diff options
| -rw-r--r-- | uploader/phenotypes/views.py | 85 | ||||
| -rw-r--r-- | uploader/static/css/styles.css | 7 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/edit-phenotype.html | 195 |
3 files changed, 287 insertions, 0 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 5ae9588..fe591f1 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -234,6 +234,7 @@ def view_phenotype(# pylint: disable=[unused-argument] species=species, population=population, dataset=dataset, + xref_id=xref_id, phenotype=phenotype, has_se=all(bool(item.get("error")) for item in phenotype["data"]), publish_data={ @@ -589,3 +590,87 @@ def review_job_data( job=job, summary=summary, activelink="add-phenotypes") + + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/phenotype/<int:xref_id>/edit", + methods=["GET", "POST"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def edit_phenotype_data( + species: dict, + population: dict, + dataset: dict, + xref_id: int, + **kwargs +): + """Edit the data for a particular phenotype.""" + def __render__(**kwargs): + processed_kwargs = { + **kwargs, + "privileges": (kwargs.get("privileges", tuple()) + ### For demo! Do not commit this part + + ("group:resource:edit-resource", + "group:resource:delete-resource",) + ### END: For demo! Do not commit this part + ) + } + return render_template( + "phenotypes/edit-phenotype.html", + species=species, + population=population, + dataset=dataset, + xref_id=xref_id, + families_with_se_and_n=_FAMILIES_WITH_SE_AND_N_, + **processed_kwargs, + activelink="edit-phenotype") + + with database_connection(app.config["SQL_URI"]) as conn: + def __fetch_phenotype__(privileges): + phenotype = phenotype_by_id(conn, + species["SpeciesId"], + population["Id"], + dataset["Id"], + xref_id) + if phenotype is None: + msg = ("Could not find the phenotype with cross-reference ID" + f" '{xref_id}' from dataset '{dataset['FullName']}' " + f" from the '{population['FullName']}' population of " + f" species '{species['FullName']}'.") + return Left({"privileges": privileges, "phenotype-error": msg}) + return {"privileges": privileges, "phenotype": phenotype} + + def __fetch_publication_data__(**kwargs): + pheno = kwargs["phenotype"] + return { + **kwargs, + "publication_data": phenotype_publication_data( + conn, pheno["Id"]) + } + + def __fail__(failure_object): + # process the object + return __render__(failure_object=failure_object) + + return oauth2_post( + "/auth/resource/phenotypes/individual/linked-resource", + json={ + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": dataset["Id"], + "xref_id": xref_id + } + ).then( + lambda resource: tuple( + privilege["privilege_id"] for role in resource["roles"] + for privilege in role["privileges"]) + ).then( + __fetch_phenotype__ + ).then( + lambda args: __fetch_publication_data__(**args) + ).either(__fail__, lambda args: __render__(**args)) diff --git a/uploader/static/css/styles.css b/uploader/static/css/styles.css index 1c3e677..7bd51a9 100644 --- a/uploader/static/css/styles.css +++ b/uploader/static/css/styles.css @@ -136,11 +136,13 @@ input[type="submit"], .btn { .heading { border-bottom: solid #EEBB88; + text-transform: capitalize; } .subheading { padding: 1em 0 0.1em 0.5em; border-bottom: solid #88BBEE; + text-transform: capitalize; } form { @@ -154,6 +156,11 @@ form .form-control { background-color: #EAEAFF; } +.table-form-table thead { + background: #E5E5FF; +} + + .sidebar-content .card .card-title { font-size: 1.5em; } diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html new file mode 100644 index 0000000..8b1642c --- /dev/null +++ b/uploader/templates/phenotypes/edit-phenotype.html @@ -0,0 +1,195 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="edit-phenotype"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2 class="heading">edit phenotype data</h2> + <p>The two (2) forms provided in this page help you update the data for the + phenotypes, and the publication information for the phenotype, + respectively.