fractal-server 2.9.0a5__tar.gz → 2.9.0a7__tar.gz

{fractal_server-2.9.0a5 → fractal_server-2.9.0a7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.9.0a5
+Version: 2.9.0a7
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

fractal_server-2.9.0a7/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.9.0a7"

{fractal_server-2.9.0a5 → fractal_server-2.9.0a7}/fractal_server/app/models/v2/task_group.py

@@ -1,4 +1,5 @@
 from datetime import datetime
+from datetime import timezone
 from typing import Optional
 
 from sqlalchemy import Column
@@ -48,9 +49,15 @@ class TaskGroupV2(SQLModel, table=True):
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),
     )
-    timestamp_last_used: Optional[datetime] = Field(
+    timestamp_last_used: datetime = Field(
         default_factory=get_timestamp,
-        sa_column=Column(DateTime(timezone=True), nullable=False),
+        sa_column=Column(
+            DateTime(timezone=True),
+            nullable=False,
+            server_default=(
+                datetime(2024, 11, 20, tzinfo=timezone.utc).isoformat()
+            ),
+        ),
     )
 
     @property

{fractal_server-2.9.0a5 → fractal_server-2.9.0a7}/fractal_server/app/routes/api/v1/project.py

@@ -1,5 +1,5 @@
+import json
 import os
-from datetime import datetime
 from datetime import timedelta
 from datetime import timezone
 from typing import Optional
@@ -50,10 +50,6 @@ router = APIRouter()
 logger = set_logger(__name__)
 
 
-def _encode_as_utc(dt: datetime):
-    return dt.replace(tzinfo=timezone.utc).isoformat()
-
-
 @router.get("/", response_model=list[ProjectReadV1])
 async def get_list_project(
     user: UserOAuth = Depends(current_active_user),
@@ -393,33 +389,25 @@ async def apply_workflow(
         workflow_id=workflow_id,
         user_email=user.email,
         input_dataset_dump=dict(
-            **input_dataset.model_dump(
-                exclude={"resource_list", "history", "timestamp_created"}
+            **json.loads(
+                input_dataset.json(exclude={"resource_list", "history"})
             ),
-            timestamp_created=_encode_as_utc(input_dataset.timestamp_created),
             resource_list=[
                 resource.model_dump()
                 for resource in input_dataset.resource_list
             ],
         ),
         output_dataset_dump=dict(
-            **output_dataset.model_dump(
-                exclude={"resource_list", "history", "timestamp_created"}
+            **json.loads(
+                output_dataset.json(exclude={"resource_list", "history"})
             ),
-            timestamp_created=_encode_as_utc(output_dataset.timestamp_created),
             resource_list=[
                 resource.model_dump()
                 for resource in output_dataset.resource_list
             ],
         ),
-        workflow_dump=dict(
-            **workflow.model_dump(exclude={"task_list", "timestamp_created"}),
-            timestamp_created=_encode_as_utc(workflow.timestamp_created),
-        ),
-        project_dump=dict(
-            **project.model_dump(exclude={"user_list", "timestamp_created"}),
-            timestamp_created=_encode_as_utc(project.timestamp_created),
-        ),
+        workflow_dump=json.loads(workflow.json(exclude={"task_list"})),
+        project_dump=json.loads(project.json(exclude={"user_list"})),
         **apply_workflow.dict(),
     )
 

{fractal_server-2.9.0a5 → fractal_server-2.9.0a7}/fractal_server/app/routes/api/v2/submit.py

@@ -1,6 +1,5 @@
+import json
 import os
-from datetime import datetime
-from datetime import timezone
 from pathlib import Path
 from typing import Optional
 
@@ -37,10 +36,6 @@ from fractal_server.app.routes.api.v2._aux_functions_tasks import (
 from fractal_server.app.routes.auth import current_active_verified_user
 
 
-def _encode_as_utc(dt: datetime):
-    return dt.replace(tzinfo=timezone.utc).isoformat()
-
-
 router = APIRouter()
 logger = set_logger(__name__)
 
@@ -164,20 +159,9 @@ async def apply_workflow(
         dataset_id=dataset_id,
         workflow_id=workflow_id,
         user_email=user.email,
-        dataset_dump=dict(
-            **dataset.model_dump(
-                exclude={"images", "history", "timestamp_created"}
-            ),
-            timestamp_created=_encode_as_utc(dataset.timestamp_created),
-        ),
-        workflow_dump=dict(
-            **workflow.model_dump(exclude={"task_list", "timestamp_created"}),
-            timestamp_created=_encode_as_utc(workflow.timestamp_created),
-        ),
-        project_dump=dict(
-            **project.model_dump(exclude={"user_list", "timestamp_created"}),
-            timestamp_created=_encode_as_utc(project.timestamp_created),
-        ),
+        dataset_dump=json.loads(dataset.json(exclude={"images", "history"})),
+        workflow_dump=json.loads(workflow.json(exclude={"task_list"})),
+        project_dump=json.loads(project.json(exclude={"user_list"})),
         **job_create.dict(),
     )
 

