diff options
| -rw-r--r-- | uploader/genotypes/views.py | 27 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-genotypes.html | 87 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-markers.html | 102 |
3 files changed, 146 insertions, 70 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 0618949..2ff9965 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -90,6 +90,26 @@ def list_genotypes(species_id: int, population_id: int): "species.populations.genotypes.select_population", species_id=species_id)) + return render_template("genotypes/list-genotypes.html", + species=species, + population=population, + genocode=genocode_by_population( + conn, population_id), + total_markers=genotype_markers_count( + conn, species_id), + activelink="list-genotypes") + + +@genotypesbp.route("/<int:species_id>/genotypes/list-markers", methods=["GET"]) +@require_login +def list_markers(species_id: int): + """List a species' genetic markers.""" + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, species_id) + if not bool(species): + flash("Invalid species provided!", "alert-danger") + return redirect(url_for("species.populations.genotypes.index")) + start_from = safe_int(request.args.get("start_from") or 0) if start_from < 0: start_from = 0 @@ -97,14 +117,11 @@ def list_genotypes(species_id: int, population_id: int): markers = enumerate_sequence( genotype_markers(conn, species_id, offset=start_from, limit=count), start=start_from+1) - return render_template("genotypes/list-genotypes.html", + return render_template("genotypes/list-markers.html", species=species, - population=population, - genocode=genocode_by_population( - conn, population_id), total_markers=genotype_markers_count( conn, species_id), start_from=start_from, count=count, markers=markers, - activelink="list-genotypes") + activelink="list-markers") diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html index 9b27540..0efc693 100644 --- a/uploader/templates/genotypes/list-genotypes.html +++ b/uploader/templates/genotypes/list-genotypes.html @@ -22,12 +22,24 @@ {{flash_all_messages()}} <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)}}" + title="View genetic markers for species '{{species.FullName}}"> + this link to view the genetic markers + </a>. + </p> +</div> + +<div class="row"> + <h2>Genotype Encoding</h2> <p> The genotype encoding used for the "{{population.FullName}}" population from the "{{species.FullName}}" species is as shown in the table below. </p> <table class="table"> - <legend>Genotype Encoding</legend> <thead> <tr> @@ -54,6 +66,14 @@ {%endfor%} </tbody> </table> + + {%if genocode | length < 1%} + <a href="#add-genotype-encoding" + title="Add a genotype encoding system for this population" + class="btn btn-primary"> + add genotype encoding + </a> + {%endif%} </div> <div class="row text-danger"> @@ -65,75 +85,12 @@ <h3>Possible references</h3> <ul> <li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li> + <li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li> </ul> </div> <div class="row"> - <p> - There are a total of {{total_markers}} genotype markers for this species. - </p> - <div class="row"> - <div class="col-md-2" style="text-align: start;"> - {%if start_from > 0%} - <a href="{{url_for('species.populations.genotypes.list_genotypes', - species_id=species.SpeciesId, - population_id=population.Id, - 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 markers {{start_from+1}} to {{start_from + count}} of - {{total_markers}} - </div> - <div class="col-md-2" style="text-align: end;"> - {%if start_from + count < total_markers%} - <a href="{{url_for('species.populations.genotypes.list_genotypes', - species_id=species.SpeciesId, - population_id=population.Id, - start_from=start_from+count, - count=count)}}"> - Next - <span class="glyphicon glyphicon-forward"></span> - </a> - {%endif%} - </div> - </div> - <table class="table"> - <thead> - <tr> - <th title="">#</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>{{marker.sequence_number}}</td> - <td>{{marker.Marker_Name}}</td> - <td>{{marker.Chr}}</td> - <td>{{marker.Mb}}</td> - <td>{{marker.Source}}</td> - <td>{{marker.Source2}}</td> - </tr> - {%else%} - <tr> - <td colspan="7" class="text-info"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - No markers to display! - </td> - </tr> - {%endfor%} - </tbody> - </table> </div> {%endblock%} diff --git a/uploader/templates/genotypes/list-markers.html b/uploader/templates/genotypes/list-markers.html new file mode 100644 index 0000000..9198b44 --- /dev/null +++ b/uploader/templates/genotypes/list-markers.html @@ -0,0 +1,102 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Genotypes: List Markers{%endblock%} + +{%block pagetitle%}Genotypes: List Markers{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="list-markers"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.list_markers', + species_id=species.SpeciesId)}}">List markers</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +{%if markers | length > 0%} +<div class="row"> + <p> + There are a total of {{total_markers}} genotype markers for this species. + </p> + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%if start_from > 0%} + <a href="{{url_for('species.populations.genotypes.list_markers', + 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 markers {{start_from+1}} to {{start_from+count if start_from+count < total_markers else total_markers}} of + {{total_markers}} + </div> + <div class="col-md-2" style="text-align: end;"> + {%if start_from + count < total_markers%} + <a href="{{url_for('species.populations.genotypes.list_markers', + 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 title="">#</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>{{marker.sequence_number}}</td> + <td>{{marker.Marker_Name}}</td> + <td>{{marker.Chr}}</td> + <td>{{marker.Mb}}</td> + <td>{{marker.Source}}</td> + <td>{{marker.Source2}}</td> + </tr> + {%endfor%} + </tbody> + </table> +</div> +{%else%} +<div class="row"> + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + This species does not currently have any genetic markers uploaded, therefore, + there is nothing to display here. + </p> + <p> + <a href="#add-genetic-markers-for-species-{{species.SpeciesId}}" + title="Add genetic markers for this species" + class="btn btn-primary"> + add genetic markers + </a> + </p> +</div> +{%endif%} +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} |