diff options
Diffstat (limited to 'uploader/phenotypes/views.py')
| -rw-r--r-- | uploader/phenotypes/views.py | 18 |
1 files changed, 12 insertions, 6 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 97bcafe..834a450 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -374,10 +374,15 @@ def process_phenotypes_individual_files(error_uri): bundlepath = Path(app.config["UPLOAD_FOLDER"], f"{str(uuid.uuid4()).replace('-', '')}.zip") with ZipFile(bundlepath,mode="w") as zfile: - for rqtlkey, formkey in (("phenocovar", "phenotype-descriptions"), - ("pheno", "phenotype-data"), - ("phenose", "phenotype-se"), - ("phenonum", "phenotype-n")): + for rqtlkey, formkey, _type in ( + ("phenocovar", "phenotype-descriptions", "mandatory"), + ("pheno", "phenotype-data", "mandatory"), + ("phenose", "phenotype-se", "optional"), + ("phenonum", "phenotype-n", "optional")): + if _type == "optional" and not bool(form.get(formkey)): + # skip if an optional key does not exist. + continue + cdata[f"{rqtlkey}_transposed"] = ( (form.get(f"{formkey}-transposed") or "off") == "on") @@ -1010,8 +1015,9 @@ def load_data_success( gn2_uri = urlparse(app.config["GN2_SERVER_URL"]) job = gnlibs_jobs.job(jobsconn, job_id, fulldetails=True) app.logger.debug("THE JOB: %s", job) - _xref_ids = (str(item) for item - in json.loads(job["metadata"].get("xref_ids", "[]"))) + _xref_ids = tuple( + str(item) for item + in json.loads(job["metadata"].get("xref_ids", "[]"))) _publication = fetch_publication_by_id( conn, int(job["metadata"].get("publication_id", "0"))) _search_terms = (item for item in |