Merge pull request #1723 from microbiomedata/issue-1722-submission-schema-11.10.0-rc.1

Upgrade to nmdc-submission-schema v11.10.0-rc.1

Author: pkalita-lbl

nmdc_server/migrations/versions/0cb677fa8d5e_update_jgi_submission-schema_slot_names.py

@@ -0,0 +1,119 @@
+"""Update JGI submission-schema slot names
+
+Revision ID: 0cb677fa8d5e
+Revises: e27443f0837e
+Create Date: 2025-08-06 19:53:09.430148
+
+"""
+
+from collections import namedtuple
+from typing import Optional
+from uuid import uuid4
+
+from alembic import op
+from sqlalchemy import Column, orm
+from sqlalchemy.dialects.postgresql import JSONB, UUID
+from sqlalchemy.ext.declarative import declarative_base
+
+# revision identifiers, used by Alembic.
+revision: str = "0cb677fa8d5e"
+down_revision: Optional[str] = "e27443f0837e"
+branch_labels: Optional[str] = None
+depends_on: Optional[str] = None
+
+
+Base = declarative_base()
+
+
+class SubmissionMetadata(Base):
+    __tablename__ = "submission_metadata"
+
+    id = Column(UUID(as_uuid=True), primary_key=True, default=uuid4)
+    metadata_submission = Column(JSONB, nullable=False)
+
+
+RenamedSlot = namedtuple("RenamedSlot", ["old_name_mg", "old_name_mt", "new_name"])
+
+
+RENAMED_SLOTS: list[RenamedSlot] = [
+    RenamedSlot("dna_absorb1", "rna_absorb1", "nuc_acid_absorb1"),
+    RenamedSlot("dna_absorb2", "rna_absorb2", "nuc_acid_absorb2"),
+    RenamedSlot("dna_concentration", "rna_concentration", "nuc_acid_concentration"),
+    RenamedSlot("dna_cont_type", "rna_cont_type", "cont_type"),
+    RenamedSlot("dna_cont_well", "rna_cont_well", "cont_well"),
+    RenamedSlot("dna_container_id", "rna_container_id", "container_name"),
+    RenamedSlot("dna_dnase", "dnase_rna", "dnase"),
+    RenamedSlot("dna_samp_id", "rna_samp_id", "jgi_samp_id"),
+    RenamedSlot("dna_sample_format", "rna_sample_format", "jgi_sample_format"),
+    RenamedSlot("dna_sample_name", "rna_sample_name", "jgi_sample_name"),
+    RenamedSlot("dna_seq_project", "rna_seq_project", "jgi_seq_project"),
+    RenamedSlot("dna_seq_project_name", "rna_seq_project_name", "jgi_seq_project_name"),
+    RenamedSlot("dna_volume", "rna_volume", "jgi_sample_volume"),
+]
+
+
+def upgrade():
+    session = orm.Session(bind=op.get_bind())
+    mappings = []
+    for submission_metadata in session.query(SubmissionMetadata):
+        metadata_submission = submission_metadata.metadata_submission
+
+        if isinstance(metadata_submission, list):
+            continue
+
+        sample_data = metadata_submission.get("sampleData")
+
+        if sample_data is None or not isinstance(sample_data, dict):
+            print(f"WARNING: sampleData not in migratable format for {submission_metadata.id}")
+            continue
+
+        for tab_key, rows in sample_data.items():
+            if not isinstance(rows, list):
+                continue
+            for row in rows:
+                if not isinstance(row, dict):
+                    continue
+                for rename in RENAMED_SLOTS:
+                    if "jgi_mg" in tab_key and rename.old_name_mg in row:
+                        row[rename.new_name] = row.pop(rename.old_name_mg)
+                    elif "jgi_mt" in tab_key and rename.old_name_mt in row:
+                        row[rename.new_name] = row.pop(rename.old_name_mt)
+
+        mappings.append({"id": submission_metadata.id, "metadata_submission": metadata_submission})
+
+    session.bulk_update_mappings(SubmissionMetadata, mappings)
+    session.commit()
+
+
+def downgrade():
+    session = orm.Session(bind=op.get_bind())
+    mappings = []
+    for submission_metadata in session.query(SubmissionMetadata):
+        metadata_submission = submission_metadata.metadata_submission
+
+        if isinstance(metadata_submission, list):
+            continue
+
+        sample_data = metadata_submission.get("sampleData")
+
+        if sample_data is None or not isinstance(sample_data, dict):
+            print(f"WARNING: sampleData not in migratable format for {submission_metadata.id}")
+            continue
+
+        for tab_key, rows in sample_data.items():
+            if not isinstance(rows, list):
+                continue
+            for row in rows:
+                if not isinstance(row, dict):
+                    continue
+                for rename in RENAMED_SLOTS:
+                    if rename.new_name in row:
+                        if "jgi_mg" in tab_key:
+                            row[rename.old_name_mg] = row.pop(rename.new_name)
+                        elif "jgi_mt" in tab_key:
+                            row[rename.old_name_mt] = row.pop(rename.new_name)
+
+        mappings.append({"id": submission_metadata.id, "metadata_submission": metadata_submission})
+
+    session.bulk_update_mappings(SubmissionMetadata, mappings)
+    session.commit()

pyproject.toml

@@ -97,7 +97,7 @@ dependencies = [
     "mypy==1.11.2",
     "mypy-extensions==1.0.0",
     "nmdc-schema==11.9.1",
-    "nmdc-submission-schema==11.9.1",
+    "nmdc-submission-schema==11.10.0-rc.1",
     "nmdc-geoloc-tools==0.2.0",
     "openpyxl==3.1.5",
     "packaging==24.1",

web/src/views/SubmissionPortal/HarmonizerView.vue

@@ -92,18 +92,9 @@ const TYPE_FIELD = ANALYSIS_TYPE;
 const COMMON_COLUMNS = [SAMP_NAME, SOURCE_MAT_ID, ANALYSIS_TYPE];
 
 const ALWAYS_READ_ONLY_COLUMNS = [
-  'dna_seq_project',
-  'rna_seq_project',
-  'dna_samp_id',
-  'rna_samp_id',
-  'rna_seq_project_pi',
-  'dna_seq_project_pi',
-  'dna_project_contact',
-  'rna_project_contact',
-  'proposal_rna',
-  'proposal_dna',
-  'rna_seq_project_name',
-  'dna_seq_project_name',
+  'jgi_seq_project',
+  'jgi_samp_id',
+  'jgi_seq_project_name',
 ];
 
 export default defineComponent({