diff options
Diffstat (limited to 'uploader/templates/samples')
| -rw-r--r-- | uploader/templates/samples/base.html | 12 | ||||
| -rw-r--r-- | uploader/templates/samples/index.html | 23 | ||||
| -rw-r--r-- | uploader/templates/samples/list-samples.html | 130 | ||||
| -rw-r--r-- | uploader/templates/samples/select-population.html | 105 | ||||
| -rw-r--r-- | uploader/templates/samples/select-species.html | 30 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-failure.html | 14 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-progress.html | 15 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-samples.html | 281 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-success.html | 34 |
9 files changed, 382 insertions, 262 deletions
diff --git a/uploader/templates/samples/base.html b/uploader/templates/samples/base.html new file mode 100644 index 0000000..291782b --- /dev/null +++ b/uploader/templates/samples/base.html @@ -0,0 +1,12 @@ +{%extends "populations/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="samples"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.samples.index')}}">Samples</a> +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html new file mode 100644 index 0000000..ee98734 --- /dev/null +++ b/uploader/templates/samples/index.html @@ -0,0 +1,23 @@ +{%extends "samples/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Populations{%endblock%} + +{%block pagetitle%}Populations{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>GeneNetwork has a selection of different species of organisms to choose from. Within those species, there are the populations of interest for a variety of experiments, from which you, the researcher, picked your samples (or individuals or cases) from. Here you can provide some basic details about your samples.</p> + <p>To start off, we will need to know what species and population your samples belong to. Please provide that information in the next sections.</p> + + {{select_species_form(url_for("species.populations.samples.index"), species)}} +</div> +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html new file mode 100644 index 0000000..aed27c3 --- /dev/null +++ b/uploader/templates/samples/list-samples.html @@ -0,0 +1,130 @@ +{%extends "samples/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-select-population.html" import select_population_form%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Samples — List Samples{%endblock%} + +{%block pagetitle%}Samples — List Samples{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="list-samples"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}">List</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p> + You selected the population "{{population.FullName}}" from the + "{{species.FullName}}" species. + </p> +</div> + +<div class="row"> + <p> + <a href="{{url_for('species.populations.samples.upload_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Add samples for population '{{population.FullName}}' from species + '{{species.FullName}}'." + class="btn btn-primary"> + add samples + </a> + </p> +</div> + +{%if samples | length > 0%} +<div class="row"> + <p> + This population already has <strong>{{total_samples}}</strong> + samples/individuals entered. You can explore the list of samples in this + population in the table below. + </p> +</div> + +<div class="row"> + <div class="col-md-2"> + {%if offset > 0:%} + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id, + from=offset-count, + count=count)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + + <div class="col-md-8" style="text-align: center;"> + Samples {{offset}} — {{offset+(count if offset + count < total_samples else total_samples - offset)}} / {{total_samples}} + </div> + + <div class="col-md-2"> + {%if offset + count < total_samples:%} + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id, + from=offset+count, + count=count)}}"> + Next + <span class="glyphicon glyphicon-forward"></span> + </a> + {%endif%} + </div> +</div> +<div class="row"> + <table class="table"> + <thead> + <tr> + <th></th> + <th>Name</th> + <th>Auxilliary Name</th> + <th>Symbol</th> + <th>Alias</th> + </tr> + </thead> + + <tbody> + {%for sample in samples%} + <tr> + <td>{{sample.sequence_number}}</td> + <td>{{sample.Name}}</td> + <td>{{sample.Name2}}</td> + <td>{{sample.Symbol or "-"}}</td> + <td>{{sample.Alias or "-"}}</td> + </tr> + {%endfor%} + </tbody> + </table> + + <p> + <a href="#" + title="Delete samples from population '{{population.FullName}}' from species + '{{species.FullName}}'." + class="btn btn-danger not-implemented"> + delete all samples + </a> + </p> +</div> +{%else%} +<div class="row"> + <p>There are no samples entered for this population. Click the "Add Samples" + button above, to add some new samples.</p> +</div> +{%endif%} + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html index da19ddc..1cc7573 100644 --- a/uploader/templates/samples/select-population.html +++ b/uploader/templates/samples/select-population.html @@ -1,99 +1,26 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} +{%extends "samples/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-select-population.html" import select_population_form%} +{%from "species/macro-display-species-card.html" import display_species_card%} -{%block title%}Select Grouping/Population{%endblock%} +{%block title%}Samples — Select 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")}} +{%block pagetitle%}Samples — Select Population{%endblock%} - <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> +{%block contents%} +{{flash_all_messages()}} +<div class="row"> + {{select_population_form( + url_for("species.populations.samples.select_population", species_id=species.SpeciesId), species, populations)}} +</div> {%endblock%} +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} {%block javascript%} +<script type="text/javascript" src="/static/js/populations.js"></script> {%endblock%} diff --git a/uploader/templates/samples/select-species.html b/uploader/templates/samples/select-species.html deleted file mode 100644 index edadc61..0000000 --- a/uploader/templates/samples/select-species.html +++ /dev/null @@ -1,30 +0,0 @@ -{%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 index 09e2ecf..2cf8053 100644 --- a/uploader/templates/samples/upload-failure.html +++ b/uploader/templates/samples/upload-failure.html @@ -1,10 +1,12 @@ {%extends "base.html"%} {%from "cli-output.html" import cli_output%} +{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Samples Upload Failure{%endblock%} {%block contents%} -<h1 class="heading">{{job.job_name}}</h2> +<div class="row"> +<h2 class="heading">{{job.job_name[0:50]}}…</h2> <p>There was a failure attempting to upload the samples.