From 1b6b9a90a4dbe38aefc00293309fb48d9f478b13 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 26 Sep 2024 17:03:31 -0500 Subject: Start building up the view dataset endpoint --- uploader/phenotypes/models.py | 31 ++++++++++ uploader/phenotypes/views.py | 17 ++++- uploader/templates/phenotypes/view-dataset.html | 82 +++++++++++++++++++++++++ 3 files changed, 129 insertions(+), 1 deletion(-) create mode 100644 uploader/templates/phenotypes/view-dataset.html (limited to 'uploader') diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index 1f72dbd..4ef674f 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -20,3 +20,34 @@ def datasets_by_population( "WHERE s.Id=%s AND iset.Id=%s;", (species_id, population_id)) return tuple(dict(row) for row in cursor.fetchall()) + + +def phenotypes_data(conn: mdb.Connection, + population_id: int, + dataset_id: int, + offset: int = 0, + limit: Optional[int] = None) -> tuple[dict, ...]: + """Fetch the data for the phenotypes.""" + #TODO: This query isn't exactly right, it misses some data. + # — Phenotype -> PublishXRef -> PublishData -> Strain -> PublishFreeze + _query = ("SELECT pxr.*, pd.*, str.* FROM PublishFreeze AS pf " + "INNER JOIN PublishXRef AS pxr ON pf.InbredSetId=pxr.InbredSetId " + "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id " + "INNER JOIN Strain AS str ON pd.StrainId=str.Id " + "WHERE pf.InbredSetId=%s AND pf.Id=%s " + "ORDER BY pxr.DataId ASC, str.Id ASC") + ( + 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_se(conn: mdb.Connection, dataset_id: int) -> tuple[dict, ...]: + """Fetch the standard errors for the phenotypes.""" + return tuple() + + +def phenotypes_sample_counts(conn: mdb.Connection, dataset_id: int) -> tuple[dict, ...]: + """Fetch the standard errors for the phenotypes.""" + return tuple() diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 7ad32ad..88cb89c 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -14,7 +14,7 @@ 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 +from .models import datasets_by_population, phenotypes_data phenotypesbp = Blueprint("phenotypes", __name__) @@ -83,3 +83,18 @@ def list_datasets(species: int, population: int, **kwargs): species["SpeciesId"], population["Id"]), activelink="list-datasets") + + +@phenotypesbp.route( + "/populations//phenotypes/datasets" + "//view", + methods=["GET"]) +@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): + """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)) diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html new file mode 100644 index 0000000..219e61e --- /dev/null +++ b/uploader/templates/phenotypes/view-dataset.html @@ -0,0 +1,82 @@ +{%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%} + +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +
+

The basic dataset details are:

+ + + + + + + + + + + + + + + + + +
NameFull NameShort Name
{{dataset.Name}}{{dataset.FullName}}{{dataset.ShortName}}
+
+ +
+

Phenotype Data

+ +

The dataset has the following phenotypes:

+ + + + + + + + + + + + + {%for pheno in phenotypes%} + + + + + + + {%else%} + + {%endfor%} + +
#NameFull NameShort Name
{{pheno.sequence_number}}{{pheno.Id}}{{pheno.FullName}}{{pheno.ShortName}}
+
+{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} -- cgit v1.2.3