diff options
Diffstat (limited to 'uploader')
| -rw-r--r-- | uploader/phenotypes/views.py | 15 | ||||
| -rw-r--r-- | uploader/static/css/theme.css | 4 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-genotypes.html | 58 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/review-job-data.html | 37 |
4 files changed, 97 insertions, 17 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 23bc682..c03f3f5 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -317,6 +317,11 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable= dataset_shortname = ( form["dataset-shortname"] or form["dataset-name"]).strip() _pheno_dataset = save_new_dataset( + # It's not necessary to update the authorisation server to register + # new phenotype resource here, since each phenotype trait can, in + # theory, have its own access control allowing/disallowing access to + # it. In practice, however, we tend to gather multiple traits into a + # single resource for access control. cursor, population["Id"], form["dataset-name"].strip(), @@ -662,6 +667,8 @@ def review_job_data( conn, int(_job_metadata["publicationid"])) if _job_metadata.get("publicationid") else None), + user=session.user_details(), + timestamp=datetime.datetime.now().isoformat(), activelink="add-phenotypes") @@ -741,9 +748,15 @@ def load_data_to_database( "publication_id": _meta["publicationid"], "authserver": oauth2client.authserver_uri(), "token": token["access_token"], + "dataname": request.form["data_name"].strip(), "success_handler": ( "uploader.phenotypes.views" - ".load_phenotypes_success_handler") + ".load_phenotypes_success_handler"), + **{ + key: request.form[key] + for key in ("data_description",) + if key in request.form.keys() + } }, external_id=session.logged_in_user_id()) ).then( diff --git a/uploader/static/css/theme.css b/uploader/static/css/theme.css index 276978f..6f5cb0c 100644 --- a/uploader/static/css/theme.css +++ b/uploader/static/css/theme.css @@ -81,10 +81,10 @@ table.dataTable tbody tr.selected td { background-color: #ffee99 !important; } -.form-group { +#frm-add-phenotypes .form-group { margin-bottom: 2em; padding-bottom: 0.2em; - border-bottom: solid gray 1px; + border-bottom: solid #A9A9A9 1px; } diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html index fd84c2f..be297a4 100644 --- a/uploader/templates/genotypes/list-genotypes.html +++ b/uploader/templates/genotypes/list-genotypes.html @@ -54,17 +54,34 @@ </div> <div class="row"> - <h2>Genetic Markers</h2> - <p>There are a total of {{total_markers}} currently registered genetic markers - for the "{{species.FullName}}" species. You can click - <a href="{{url_for('species.populations.genotypes.list_markers', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="View genetic markers for species '{{species.FullName}}" - target="_blank"> - here to view the genetic markers - </a>. - </p> + <h2 class="subheading">Genetic Markers</h2> + + <table id="tbl-genetic-markers" class="table compact stripe cell-border" + data-genetic-markers='{{genetic_markers | tojson}}'> + <thead> + <tr> + <th title="">Index</th> + <th title="">Marker Name</th> + <th title="Chromosome">Chr</th> + <th title="Physical location of the marker in megabasepairs"> + Location (Mb)</th> + <th title="">Source</th> + <th title="">Source2</th> + </thead> + + <tbody> + {%for marker in markers%} + <tr> + <td></td> + <td></td> + <td></td> + <td></td> + <td></td> + <td></td> + </tr> + {%endfor%} + </tbody> + </table> </div> <div class="row text-danger"> @@ -133,3 +150,22 @@ all the rest.</p> </div> {%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() { + var dtGeneticMarkers = buildDataTable( + "#tbl-genetic-markers", + JSON.parse($("#tbl-genetic-markers").attr("data-genetic-markers")), + [ + {data: 'index'}, + {data: 'Name'}, + {data: 'Chr'}, + {data: 'Mb'}, + {data: 'Source'}, + {data: 'Source2'} + ]); + }) +</script> +{%endblock%} diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html index c8355b2..0e8f119 100644 --- a/uploader/templates/phenotypes/review-job-data.html +++ b/uploader/templates/phenotypes/review-job-data.html @@ -70,6 +70,9 @@ {%endif%} {%endfor%} </ul> +</div> + +<div class="row"> <form id="frm-review-phenotype-data" method="POST" @@ -78,10 +81,38 @@ population_id=population.Id, dataset_id=dataset.Id)}}"> <input type="hidden" name="data-qc-job-id" value="{{job.jobid}}" /> - <input type="submit" - value="continue" - class="btn btn-primary" /> + <div class="form-group"> + <label for="txt-data-name">data name</label> + <input type="text" + id="txt-data-name" + class="form-control" + name="data_name" + title="A short, descriptive name for this data." + placeholder="{{user.email}} - {{dataset.Name}} - {{timestamp}}" + value="{{user.email}} - {{dataset.Name}} - {{timestamp}}" + required="required"> + <span class="form-text text-muted"> + This is a short, descriptive name for the data. It is useful to humans, + enabling them identify what traits each data "resource" wraps around. + </span> + </div> + + {%if view_under_construction%} + <div class="form-group"> + <label for="txt-data-description">data description</label> + <textarea id="txt-data-description" + class="form-control" + name="data_description" + title="A longer description for this data." + rows="5"></textarea> + <span class="form-text text-muted"> + </span> + </div> + {%endif%} + + <button type="submit" class="btn btn-primary">continue</button> </form> + </div> {%else%} <div class="row"> |