diff options
Diffstat (limited to 'uploader/templates/genotypes')
| -rw-r--r-- | uploader/templates/genotypes/base.html | 11 | ||||
| -rw-r--r-- | uploader/templates/genotypes/create-dataset.html | 82 | ||||
| -rw-r--r-- | uploader/templates/genotypes/index.html | 4 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-genotypes.html | 40 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-markers.html | 5 | ||||
| -rw-r--r-- | uploader/templates/genotypes/select-population.html | 16 | ||||
| -rw-r--r-- | uploader/templates/genotypes/view-dataset.html | 61 |
7 files changed, 192 insertions, 27 deletions
diff --git a/uploader/templates/genotypes/base.html b/uploader/templates/genotypes/base.html index 1b274bf..7d61312 100644 --- a/uploader/templates/genotypes/base.html +++ b/uploader/templates/genotypes/base.html @@ -6,7 +6,18 @@ {%else%} class="breadcrumb-item" {%endif%}> + {%if population is mapping%} + <a href="{{url_for('species.populations.genotypes.list_genotypes', + species_id=species.SpeciesId, + population_id=population.Id)}}"> + {%if dataset is defined and dataset is mapping%} + {{dataset.Name}} + {%else%} + Genotypes + {%endif%}</a> + {%else%} <a href="{{url_for('species.populations.genotypes.index')}}">Genotypes</a> + {%endif%} </li> {%block lvl4_breadcrumbs%}{%endblock%} {%endblock%} diff --git a/uploader/templates/genotypes/create-dataset.html b/uploader/templates/genotypes/create-dataset.html new file mode 100644 index 0000000..10331c1 --- /dev/null +++ b/uploader/templates/genotypes/create-dataset.html @@ -0,0 +1,82 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes — Create Dataset{%endblock%} + +{%block pagetitle%}Genotypes — Create Dataset{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="create-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}">Create Dataset</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-geno-create-dataset" + method="POST" + action="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}"> + <legend>Create a new Genotype Dataset</legend> + + <div class="form-group"> + <label for="txt-geno-dataset-name" class="form-label">Name</label> + <input type="text" + id="txt-geno-dataset-name" + name="geno-dataset-name" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a short representative, but constrained name for the genotype + dataset.<br /> + The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens + and underscores. Any other character will cause the name to be + rejected.</p></small> + </div> + + <div class="form-group"> + <label for="txt-geno-dataset-fullname" class="form-label">Full Name</label> + <input type="text" + id="txt-geno-dataset-fullname" + name="geno-dataset-fullname" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a longer, more descriptive name for your dataset.</p></small> + </div> + + <div class="form-group"> + <label for="txt-geno-dataset-shortname" + class="form-label">Short Name</label> + <input type="text" + id="txt-geno-dataset-shortname" + name="geno-dataset-shortname" + class="form-control" /> + <small class="form-text text-muted"> + <p>A short name for your dataset. If you leave this field blank, the + short name will be set to the same value as the + "<strong>Name</strong>" field above.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + class="btn btn-primary" + value="create dataset" /> + </div> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html index e749f5a..b50ebc5 100644 --- a/uploader/templates/genotypes/index.html +++ b/uploader/templates/genotypes/index.html @@ -26,3 +26,7 @@ species)}} </div> {%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html index 8afd591..0f074fd 100644 --- a/uploader/templates/genotypes/list-genotypes.html +++ b/uploader/templates/genotypes/list-genotypes.html @@ -26,7 +26,8 @@ <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)}}" + species_id=species.SpeciesId, + population_id=population.Id)}}" title="View genetic markers for species '{{species.FullName}}"> this link to view the genetic markers </a>. @@ -70,7 +71,7 @@ {%if genocode | length < 1%} <a href="#add-genotype-encoding" title="Add a genotype encoding system for this population" - class="btn btn-primary"> + class="btn btn-primary not-implemented"> add genotype encoding </a> {%endif%} @@ -95,14 +96,8 @@ <p>The genotype data is organised under various genotype datasets. You can click on the link for the relevant dataset to view a little more information about it.