fractal-server 2.15.0a5__py3-none-any.whl → 2.15.1__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.15.0a5"
+__VERSION__ = "2.15.1"

fractal_server/app/models/security.py

@@ -15,8 +15,8 @@ from typing import Optional
 from pydantic import ConfigDict
 from pydantic import EmailStr
 from sqlalchemy import Column
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
-from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
@@ -124,5 +124,5 @@ class UserGroup(SQLModel, table=True):
         sa_column=Column(DateTime(timezone=True), nullable=False),
     )
     viewer_paths: list[str] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
+        sa_column=Column(JSONB, server_default="[]", nullable=False)
     )

fractal_server/app/models/user_settings.py

@@ -1,5 +1,5 @@
 from sqlalchemy import Column
-from sqlalchemy.types import JSON
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlmodel import Field
 from sqlmodel import SQLModel
 
@@ -25,7 +25,7 @@ class UserSettings(SQLModel, table=True):
 
     id: int | None = Field(default=None, primary_key=True)
     slurm_accounts: list[str] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
+        sa_column=Column(JSONB, server_default="[]", nullable=False)
     )
     ssh_host: str | None = None
     ssh_username: str | None = None

fractal_server/app/models/v2/dataset.py

@@ -3,8 +3,8 @@ from typing import Any
 
 from pydantic import ConfigDict
 from sqlalchemy import Column
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
-from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
@@ -24,7 +24,7 @@ class DatasetV2(SQLModel, table=True):
     )
 
     history: list[dict[str, Any]] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
+        sa_column=Column(JSONB, server_default="[]", nullable=False)
     )
 
     timestamp_created: datetime = Field(
@@ -34,7 +34,7 @@ class DatasetV2(SQLModel, table=True):
 
     zarr_dir: str
     images: list[dict[str, Any]] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
+        sa_column=Column(JSONB, server_default="[]", nullable=False)
     )
 
     @property

fractal_server/app/models/v2/job.py

@@ -3,8 +3,8 @@ from typing import Any
 
 from pydantic import ConfigDict
 from sqlalchemy import Column
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
-from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import SQLModel
 
@@ -31,13 +31,13 @@ class JobV2(SQLModel, table=True):
     slurm_account: str | None = None
 
     dataset_dump: dict[str, Any] = Field(
-        sa_column=Column(JSON, nullable=False)
+        sa_column=Column(JSONB, nullable=False)
     )
     workflow_dump: dict[str, Any] = Field(
-        sa_column=Column(JSON, nullable=False)
+        sa_column=Column(JSONB, nullable=False)
     )
     project_dump: dict[str, Any] = Field(
-        sa_column=Column(JSON, nullable=False)
+        sa_column=Column(JSONB, nullable=False)
     )
 
     worker_init: str | None = None
@@ -57,8 +57,8 @@ class JobV2(SQLModel, table=True):
     log: str | None = None
 
     attribute_filters: AttributeFilters = Field(
-        sa_column=Column(JSON, nullable=False, server_default="{}")
+        sa_column=Column(JSONB, nullable=False, server_default="{}")
     )
     type_filters: dict[str, bool] = Field(
-        sa_column=Column(JSON, nullable=False, server_default="{}")
+        sa_column=Column(JSONB, nullable=False, server_default="{}")
     )

fractal_server/app/models/v2/task.py

@@ -1,7 +1,8 @@
 from typing import Any
 
 from sqlalchemy import Column
-from sqlalchemy.types import JSON
+from sqlalchemy.dialects.postgresql import JSON
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlmodel import Field
 from sqlmodel import SQLModel
 
@@ -33,8 +34,8 @@ class TaskV2(SQLModel, table=True):
     docs_info: str | None = None
     docs_link: str | None = None
 
-    input_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
-    output_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
+    input_types: dict[str, bool] = Field(sa_column=Column(JSONB), default={})
+    output_types: dict[str, bool] = Field(sa_column=Column(JSONB), default={})
 
     taskgroupv2_id: int = Field(foreign_key="taskgroupv2.id")
 
