Merge branch 'dev' into feat/support-solver-v87

.github/workflows/commitlint.yml

@@ -0,0 +1,13 @@
+name: Lint Commit Messages
+on: [pull_request]
+
+permissions:
+  contents: read
+  pull-requests: read
+
+jobs:
+  commitlint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: wagoid/commitlint-github-action@v5

.github/workflows/compatibility.yml

@@ -43,7 +43,7 @@ jobs:
         with:
           node-version: ${{ matrix.node-version }}
       - name: Install dependencies
-        run: npm install --legacy-peer-deps
+        run: npm install
         working-directory: webapp
       - name: Build
         run: npm run build

.github/workflows/deploy.yml

@@ -30,7 +30,7 @@ jobs:
           node-version: 18.16.1
 
       - name: 💚 Install dependencies
-        run: npm install --legacy-peer-deps
+        run: npm install
         working-directory: webapp
 
       - name: 💚 Build webapp

.github/workflows/main.yml

@@ -78,7 +78,7 @@ jobs:
         with:
           node-version: 18.16.1
       - name: Install dependencies
-        run: npm install --legacy-peer-deps
+        run: npm install
         working-directory: webapp
       - name: Build
         run: npm run build
@@ -89,16 +89,6 @@ jobs:
       - name: Lint
         run: npm run lint
         working-directory: webapp
-      - name: Run tests
-        run: npm run test-coverage
-        working-directory: webapp
-        env:
-          CI: true
-      - name: Archive code coverage results
-        uses: actions/upload-artifact@v3
-        with:
-          name: js-code-coverage-report
-          path: webapp/coverage/lcov.info
 
   sonarcloud:
     runs-on: ubuntu-20.04
@@ -109,11 +99,6 @@ jobs:
         uses: actions/download-artifact@v3
         with:
           name: python-code-coverage-report
-      - name: Download js coverage report
-        uses: actions/download-artifact@v3
-        with:
-          name: js-code-coverage-report
-          path: webapp/coverage
       - name: SonarCloud Scan
         uses: sonarsource/sonarcloud-github-action@master
         env:

README.md

@@ -31,7 +31,7 @@ Install the front-end dependencies:
 
 ```shell script
 cd webapp
-npm install --legacy-peer-deps
+npm install
 cd ..
 ```
 

alembic/versions/3c70366b10ea_add_tag_and_study_tag_tables.py

@@ -0,0 +1,58 @@
+"""Add tag and study_tag tables
+
+Revision ID: 3c70366b10ea
+Revises: 1f5db5dfad80
+Create Date: 2024-02-02 13:06:47.627554
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "3c70366b10ea"
+down_revision = "1f5db5dfad80"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "tag",
+        sa.Column("label", sa.String(length=40), nullable=False),
+        sa.Column("color", sa.String(length=20), nullable=True),
+        sa.PrimaryKeyConstraint("label"),
+    )
+    with op.batch_alter_table("tag", schema=None) as batch_op:
+        batch_op.create_index(batch_op.f("ix_tag_color"), ["color"], unique=False)
+        batch_op.create_index(batch_op.f("ix_tag_label"), ["label"], unique=False)
+
+    op.create_table(
+        "study_tag",
+        sa.Column("study_id", sa.String(length=36), nullable=False),
+        sa.Column("tag_label", sa.String(length=40), nullable=False),
+        sa.ForeignKeyConstraint(["study_id"], ["study.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["tag_label"], ["tag.label"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("study_id", "tag_label"),
+    )
+    with op.batch_alter_table("study_tag", schema=None) as batch_op:
+        batch_op.create_index(batch_op.f("ix_study_tag_study_id"), ["study_id"], unique=False)
+        batch_op.create_index(batch_op.f("ix_study_tag_tag_label"), ["tag_label"], unique=False)
+
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("study_tag", schema=None) as batch_op:
+        batch_op.drop_index(batch_op.f("ix_study_tag_tag_label"))
+        batch_op.drop_index(batch_op.f("ix_study_tag_study_id"))
+
+    op.drop_table("study_tag")
+    with op.batch_alter_table("tag", schema=None) as batch_op:
+        batch_op.drop_index(batch_op.f("ix_tag_label"))
+        batch_op.drop_index(batch_op.f("ix_tag_color"))
+
+    op.drop_table("tag")
+    # ### end Alembic commands ###