</p> - <p>You can also create a new genotype dataset by clicking the button below. - <br /> - <a href="#create-new-genotype-dataset" - title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species." - class="btn btn-primary"> - create new genotype dataset</a></p> - {%if datasets | length > 0%} + {%if dataset is not none%} <table class="table"> <thead> <tr> @@ -112,7 +107,6 @@ </thead> <tbody> - {%for dataset in datasets%} <tr> <td>{{dataset.Name}}</td> <td><a href="{{url_for('species.populations.genotypes.view_dataset', @@ -122,16 +116,32 @@ title="View details regarding and manage dataset '{{dataset.FullName}}'"> {{dataset.FullName}}</a></td> </tr> - {%endfor%} </tbody> </table> {%else%} - <p class="text-warning"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - There are no genotype datasets to display, yet! - </p> + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There is no genotype dataset defined for this population. + </p> + <p> + <a href="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species." + class="btn btn-primary"> + create new genotype dataset</a></p> {%endif%} </div> +<div class="row text-warning"> + <p> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a + single genotype dataset. If there is more than one, the system apparently + fails in unpredictable ways. + </p> + <p>Fix this to allow multiple datasets, each with a different assembly from + all the rest.</p> +</div> {%endblock%} {%block sidebarcontents%} diff --git a/uploader/templates/genotypes/list-markers.html b/uploader/templates/genotypes/list-markers.html index 9198b44..a705ae3 100644 --- a/uploader/templates/genotypes/list-markers.html +++ b/uploader/templates/genotypes/list-markers.html @@ -13,7 +13,8 @@ class="breadcrumb-item" {%endif%}> <a href="{{url_for('species.populations.genotypes.list_markers', - species_id=species.SpeciesId)}}">List markers</a> + species_id=species.SpeciesId, + population_id=population.Id)}}">List markers</a> </li> {%endblock%} @@ -30,6 +31,7 @@ {%if start_from > 0%} <a href="{{url_for('species.populations.genotypes.list_markers', species_id=species.SpeciesId, + population_id=population.Id, start_from=start_from-count, count=count)}}"> <span class="glyphicon glyphicon-backward"></span> @@ -45,6 +47,7 @@ {%if start_from + count < total_markers%} <a href="{{url_for('species.populations.genotypes.list_markers', species_id=species.SpeciesId, + population_id=population.Id, start_from=start_from+count, count=count)}}"> Next diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html index 7c81943..acdd063 100644 --- a/uploader/templates/genotypes/select-population.html +++ b/uploader/templates/genotypes/select-population.html @@ -12,20 +12,14 @@ {{flash_all_messages()}} <div class="row"> - <p> - You have indicated that you intend to upload the genotypes for species - '{{species.FullName}}'. We now just require the population for your - experiment/study, and you should be good to go. - </p> -</div> - -<div class="row"> - {{select_population_form(url_for("species.populations.genotypes.select_population", - species_id=species.SpeciesId), - populations)}} + {{select_population_form(url_for("species.populations.genotypes.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/genotypes/view-dataset.html b/uploader/templates/genotypes/view-dataset.html new file mode 100644 index 0000000..e7ceb36 --- /dev/null +++ b/uploader/templates/genotypes/view-dataset.html @@ -0,0 +1,61 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes: View Dataset{%endblock%} + +{%block pagetitle%}Genotypes: View Dataset{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">view dataset</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Genotype Dataset Details</h2> + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td>{{dataset.FullName}}</td> + </tr> + </tbody> + </table> +</div> + +<div class="row text-warning"> + <h2>Assembly Details</h2> + + <p>Maybe include the assembly details here if found to be necessary.</p> +</div> + +<div class="row"> + <h2>Genotype Data</h2> + + <p class="text-danger"> + Provide link to enable uploading of genotype data here.</p> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} |