diff options
Diffstat (limited to 'uploader/templates/samples')
| -rw-r--r-- | uploader/templates/samples/index.html | 4 | ||||
| -rw-r--r-- | uploader/templates/samples/list-samples.html | 38 | ||||
| -rw-r--r-- | uploader/templates/samples/select-population.html | 23 | ||||
| -rw-r--r-- | uploader/templates/samples/sui-base.html | 25 | ||||
| -rw-r--r-- | uploader/templates/samples/sui-list-samples.html | 98 | ||||
| -rw-r--r-- | uploader/templates/samples/sui-upload-failure.html | 32 | ||||
| -rw-r--r-- | uploader/templates/samples/sui-upload-progress.html | 26 | ||||
| -rw-r--r-- | uploader/templates/samples/sui-upload-samples.html | 153 | ||||
| -rw-r--r-- | uploader/templates/samples/sui-upload-success.html | 31 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-failure.html | 2 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-samples.html | 18 |
11 files changed, 402 insertions, 48 deletions
diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html index ee4a63e..ee98734 100644 --- a/uploader/templates/samples/index.html +++ b/uploader/templates/samples/index.html @@ -17,3 +17,7 @@ {{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 index 13e5cec..aed27c3 100644 --- a/uploader/templates/samples/list-samples.html +++ b/uploader/templates/samples/list-samples.html @@ -29,6 +29,19 @@ </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> @@ -73,7 +86,7 @@ <table class="table"> <thead> <tr> - <th>#</th> + <th></th> <th>Name</th> <th>Auxilliary Name</th> <th>Symbol</th> @@ -96,32 +109,17 @@ <p> <a href="#" - title="Add samples for population '{{population.FullName}}' from species + title="Delete samples from population '{{population.FullName}}' from species '{{species.FullName}}'." - class="btn btn-danger"> + 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. Do please go ahead and add - the samples for this population by clicking on the button below. - </p> - - <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> + <p>There are no samples entered for this population. Click the "Add Samples" + button above, to add some new samples.</p> </div> {%endif%} diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html index f437780..1cc7573 100644 --- a/uploader/templates/samples/select-population.html +++ b/uploader/templates/samples/select-population.html @@ -12,28 +12,15 @@ {{flash_all_messages()}} <div class="row"> - <p>You have selected "{{species.FullName}}" as the species that your data relates to.</p> - <p>Next, we need information regarding the population your data relates to. Do please select the population from the existing ones below</p> -</div> - -<div class="row"> {{select_population_form( - url_for("species.populations.samples.select_population", species_id=species.SpeciesId), - populations)}} -</div> - -<div class="row"> - <p> - If you cannot find the population your data relates to in the drop-down - above, you might want to - <a href="{{url_for('species.populations.create_population', - species_id=species.SpeciesId)}}" - title="Create a new population for species '{{species.FullName}},"> - add a new population to GeneNetwork</a> - instead. + 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/sui-base.html b/uploader/templates/samples/sui-base.html new file mode 100644 index 0000000..8ec7505 --- /dev/null +++ b/uploader/templates/samples/sui-base.html @@ -0,0 +1,25 @@ +{%extends "populations/sui-base.html"%} +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species['SpeciesId'], + population_id=population.Id)}}"> + Samples + </a> +</li> +{%endblock%} + +{%block contents%} +<div class="row"> + <h2 class="heading">{{population.FullName}} ({{population.Name}})</h2> +</div> +{%endblock%} + + + +{%block sidebarcontents%} +{{display_sui_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/samples/sui-list-samples.html b/uploader/templates/samples/sui-list-samples.html new file mode 100644 index 0000000..e9ed71a --- /dev/null +++ b/uploader/templates/samples/sui-list-samples.html @@ -0,0 +1,98 @@ +{%extends "samples/sui-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-select-population.html" import select_population_form%} + +{%block title%}Samples — List Samples{%endblock%} + +{%block contents%} +{{super()}} + +<div class="row"> + <h3 class="subheading">manage samples</h3> + {{flash_all_messages()}} +</div> + +<div class="row"> + <div class="col"> + <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 new samples</a> + </div> +</div> + +{%if samples | length > 0%} +<div class="row"> + <p> + Population "{{population.FullName}} ({{population.Name}})" already has + <strong>{{total_samples}}</strong> samples/individuals entered. You can + explore the list of samples 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> +</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%} diff --git a/uploader/templates/samples/sui-upload-failure.html b/uploader/templates/samples/sui-upload-failure.html new file mode 100644 index 0000000..d950c50 --- /dev/null +++ b/uploader/templates/samples/sui-upload-failure.html @@ -0,0 +1,32 @@ +{%extends "sui-base.html"%} +{%from "cli-output.html" import cli_output%} + +{%block title%}Samples Upload Failure{%endblock%} + +{%block contents%} +<div class="row"> +<h2 class="heading">{{job.job_name[0:50]}}…</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.