From 190e1c7cb924ac9598956ac0f2be37ed3915ab23 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 23 Jan 2025 11:23:05 -0600
Subject: Provide summary for review before entering data to database.
---
uploader/phenotypes/views.py | 76 +++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 75 insertions(+), 1 deletion(-)
(limited to 'uploader/phenotypes/views.py')
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index ec4c840..53e68d1 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -5,7 +5,7 @@ import json
import datetime
from pathlib import Path
from zipfile import ZipFile
-from functools import wraps
+from functools import wraps, reduce
from logging import INFO, ERROR, DEBUG, FATAL, CRITICAL, WARNING
from redis import Redis
@@ -502,3 +502,77 @@ def job_status(
metadata=jobs.job_files_metadata(
rconn, jobs.jobsnamespace(), job['jobid']),
activelink="add-phenotypes")
+
+
+@phenotypesbp.route(
+ "<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
+ "/<int:dataset_id>/review-job/<uuid:job_id>",
+ methods=["GET"])
+@require_login
+@with_dataset(
+ species_redirect_uri="species.populations.phenotypes.index",
+ population_redirect_uri="species.populations.phenotypes.select_population",
+ redirect_uri="species.populations.phenotypes.list_datasets")
+def review_job_data(
+ species: dict,
+ population: dict,
+ dataset: dict,
+ job_id: uuid.UUID,
+ **kwargs
+):# pylint: disable=[unused-argument]
+ """Review data one more time before entering it into the database."""
+ with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+ try:
+ job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id))
+ except jobs.JobNotFound as _jnf:
+ job = None
+
+ def __metadata_by_type__(by_type, item):
+ filetype = item[1]["filetype"]
+ return {
+ **by_type,
+ filetype: (by_type.get(filetype, tuple())
+ + ({"filename": item[0], **item[1]},))
+ }
+ metadata = reduce(__metadata_by_type__,
+ (jobs.job_files_metadata(
+ rconn, jobs.jobsnamespace(), job['jobid'])
+ if job else {}).items(),
+ {})
+
+ def __desc__(filetype):
+ match filetype:
+ case "phenocovar":
+ desc = "phenotypes"
+ case "pheno":
+ desc = "phenotypes data"
+ case "phenose":
+ desc = "phenotypes standard-errors"
+ case "phenonum":
+ desc = "phenotypes samples"
+ case _:
+ desc = f"unknown file type '{filetype}'."
+
+ return desc
+
+ def __summarise__(filetype, files):
+ return {
+ "filetype": filetype,
+ "number-of-files": len(files),
+ "total-data-rows": sum(
+ int(afile["linecount"]) - 1 for afile in files),
+ "description": __desc__(filetype)
+ }
+
+ summary = {
+ filetype: __summarise__(filetype, meta)
+ for filetype,meta in metadata.items()
+ }
+ return render_template("phenotypes/review-job-data.html",
+ species=species,
+ population=population,
+ dataset=dataset,
+ job_id=job_id,
+ job=job,
+ summary=summary,
+ activelink="add-phenotypes")
--
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