@@ -42,5 +43,5 @@ class TaskV2(SQLModel, table=True):
     modality: str | None = None
     authors: str | None = None
     tags: list[str] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
+        sa_column=Column(JSONB, server_default="[]", nullable=False)
     )

fractal_server/app/models/v2/task_group.py

@@ -2,8 +2,8 @@ from datetime import datetime
 from datetime import timezone
 
 from sqlalchemy import Column
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
-from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
@@ -35,7 +35,7 @@ class TaskGroupV2(SQLModel, table=True):
     pip_extras: str | None = None
     pinned_package_versions: dict[str, str] = Field(
         sa_column=Column(
-            JSON,
+            JSONB,
             server_default="{}",
             default={},
             nullable=True,

fractal_server/app/models/v2/workflowtask.py

@@ -2,7 +2,8 @@ from typing import Any
 
 from pydantic import ConfigDict
 from sqlalchemy import Column
-from sqlalchemy.types import JSON
+from sqlalchemy.dialects.postgresql import JSON
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
@@ -24,14 +25,14 @@ class WorkflowTaskV2(SQLModel, table=True):
         sa_column=Column(JSON), default=None
     )
     args_parallel: dict[str, Any] | None = Field(
-        sa_column=Column(JSON), default=None
+        sa_column=Column(JSONB), default=None
     )
     args_non_parallel: dict[str, Any] | None = Field(
-        sa_column=Column(JSON), default=None
+        sa_column=Column(JSONB), default=None
     )
 
     type_filters: dict[str, bool] = Field(
-        sa_column=Column(JSON, nullable=False, server_default="{}")
+        sa_column=Column(JSONB, nullable=False, server_default="{}")
     )
 
     # Task

fractal_server/app/runner/executors/slurm_common/_slurm_config.py

@@ -48,6 +48,8 @@ class _SlurmConfigSet(BaseModel):
         constraint:
         gres:
         time:
+        exclude:
+        nodelist:
         account:
         extra_lines:
     """
@@ -59,6 +61,8 @@ class _SlurmConfigSet(BaseModel):
     mem: int | str | None = None
     constraint: str | None = None
     gres: str | None = None
+    exclude: str | None = None
+    nodelist: str | None = None
     time: str | None = None
     account: str | None = None
     extra_lines: list[str] | None = None
@@ -227,6 +231,8 @@ class SlurmConfig(BaseModel):
         account: Corresponds to SLURM option.
         gpus: Corresponds to SLURM option.
         time: Corresponds to SLURM option (WARNING: not fully supported).
+        nodelist: Corresponds to SLURM option.
+        exclude: Corresponds to SLURM option.
         prefix: Prefix of configuration lines in SLURM submission scripts.
         shebang_line: Shebang line for SLURM submission scripts.
         extra_lines: Additional lines to include in SLURM submission scripts.
@@ -268,6 +274,8 @@ class SlurmConfig(BaseModel):
     gpus: str | None = None
     time: str | None = None
     account: str | None = None
+    nodelist: str | None = None
+    exclude: str | None = None
 
     # Free-field attribute for extra lines to be added to the SLURM job
     # preamble
@@ -361,6 +369,8 @@ class SlurmConfig(BaseModel):
             "gpus",
             "time",
             "account",
+            "exclude",
+            "nodelist",
         ]:
             value = getattr(self, key)
             if value is not None:

fractal_server/app/runner/executors/slurm_common/base_slurm_runner.py

@@ -182,33 +182,53 @@ class BaseSlurmRunner(BaseRunner):
     def _mkdir_remote_folder(self, folder: str) -> None:
         raise NotImplementedError("Implement in child class.")
 
