diff options
Diffstat (limited to 'uploader/phenotypes/views.py')
| -rw-r--r-- | uploader/phenotypes/views.py | 99 |
1 files changed, 92 insertions, 7 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index ec4c840..8ecd305 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 @@ -44,7 +44,8 @@ from .models import (dataset_by_id, phenotypes_count, save_new_dataset, dataset_phenotypes, - datasets_by_population) + datasets_by_population, + phenotype_publication_data) phenotypesbp = Blueprint("phenotypes", __name__) render_template = make_template_renderer("phenotypes") @@ -220,16 +221,26 @@ def view_phenotype(# pylint: disable=[unused-argument] ): """View an individual phenotype from the dataset.""" def __render__(privileges): + phenotype = phenotype_by_id(conn, + species["SpeciesId"], + population["Id"], + dataset["Id"], + xref_id) return render_template( "phenotypes/view-phenotype.html", species=species, population=population, dataset=dataset, - phenotype=phenotype_by_id(conn, - species["SpeciesId"], - population["Id"], - dataset["Id"], - xref_id), + phenotype=phenotype, + has_se=all(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() is not "") + }, privileges=(privileges ### For demo! Do not commit this part + ("group:resource:edit-resource", @@ -502,3 +513,77 @@ 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") |