endif%}
{%endwith%}
- <legend>Create new study</legend>
+ <legend class="heading">Create new study</legend>
{{hidden_fields(filename, filetype, species=species, genechipid=genechipid,
totallines=totallines)}}
- <fieldset>
- <label for="studyname" class="form-col-1">name:</label>
- <input type="text" id="studyname" name="studyname" class="form-col-2"
+ <div class="form-group">
+ <label class="form-label" for="studyname">name:</label>
+ <input type="text" id="studyname" name="studyname" class="form-control"
required="required"
{%if studyname:%}
value="{{studyname}}"
{%endif%} />
- </fieldset>
+ </div>
- <fieldset>
- <label for="group" class="form-col-1">group:</label>
- <select id="group" name="inbredsetid" class="form-col-2"
+ <div class="form-group">
+ <label class="form-label" for="group">group:</label>
+ <select id="group" name="inbredsetid" class="form-control"
required="required">
<option value="">Select group</option>
{%for family in groups:%}
@@ -81,11 +83,11 @@
</optgroup>
{%endfor%}
</select>
- </fieldset>
+ </div>
- <fieldset>
- <label for="tissue" class="form-col-1">tissue:</label>
- <select id="tissue" name="tissueid" class="form-col-2"
+ <div class="form-group">
+ <label class="form-label" for="tissue">tissue:</label>
+ <select id="tissue" name="tissueid" class="form-control"
required="required">
<option value="">Select type</option>
{%for tissue in tissues:%}
@@ -97,12 +99,9 @@
</option>
{%endfor%}
</select>
- </fieldset>
+ </div>
- <fieldset>
- <input type="submit" value="create study"
- class="btn btn-primary form-col-2" />
- </fieldset>
+ <button type="submit" class="btn btn-primary">create study</button>
</form>
</div>
diff --git a/qc_app/templates/stdout_output.html b/qc_app/templates/stdout_output.html
index f3fcde5..85345a9 100644
--- a/qc_app/templates/stdout_output.html
+++ b/qc_app/templates/stdout_output.html
@@ -2,9 +2,7 @@
<h4>STDOUT Output</h4>
<div class="cli-output">
- {%for line in job.get("stdout", "").split("\n\n"):%}
- <p>{{line}}</p>
- {%endfor%}
+ <pre>{{job.get("stdout", "")}}</pre>
</div>
{%endmacro%}