-    def _submit_single_sbatch(
+    def _enrich_slurm_config(
         self,
-        *,
-        base_command: str,
-        slurm_job: SlurmJob,
         slurm_config: SlurmConfig,
-    ) -> str:
-        logger.debug("[_submit_single_sbatch] START")
+    ) -> SlurmConfig:
+        """
+        Return an enriched `SlurmConfig` object
 
-        # Include SLURM account in `slurm_config`. Note: we make this change
-        # here, rather than exposing a new argument of `get_slurm_config`,
-        # because it's a backend-specific argument while `get_slurm_config` has
-        # a generic interface.
+        Include `self.account` and `self.common_script_lines` into a
+        `SlurmConfig` object. Extracting this logic into an independent
+        class method is useful to fix issue #2659 (which was due to
+        performing this same operation multiple times rather than once).
+
+        Args:
+            slurm_config: The original `SlurmConfig` object.
+
+        Returns:
+            A new, up-to-date, `SlurmConfig` object.
+        """
+
+        new_slurm_config = slurm_config.model_copy()
+
+        # Include SLURM account in `slurm_config`.
         if self.slurm_account is not None:
-            slurm_config.account = self.slurm_account
+            new_slurm_config.account = self.slurm_account
 
         # Include common_script_lines in extra_lines
         if len(self.common_script_lines) > 0:
             logger.debug(
                 f"Add {self.common_script_lines} to "
-                f"{slurm_config.extra_lines=}."
+                f"{new_slurm_config.extra_lines=}."
             )
-            current_extra_lines = slurm_config.extra_lines or []
-            slurm_config.extra_lines = (
+            current_extra_lines = new_slurm_config.extra_lines or []
+            new_slurm_config.extra_lines = (
                 current_extra_lines + self.common_script_lines
             )
 
+        return new_slurm_config
+
+    def _submit_single_sbatch(
+        self,
+        *,
+        base_command: str,
+        slurm_job: SlurmJob,
+        slurm_config: SlurmConfig,
+    ) -> str:
+        logger.debug("[_submit_single_sbatch] START")
+
         for task in slurm_job.tasks:
             # Write input file
             if self.slurm_runner_type == "ssh":
@@ -508,6 +528,9 @@ class BaseSlurmRunner(BaseRunner):
         user_id: int,
     ) -> tuple[Any, Exception]:
         logger.debug("[submit] START")
+
+        config = self._enrich_slurm_config(config)
+
         try:
             workdir_local = task_files.wftask_subfolder_local
             workdir_remote = task_files.wftask_subfolder_remote
@@ -649,6 +672,8 @@ class BaseSlurmRunner(BaseRunner):
         input images, while for compound tasks these can differ.
         """
 
+        config = self._enrich_slurm_config(config)
+
         logger.debug(f"[multisubmit] START, {len(list_parameters)=}")
         try:
             if self.is_shutdown():

fractal_server/app/runner/executors/slurm_common/get_slurm_config.py

@@ -125,7 +125,14 @@ def get_slurm_config_internal(
             )
             logger.error(error_msg)
             raise SlurmConfigError(error_msg)
-        for key in ["time", "gres", "gpus", "constraint"]:
+        for key in [
+            "time",
+            "gres",
+            "gpus",
+            "constraint",
+            "nodelist",
+            "exclude",
+        ]:
             value = wftask_meta.get(key, None)
             if value is not None:
                 slurm_dict[key] = value