alembic/versions/c0c4aaf84861_add_delete_cascade_variant_studies.py

@@ -0,0 +1,51 @@
+"""
+Add delete cascade constraint to variant study foreign keys
+
+Revision ID: c0c4aaf84861
+Revises: fd73601a9075
+Create Date: 2024-02-21 17:29:48.736664
+"""
+from alembic import op  # type: ignore
+
+# revision identifiers, used by Alembic.
+revision = "c0c4aaf84861"
+down_revision = "fd73601a9075"
+branch_labels = None
+depends_on = None
+
+COMMAND_BLOCK_FK = "commandblock_study_id_fkey"
+SNAPSHOT_FK = "variant_study_snapshot_id_fkey"
+
+
+def upgrade() -> None:
+    dialect_name: str = op.get_context().dialect.name
+
+    # SQLite doesn't support dropping foreign keys, so we need to ignore it here
+    if dialect_name == "postgresql":
+        # ### commands auto generated by Alembic - please adjust! ###
+        with op.batch_alter_table("commandblock", schema=None) as batch_op:
+            batch_op.drop_constraint(COMMAND_BLOCK_FK, type_="foreignkey")
+            batch_op.create_foreign_key(COMMAND_BLOCK_FK, "variantstudy", ["study_id"], ["id"], ondelete="CASCADE")
+
+        with op.batch_alter_table("variant_study_snapshot", schema=None) as batch_op:
+            batch_op.drop_constraint(SNAPSHOT_FK, type_="foreignkey")
+            batch_op.create_foreign_key(SNAPSHOT_FK, "variantstudy", ["id"], ["id"], ondelete="CASCADE")
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    dialect_name: str = op.get_context().dialect.name
+
+    # SQLite doesn't support dropping foreign keys, so we need to ignore it here
+    if dialect_name == "postgresql":
+        # ### commands auto generated by Alembic - please adjust! ###
+        with op.batch_alter_table("variant_study_snapshot", schema=None) as batch_op:
+            batch_op.drop_constraint(SNAPSHOT_FK, type_="foreignkey")
+            batch_op.create_foreign_key(SNAPSHOT_FK, "variantstudy", ["id"], ["id"])
+
+        with op.batch_alter_table("commandblock", schema=None) as batch_op:
+            batch_op.drop_constraint(COMMAND_BLOCK_FK, type_="foreignkey")
+            batch_op.create_foreign_key(COMMAND_BLOCK_FK, "variantstudy", ["study_id"], ["id"])
+
+    # ### end Alembic commands ###

