diff options
| -rw-r--r-- | uploader/templates/genotypes/create-dataset.html | 6 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-genotypes.html | 128 |
2 files changed, 71 insertions, 63 deletions
diff --git a/uploader/templates/genotypes/create-dataset.html b/uploader/templates/genotypes/create-dataset.html index 5a6d3d2..ff174fb 100644 --- a/uploader/templates/genotypes/create-dataset.html +++ b/uploader/templates/genotypes/create-dataset.html @@ -41,9 +41,9 @@ <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> + It is used internally by the Genenetwork system. Do not change this + value.</p> + </small> </div> <div class="form-group"> diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html index be297a4..5b970ff 100644 --- a/uploader/templates/genotypes/list-genotypes.html +++ b/uploader/templates/genotypes/list-genotypes.html @@ -54,81 +54,72 @@ </div> <div class="row"> - <h2 class="subheading">Genetic Markers</h2> + <h2>Genotype Dataset</h2> - <table id="tbl-genetic-markers" class="table compact stripe cell-border" - data-genetic-markers='{{genetic_markers | tojson}}'> + {%if dataset is not none%} + + <table class="table"> <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> + <th>Name</th> + <th>Full Name</th> + </tr> </thead> <tbody> - {%for marker in markers%} <tr> - <td></td> - <td></td> - <td></td> - <td></td> - <td></td> - <td></td> + <td>{{dataset.Name}}</td> + <td><a href="{{url_for('species.populations.genotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="View details regarding and manage dataset '{{dataset.FullName}}'"> + {{dataset.FullName}}</a></td> </tr> - {%endfor%} </tbody> </table> -</div> - -<div class="row text-danger"> - <h3>Some Important Concepts to Consider/Remember</h3> - <ul> - <li>Reference vs. Non-reference alleles</li> - <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li> - </ul> - <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"> - <h2>Genotype Datasets</h2> - <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> + <div class="row"> + <h3 class="subsubheading">Genetic Markers</h3> - {%if dataset is not none%} - <table class="table"> + <table id="tbl-genetic-markers" class="table compact stripe cell-border" + data-genetic-markers='{{genetic_markers | tojson}}'> <thead> <tr> - <th>Name</th> - <th>Full Name</th> - </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>{{dataset.Name}}</td> - <td><a href="{{url_for('species.populations.genotypes.view_dataset', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}" - title="View details regarding and manage dataset '{{dataset.FullName}}'"> - {{dataset.FullName}}</a></td> + <td></td> + <td></td> + <td></td> + <td></td> + <td></td> + <td></td> </tr> + {%endfor%} </tbody> </table> + </div> + {%else%} + + <p> + Your genotype data will need to be under a dataset. Unfortunately there is + currently no dataset defined for this population. + </p> + <p class="text-warning"> <span class="glyphicon glyphicon-exclamation-sign"></span> - There is no genotype dataset defined for this population. + Click the button below to define the genotype dataset for this population. </p> <p> <a href="{{url_for('species.populations.genotypes.create_dataset', @@ -139,16 +130,33 @@ 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 class="row"> + <h2>Notes</h2> + <div class="row text-danger"> + <h3>Genetic Markers: Some Important Concepts to Consider/Remember</h3> + <ul> + <li>Reference vs. Non-reference alleles</li> + <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li> + </ul> + <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 text-warning"> + <h3>Genotype Dataset</h3> + <p> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a + single genotype dataset per population. If there is more than one, the + system apparently fails in unpredictable ways. + </p> + </div> </div> + {%endblock%} |