Fix display issues

README.md

@@ -32,3 +32,9 @@ When running, it will default to using a SQLite3 database located in the root of
 ## Using the library
 
 The `sample_registry` library can be installed and run anywhere by following the instructions in Development (you don't need to do the `create_test_db` and running the site (bottom two commands)). To connect it to a Postgres backend, you'll need to also set the environment variables `DB_HOST`, `DB_USER`, `DB_NAME`, and `DB_PSWD`.
+
+## Manually build Docker image
+
+If you want to iterate over a feature you can only test on the K8s deployment, you can manually build the Docker image instead of relying on the release workflow. Use `docker build -t ctbushman/sample_registry:latest -f Dockerfile .` to build the image and then `docker push ctbushman/sample_registry:latest` to push it to DockerHub. You can then trigger the K8s deployment to grab the new image.
+
+N.B. You might want to use a different tag than `latest` if you're testing something volatile so that if someone else is trying to use the image as you're developing, they won't pull your wonky changes.

app/sample_registry/src/sample_registry/register.py

@@ -46,6 +46,8 @@ def unregister_samples(argv=None, session: Session = None, out=sys.stdout):
     samples_removed = registry.remove_samples(args.run_accession)
     out.write("Removed {0} samples: {1}".format(len(samples_removed), samples_removed))
 
+    session.commit()
+
 
 def register_samples():
     return register_sample_annotations(None, True)
@@ -78,6 +80,8 @@ def register_sample_annotations(
         registry.register_samples(args.run_accession, sample_table)
     registry.register_annotations(args.run_accession, sample_table)
 
+    session.commit()
+
 
 def parse_tsv_ncol(f, ncol: int) -> Generator[tuple[str], None, None]:
     assert ncol > 0
@@ -107,6 +111,8 @@ def register_sample_types(argv=None, session: Session = None):
     registry.remove_standard_sample_types()
     registry.register_standard_sample_types(sample_types)
 
+    session.commit()
+
 
 def register_host_species(argv=None, session: Session = None):
     p = argparse.ArgumentParser(
@@ -120,6 +126,8 @@ def register_host_species(argv=None, session: Session = None):
     registry.remove_standard_host_species()
     registry.register_standard_host_species(host_species)
 
+    session.commit()
+
 
 def register_illumina_file(argv=None, session: Session = None, out=sys.stdout):
     p = argparse.ArgumentParser(
@@ -136,6 +144,8 @@ def register_illumina_file(argv=None, session: Session = None, out=sys.stdout):
     )
     out.write("Registered run {0} in the database\n".format(acc))
 
+    session.commit()
+
 
 def register_run(argv=None, session: Session = None, out=sys.stdout):
     p = argparse.ArgumentParser(description="Add a new run to the registry")
@@ -156,3 +166,5 @@ def register_run(argv=None, session: Session = None, out=sys.stdout):
         args.date, args.type, "Nextera XT", args.lane, args.file, args.comment
     )
     out.write("Registered run %s in the database\n" % acc)
+
+    session.commit()

app/sample_registry/src/sample_registry/registrar.py

@@ -43,7 +43,7 @@ def register_run(
         data_uri: str,
         comment: str,
     ) -> int:
-        run_acc = self.session.scalar(
+        return self.session.scalar(
             insert(Run)
             .returning(Run.run_accession)
             .values(
@@ -58,9 +58,6 @@ def register_run(
             )
         )
 
-        self.session.commit()
-        return run_acc
-
     def register_samples(
         self, run_accession: int, sample_table: SampleTable
     ) -> list[int]:
@@ -79,7 +76,7 @@ def register_samples(
         ).first():
             raise ValueError("Samples already registered for run %s" % run_accession)
 
-        sample_accs = self.session.scalars(
+        return self.session.scalars(
             insert(Sample)
             .returning(Sample.sample_accession)
             .values(
@@ -94,9 +91,6 @@ def register_samples(
             )
         )
 
-        self.session.commit()
-        return sample_accs
-
     def remove_samples(self, run_accession: int) -> list[int]:
         samples = self.session.scalars(
             select(Sample.sample_accession).where(Sample.run_accession == run_accession)
@@ -108,7 +102,6 @@ def remove_samples(self, run_accession: int) -> list[int]:
             delete(Sample).where(Sample.run_accession == run_accession)
         )
 
-        self.session.commit()
         return samples
 
     def register_annotations(self, run_accession: int, sample_table: SampleTable):
@@ -152,7 +145,6 @@ def register_annotations(self, run_accession: int, sample_table: SampleTable):
                 )
             )
 
-        self.session.commit()
         return annotation_keys
 
     def _get_sample_accessions(
@@ -182,7 +174,6 @@ def _get_sample_accessions(
 
     def remove_standard_sample_types(self):
         self.session.execute(delete(StandardSampleType))
-        self.session.commit()
 
     def register_standard_sample_types(self, sample_types: list[tuple[str, str, bool]]):
         self.session.execute(
@@ -198,11 +189,8 @@ def register_standard_sample_types(self, sample_types: list[tuple[str, str, bool
             )
         )
 
-        self.session.commit()
-
     def remove_standard_host_species(self):
         self.session.execute(delete(StandardHostSpecies))
-        self.session.commit()
 
     def register_standard_host_species(
         self, host_species
@@ -219,5 +207,3 @@ def register_standard_host_species(
                 ]
             )
         )
-
-        self.session.commit()