Retrieve ALL markers for a species regardless of data.

Retrieve all the genetic markers that exist for a particular species
regardless of whether or not a particular marker has corresponding
samples allele data.

3 files changed, 24 insertions, 27 deletions

diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
index 4f09b02..34d2cfe 100644
--- a/uploader/genotypes/models.py
+++ b/uploader/genotypes/models.py
@@ -29,29 +29,28 @@ def genotype_markers_count(conn: mdb.Connection, species_id: int) -> int:
 def genotype_markers(
         conn: mdb.Connection,
         species_id: int,
-        dataset_id: int,
         offset: int = 0,
         limit: Optional[int] = None
 ) -> tuple[tuple[dict, ...], int]:
     """Retrieve markers from the database."""
     _query_template = (
-        "SELECT %%COLS%% FROM GenoXRef AS gxr INNER JOIN Geno AS gno "
-        "ON gxr.GenoId=gno.Id WHERE gxr.GenoFreezeId=%s AND gno.SpeciesId=%s "
+        "SELECT %%COLS%% FROM Geno AS gno "
+        "WHERE gno.SpeciesId=%s "
         "%%LIMIT%%")
 
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(
             _query_template.replace("%%LIMIT%%", "").replace(
-                "%%COLS%%", "COUNT(gxr.GenoId) AS total_records"),
-            (species_id, dataset_id))
+                "%%COLS%%", "COUNT(gno.Id) AS total_records"),
+            (species_id,))
         _total_records = cursor.fetchone()["total_records"]
         cursor.execute(
-            _query_template.replace("%%COLS%%", "gxr.GenoFreezeId, gno.*").replace(
+            _query_template.replace("%%COLS%%", "gno.*").replace(
                 "%%LIMIT%%",
                 (f"LIMIT {int(limit)} OFFSET {int(offset)}"
                  if bool(limit) and limit > 0
                  else "")),
-            (species_id, dataset_id))
+            (species_id,))
         debug_query(cursor, app.logger)
         return tuple(dict(row) for row in cursor.fetchall()), _total_records
 
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 42f41a8..f27671c 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -60,17 +60,15 @@ def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable=
     "/<int:species_id>/populations/<int:population_id>/genotypes/<int:dataset_id>/list-markers",
     methods=["GET"])
 @require_login
-@with_dataset(species_redirect_uri="species.list_species",
-              population_redirect_uri="species.populations.list_species_populations",
-              redirect_uri="species.populations.genotypes.list_genotypes",
-              dataset_by_id=genotype_dataset)
-def list_markers(species: dict, population: dict, dataset: dict, **_kwargs):
-    """List the markers uploaded for this dataset."""
+@with_species(redirect_uri="species.populations.genotypes.list_genotypes")
+def list_markers(species: dict, **_kwargs):
+    """List the markers that exist for this species."""
     args = request.args
     offset = int(args.get("start") or 0)
     with database_connection(app.config["SQL_URI"]) as conn:
         markers, total_records = genotype_markers(
-            conn, species["SpeciesId"], dataset["Id"],
+            conn,
+            species["SpeciesId"],
             offset=offset,
             limit=int(args.get("length") or 0))
         return jsonify({
diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html
index 38a1b8f..131576f 100644
--- a/uploader/templates/genotypes/list-genotypes.html
+++ b/uploader/templates/genotypes/list-genotypes.html
@@ -60,6 +60,7 @@
 {%if dataset is not none%}
 
 <div class="row">
+  <h3>Dataset Details</h3>
   <table class="table">
     <thead>
       <tr>
@@ -81,17 +82,22 @@
       </tr>
     </tbody>
   </table>
-</div>
-
-<div class="row">
-  <h3>Genotype Data</h3>
 
-  <div class="col" style="margin-bottom: 3px;">
-    <a href="#" class="btn btn-primary">upload genotypes</a>
-  </div>
+  <p>
+    To see more information regarding this dataset (e.g. which markers have
+    sample allele data, the allele data itself, etc) click on the "Full Name"
+    link above.</p>
 </div>
 
 <div class="row">
+  <h3>Genotype Markers</h3>
+
+  <div class="row">
+    <p>
+      The table below lists all of the markers that exist for species
+      {{species.SpeciesName}} ({{species.FullName}}), regardless of whether
+      (or not) we have corresponding sample allele data for a particular marker.
+    </p>
   <table id="tbl-genetic-markers" class="table compact stripe cell-border">
     <thead>
       <tr>
@@ -121,12 +127,6 @@
   </table>
 </div>
 
-<div class="row text-warning">
-  <h3>Assembly Details</h3>
-
-  <p>Maybe include the assembly details here if found to be necessary.</p>
-</div>
-
 {%else%}
 
 <div class="row">