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-rw-r--r--uploader/genotypes/models.py21
-rw-r--r--uploader/genotypes/views.py29
-rw-r--r--uploader/templates/genotypes/list-genotypes.html10
-rw-r--r--uploader/templates/genotypes/view-dataset.html61
4 files changed, 112 insertions, 9 deletions
diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
index 29acd0b..1fe5929 100644
--- a/uploader/genotypes/models.py
+++ b/uploader/genotypes/models.py
@@ -44,19 +44,26 @@ def genotype_markers(
def genotype_dataset(
conn: mdb.Connection,
species_id: int,
- population_id: int
+ population_id: int,
+ dataset_id: Optional[int] = None
) -> Optional[dict]:
"""Retrieve genotype datasets from the database.
Apparently, you should only ever have one genotype dataset for a population.
"""
+ _query = (
+ "SELECT gf.* FROM Species AS s INNER JOIN InbredSet AS iset "
+ "ON s.Id=iset.SpeciesId INNER JOIN GenoFreeze AS gf "
+ "ON iset.Id=gf.InbredSetId "
+ "WHERE s.Id=%s AND iset.Id=%s")
+ _params = (species_id, population_id)
+ if bool(dataset_id):
+ _query = _query + " AND gf.Id=%s"
+ _params = _params + (dataset_id,)
+
with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute(
- "SELECT gf.* FROM Species AS s INNER JOIN InbredSet AS iset "
- "ON s.Id=iset.SpeciesId INNER JOIN GenoFreeze AS gf "
- "ON iset.Id=gf.InbredSetId "
- "WHERE s.Id=%s AND iset.Id=%s",
- (species_id, population_id))
+ cursor.execute(_query, _params)
+ debug_query(cursor)
result = cursor.fetchone()
if bool(result):
return dict(result)
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 8752b02..4158491 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -136,5 +136,30 @@ def list_markers(species_id: int):
@require_login
def view_dataset(species_id: int, population_id: int, dataset_id: int):
"""View details regarding a specific dataset."""
- return (f"Genotype dataset '{dataset_id}, from population '{population_id}' "
- f"of species '{species_id}'.")
+ 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"))
+
+ population = population_by_species_and_id(
+ conn, species_id, population_id)
+ if not bool(population):
+ flash("Invalid population selected!", "alert-danger")
+ return redirect(url_for(
+ "species.populations.genotypes.select_population",
+ species_id=species_id))
+
+ dataset = genotype_dataset(conn, species_id, population_id, dataset_id)
+ if not bool(dataset):
+ flash("Could not find such a dataset!", "alert-danger")
+ return redirect(url_for(
+ "species.populations.genotypes.list_genotypes",
+ species_id=species_id,
+ population_id=population_id))
+
+ return render_template("genotypes/view-dataset.html",
+ species=species,
+ population=population,
+ dataset=dataset,
+ activelink="view-dataset")
diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html
index 3780f85..864e1ec 100644
--- a/uploader/templates/genotypes/list-genotypes.html
+++ b/uploader/templates/genotypes/list-genotypes.html
@@ -129,6 +129,16 @@
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/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%}