</p> @@ -13,15 +15,23 @@ <h3>Debugging Information</h3> <ul> - <li><strong>job id</strong>: {{job.job_id}}</li> + <li><strong>job id</strong>: {{job.jobid}}</li> <li><strong>status</strong>: {{job.status}}</li> <li><strong>job type</strong>: {{job["job-type"]}}</li> </ul> +</div> +<div class="row"> <h4>stdout</h4> {{cli_output(job, "stdout")}} +</div> +<div class="row"> <h4>stderr</h4> {{cli_output(job, "stderr")}} +</div> +{%endblock%} +{%block sidebarcontents%} +{{display_population_card(species, population)}} {%endblock%} diff --git a/uploader/templates/samples/upload-progress.html b/uploader/templates/samples/upload-progress.html index 7bb02be..677d457 100644 --- a/uploader/templates/samples/upload-progress.html +++ b/uploader/templates/samples/upload-progress.html @@ -1,5 +1,6 @@ -{%extends "base.html"%} +{%extends "samples/base.html"%} {%from "cli-output.html" import cli_output%} +{%from "populations/macro-display-population-card.html" import display_population_card%} {%block extrameta%} <meta http-equiv="refresh" content="5"> @@ -8,7 +9,8 @@ {%block title%}Job Status{%endblock%} {%block contents%} -<h1 class="heading">{{job.job_name}}</h2> +<div class="row" style="overflow-x: clip;"> +<h2 class="heading">{{job.job_name[0:50]}}…</h2> <p> <strong>status</strong>: @@ -16,7 +18,14 @@ </p> <p>saving to database...</p> +</div> -{{cli_output(job, "stdout")}} +<div class="row"> + {{cli_output(job, "stdout")}} +</div> {%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html index e62de57..6422094 100644 --- a/uploader/templates/samples/upload-samples.html +++ b/uploader/templates/samples/upload-samples.html @@ -1,138 +1,159 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload Samples{%endblock%} - -{%block css%}{%endblock%} +{%extends "samples/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-select-population.html" import select_population_form%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Samples — Upload Samples{%endblock%} + +{%block pagetitle%}Samples — Upload Samples{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="uploade-samples"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.samples.upload_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}">List</a> +</li> +{%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> +{{flash_all_messages()}} + +<div class="row"> + <p> + You can now upload the samples for the "{{population.FullName}}" population + from the "{{species.FullName}}" species here. + </p> + <p> + Upload a <strong>character-separated value (CSV)</strong> file that contains + details about your samples. The CSV file should have the following fields: + <dl> + <dt>Name</dt> + <dd>The primary name/identifier for the sample/individual.</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. This can be a strain name, e.g. 'BXD60' for + species that have strains. This field can be left empty for species like + Humans that do not have strains..</dd> + + <dt>Alias</dt> + <dd>An alias for the sample. Can be an empty field, or take on the same + value as that of the Symbol.</dd> + </dl> + </p> +</div> + +<div class="row"> + <form id="form-samples" + method="POST" + action="{{url_for('species.populations.samples.upload_samples', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + enctype="multipart/form-data"> + <legend class="heading">upload samples</legend> + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" value="{{population.Id}}" /> + + <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, text/plain" + 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> +</div> + +<div class="row"> + <h3>Preview File Content</h3> + + <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 in the form above to preview the data.</td> + </tr> + </tbody> + </table> +</div> {%endblock%} +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} {%block javascript%} <script src="/static/js/upload_samples.js" type="text/javascript"></script> diff --git a/uploader/templates/samples/upload-success.html b/uploader/templates/samples/upload-success.html index cb745c3..881d466 100644 --- a/uploader/templates/samples/upload-success.html +++ b/uploader/templates/samples/upload-success.html @@ -1,18 +1,36 @@ -{%extends "base.html"%} +{%extends "samples/base.html"%} {%from "cli-output.html" import cli_output%} +{%from "populations/macro-display-population-card.html" import display_population_card%} {%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> +<div class="row" style="overflow-x: clip;"> + <h2 class="heading">{{job.job_name[0:50]}}…</h2> -<p>Successfully uploaded the samples.</p> + <p> + <strong>status</strong>: + <span>{{job["status"]}} ({{job.get("message", "-")}})</span><br /> + </p> -{{cli_output(job, "stdout")}} + <p>Successfully uploaded the samples.</p> + <p> + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="View population samples"> + View samples + </a> + </p> +</div> +<div class="row"> + {{cli_output(job, "stdout")}} +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} {%endblock%} |