</p> +</div> + +<div class="row"> + <h3 class="subheading">phenotype data</h3> + <form id="frm-edit-phenotype-data"> + <div style="max-height: 23.37em;overflow-y: scroll;"> + <table class="table table-striped table-responsive table-form-table"> + <thead style="position: sticky; top: 0;"> + <tr> + <th>#</th> + <th>Sample</th> + <th>Value</th> + {%if population.Family in families_with_se_and_n%} + <th>Standard-Error</th> + <th>Number of Samples</th> + {%endif%} + </tr> + </thead> + + <tbody> + {%for item in phenotype.data%} + <tr> + <td>{{loop.index}}</td> + <td>{{item.StrainName}}</td> + <td> + <input type="text" + name="value::{{item.DataId}}::{{item.StrainId}}" + value="{{item.value}}" + data-original-value="{{item.value}}" + class="form-control" /></td> + {%if population.Family in families_with_se_and_n%} + <td> + <input type="text" + name="se::{{item.DataId}}::{{item.StrainId}}" + value="{{item.error or ''}}" + data-original-value="{{item.error or ''}}" + class="form-control" /></td> + <td><input type="text" + name="n::{{item.DataId}}::{{item.StrainId}}" + value="{{item.count or ''}}" + data-original-value="{{item.count or "-"}}" + class="form-control" /></td> + {%endif%} + </tr> + {%endfor%} + </tbody> + </table> + </div> + <div class="form-group"> + <input type="submit" + name="submit" + class="btn btn-primary not-implemented" + value="update data" /> + </div> + </form> +</div> + +<div class="row"> + <h3 class="subheading">publication information</h3> + <p>Use the form below to update the publication information for this + phenotype.</p> + <form id="frm-edit-phenotype-pub-data" + method="POST" + action="#"> + <div class="form-group"> + <label for="txt-pubmed-id" class="form-label">Pubmed ID</label> + <input id="txt-pubmed-id" name="pubmed-id" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter your publication's PubMed ID. + </span> + </div> + + <div class="form-group"> + <label for="txt-publication-authors" class="form-label">Authors</label> + <input id="txt-publication-authors" name="publication-authors" + type="text" class="form-control" /> + <span class="form-text text-muted"> + Enter the authors.</span> + </div> + + <div class="form-group"> + <label for="txt-publication-title" class="form-label"> + Publication Title</label> + <input id="txt-publication-title" name="publication-title" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter your publication's title.</span> + </div> + + <div class="form-group"> + <label for="txt-publication-abstract" class="form-label"> + Publication Abstract</label> + <textarea id="txt-publication-abstract" name="publication-abstract" + class="form-control" rows="10"></textarea> + <span class="form-text text-muted"> + Enter the abstract for your publication.</span> + </div> + + <div class="form-group"> + <label for="txt-publication-journal" class="form-label">Journal</label> + <input id="txt-publication-journal" name="journal" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the name of the journal where your work was published.</span> + </div> + + <div class="form-group"> + <label for="txt-publication-volume" class="form-label">Volume</label> + <input id="txt-publication-volume" name="publication-volume" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the volume in the following format …</span> + </div> + + <div class="form-group"> + <label for="txt-publication-pages" class="form-label">Pages</label> + <input id="txt-publication-pages" name="publication-pages" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the journal volume where your work was published.</span> + </div> + + <div class="form-group"> + <label for="select-publication-month" class="form-label"> + Publication Month</label> + <select id="select-publication-month" name="publication-month" + class="form-control"> + {%for month in monthnames%} + <option value="{{month | lower}}" + {%if current_month | lower == month | lower%} + selected="selected" + {%endif%}>{{month | capitalize}}</option> + {%endfor%} + </select> + <span class="form-text text-muted"> + Select the month when the work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span></span> + </div> + + <div class="form-group"> + <label for="txt-publication-year" class="form-label">Publication Year</label> + <input id="txt-publication-year" name="publication-year" type="text" + class="form-control" value="{{current_year}}" /> + <span class="form-text text-muted"> + Enter the year your work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span> + </span> + </div> + <div class="form-group"> + <input type="submit" + name="submit" + class="btn btn-primary not-implemented" + value="update publication" /> + </div> + </form> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} |