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authorFrederick Muriuki Muriithi2024-09-27 11:43:48 -0500
committerFrederick Muriuki Muriithi2024-09-27 11:43:48 -0500
commitf04e340323d0e289aaa379ab1a8d82033da73e62 (patch)
treebe44d5f39b9dfbc4d78cf2f296bc5f6ec8c2830d /uploader
parent0729e38e2f5bbc5ab23153adfed3d35ee59dc3d5 (diff)
downloadgn-uploader-f04e340323d0e289aaa379ab1a8d82033da73e62.tar.gz
Show some details for a phenotype dataset.
Diffstat (limited to 'uploader')
-rw-r--r--uploader/phenotypes/models.py48
-rw-r--r--uploader/phenotypes/views.py47
-rw-r--r--uploader/templates/phenotypes/view-dataset.html23
3 files changed, 98 insertions, 20 deletions
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index 4ef674f..c3b6dfb 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -22,6 +22,54 @@ def datasets_by_population(
return tuple(dict(row) for row in cursor.fetchall())
+def dataset_by_id(conn: mdb.Connection,
+ species_id: int,
+ population_id: int,
+ dataset_id: int) -> dict:
+ """Fetch dataset details by identifier"""
+ 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 AND pf.Id=%s",
+ (species_id, population_id, dataset_id))
+ return dict(cursor.fetchone())
+
+
+def phenotypes_count(conn: mdb.Connection,
+ population_id: int,
+ dataset_id: int) -> int:
+ """Count the number of phenotypes in the dataset."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "SELECT COUNT(*) AS total_phenos FROM Phenotype AS pheno "
+ "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
+ "INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId "
+ "WHERE pxr.InbredSetId=%s AND pf.Id=%s",
+ (population_id, dataset_id))
+ return int(cursor.fetchone()["total_phenos"])
+
+
+def dataset_phenotypes(conn: mdb.Connection,
+ population_id: int,
+ dataset_id: int,
+ offset: int = 0,
+ limit: Optional[int] = None) -> tuple[dict, ...]:
+ """Fetch the actual phenotypes."""
+ _query = (
+ "SELECT pheno.*, pxr.Id, ist.InbredSetCode FROM Phenotype AS pheno "
+ "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
+ "INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId "
+ "INNER JOIN InbredSet AS ist ON pf.InbredSetId=ist.Id "
+ "WHERE pxr.InbredSetId=%s AND pf.Id=%s") + (
+ f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(_query, (population_id, dataset_id))
+ debug_query(cursor)
+ return tuple(dict(row) for row in cursor.fetchall())
+
+
def phenotypes_data(conn: mdb.Connection,
population_id: int,
dataset_id: int,
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 88cb89c..4565844 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -1,20 +1,24 @@
"""Views handling ('classical') phenotypes."""
-from flask import (request,
+from flask import (flash,
+ request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
-from uploader.datautils import order_by_family
from uploader.authorisation import require_login
from uploader.db_utils import database_connection
from uploader.species.models import all_species, species_by_id
from uploader.request_checks import with_species, with_population
+from uploader.datautils import safe_int, order_by_family, enumerate_sequence
from uploader.population.models import (populations_by_species,
population_by_species_and_id)
-from .models import datasets_by_population, phenotypes_data
+from .models import (dataset_by_id,
+ phenotypes_count,
+ dataset_phenotypes,
+ datasets_by_population)
phenotypesbp = Blueprint("phenotypes", __name__)
@@ -40,7 +44,7 @@ def index():
methods=["GET"])
@require_login
@with_species(redirect_uri="species.populations.phenotypes.index")
-def select_population(species: dict, **kwargs):
+def select_population(species: dict, **kwargs):# pylint: disable=[unused-argument]
"""Select the population for your phenotypes."""