{fractal_server-2.9.0a5 → fractal_server-2.9.0a7}/fractal_server/app/runner/executors/slurm/ssh/executor.py

@@ -1500,7 +1500,11 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         logger.info("[FractalSlurmSSHExecutor.ssh_handshake] START")
         cmd = f"{self.python_remote} -m fractal_server.app.runner.versions"
         stdout = self.fractal_ssh.run_command(cmd=cmd)
-        remote_versions = json.loads(stdout.strip("\n"))
+        try:
+            remote_versions = json.loads(stdout.strip("\n"))
+        except json.decoder.JSONDecodeError as e:
+            logger.error("Fractal server versions not available")
+            raise e
 
         # Check compatibility with local versions
         local_versions = get_versions()

fractal_server-2.9.0a5/fractal_server/migrations/versions/3082479ac4ea_taskgroup_activity_and_venv_info_to_.py → fractal_server-2.9.0a7/fractal_server/migrations/versions/d256a7379ab8_taskgroup_activity_and_venv_info_to_.py

@@ -1,16 +1,17 @@
 """TaskGroup Activity and venv-info to TaskGroup
 
-Revision ID: 3082479ac4ea
+Revision ID: d256a7379ab8
 Revises: 19eca0dd47a9
-Create Date: 2024-11-12 14:39:34.035859
+Create Date: 2024-11-20 15:01:52.659832
 
 """
 import sqlalchemy as sa
 import sqlmodel
 from alembic import op
+from sqlalchemy.dialects import postgresql
 
 # revision identifiers, used by Alembic.
-revision = "3082479ac4ea"
+revision = "d256a7379ab8"
 down_revision = "19eca0dd47a9"
 branch_labels = None
 depends_on = None
@@ -71,6 +72,7 @@ def upgrade() -> None:
             sa.Column(
                 "timestamp_last_used",
                 sa.DateTime(timezone=True),
+                server_default="2024-11-20T00:00:00+00:00",
                 nullable=False,
             )
         )
@@ -91,12 +93,14 @@ def downgrade() -> None:
         sa.Column("id", sa.INTEGER(), autoincrement=True, nullable=False),
         sa.Column(
             "data",
-            sa.JSON(),
+            postgresql.JSON(astext_type=sa.Text()),
+            autoincrement=False,
             nullable=True,
         ),
         sa.Column(
             "timestamp",
-            sa.DateTime(timezone=True),
+            postgresql.TIMESTAMP(timezone=True),
+            autoincrement=False,
             nullable=True,
         ),
         sa.Column(

{fractal_server-2.9.0a5 → fractal_server-2.9.0a7}/fractal_server/tasks/v2/local/deactivate.py

@@ -109,11 +109,12 @@ def deactivate_local(
                         ),
                         logger_name=LOGGER_NAME,
                     )
+
+                    # Update pip-freeze data
                     pip_freeze_stdout = _customize_and_run_template(
                         template_filename="3_pip_freeze.sh",
                         **common_args,
                     )
-                    # Update pip-freeze data
                     logger.info("Add pip freeze stdout to TaskGroupV2 - start")
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)

{fractal_server-2.9.0a5 → fractal_server-2.9.0a7}/fractal_server/tasks/v2/ssh/deactivate.py

@@ -119,10 +119,13 @@ def deactivate_ssh(
                         python_bin="/not/applicable",
                     )
 
-                    # Prepare arguments for `_customize_and_run_template`
+                    # Define script_dir_remote and create it if missing
                     script_dir_remote = (
                         Path(task_group.path) / SCRIPTS_SUBFOLDER
                     ).as_posix()
+                    fractal_ssh.mkdir(folder=script_dir_remote, parents=True)
+
+                    # Prepare arguments for `_customize_and_run_template`
                     common_args = dict(
                         replacements=replacements,
                         script_dir_local=(

{fractal_server-2.9.0a5 → fractal_server-2.9.0a7}/fractal_server/tasks/v2/ssh/reactivate.py

@@ -128,10 +128,13 @@ def reactivate_ssh(
                     ("__PIP_FREEZE_FILE__", pip_freeze_file_remote)
                 )
 
-                # Prepare common arguments for `_customize_and_run_template``
+                # Define script_dir_remote and create it if missing
                 script_dir_remote = (
                     Path(task_group.path) / SCRIPTS_SUBFOLDER
                 ).as_posix()
+                fractal_ssh.mkdir(folder=script_dir_remote, parents=True)
+
+                # Prepare common arguments for `_customize_and_run_template`
                 common_args = dict(
                     replacements=replacements,
                     script_dir_local=(

{fractal_server-2.9.0a5 → fractal_server-2.9.0a7}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.9.0a5"
+version = "2.9.0a7"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Tommaso Comparin <tommaso.comparin@exact-lab.it>",
@@ -86,7 +86,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.9.0a5"
+current_version = "2.9.0a7"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.9.0a5/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.9.0a5"