diff options
| -rw-r--r-- | uploader/platforms/views.py | 6 | ||||
| -rw-r--r-- | uploader/templates/platforms/sui-base.html | 17 | ||||
| -rw-r--r-- | uploader/templates/platforms/sui-create-platform.html | 116 | ||||
| -rw-r--r-- | uploader/templates/platforms/sui-list-platforms.html | 88 |
4 files changed, 225 insertions, 2 deletions
diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py index ba0f0ef..0092760 100644 --- a/uploader/platforms/views.py +++ b/uploader/platforms/views.py @@ -8,6 +8,8 @@ from flask import ( Blueprint, current_app as app) +from uploader.sui import sui_template + from uploader.flask_extensions import url_for from uploader.ui import make_template_renderer from uploader.authorisation import require_login @@ -60,7 +62,7 @@ def list_platforms(species_id: int): start_from = max(safe_int(request.args.get("start_from") or 0), 0) count = safe_int(request.args.get("count") or 20) return render_template( - "platforms/list-platforms.html", + sui_template("platforms/list-platforms.html"), species=species, platforms=enumerate_sequence( platforms_by_species(conn, @@ -87,7 +89,7 @@ def create_platform(species_id: int): if request.method == "GET": return render_template( - "platforms/create-platform.html", + sui_template("platforms/create-platform.html"), species=species, activelink="create-platform") diff --git a/uploader/templates/platforms/sui-base.html b/uploader/templates/platforms/sui-base.html new file mode 100644 index 0000000..136b956 --- /dev/null +++ b/uploader/templates/platforms/sui-base.html @@ -0,0 +1,17 @@ +{%extends "species/sui-base.html"%} +{%from "species/macro-display-species-card.html" import display_sui_species_card%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.platforms.list_platforms', + species_id=species['SpeciesId'])}}"> + Platforms + </a> +</li> +{%endblock%} + + +{%block sidebarcontents%} +{{display_sui_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/platforms/sui-create-platform.html b/uploader/templates/platforms/sui-create-platform.html new file mode 100644 index 0000000..25977a7 --- /dev/null +++ b/uploader/templates/platforms/sui-create-platform.html @@ -0,0 +1,116 @@ +{%extends "platforms/sui-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Platforms — Create Platforms{%endblock%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.platforms.create_platform', + species_id=species['SpeciesId'])}}"> + Create + </a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Create New Platform</h2> + + <p>You can create a new genetic sequencing platform below.</p> +</div> + +<div class="row"> + <form id="frm-create-platform" + method="POST" + action="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}"> + + <div class="form-group"> + <label for="txt-geo-platform" class="form-label">GEO Platform</label> + <input type="text" + id="txt-geo-platform" + name="geo-platform" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is the platform's + <a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}" + title="Platforms for '{{species.FullName}}' on NCBI"> + accession value on NCBI</a>. If you do not know the value, click the + link and search on NCBI for species '{{species.FullName}}'.</p></small> + </div> + + <div class="form-group"> + <label for="txt-platform-name" class="form-label">Platform Name</label> + <input type="text" + id="txt-platform-name" + name="platform-name" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is name of the genetic sequencing platform.</p></small> + </div> + + <div class="form-group"> + <label for="txt-platform-shortname" class="form-label"> + Platform Short Name</label> + <input type="text" + id="txt-platform-shortname" + name="platform-shortname" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>Use the following conventions for this field: + <ol> + <li>Start with a 4-letter vendor code, e.g. "Affy" for "Affymetrix", "Illu" for "Illumina", etc.</li> + <li>Append an underscore to the 4-letter vendor code</li> + <li>Use the name of the array given by the vendor, e.g. U74AV2, MOE430A, etc.</li> + </ol> + </p> + </small> + </div> + + <div class="form-group"> + <label for="txt-platform-title" class="form-label">Platform Title</label> + <input type="text" + id="txt-platform-title" + name="platform-title" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>The full platform title. Sometimes, this is the same as the Platform + Name above.</p></small> + </div> + + <div class="form-group"> + <label for="txt-go-tree-value" class="form-label">GO Tree Value</label> + <input type="text" + id="txt-go-tree-value" + name="go-tree-value" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a Chip identification value useful for analysis with the + <strong> + <a href="https://www.geneweaver.org/" + title="Go to the GeneWeaver site." + target="_blank">GeneWeaver</a></strong> + and + <strong> + <a href="https://www.webgestalt.org/" + title="Go to the WEB-based GEne SeT AnaLysis Toolkit site." + target="_blank">WebGestalt</a></strong> + tools.<br /> + This can be left blank for custom platforms.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + value="create new platform" + class="btn btn-primary" /> + </div> + </form> +</div> +{%endblock%} diff --git a/uploader/templates/platforms/sui-list-platforms.html b/uploader/templates/platforms/sui-list-platforms.html new file mode 100644 index 0000000..f4c17e8 --- /dev/null +++ b/uploader/templates/platforms/sui-list-platforms.html @@ -0,0 +1,88 @@ +{%extends "platforms/sui-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Platforms — List Platforms{%endblock%} + +{%block pagetitle%}Platforms — List Platforms{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>View the list of the genetic sequencing platforms that are currently + supported by GeneNetwork.</p> + <p>If you cannot find the platform you wish to use, you can add it by clicking + the "New Platform" button below.</p> + <p><a href="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}" + title="Create a new genetic sequencing platform for species {{species.FullName}}" + class="btn btn-primary">Create Platform</a></p> +</div> + +<div class="row"> + <h2>Supported Platforms</h2> + {%if platforms is defined and platforms | length > 0%} + <p>There are {{total_platforms}} platforms supported by GeneNetwork</p> + + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%if start_from > 0%} + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId, + start_from=start_from-count, + count=count)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + <div class="col-md-8" style="text-align: center;"> + Displaying platforms {{start_from+1}} to {{start_from+count if start_from+count < total_platforms else total_platforms}} of + {{total_platforms}} + </div> + <div class="col-md-2" style="text-align: end;"> + {%if start_from + count < total_platforms%} + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId, + start_from=start_from+count, + count=count)}}"> + Next + <span class="glyphicon glyphicon-forward"></span> + </a> + {%endif%} + </div> + </div> + + <table class="table"> + <thead> + <tr> + <th></th> + <th>Platform Name</th> + <th><a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}" + title="Gene Expression Omnibus: Platforms section" + target="_blank">GEO Platform</a></th> + <th>Title</th> + </tr> + </thead> + + <tbody> + {%for platform in platforms%} + <tr> + <td>{{platform.sequence_number}}</td> + <td>{{platform.GeneChipName}}</td> + <td><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{platform.GeoPlatform}}" + title="View platform on the Gene Expression Omnibus" + target="_blank">{{platform.GeoPlatform}}</a></td> + <td>{{platform.Title}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There are no platforms supported at this time!</p> + {%endif%} +</div> +{%endblock%} |