diff options
Diffstat (limited to 'uploader/templates/samples')
| -rw-r--r-- | uploader/templates/samples/index.html | 10 | ||||
| -rw-r--r-- | uploader/templates/samples/list-samples.html | 113 | ||||
| -rw-r--r-- | uploader/templates/samples/select-population.html | 18 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-failure.html | 2 | ||||
| -rw-r--r-- | uploader/templates/samples/upload-samples.html | 9 |
5 files changed, 83 insertions, 69 deletions
diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html index 7c88c01..ee98734 100644 --- a/uploader/templates/samples/index.html +++ b/uploader/templates/samples/index.html @@ -11,11 +11,13 @@ {{flash_all_messages()}} <div class="row"> - <p>Here, you can upload the samples/individuals that were used in your - experiments.</p> - <p>Since the samples are linked to specific species and populations, we will - need to first select them in the next few steps.</p> + <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 index 8f1bf16..aed27c3 100644 --- a/uploader/templates/samples/list-samples.html +++ b/uploader/templates/samples/list-samples.html @@ -24,45 +24,69 @@ <div class="row"> <p> - Samples for population "{{population.FullName}}" from the + You selected the population "{{population.FullName}}" from the "{{species.FullName}}" species. </p> +</div> - {%if samples | length > 0%} - <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="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> - <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> +{%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="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 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> @@ -73,6 +97,7 @@ <tbody> {%for sample in samples%} <tr> + <td>{{sample.sequence_number}}</td> <td>{{sample.Name}}</td> <td>{{sample.Name2}}</td> <td>{{sample.Symbol or "-"}}</td> @@ -84,30 +109,20 @@ <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> - {%else%} - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - There are no samples for this population at this time. - </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> - {%endif%} </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%} diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html index 8e22ac1..1cc7573 100644 --- a/uploader/templates/samples/select-population.html +++ b/uploader/templates/samples/select-population.html @@ -12,23 +12,15 @@ {{flash_all_messages()}} <div class="row"> - <p>Select the population to use with your samples:</p> {{select_population_form( - url_for("species.populations.samples.select_population", species_id=species.SpeciesId), - populations)}} -</div> -<div class="row"> - <p><strong>Cannot find your population in the list?</strong></p> - - <p>If you cannot find the population you want in the drop-down above, you can - instead, - <a href="{{url_for('species.populations.create_population', - species_id=species.SpeciesId)}}" - title="Create a new population for species '{{species.FullName}},"> - create a new population</a>. + 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/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 b101b2e..6422094 100644 --- a/uploader/templates/samples/upload-samples.html +++ b/uploader/templates/samples/upload-samples.html @@ -23,7 +23,12 @@ {{flash_all_messages()}} <div class="row"> - <p>You can now upload a character-separated value (CSV) file that contains + <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> @@ -61,7 +66,7 @@ <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" + accept="text/csv, text/tab-separated-values, text/plain" class="form-control" /> </div> |