fractal_server/migrations/versions/b3ffb095f973_json_to_jsonb.py

@@ -0,0 +1,264 @@
+"""JSON to JSONB
+
+Revision ID: b3ffb095f973
+Revises: b1e7f7a1ff71
+Create Date: 2025-06-19 10:12:06.699107
+
+"""
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = "b3ffb095f973"
+down_revision = "b1e7f7a1ff71"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("datasetv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "history",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'[]'::json"),
+        )
+        batch_op.alter_column(
+            "images",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'[]'::json"),
+        )
+
+    with op.batch_alter_table("jobv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "dataset_dump",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+        )
+        batch_op.alter_column(
+            "workflow_dump",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+        )
+        batch_op.alter_column(
+            "project_dump",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+        )
+        batch_op.alter_column(
+            "attribute_filters",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'{}'::json"),
+        )
+        batch_op.alter_column(
+            "type_filters",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'{}'::json"),
+        )
+
+    with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "pinned_package_versions",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=True,
+            existing_server_default=sa.text("'{}'::json"),
+        )
+
+    with op.batch_alter_table("taskv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "input_types",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=True,
+        )
+        batch_op.alter_column(
+            "output_types",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=True,
+        )
+        batch_op.alter_column(
+            "tags",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'[]'::json"),
+        )
+
+    with op.batch_alter_table("user_settings", schema=None) as batch_op:
+        batch_op.alter_column(
+            "slurm_accounts",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'[]'::json"),
+        )
+
+    with op.batch_alter_table("usergroup", schema=None) as batch_op:
+        batch_op.alter_column(
+            "viewer_paths",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'[]'::json"),
+        )
+
+    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "args_parallel",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=True,
+        )
+        batch_op.alter_column(
+            "args_non_parallel",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=True,
+        )
+        batch_op.alter_column(
+            "type_filters",
+            existing_type=postgresql.JSON(astext_type=sa.Text()),
+            type_=postgresql.JSONB(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'{}'::json"),
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "type_filters",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'{}'::json"),
+        )
+        batch_op.alter_column(
+            "args_non_parallel",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=True,
+        )
+        batch_op.alter_column(
+            "args_parallel",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=True,
+        )
+
+    with op.batch_alter_table("usergroup", schema=None) as batch_op:
+        batch_op.alter_column(
+            "viewer_paths",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'[]'::json"),
+        )
+
+    with op.batch_alter_table("user_settings", schema=None) as batch_op:
+        batch_op.alter_column(
+            "slurm_accounts",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'[]'::json"),
+        )
+
+    with op.batch_alter_table("taskv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "tags",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'[]'::json"),
+        )
+        batch_op.alter_column(
+            "output_types",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=True,
+        )
+        batch_op.alter_column(
+            "input_types",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=True,
+        )
+
+    with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "pinned_package_versions",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=True,
+            existing_server_default=sa.text("'{}'::json"),
+        )
+
+    with op.batch_alter_table("jobv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "type_filters",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'{}'::json"),
+        )
+        batch_op.alter_column(
+            "attribute_filters",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'{}'::json"),
+        )
+        batch_op.alter_column(
+            "project_dump",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+        )
+        batch_op.alter_column(
+            "workflow_dump",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+        )
+        batch_op.alter_column(
+            "dataset_dump",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+        )
+
+    with op.batch_alter_table("datasetv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "images",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'[]'::json"),
+        )
+        batch_op.alter_column(
+            "history",
+            existing_type=postgresql.JSONB(astext_type=sa.Text()),
+            type_=postgresql.JSON(astext_type=sa.Text()),
+            existing_nullable=False,
+            existing_server_default=sa.text("'[]'::json"),
+        )
+
+    # ### end Alembic commands ###

fractal_server/tasks/v2/ssh/collect_pixi.py

@@ -182,19 +182,21 @@ def collect_ssh_pixi(
                     )
 
                     # Run the three pixi-related scripts
-                    _customize_and_run_template(
+                    stdout = _customize_and_run_template(
                         template_filename="pixi_1_extract.sh",
                         replacements=replacements,
                         **common_args,
                     )
+                    logger.debug(f"STDOUT: {stdout}")
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
-                    _customize_and_run_template(
+                    stdout = _customize_and_run_template(
                         template_filename="pixi_2_install.sh",
                         replacements=replacements,
                         **common_args,
                     )
+                    logger.debug(f"STDOUT: {stdout}")
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
@@ -203,6 +205,7 @@ def collect_ssh_pixi(
                         replacements=replacements,
                         **common_args,
                     )
+                    logger.debug(f"STDOUT: {stdout}")
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 

fractal_server/tasks/v2/ssh/reactivate_pixi.py

@@ -152,11 +152,12 @@ def reactivate_ssh_pixi(
                     )
 
                     # Run script 1 - extract tar.gz into `source_dir`
-                    _customize_and_run_template(
+                    stdout = _customize_and_run_template(
                         template_filename="pixi_1_extract.sh",
                         replacements=replacements,
                         **common_args,
                     )
+                    logger.debug(f"STDOUT: {stdout}")
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
@@ -176,20 +177,22 @@ def reactivate_ssh_pixi(
                     )
 
