diff options
Diffstat (limited to 'uploader/templates/samples')
| -rw-r--r-- | uploader/templates/samples/select-population.html | 99 | ||||
| -rw-r--r-- | uploader/templates/samples/select-species.html | 30 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-failure.html | 27 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-progress.html | 22 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-samples.html | 139 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-success.html | 18 |
6 files changed, 335 insertions, 0 deletions
diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html new file mode 100644 index 0000000..da19ddc --- /dev/null +++ b/uploader/templates/samples/select-population.html @@ -0,0 +1,99 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Select Grouping/Population{%endblock%} + +{%block contents%} +<h1 class="heading">Select grouping/population</h1> + +<div> + <p>We organise the samples/cases/strains in a hierarchichal form, starting + with <strong>species</strong> at the very top. Under species, we have a + grouping in terms of the relevant population + (e.g. Inbred populations, cell tissue, etc.)</p> +</div> + +<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}}" /> + + <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-control"> + <option value="">Select a grouping/population</option> + {%for pop in populations%} + <option value="{{pop.InbredSetId}}"> + {{pop.InbredSetName}} ({{pop.FullName}})</option> + {%endfor%} + </select> + </div> + + <button type="submit" class="btn btn-primary">select population</button> +</form> + +<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> + +<form method="POST" action="{{url_for('samples.create_population', + species_id=species.SpeciesId)}}"> + <legend class="heading">create new grouping/population</legend> + {{flash_messages("error-create-population")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <div class="form-group"> + <legend>mandatory</legend> + + <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-control" /> + + <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-control" /> + </div> + <div class="form-group"> + <legend>Optional</legend> + + <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-control" /> + + <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" /> + + <label for="txtarea:" class="form-label">Description</label> + <textarea id="txtarea:description" + name="description" + rows="5" + placeholder="Enter a description of this grouping/population" + class="form-control"></textarea> + </div> + + <button type="submit" class="btn btn-primary">create grouping/population</button> +</form> + +{%endblock%} + + +{%block javascript%} +{%endblock%} diff --git a/uploader/templates/samples/select-species.html b/uploader/templates/samples/select-species.html new file mode 100644 index 0000000..edadc61 --- /dev/null +++ b/uploader/templates/samples/select-species.html @@ -0,0 +1,30 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Select Grouping/Population{%endblock%} + +{%block contents%} +<h2 class="heading">upload samples/cases</h2> + +<p>We need to know what species your data belongs to.</p> + +{{flash_all_messages()}} + +<form method="POST" action="{{url_for('samples.select_species')}}"> + <legend class="heading">upload samples</legend> + <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> + </div> + + <button type="submit" class="btn btn-primary">submit</button> +</form> +{%endblock%} diff --git a/uploader/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html new file mode 100644 index 0000000..09e2ecf --- /dev/null +++ b/uploader/templates/samples/upload-failure.html @@ -0,0 +1,27 @@ +{%extends "base.html"%} +{%from "cli-output.html" import cli_output%} + +{%block title%}Samples Upload Failure{%endblock%} + +{%block contents%} +<h1 class="heading">{{job.job_name}}</h2> + +<p>There was a failure attempting to upload the samples.</p> + +<p>Here is some information to help with debugging the issue. Provide this + information to the developer/maintainer.</p> + +<h3>Debugging Information</h3> +<ul> + <li><strong>job id</strong>: {{job.job_id}}</li> + <li><strong>status</strong>: {{job.status}}</li> + <li><strong>job type</strong>: {{job["job-type"]}}</li> +</ul> + +<h4>stdout</h4> +{{cli_output(job, "stdout")}} + +<h4>stderr</h4> +{{cli_output(job, "stderr")}} + +{%endblock%} diff --git a/uploader/templates/samples/upload-progress.html b/uploader/templates/samples/upload-progress.html new file mode 100644 index 0000000..7bb02be --- /dev/null +++ b/uploader/templates/samples/upload-progress.html @@ -0,0 +1,22 @@ +{%extends "base.html"%} +{%from "cli-output.html" import cli_output%} + +{%block extrameta%} +<meta http-equiv="refresh" content="5"> +{%endblock%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} +<h1 class="heading">{{job.job_name}}</h2> + +<p> +<strong>status</strong>: +<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br /> +</p> + +<p>saving to database...</p> + +{{cli_output(job, "stdout")}} + +{%endblock%} diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html new file mode 100644 index 0000000..e62de57 --- /dev/null +++ b/uploader/templates/samples/upload-samples.html @@ -0,0 +1,139 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Upload Samples{%endblock%} + +{%block css%}{%endblock%} + +{%block contents%} +<h1 class="heading">upload samples</h1> + +{{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> + + <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>Alias</dt> + <dd>An alias for the sample. Can be an empty field.</dd> + </dl> +</p> + +<form id="form-samples" + method="POST" + action="{{url_for('samples.upload_samples', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + enctype="multipart/form-data"> + <legend class="heading">upload samples</legend> + + <div class="form-group"> + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <label class="form-label">species:</label> + <span class="form-text">{{species.SpeciesName}} [{{species.MenuName}}]</span> + </div> + + <div class="form-group"> + <input type="hidden" name="inbredset_id" value="{{population.InbredSetId}}" /> + <label class="form-label">grouping/population:</label> + <span class="form-text">{{population.Name}} [{{population.FullName}}]</span> + </div> + + <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> + + <div class="form-group"> + <label for="select:separator" class="form-label">field separator</label> + <select id="select:separator" + name="separator" + required="required" + class="form-control"> + <option value="">Select separator for your file: (default is comma)</option> + <option value="	">TAB</option> + <option value=" ">Space</option> + <option value=",">Comma</option> + <option value=";">Semicolon</option> + <option value="other">Other</option> + </select> + <input id="txt:separator" + type="text" + name="other_separator" + 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-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. + </small> + </div> + + <button type="submit" + class="btn btn-primary">upload samples file</button> +</form> + +<table id="tbl:samples-preview" class="table"> + <caption class="heading">preview content</caption> + + <thead> + <tr> + <th>Name</th> + <th>Name2</th> + <th>Symbol</th> + <th>Alias</th> + </tr> + </thead> + + <tbody> + <tr id="default-row"> + <td colspan="4"> + Please make some selections to preview the data.</td> + </tr> + </tbody> +</table> + +{%endblock%} + + +{%block javascript%} +<script src="/static/js/upload_samples.js" type="text/javascript"></script> +{%endblock%} diff --git a/uploader/templates/samples/upload-success.html b/uploader/templates/samples/upload-success.html new file mode 100644 index 0000000..cb745c3 --- /dev/null +++ b/uploader/templates/samples/upload-success.html @@ -0,0 +1,18 @@ +{%extends "base.html"%} +{%from "cli-output.html" import cli_output%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} +<h1 class="heading">{{job.job_name}}</h2> + +<p> +<strong>status</strong>: +<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br /> +</p> + +<p>Successfully uploaded the samples.</p> + +{{cli_output(job, "stdout")}} + +{%endblock%} |