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("population_id")):
@@ -58,7 +62,7 @@ def select_population(species: dict, **kwargs):
flash("No such population found!", "alert-danger")
return redirect(url_for(
"species.populations.phenotypes.select_population",
- species_id=species_id))
+ species_id=species["SpeciesId"]))
return redirect(url_for("species.populations.phenotypes.list_datasets",
species_id=species["SpeciesId"],
@@ -72,7 +76,7 @@ def select_population(species: dict, **kwargs):
@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):
+def list_datasets(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
"""List available phenotype datasets."""
with database_connection(app.config["SQL_URI"]) as conn:
return render_template("phenotypes/list-datasets.html",
@@ -92,9 +96,32 @@ def list_datasets(species: int, population: int, **kwargs):
@require_login
@with_population(species_redirect_uri="species.populations.phenotypes.index",
redirect_uri="species.populations.phenotypes.select_population")
-def view_dataset(species: int, population: int, dataset_id: int, **kwargs):
+def view_dataset(# pylint: disable=[unused-argument]
+ species: dict, population: dict, dataset_id: int, **kwargs):
"""View a specific dataset"""
with database_connection(app.config["SQL_URI"]) as conn:
- from flask import jsonify
- return jsonify(phenotypes_data(
- conn, population["Id"], dataset_id, offset=0, limit=20))
+ dataset = dataset_by_id(
+ conn, species["SpeciesId"], population["Id"], dataset_id)
+ if not bool(dataset):
+ flash("Could not find such a phenotype dataset!", "alert-danger")
+ return redirect(url_for(
+ "species.populations.phenotypes.list_datasets",
+ species_id=species["SpeciesId"],
+ population_id=population["Id"]))
+
+ start_at = max(safe_int(request.args.get("start_at") or 0), 0)
+ count = int(request.args.get("count") or 20)
+ return render_template("phenotypes/view-dataset.html",
+ species=species,
+ population=population,
+ dataset={"Id": dataset_id},
+ phenotype_count=phenotypes_count(
+ conn, population["Id"], dataset_id),
+ phenotypes=enumerate_sequence(
+ dataset_phenotypes(conn,
+ population["Id"],
+ dataset_id,
+ offset=start_at,
+ limit=count),
+ start=start_at+1),
+ activelink="view-dataset")
diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html
index 219e61e..fc393d6 100644
--- a/uploader/templates/phenotypes/view-dataset.html
+++ b/uploader/templates/phenotypes/view-dataset.html
@@ -7,14 +7,15 @@
{%block pagetitle%}Phenotypes{%endblock%}
{%block lvl4_breadcrumbs%}
-<li {%if activelink=="view-datasets"%}
+<li {%if activelink=="view-dataset"%}
class="breadcrumb-item active"
{%else%}
class="breadcrumb-item"
{%endif%}>
- <a href="{{url_for('species.populations.phenotypes.view_datasets',
+ <a href="{{url_for('species.populations.phenotypes.view_dataset',
species_id=species.SpeciesId,
- population_id=population.Id)}}">View Datasets</a>
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}">View Datasets</a>
</li>
{%endblock%}
@@ -49,15 +50,18 @@
<div class="row">
<h2>Phenotype Data</h2>
- <p>The dataset has the following phenotypes:</p>
+ <p>This dataset has a total of {{phenotype_count}} phenotypes.</p>
+ <p class="text-danger">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ Limit access here, according to the authorisation privileges the user has on
+ this dataset!</p>
<table class="table">
<thead>
<tr>
<th>#</th>
- <th>Name</th>
- <th>Full Name</th>
- <th>Short Name</th>
+ <th>Record</th>
+ <th>Description</th>
</tr>
</thead>
@@ -65,9 +69,8 @@
{%for pheno in phenotypes%}
<tr>
<td>{{pheno.sequence_number}}</td>
- <td>{{pheno.Id}}</td>
- <td>{{pheno.FullName}}</td>
- <td>{{pheno.ShortName}}</td>
+ <td>{{pheno.InbredSetCode}}_{{pheno["pxr.Id"]}}</td>
+ <td>{{pheno.Post_publication_description or pheno.Pre_publication_abbreviation or pheno.Original_description}}</td>
</tr>
{%else%}
<tr><td colspan="5"></td></tr>