diff options
| -rw-r--r-- | uploader/samples/views.py | 8 | ||||
| -rw-r--r-- | uploader/static/css/theme.css | 4 | ||||
| -rw-r--r-- | uploader/templates/cli-output.html | 2 | ||||
| -rw-r--r-- | uploader/templates/samples/sui-base.html | 8 | ||||
| -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 |
8 files changed, 258 insertions, 6 deletions
diff --git a/uploader/samples/views.py b/uploader/samples/views.py index fcb895d..93f0c29 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -149,7 +149,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma code=307) if request.method == "GET" or request.files.get("samples_file") is None: - return render_template("samples/upload-samples.html", + return render_template(sui_template("samples/upload-samples.html"), species=species, population=population) @@ -216,7 +216,7 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): if job: status = job["status"] if status == "success": - return render_template("samples/upload-success.html", + return render_template(sui_template("samples/upload-success.html"), job=job, species=species, population=population,) @@ -236,7 +236,7 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): return redirect(url_for( "samples.upload_failure", job_id=job_id)) - return render_template("samples/upload-progress.html", + return render_template(sui_template("samples/upload-progress.html"), species=species, population=population, job=job) # maybe also handle this? @@ -267,7 +267,7 @@ def upload_failure(species: dict, population: dict, job_id: uuid.UUID, **kwargs) if stat.st_size > 0: return render_template("worker_failure.html", job_id=job_id) - return render_template("samples/upload-failure.html", + return render_template(sui_template("samples/upload-failure.html"), species=species, population=population, job=job) diff --git a/uploader/static/css/theme.css b/uploader/static/css/theme.css index 2acce5f..99b7af3 100644 --- a/uploader/static/css/theme.css +++ b/uploader/static/css/theme.css @@ -56,6 +56,10 @@ body { text-transform: capitalize; } +label { + text-transform: Capitalize; +} + input[type="search"] { border-radius: 5px; } diff --git a/uploader/templates/cli-output.html b/uploader/templates/cli-output.html index 64b1a9a..9cff09d 100644 --- a/uploader/templates/cli-output.html +++ b/uploader/templates/cli-output.html @@ -1,7 +1,7 @@ {%macro cli_output(job, stream)%} <h4 class="subheading">{{stream | upper}} Output</h4> -<div class="cli-output" style="max-height: 10em; overflow: auto;"> +<div class="cli-output" style="overflow: auto;"> <pre>{{job.get(stream, "")}}</pre> </div> diff --git a/uploader/templates/samples/sui-base.html b/uploader/templates/samples/sui-base.html index ee08e2e..8ec7505 100644 --- a/uploader/templates/samples/sui-base.html +++ b/uploader/templates/samples/sui-base.html @@ -3,7 +3,13 @@ {%block breadcrumbs%} {{super()}} -<li class="breadcrumb-item">Manage Samples</li> +<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%} 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%} |