                     # Run script 2 - run pixi-install command
-                    _customize_and_run_template(
+                    stdout = _customize_and_run_template(
                         template_filename="pixi_2_install.sh",
                         replacements=replacements,
                         **common_args,
                     )
+                    logger.debug(f"STDOUT: {stdout}")
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
                     # Run script 3 - post-install
-                    _customize_and_run_template(
+                    stdout = _customize_and_run_template(
                         template_filename="pixi_3_post_install.sh",
                         replacements=replacements,
                         **common_args,
                     )
+                    logger.debug(f"STDOUT: {stdout}")
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 

fractal_server/tasks/v2/templates/pixi_1_extract.sh

@@ -2,7 +2,7 @@ set -e
 
 write_log(){
     TIMESTAMP=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
-    echo "[collect-task-pixi, ${TIMESTAMP}] ${1}"
+    echo "[extract-tar-gz-pixi, ${TIMESTAMP}] ${1}"
 }
 
 # Replacements

fractal_server/tasks/v2/templates/pixi_2_install.sh

@@ -2,7 +2,7 @@ set -e
 
 write_log(){
     TIMESTAMP=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
-    echo "[collect-task-pixi, ${TIMESTAMP}] ${1}"
+    echo "[install-tasks-pixi, ${TIMESTAMP}] ${1}"
 }
 
 # Replacements
@@ -31,7 +31,7 @@ export TOKIO_WORKER_THREADS="${TOKIO_WORKER_THREADS}"
 
 TIME_START=$(date +%s)
 
-echo "Hostname: $(hostname)"
+write_log "Hostname: $(hostname)"
 
 cd "${PACKAGE_DIR}"
 write_log "Changed working directory to ${PACKAGE_DIR}"

fractal_server/tasks/v2/templates/pixi_3_post_install.sh

@@ -2,7 +2,7 @@ set -e
 
 write_log(){
     TIMESTAMP=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
-    echo "[collect-task-pixi, ${TIMESTAMP}] ${1}"
+    echo "[after-install-pixi, ${TIMESTAMP}] ${1}"
 }
 
 # Replacements

{fractal_server-2.15.0a5.dist-info → fractal_server-2.15.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.15.0a5
+Version: 2.15.1
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin

