Small updates after testing.

loculus-project · Jul 23, 2024 · 7147777 · 7147777
1 parent 992d254
commit 7147777
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Showing 5 changed files with 22 additions and 5 deletions.
diff --git a/ena-submission/Snakefile b/ena-submission/Snakefile
@@ -96,6 +96,21 @@ rule create_project:
             --log-level {params.log_level} \
         """
 
+rule create_sample:
+    input:
+        script="scripts/create_sample.py",
+        config="results/config.yaml",
+    output:
+        sample_created=touch("results/sample_created"),
+    params:
+        log_level=LOG_LEVEL,
+    shell:
+        """
+        python {input.script} \
+            --config-file {input.config} \
+            --log-level {params.log_level} \
+        """
+
 rule get_ena_submission_list_and_sleep:
     input:
         file="results/ena_submission_list.json"

diff --git a/ena-submission/scripts/create_project.py b/ena-submission/scripts/create_project.py
@@ -61,6 +61,9 @@ def construct_project_set_object(
     project_type = ProjectType(
         center_name=XmlAttribute(group_info["institution"]),
         alias=XmlAttribute(f"{row["group_id"]}:{row["organism"]}:{config.unique_project_suffix}"),
+        # alias=XmlAttribute(
+        #     f"{row["group_id"]}:{row["organism"]}:{config.unique_project_suffix}:{datetime.now(tz=pytz.utc)}"  # For testing
+        # ),
         name=metadata_dict["scientific_name"],
         title=f"{metadata_dict["scientific_name"]}: Genome sequencing",
         description=(
@@ -275,7 +278,7 @@ def create_project(log_level, config_file):
             f"Found {len(entries_with_errors)} entries in project_table in status HAS_ERRORS",
             f" for {time_threshold}m",
         )
-        for row in ready_to_submit_project:
+        for row in entries_with_errors:
             # TODO: Query ENA to check if project has in fact been created
             # If created update project_table
             # If not retry 3 times, then raise for manual intervention

diff --git a/ena-submission/scripts/ena_submission_helper.py b/ena-submission/scripts/ena_submission_helper.py
@@ -131,7 +131,7 @@ def get_sample_xml(sample_set):
         submission_set = get_submission_dict()
         files = {
             "SUBMISSION": xmltodict.unparse(submission_set, pretty=True),
-            "SAMPLE": dataclass_to_xml(sample_set, root_name="PROJECT_SET"),
+            "SAMPLE": dataclass_to_xml(sample_set, root_name="SAMPLE_SET"),
         }
         return files
 

diff --git a/ena-submission/scripts/submission_db_helper.py b/ena-submission/scripts/submission_db_helper.py
@@ -76,8 +76,7 @@ class SubmissionTableEntry:
 
 @dataclass
 class ProjectTableEntry:
-    accession: str
-    version: str
+    group_id: int
     organism: str
     errors: str | None = None
     warnings: str | None = None

diff --git a/ena-submission/scripts/test_ena_submission.py b/ena-submission/scripts/test_ena_submission.py
@@ -159,7 +159,7 @@ def test_sample_set_construction(self):
         organism_metadata["taxon_id"] = "Test taxon"
         center_name = "Fake center name"
         config = mock.Mock()
-        config.metadata_map = {
+        config.metadata_mapping = {
             "subject exposure": {"loculus_fields": ["exposure_event"]},
             "type exposure": {"loculus_fields": ["exposure_event"]},
             "hospitalisation": {