alembic/versions/dae93f1d9110_populate_tag_and_study_tag_tables_with_.py

@@ -0,0 +1,123 @@
+"""
+Populate `tag` and `study_tag` tables from `patch` field in `study_additional_data` table
+
+Revision ID: dae93f1d9110
+Revises: 3c70366b10ea
+Create Date: 2024-02-08 10:30:20.590919
+"""
+import collections
+import itertools
+import json
+import secrets
+import typing as t
+
+import sqlalchemy as sa  # type: ignore
+from alembic import op
+from sqlalchemy.engine import Connection  # type: ignore
+
+from antarest.study.css4_colors import COLOR_NAMES
+
+# revision identifiers, used by Alembic.
+revision = "dae93f1d9110"
+down_revision = "3c70366b10ea"
+branch_labels = None
+depends_on = None
+
+
+def _avoid_duplicates(tags: t.Iterable[str]) -> t.Sequence[str]:
+    """Avoid duplicate tags (case insensitive)"""
+
+    upper_tags = {tag.upper(): tag for tag in tags}
+    return list(upper_tags.values())
+
+
+def _load_patch_obj(patch: t.Optional[str]) -> t.MutableMapping[str, t.Any]:
+    """Load the patch object from the `patch` field in the `study_additional_data` table."""
+
+    obj: t.MutableMapping[str, t.Any] = json.loads(patch or "{}")
+    obj["study"] = obj.get("study") or {}
+    obj["study"]["tags"] = _avoid_duplicates(obj["study"].get("tags") or [])
+    return obj
+
+
+def upgrade() -> None:
+    """
+    Populate `tag` and `study_tag` tables from `patch` field in `study_additional_data` table
+
+    Four steps to proceed:
+        - Retrieve study-tags pairs from patches in `study_additional_data`.
+        - Delete all rows in `tag` and `study_tag`, as tag updates between revised 3c70366b10ea and this version,
+          do modify the data in patches alongside the two previous tables.
+        - Populate `tag` table using unique tag-labels and by randomly generating their associated colors.
+        - Populate `study_tag` using study-tags pairs.
+    """
+
+    # create connexion to the db
+    connexion: Connection = op.get_bind()
+
+    # retrieve the tags and the study-tag pairs from the db
+    study_tags = connexion.execute("SELECT study_id, patch FROM study_additional_data")
+    tags_by_ids: t.MutableMapping[str, t.Set[str]] = {}
+    for study_id, patch in study_tags:
+        obj = _load_patch_obj(patch)
+        tags_by_ids[study_id] = obj["study"]["tags"]
+
+    # delete rows in tables `tag` and `study_tag`
+    connexion.execute("DELETE FROM study_tag")
+    connexion.execute("DELETE FROM tag")
+
+    # insert the tags in the `tag` table
+    all_labels = {lbl.upper(): lbl for lbl in itertools.chain.from_iterable(tags_by_ids.values())}
+    bulk_tags = [{"label": label, "color": secrets.choice(COLOR_NAMES)} for label in all_labels.values()]
+    if bulk_tags:
+        sql = sa.text("INSERT INTO tag (label, color) VALUES (:label, :color)")
+        connexion.execute(sql, *bulk_tags)
+
+    # Create relationships between studies and tags in the `study_tag` table
+    bulk_study_tags = [
+        # fmt: off
+        {"study_id": id_, "tag_label": all_labels[lbl.upper()]}
+        for id_, tags in tags_by_ids.items()
+        for lbl in tags
+        # fmt: on
+    ]
+    if bulk_study_tags:
+        sql = sa.text("INSERT INTO study_tag (study_id, tag_label) VALUES (:study_id, :tag_label)")
+        connexion.execute(sql, *bulk_study_tags)
+
+
+def downgrade() -> None:
+    """
+    Restore `patch` field in `study_additional_data` from `tag` and `study_tag` tables
+
+    Three steps to proceed:
+        - Retrieve study-tags pairs from `study_tag` table.
+        - Update patches study-tags in `study_additional_data` using these pairs.
+        - Delete all rows from `tag` and `study_tag`.
+    """
+    # create a connection to the db
+    connexion: Connection = op.get_bind()
+
+    # Creating the `tags_by_ids` mapping from data in the `study_tags` table
+    tags_by_ids: t.MutableMapping[str, t.Set[str]] = collections.defaultdict(set)
+    study_tags = connexion.execute("SELECT study_id, tag_label FROM study_tag")
+    for study_id, tag_label in study_tags:
+        tags_by_ids[study_id].add(tag_label)
+
+    # Then, we read objects from the `patch` field of the `study_additional_data` table
+    objects_by_ids = {}
+    study_tags = connexion.execute("SELECT study_id, patch FROM study_additional_data")
+    for study_id, patch in study_tags:
+        obj = _load_patch_obj(patch)
+        obj["study"]["tags"] = _avoid_duplicates(tags_by_ids[study_id] | set(obj["study"]["tags"]))
+        objects_by_ids[study_id] = obj
+
+    # Updating objects in the `study_additional_data` table
+    bulk_patches = [{"study_id": id_, "patch": json.dumps(obj)} for id_, obj in objects_by_ids.items()]
+    if bulk_patches:
+        sql = sa.text("UPDATE study_additional_data SET patch = :patch WHERE study_id = :study_id")
+        connexion.execute(sql, *bulk_patches)
+
+    # Deleting study_tags and tags
+    connexion.execute("DELETE FROM study_tag")
+    connexion.execute("DELETE FROM tag")