{fractal_server-2.15.0a5.dist-info → fractal_server-2.15.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=EiSBiIGr3J4HykWpwvOxbtsBmNSbQnrB9Kqpelw5XWA,25
+fractal_server/__init__.py,sha256=6A0nKt1r_WHhSOgKEGX5ueD-wRkklKFCyvI9s88a16s,23
 fractal_server/__main__.py,sha256=rkM8xjY1KeS3l63irB8yCrlVobR-73uDapC4wvrIlxI,6957
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -6,18 +6,18 @@ fractal_server/app/db/__init__.py,sha256=EFzcf6iKemWlOSRj4vtDT63hAE9HBYWh4abYOdD
 fractal_server/app/models/__init__.py,sha256=xJWiGAwpXmCpnFMC4c_HTqoUCzMOXrakoGLUH_uMvdA,415
 fractal_server/app/models/linkusergroup.py,sha256=3KkkE4QIUAlTrBAZs_tVy0pGvAxUAq6yOEjflct_z2M,678
 fractal_server/app/models/linkuserproject.py,sha256=hvaxh3Lkiy2uUCwB8gvn8RorCpvxSSdzWdCS_U1GL7g,315
-fractal_server/app/models/security.py,sha256=PVZ3nTZO3TYpOTLiMARNy2mHAET49i6nE7bKxn1H-vQ,3836
-fractal_server/app/models/user_settings.py,sha256=RxzRBGLHF_wc5csrTeHGUSV77Md_X0Lf-SnYVOsEWHc,1263
+fractal_server/app/models/security.py,sha256=NfR0I4dRbOEmCWOKeEHyFO-uqhSJ11dS0B6yWtZRqs4,3852
+fractal_server/app/models/user_settings.py,sha256=WdnrLOP2w8Nqh_3K-4-b-8a7XEC9ILrE6SfbYoTk-7Y,1279
 fractal_server/app/models/v2/__init__.py,sha256=vjHwek7-IXmaZZL9VF0nD30YL9ca4wNc8P4RXJK_kDc,832
 fractal_server/app/models/v2/accounting.py,sha256=i-2TsjqyuclxFQ21C-TeDoss7ZBTRuXdzIJfVr2UxwE,1081
-fractal_server/app/models/v2/dataset.py,sha256=B_bPnYCSLRFN-vBIOc5nJ31JTruQPxLda9mqpPIJmGk,1209
+fractal_server/app/models/v2/dataset.py,sha256=P_zy4dPQAqrCALQ6737VkAFk1SvcgYjnslGUZhPI8sc,1226
 fractal_server/app/models/v2/history.py,sha256=CBN2WVg9vW5pHU1RP8TkB_nnJrwnuifCcxgnd53UtEE,2163
-fractal_server/app/models/v2/job.py,sha256=LfpwAedMVcA_6Ne0Rr4g3tt0asAQkWz3LSPm7IwZhYc,1978
+fractal_server/app/models/v2/job.py,sha256=e3Un_rUgWC-KazGLDQqy17NQK_2ZsL3EmEmDAky_bN0,1998
 fractal_server/app/models/v2/project.py,sha256=RmU5BQR4HD6xifRndUhvPBy30wntml-giBRoEysdWXw,755
-fractal_server/app/models/v2/task.py,sha256=P7nsS5mCmVyzr4WtcjoiedesqkWvkHA2cQPsMbQt-7o,1427
-fractal_server/app/models/v2/task_group.py,sha256=Q78ommMWEG2Sqvg2Y8ICgYA_aGH-N7LdLbnmnDl1l1M,3841
+fractal_server/app/models/v2/task.py,sha256=iBIQB8POQE5MyKvLZhw7jZWlBhbrThzCDzRTcgiAczQ,1493
+fractal_server/app/models/v2/task_group.py,sha256=1cn14RKKOOCCjh42iaT-HyuRrRpCPcYhWRrlMK-Enwc,3857
 fractal_server/app/models/v2/workflow.py,sha256=wuK9SV1TXrlYcieYLYj5fGvV3K3bW7g9jCM1uv9HHjA,1058
-fractal_server/app/models/v2/workflowtask.py,sha256=tph237DXitOnzSv88rk9qgN2VmlI1smWS5fNYHR8jMo,1200
+fractal_server/app/models/v2/workflowtask.py,sha256=qkTc-hcFLpJUVsEUbnDq2BJL0qg9jagy2doZeusF1ek,1266
 fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/admin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/admin/v2/__init__.py,sha256=_5lqb6-M8-fZqE1HRMep6pAFYRUKMxrvbZOKs-RXWkw,933
@@ -80,9 +80,9 @@ fractal_server/app/runner/executors/local/runner.py,sha256=DZK_oVxjIewyo7tjB7HvT
 fractal_server/app/runner/executors/slurm_common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm_common/_batching.py,sha256=gbHZIxt90GjUwhB9_UInwVqpX-KdxRQMDeXzUagdL3U,8816
