Include the publication when provided.

1 files changed, 12 insertions, 2 deletions

diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 92a7c4b..20b95e2 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -40,6 +40,7 @@ from uploader.route_utils import generic_select_population
 from uploader.datautils import safe_int, enumerate_sequence
 from uploader.species.models import all_species, species_by_id
 from uploader.monadic_requests import make_either_error_handler
+from uploader.publications.models import fetch_publication_by_id
 from uploader.request_checks import with_species, with_population
 from uploader.samples.models import samples_by_species_and_population
 from uploader.input_validation import (encode_errors,
@@ -465,7 +466,9 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p
                     "speciesid": species["SpeciesId"],
                     "populationid": population["Id"],
                     "datasetid": dataset["Id"],
-                    "bundle": str(phenobundle.absolute())})}),
+                    "bundle": str(phenobundle.absolute()),
+                    **({"publicationid": request.form["publication-id"]}
+                       if request.form.get("publication-id") else {})})}),
             _redisuri,
             f"{app.config['UPLOAD_FOLDER']}/job_errors")
 
@@ -538,7 +541,8 @@ def review_job_data(
         **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:
+    with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn,
+          database_connection(app.config["SQL_URI"]) as conn):
         try:
             job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id))
         except jobs.JobNotFound as _jnf:
@@ -586,6 +590,7 @@ def review_job_data(
             filetype: __summarise__(filetype, meta)
             for filetype,meta in metadata.items()
         }
+        _job_metadata = json.loads(job["job-metadata"])
         return render_template("phenotypes/review-job-data.html",
                                species=species,
                                population=population,
@@ -593,6 +598,11 @@ def review_job_data(
                                job_id=job_id,
                                job=job,
                                summary=summary,
+                               publication=(
+                                   fetch_publication_by_id(
+                                       conn, int(_job_metadata["publicationid"]))
+                                   if _job_metadata.get("publicationid")
+                                   else None),
                                activelink="add-phenotypes")