diff options
Diffstat (limited to 'uploader/phenotypes/views.py')
| -rw-r--r-- | uploader/phenotypes/views.py | 67 |
1 files changed, 46 insertions, 21 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index d283e47..ddec54c 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -3,12 +3,14 @@ import sys import uuid import json import datetime +from typing import Any from pathlib import Path from zipfile import ZipFile from functools import wraps, reduce from logging import INFO, ERROR, DEBUG, FATAL, CRITICAL, WARNING from redis import Redis +from pymonad.either import Left from requests.models import Response from MySQLdb.cursors import DictCursor from gn_libs.mysqldb import database_connection @@ -195,12 +197,10 @@ def view_dataset(# pylint: disable=[unused-argument] 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), + dataset_phenotypes( + conn, + population["Id"], + dataset["Id"])), start_from=start_at, count=count, activelink="view-dataset") @@ -229,6 +229,11 @@ def view_phenotype(# pylint: disable=[unused-argument] population["Id"], dataset["Id"], xref_id) + def __non_empty__(value) -> bool: + if isinstance(value, str): + return value.strip() != "" + return bool(value) + return render_template( "phenotypes/view-phenotype.html", species=species, @@ -236,14 +241,13 @@ def view_phenotype(# pylint: disable=[unused-argument] dataset=dataset, xref_id=xref_id, phenotype=phenotype, - has_se=all(bool(item.get("error")) for item in phenotype["data"]), + has_se=any(bool(item.get("error")) for item in phenotype["data"]), publish_data={ key.replace("_", " "): val for key,val in (phenotype_publication_data(conn, phenotype["Id"]) or {}).items() if (key in ("PubMed_ID", "Authors", "Title", "Journal") - and val is not None - and val.strip() != "") + and __non_empty__(val)) }, privileges=(privileges ### For demo! Do not commit this part @@ -520,7 +524,7 @@ def job_status( @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" - "/<int:dataset_id>/review-job/<uuid:job_id>", + "/<int:dataset_id>/job/<uuid:job_id>/review", methods=["GET"]) @require_login @with_dataset( @@ -548,11 +552,12 @@ def review_job_data( 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(), - {}) + metadata: dict[str, Any] = reduce( + __metadata_by_type__, + (jobs.job_files_metadata( + rconn, jobs.jobsnamespace(), job['jobid']) + if job else {}).items(), + {}) def __desc__(filetype): match filetype: @@ -593,6 +598,7 @@ def review_job_data( def update_phenotype_metadata(conn, metadata: dict): + """Update a phenotype's basic metadata values.""" with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute("SELECT * FROM Phenotype WHERE Id=%(phenotype-id)s", metadata) @@ -623,6 +629,7 @@ def update_phenotype_metadata(conn, metadata: dict): def update_phenotype_values(conn, values): + """Update a phenotype's data values.""" with conn.cursor() as cursor: cursor.executemany( "UPDATE PublishData SET value=%(new)s " @@ -637,6 +644,7 @@ def update_phenotype_values(conn, values): def update_phenotype_se(conn, serrs): + """Update a phenotype's standard-error values.""" with conn.cursor() as cursor: cursor.executemany( "INSERT INTO PublishSE(DataId, StrainId, error) " @@ -652,6 +660,7 @@ def update_phenotype_se(conn, serrs): def update_phenotype_n(conn, counts): + """Update a phenotype's strain counts.""" with conn.cursor() as cursor: cursor.executemany( "INSERT INTO NStrain(DataId, StrainId, count) " @@ -680,9 +689,25 @@ def update_phenotype_data(conn, data: dict): def __separate_items__(acc, row): key, val = row - return ({**acc[0], key: {**val["value"], "changed?": (not val["value"]["new"] == val["value"]["original"])}}, - {**acc[1], key: {**val["se"] , "changed?": (not val["se"]["new"] == val["se"]["original"])}}, - {**acc[2], key: {**val["n"] , "changed?": (not val["n"]["new"] == val["n"]["original"])}}) + return ({ + **acc[0], + key: { + **val["value"], + "changed?": (not val["value"]["new"] == val["value"]["original"]) + } + }, { + **acc[1], + key: { + **val["se"], + "changed?": (not val["se"]["new"] == val["se"]["original"]) + } + },{ + **acc[2], + key: { + **val["n"], + "changed?": (not val["n"]["new"] == val["n"]["original"]) + } + }) values, serrs, counts = tuple( tuple({ @@ -691,8 +716,8 @@ def update_phenotype_data(conn, data: dict): "new": row[1]["new"] } for row in item) for item in ( - filter(lambda val: val[1]["changed?"], item.items()) - for item in reduce( + filter(lambda val: val[1]["changed?"], item.items())# type: ignore[arg-type] + for item in reduce(# type: ignore[var-annotated] __separate_items__, reduce(__organise_by_dataid_and_strainid__, data.items(), @@ -713,7 +738,7 @@ def update_phenotype_data(conn, data: dict): species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", redirect_uri="species.populations.phenotypes.list_datasets") -def edit_phenotype_data( +def edit_phenotype_data(# pylint: disable=[unused-argument] species: dict, population: dict, dataset: dict, |