 fractal_server/app/runner/executors/slurm_common/_job_states.py,sha256=nuV-Zba38kDrRESOVB3gaGbrSPZc4q7YGichQaeqTW0,238
-fractal_server/app/runner/executors/slurm_common/_slurm_config.py,sha256=Zv2l_6X1EfSHGRqcBMj2dbai_kP8hfuMfh-WoIUj0tY,15646
-fractal_server/app/runner/executors/slurm_common/base_slurm_runner.py,sha256=2F2zgg3DJKAJ5LecFAzMSGLFmsMiM4lMk4Kh9It35F4,35626
-fractal_server/app/runner/executors/slurm_common/get_slurm_config.py,sha256=VJNryceLzF5_fx9_lS1nGq85EW8rOQ0KrgtMATcfdQc,7271
+fractal_server/app/runner/executors/slurm_common/_slurm_config.py,sha256=U9BONnnwn8eDqDevwUtFSBcvIsxvNgDHirhcQGJ9t9E,15947
+fractal_server/app/runner/executors/slurm_common/base_slurm_runner.py,sha256=iXRlTuPvBqqq_I-WYF2IRocPEayMCBxCSJkn_eop6t4,36226
+fractal_server/app/runner/executors/slurm_common/get_slurm_config.py,sha256=jhoFHauWJm55bIC_v7pFylbK8WgcRJemGu2OjUiRbpQ,7377
 fractal_server/app/runner/executors/slurm_common/remote.py,sha256=xWnI6WktHR_7cxUme72ztIeBb4osnbZNu6J2azWn9K8,3765
 fractal_server/app/runner/executors/slurm_common/slurm_job_task_models.py,sha256=K4SdJOKsUWzDlnkb8Ug_UmTx6nBMsTqn9_oKqwE4XDI,3520
 fractal_server/app/runner/executors/slurm_ssh/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -171,6 +171,7 @@ fractal_server/migrations/versions/a7f4d6137b53_add_workflow_dump_to_applyworkfl
 fractal_server/migrations/versions/af1ef1c83c9b_add_accounting_tables.py,sha256=BftudWuSGvKGBzIL5AMb3yWkgTAuaKPBGsYcOzp_gLQ,1899
 fractal_server/migrations/versions/af8673379a5c_drop_old_filter_columns.py,sha256=9sLd0F7nO5chHHm7RZ4wBA-9bvWomS-av_odKwODADM,1551
 fractal_server/migrations/versions/b1e7f7a1ff71_task_group_for_pixi.py,sha256=loDrqBB-9U3vqLKePEeJy4gK4EuPs_1F345mdrnoCt0,1293
+fractal_server/migrations/versions/b3ffb095f973_json_to_jsonb.py,sha256=Q01lPlBNQgi3hpoUquWj2QUEF7cTsyQ7uikUhWunzWY,10035
 fractal_server/migrations/versions/c90a7c76e996_job_id_in_history_run.py,sha256=Y1cPwmFOZ4mx3v2XZM6adgu8u0L0VD_R4ADURyMb2ro,1102
 fractal_server/migrations/versions/d256a7379ab8_taskgroup_activity_and_venv_info_to_.py,sha256=HN3_Pk8G81SzdYjg4K1RZAyjKSlsZGvcYE2nWOUbwxQ,3861
 fractal_server/migrations/versions/d4fe3708d309_make_applyworkflow_workflow_dump_non_.py,sha256=6cHEZFuTXiQg9yu32Y3RH1XAl71av141WQ6UMbiITIg,949
@@ -201,20 +202,20 @@ fractal_server/tasks/v2/local/reactivate_pixi.py,sha256=wF_3gcMWO_8ArJFo4iYh-51L
 fractal_server/tasks/v2/ssh/__init__.py,sha256=vX5aIM9Hbn2T_cIP_LrZ5ekRqJzYm_GSfp-4Iv7kqeI,300
 fractal_server/tasks/v2/ssh/_utils.py,sha256=ktVH7psQSAhh353fVUe-BwiBZHzTdgXnR-Xv_vfuX0Y,3857
 fractal_server/tasks/v2/ssh/collect.py,sha256=M9gFD1h9Q1Z-BFQq65dI0vFs6HPCkKQzOkxaLddmChY,14334
-fractal_server/tasks/v2/ssh/collect_pixi.py,sha256=g-dwkVbzV_4dMXAU8Ej_HmgivHmyq7p9sSOfDXNJhR4,13621
+fractal_server/tasks/v2/ssh/collect_pixi.py,sha256=q68GSL9yvezqOEc-zt4Ko1d7ZhTlJugoGspRA8JPiJw,13801
 fractal_server/tasks/v2/ssh/deactivate.py,sha256=XAIy84cLT9MSTMiN67U-wfOjxMm5s7lmrGwhW0qp7BU,12439
