diff options
Diffstat (limited to 'uploader/phenotypes/views.py')
| -rw-r--r-- | uploader/phenotypes/views.py | 24 |
1 files changed, 4 insertions, 20 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 0e626ad..94f66a7 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -29,7 +29,6 @@ from flask import (flash, Blueprint, current_app as app) -# from r_qtl import r_qtl2 as rqtl2 from r_qtl import r_qtl2_qc as rqc from r_qtl import exceptions as rqe @@ -253,12 +252,7 @@ def view_phenotype(# pylint: disable=[unused-argument] if (key in ("PubMed_ID", "Authors", "Title", "Journal") and __non_empty__(val)) }, - privileges=(privileges - ### For demo! Do not commit this part - + ("group:resource:edit-resource", - "group:resource:delete-resource",) - ### END: For demo! Do not commit this part - ), + privileges=privileges, activelink="view-phenotype") def __fail__(error): @@ -371,8 +365,7 @@ def process_phenotypes_individual_files(error_uri): ("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 + continue # skip if an optional key does not exist. cdata[f"{rqtlkey}_transposed"] = ( (form.get(f"{formkey}-transposed") or "off") == "on") @@ -424,10 +417,7 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p dataset_id=dataset["Id"])) _redisuri = app.config["REDIS_URL"] _sqluri = app.config["SQL_URI"] - with (Redis.from_url(_redisuri, decode_responses=True) as rconn, - # database_connection(_sqluri) as conn, - # conn.cursor(cursorclass=DictCursor) as cursor - ): + with Redis.from_url(_redisuri, decode_responses=True) as rconn: if request.method == "GET": today = datetime.date.today() return render_template( @@ -462,7 +452,6 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p [sys.executable, "-m", "scripts.rqtl2.phenotypes_qc", _sqluri, _redisuri, _namespace, str(_jobid), str(species["SpeciesId"]), str(population["Id"]), - # str(dataset["Id"]), str(phenobundle), "--loglevel", logging.getLevelName( @@ -855,12 +844,7 @@ def edit_phenotype_data(# pylint: disable=[unused-argument] def __render__(**kwargs): processed_kwargs = { **kwargs, - "privileges": (kwargs.get("privileges", tuple()) - ### For demo! Do not commit this part - + ("group:resource:edit-resource", - "group:resource:delete-resource",) - ### END: For demo! Do not commit this part - ) + "privileges": kwargs.get("privileges", tuple()) } return render_template( "phenotypes/edit-phenotype.html", |