Merge pull request #992 from microbiomedata/submission-schema-7.7.2

Upgrade to submission schema 7.7.2

nmdc_server/migrations/versions/dad555bb9212_submission_schema_v7_7_2.py

@@ -0,0 +1,93 @@
+"""submission schema v7.7.2
+
+* Changes the permissible values of the enum in the cur_land_use slot.
+  See https://github.com/microbiomedata/sheets_and_friends/issues/60
+
+Revision ID: dad555bb9212
+Revises: af8b2e3c91b2
+Create Date: 2023-07-14 21:12:10.113468
+
+"""
+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 = "dad555bb9212"
+down_revision: Optional[str] = "af8b2e3c91b2"
+branch_labels: Optional[str] = None
+depends_on: Optional[str] = None
+
+
+CUR_LAND_USE_RENAMES = [
+    # (old name, new name)
+    ("conifers (e.g. pine,spruce,fir,cypress)", "conifers"),
+    ("crop trees (nuts,fruit,christmas trees,nursery trees)", "crop trees"),
+    ("hardwoods (e.g. oak,hickory,elm,aspen)", "hardwoods"),
+    ("horticultural plants (e.g. tulips)", "horticultural plants"),
+    ("marshlands (grass,sedges,rushes)", "marshlands"),
+    ("meadows (grasses,alfalfa,fescue,bromegrass,timothy)", "meadows"),
+    ("pastureland (grasslands used for livestock grazing)", "pastureland"),
+    ("rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", "rainforest"),
+    ("shrub crops (blueberries,nursery ornamentals,filberts)", "shrub crops"),
+    ("shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", "shrub land"),
+    (
+        "successional shrub land (tree saplings,hazels,sumacs,chokecherry,"
+        "shrub dogwoods,blackberries)",
+        "successional shrub land",
+    ),
+    ("swamp (permanent or semi-permanent water body dominated by woody plants)", "swamp"),
+    ("tropical (e.g. mangrove,palms)", "tropical"),
+    ("tundra (mosses,lichens)", "tundra"),
+    ("vine crops (grapes)", "vine crops"),
+]
+
+
+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)
+
+
+def rename(slot, rename_map):
+    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 in sample_data.values():
+            for row in tab:
+                value = row.get(slot)
+                if value in rename_map:
+                    row[slot] = rename_map[value]
+
+        mappings.append({"id": submission_metadata.id, "metadata_submission": metadata_submission})
+    session.bulk_update_mappings(SubmissionMetadata, mappings)
+    session.commit()
+
+
+def upgrade():
+    upgrade_map = dict(CUR_LAND_USE_RENAMES)
+    rename("cur_land_use", upgrade_map)
+
+
+def downgrade():
+    downgrade_map = dict((t[1], t[0]) for t in CUR_LAND_USE_RENAMES)
+    rename("cur_land_use", downgrade_map)

web/package.json

@@ -34,7 +34,7 @@
     "lodash": "^4.17.21",
     "moment": "^2.29.2",
     "nmdc-schema": "https://github.com/microbiomedata/nmdc-schema#v6.0.4",
-    "nmdc-submission-schema": "https://files.pythonhosted.org/packages/source/n/nmdc-submission-schema/nmdc_submission_schema-7.6.5.tar.gz",
+    "nmdc-submission-schema": "https://files.pythonhosted.org/packages/source/n/nmdc-submission-schema/nmdc_submission_schema-7.7.2.tar.gz",
     "popper.js": "1.16.1",
     "protobufjs": "^6.11.3",
     "serialize-javascript": "^6.0.0",

web/yarn.lock

@@ -7566,9 +7566,9 @@ nice-try@^1.0.4:
   version "0.0.0"
   resolved "https://github.com/microbiomedata/nmdc-schema#e9b7da691079989a7e72ecc350f59058c6787557"
 
-"nmdc-submission-schema@https://files.pythonhosted.org/packages/source/n/nmdc-submission-schema/nmdc_submission_schema-7.6.5.tar.gz":
+"nmdc-submission-schema@https://files.pythonhosted.org/packages/source/n/nmdc-submission-schema/nmdc_submission_schema-7.7.2.tar.gz":
   version "0.0.0"
-  resolved "https://files.pythonhosted.org/packages/source/n/nmdc-submission-schema/nmdc_submission_schema-7.6.5.tar.gz#aab06d3093a0df621bf6a8b75f88b46dd37f4838"
+  resolved "https://files.pythonhosted.org/packages/source/n/nmdc-submission-schema/nmdc_submission_schema-7.7.2.tar.gz#60cb33a838278446219f1704fa729b70eebbc39b"
 
 no-case@^2.2.0:
   version "2.3.2"