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-rw-r--r--uploader/phenotypes/models.py22
-rw-r--r--uploader/phenotypes/views.py22
-rw-r--r--uploader/templates/phenotypes/list-datasets.html63
3 files changed, 107 insertions, 0 deletions
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
new file mode 100644
index 0000000..1f72dbd
--- /dev/null
+++ b/uploader/phenotypes/models.py
@@ -0,0 +1,22 @@
+"""Database and utility functions for phenotypes."""
+from typing import Optional
+
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+from uploader.db_utils import debug_query
+
+def datasets_by_population(
+ conn: mdb.Connection,
+ species_id: int,
+ population_id: int
+) -> tuple[dict, ...]:
+ """Retrieve all of a population's phenotype studies."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "SELECT s.SpeciesId, pf.* FROM Species AS s "
+ "INNER JOIN InbredSet AS iset ON s.Id=iset.SpeciesId "
+ "INNER JOIN PublishFreeze AS pf ON iset.Id=pf.InbredSetId "
+ "WHERE s.Id=%s AND iset.Id=%s;",
+ (species_id, population_id))
+ return tuple(dict(row) for row in cursor.fetchall())
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 9185f4c..7ad32ad 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -14,6 +14,8 @@ from uploader.request_checks import with_species, with_population
from uploader.population.models import (populations_by_species,
population_by_species_and_id)
+from .models import datasets_by_population
+
phenotypesbp = Blueprint("phenotypes", __name__)
@phenotypesbp.route("/phenotypes", methods=["GET"])
@@ -61,3 +63,23 @@ def select_population(species: dict, **kwargs):
return redirect(url_for("species.populations.phenotypes.list_datasets",
species_id=species["SpeciesId"],
population_id=population["Id"]))
+
+
+
+@phenotypesbp.route(
+ "<int:species_id>/populations/<int:population_id>/phenotypes/datasets",
+ methods=["GET"])
+@require_login
+@with_population(species_redirect_uri="species.populations.phenotypes.index",
+ redirect_uri="species.populations.phenotypes.select_population")
+def list_datasets(species: int, population: int, **kwargs):
+ """List available phenotype datasets."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ return render_template("phenotypes/list-datasets.html",
+ species=species,
+ population=population,
+ datasets=datasets_by_population(
+ conn,
+ species["SpeciesId"],
+ population["Id"]),
+ activelink="list-datasets")
diff --git a/uploader/templates/phenotypes/list-datasets.html b/uploader/templates/phenotypes/list-datasets.html
new file mode 100644
index 0000000..360fd2c
--- /dev/null
+++ b/uploader/templates/phenotypes/list-datasets.html
@@ -0,0 +1,63 @@
+{%extends "phenotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%block title%}Phenotypes{%endblock%}
+
+{%block pagetitle%}Phenotypes{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="list-datasets"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.phenotypes.list_datasets',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}">List Datasets</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ {%if datasets | length > 0%}
+ <p>The dataset(s) available for this population is/are:</p>
+
+ <table class="table">
+ <thead>
+ <tr>
+ <th>Name</th>
+ <th>Full Name</th>
+ <th>Short Name</th>
+ </tr>
+ </thead>
+
+ <tbody>
+ {%for dataset in datasets%}
+ <tr>
+ <td><a href="{{url_for('species.populations.phenotypes.view_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}">{{dataset.Name}}</a></td>
+ <td>{{dataset.FullName}}</td>
+ <td>{{dataset.ShortName}}</td>
+ </tr>
+ {%endfor%}
+ </tbody>
+ </table>
+ {%else%}
+ <p class="text-warning">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ There is no dataset for this population!</p>
+ <p><a href="#"
+ class="not-implemented btn btn-primary"
+ title="Create a new phenotype dataset.">create dataset</a></p>
+ {%endif%}
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}