Include the publication when provided.

3 files changed, 26 insertions, 4 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")
 
 
diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
index 2ff6a4f..5709491 100644
--- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html
+++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
@@ -585,6 +585,7 @@
           }));
       });
       formdata.append("resumable-upload", "true");
+      formdata.append("publication-id", $("#txt-publication-id").val());
       return formdata;
   }
 
diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html
index 7bc8c62..befb5e2 100644
--- a/uploader/templates/phenotypes/review-job-data.html
+++ b/uploader/templates/phenotypes/review-job-data.html
@@ -40,9 +40,20 @@
     species &#x201C;<strong>{{species.SpeciesName}} ({{species.FullName}})</strong>&#x201D;
     will be updated as follows:</p>
 
+  <ul>
+    {%if publication%}
+    <li>All {{summary.get("pheno", {}).get("total-data-rows", "0")}} phenotypes
+      are linked to the following publication:
+      <ul>
+        <li><strong>Publication Title:</strong>
+          {{publication.Title or "—"}}</li>
+        <li><strong>Author(s):</strong>
+          {{publication.Authors or "—"}}</li>
+      </ul>
+    </li>
+    {%endif%}
   {%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%}
   {%if summary.get(ftype, False)%}
-  <ul>
     <li>A total of {{summary[ftype]["number-of-files"]}} files will be processed
       adding {%if ftype == "phenocovar"%}(possibly){%endif%}
       {{summary[ftype]["total-data-rows"]}} new
@@ -53,9 +64,9 @@
       {%endif%}
       to the database.
     </li>
-  </ul>
   {%endif%}
   {%endfor%}
+  </ul>
 
   <a href="#" class="not-implemented btn btn-primary">continue</a>
 </div>