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%} diff --git a/uploader/templates/samples/sui-upload-progress.html b/uploader/templates/samples/sui-upload-progress.html new file mode 100644 index 0000000..8412c46 --- /dev/null +++ b/uploader/templates/samples/sui-upload-progress.html @@ -0,0 +1,26 @@ +{%extends "samples/sui-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%} +<div class="row" style="overflow-x: clip;"> +<h2 class="heading">{{job.job_name[0:50]}}…</h2> + +<p> +<strong>status</strong>: +<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br /> +</p> + +<p>saving to database...</p> +</div> + +<div class="row"> + {{cli_output(job, "stdout")}} +</div> + +{%endblock%} diff --git a/uploader/templates/samples/sui-upload-samples.html b/uploader/templates/samples/sui-upload-samples.html new file mode 100644 index 0000000..83c2061 --- /dev/null +++ b/uploader/templates/samples/sui-upload-samples.html @@ -0,0 +1,153 @@ +{%extends "samples/sui-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Samples — Upload Samples{%endblock%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.populations.samples.upload_samples', + species_id=species['SpeciesId'], + population_id=population.Id)}}"> + Upload + </a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<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" /> + <small class="form-text text-muted"> + See the <a href="#docs-samples-upload">documentation below</a> for + details on expected file format.</small> + </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> + + + +<div class="row" id="docs-samples-upload"> + <h3 class="subheading">File Format</h3> + <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> +{%endblock%} + +{%block javascript%} +<script src="/static/js/upload_samples.js" type="text/javascript"></script> +{%endblock%} diff --git a/uploader/templates/samples/sui-upload-success.html b/uploader/templates/samples/sui-upload-success.html new file mode 100644 index 0000000..054bde8 --- /dev/null +++ b/uploader/templates/samples/sui-upload-success.html @@ -0,0 +1,31 @@ +{%extends "samples/sui-base.html"%} +{%from "cli-output.html" import cli_output%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} + +<div class="row" style="overflow-x: clip;"> + <h2 class="heading">{{job.job_name[0:50]}}…</h2> + + <p> + <strong>status</strong>: + <span>{{job["status"]}} ({{job.get("message", "-")}})</span><br /> + </p> + + <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%} diff --git a/uploader/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html index 458ab55..2cf8053 100644 --- a/uploader/templates/samples/upload-failure.html +++ b/uploader/templates/samples/upload-failure.html @@ -15,7 +15,7 @@ <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> diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html index 25d3290..4aa2f7f 100644 --- a/uploader/templates/samples/upload-samples.html +++ b/uploader/templates/samples/upload-samples.html @@ -65,14 +65,14 @@ <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" + <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" + <label for="select-separator" class="form-label">field separator</label> + <select id="select-separator" name="separator" required="required" class="form-control"> @@ -83,7 +83,7 @@ <option value=";">Semicolon</option> <option value="other">Other</option> </select> - <input id="txt:separator" + <input id="txt-separator" type="text" name="other_separator" class="form-control" /> @@ -95,11 +95,11 @@ </div> <div class="form-group form-check"> - <input id="chk:heading" + <input id="chk-heading" type="checkbox" name="first_line_heading" class="form-check-input" /> - <label for="chk:heading" class="form-check-label"> + <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 @@ -108,8 +108,8 @@ </div> <div class="form-group"> - <label for="txt:delimiter" class="form-label">field delimiter</label> - <input id="txt:delimiter" + <label for="txt-delimiter" class="form-label">field delimiter</label> + <input id="txt-delimiter" type="text" name="field_delimiter" maxlength="1" |