 fractal_server/tasks/v2/ssh/deactivate_pixi.py,sha256=K0yK_NPUqhFMj6cp6G_0Kfn0Yo7oQux4kT5dFPulnos,4748
 fractal_server/tasks/v2/ssh/reactivate.py,sha256=NJIgMNFKaXMhbvK0iZOsMwMtsms6Boj9f8N4L01X9Bo,8271
-fractal_server/tasks/v2/ssh/reactivate_pixi.py,sha256=QNlY0cqZvQblsl0eAbKBPBs_QAkN0G233Hy58PpWHxs,9595
+fractal_server/tasks/v2/ssh/reactivate_pixi.py,sha256=o86FNB8pX9Sv_ROrCOJQqxIfDUhJqzzmo3JKsSfCNlA,9784
 fractal_server/tasks/v2/templates/1_create_venv.sh,sha256=PK0jdHKtQpda1zULebBaVPORt4t6V17wa4N1ohcj5ac,548
 fractal_server/tasks/v2/templates/2_pip_install.sh,sha256=jMJPQJXHKznO6fxOOXtFXKPdCmTf1VLLWj_JL_ZdKxo,1644
 fractal_server/tasks/v2/templates/3_pip_freeze.sh,sha256=JldREScEBI4cD_qjfX4UK7V4aI-FnX9ZvVNxgpSOBFc,168
 fractal_server/tasks/v2/templates/4_pip_show.sh,sha256=qm1vPy6AkKhWDjCJGXS8LqCLYO3KsAyRK325ZsFcF6U,1747
 fractal_server/tasks/v2/templates/5_get_venv_size_and_file_number.sh,sha256=q-6ZUvA6w6FDVEoSd9O63LaJ9tKZc7qAFH72SGPrd_k,284
 fractal_server/tasks/v2/templates/6_pip_install_from_freeze.sh,sha256=A2y8RngEjAcRhG-_owA6P7tAdrS_AszFuGXnaeMV8u0,1122
-fractal_server/tasks/v2/templates/pixi_1_extract.sh,sha256=1Z6sd_fTzqQkOfbFswaPZBNLUyv-OrS4euGlcoi8ces,1097
-fractal_server/tasks/v2/templates/pixi_2_install.sh,sha256=BkINfTU34vZ_zCyg_CIDEWvlAME3p6kF1qmxs4UAkPw,1595
-fractal_server/tasks/v2/templates/pixi_3_post_install.sh,sha256=uDCdjXpBMsQcexZ4pvZn3ctJenM4QMsazsWMf5aw7eA,2500
+fractal_server/tasks/v2/templates/pixi_1_extract.sh,sha256=Jdy5OyKo2jxe_qIDB9Zi4a0FL0cMBysxvBPHlUrARQM,1099
+fractal_server/tasks/v2/templates/pixi_2_install.sh,sha256=h6-M101Q1AdAfZNZyPfSUc8AlZ-uS84Hae4vJdDSglY,1601
+fractal_server/tasks/v2/templates/pixi_3_post_install.sh,sha256=99J8KXkNeQk9utuEtUxfAZS6VCThC32X7I7HAp2gdTU,2501
 fractal_server/tasks/v2/utils_background.py,sha256=_4wGETgZ3JdnJXLYKSI0Lns8LwokJL-NEzUOK5SxCJU,4811
 fractal_server/tasks/v2/utils_database.py,sha256=yi7793Uue32O59OBVUgomO42oUrVKdSKXoShBUNDdK0,1807
 fractal_server/tasks/v2/utils_package_names.py,sha256=RDg__xrvQs4ieeVzmVdMcEh95vGQYrv9Hfal-5EDBM8,2393
@@ -229,8 +230,8 @@ fractal_server/types/validators/_workflow_task_arguments_validators.py,sha256=HL
 fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=Vn35lApt1T1J8nc09sAVqd10Cy0sa3dLipcljI-hkuk,2185
 fractal_server/zip_tools.py,sha256=tqz_8f-vQ9OBRW-4OQfO6xxY-YInHTyHmZxU7U4PqZo,4885
-fractal_server-2.15.0a5.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.15.0a5.dist-info/METADATA,sha256=ItBnov8ODJ4zuzUPJQXjBLs6H5SviOLZ5K6nw1Lfjmw,4245
-fractal_server-2.15.0a5.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
-fractal_server-2.15.0a5.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.15.0a5.dist-info/RECORD,,
+fractal_server-2.15.1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.15.1.dist-info/METADATA,sha256=kxk3S8JxO5PKXtG0HSpS2jLbnQ0JMF-WHZjrqHxPatY,4243
+fractal_server-2.15.1.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
+fractal_server-2.15.1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.15.1.dist-info/RECORD,,