fractal-server 2.14.0a3__py3-none-any.whl → 2.14.0a4__py3-none-any.whl

fractal_server/config.py

@@ -28,6 +28,7 @@ from pydantic import EmailStr
 from pydantic import Field
 from pydantic import field_validator
 from pydantic import model_validator
+from pydantic import SecretStr
 from pydantic_settings import BaseSettings
 from pydantic_settings import SettingsConfigDict
 from sqlalchemy.engine import URL
@@ -54,8 +55,8 @@ class MailSettings(BaseModel):
     recipients: list[EmailStr] = Field(min_length=1)
     smtp_server: str
     port: int
-    encrypted_password: Optional[str] = None
-    encryption_key: Optional[str] = None
+    encrypted_password: Optional[SecretStr] = None
+    encryption_key: Optional[SecretStr] = None
     instance_name: str
     use_starttls: bool
     use_login: bool
@@ -97,7 +98,7 @@ class OAuthClientConfig(BaseModel):
 
     CLIENT_NAME: str
     CLIENT_ID: str
-    CLIENT_SECRET: str
+    CLIENT_SECRET: SecretStr
     OIDC_CONFIGURATION_ENDPOINT: Optional[str] = None
     REDIRECT_URL: Optional[str] = None
 
@@ -137,7 +138,7 @@ class Settings(BaseSettings):
     JWT token lifetime, in seconds.
     """
 
-    JWT_SECRET_KEY: Optional[str] = None
+    JWT_SECRET_KEY: Optional[SecretStr] = None
     """
     JWT secret
 
@@ -204,7 +205,7 @@ class Settings(BaseSettings):
     """
     User to use when connecting to the PostgreSQL database.
     """
-    POSTGRES_PASSWORD: Optional[str] = None
+    POSTGRES_PASSWORD: Optional[SecretStr] = None
     """
     Password to use when connecting to the PostgreSQL database.
     """
@@ -223,10 +224,15 @@ class Settings(BaseSettings):
 
     @property
     def DATABASE_ASYNC_URL(self) -> URL:
+        if self.POSTGRES_PASSWORD is None:
+            password = None
+        else:
+            password = self.POSTGRES_PASSWORD.get_secret_value()
+
         url = URL.create(
             drivername="postgresql+psycopg",
             username=self.POSTGRES_USER,
-            password=self.POSTGRES_PASSWORD,
+            password=password,
             host=self.POSTGRES_HOST,
             port=self.POSTGRES_PORT,
             database=self.POSTGRES_DB,
@@ -250,7 +256,7 @@ class Settings(BaseSettings):
     default admin credentials.
     """
 
-    FRACTAL_DEFAULT_ADMIN_PASSWORD: str = "1234"
+    FRACTAL_DEFAULT_ADMIN_PASSWORD: SecretStr = "1234"
     """
     Admin default password, used upon creation of the first superuser during
     server startup.
@@ -579,11 +585,11 @@ class Settings(BaseSettings):
     """
     Address of the OAuth-signup email sender.
     """
-    FRACTAL_EMAIL_PASSWORD: Optional[str] = None
+    FRACTAL_EMAIL_PASSWORD: Optional[SecretStr] = None
     """
     Password for the OAuth-signup email sender.
     """
-    FRACTAL_EMAIL_PASSWORD_KEY: Optional[str] = None
+    FRACTAL_EMAIL_PASSWORD_KEY: Optional[SecretStr] = None
     """
     Key value for `cryptography.fernet` decrypt
     """
@@ -653,8 +659,12 @@ class Settings(BaseSettings):
                     )
                 try:
                     (
-                        Fernet(self.FRACTAL_EMAIL_PASSWORD_KEY)
-                        .decrypt(self.FRACTAL_EMAIL_PASSWORD)
+                        Fernet(
+                            self.FRACTAL_EMAIL_PASSWORD_KEY.get_secret_value()
+                        )
+                        .decrypt(
+                            self.FRACTAL_EMAIL_PASSWORD.get_secret_value()
+                        )
                         .decode("utf-8")
                     )
                 except Exception as e:
@@ -663,14 +673,22 @@ class Settings(BaseSettings):
                         "FRACTAL_EMAIL_PASSWORD_KEY). "
                         f"Original error: {str(e)}."
                     )
+                password = self.FRACTAL_EMAIL_PASSWORD.get_secret_value()
+            else:
+                password = None
+
+            if self.FRACTAL_EMAIL_PASSWORD_KEY is not None:
+                key = self.FRACTAL_EMAIL_PASSWORD_KEY.get_secret_value()
+            else:
+                key = None
 
             self.email_settings = MailSettings(
                 sender=self.FRACTAL_EMAIL_SENDER,
                 recipients=self.FRACTAL_EMAIL_RECIPIENTS.split(","),
                 smtp_server=self.FRACTAL_EMAIL_SMTP_SERVER,
                 port=self.FRACTAL_EMAIL_SMTP_PORT,
-                encrypted_password=self.FRACTAL_EMAIL_PASSWORD,
-                encryption_key=self.FRACTAL_EMAIL_PASSWORD_KEY,
+                encrypted_password=password,
+                encryption_key=key,
                 instance_name=self.FRACTAL_EMAIL_INSTANCE_NAME,
                 use_starttls=use_starttls,
                 use_login=use_login,
@@ -788,25 +806,6 @@ class Settings(BaseSettings):
         self.check_db()
         self.check_runner()
 
-    def get_sanitized(self) -> dict:
-        def _must_be_sanitized(string) -> bool:
-            if not string.upper().startswith("FRACTAL") or any(
-                s in string.upper()
-                for s in ["PASSWORD", "SECRET", "PWD", "TOKEN", "KEY"]
-            ):
-                return True
-            else:
-                return False
-
-        sanitized_settings = {}
-        for k, v in self.model_dump().items():
-            if _must_be_sanitized(k):
-                sanitized_settings[k] = "***"
-            else:
-                sanitized_settings[k] = v
-
-        return sanitized_settings
-
 
 def get_settings(settings=Settings()) -> Settings:
     return settings

fractal_server/migrations/versions/fbce16ff4e47_new_history_items.py

@@ -0,0 +1,120 @@
+"""new history items
+
+Revision ID: fbce16ff4e47
+Revises: af1ef1c83c9b
+Create Date: 2025-03-14 15:25:01.083619
+
+"""
+import sqlalchemy as sa
+import sqlmodel
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = "fbce16ff4e47"
+down_revision = "af1ef1c83c9b"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "historyrun",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("dataset_id", sa.Integer(), nullable=False),
+        sa.Column("workflowtask_id", sa.Integer(), nullable=True),
+        sa.Column(
+            "workflowtask_dump",
+            postgresql.JSONB(astext_type=sa.Text()),
+            nullable=False,
+        ),
+        sa.Column(
+            "task_group_dump",
+            postgresql.JSONB(astext_type=sa.Text()),
+            nullable=False,
+        ),
+        sa.Column(
+            "timestamp_started", sa.DateTime(timezone=True), nullable=False
+        ),
+        sa.Column(
+            "status", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column("num_available_images", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["dataset_id"],
+            ["datasetv2.id"],
+            name=op.f("fk_historyrun_dataset_id_datasetv2"),
+            ondelete="CASCADE",
+        ),
+        sa.ForeignKeyConstraint(
+            ["workflowtask_id"],
+            ["workflowtaskv2.id"],
+            name=op.f("fk_historyrun_workflowtask_id_workflowtaskv2"),
+            ondelete="SET NULL",
+        ),
+        sa.PrimaryKeyConstraint("id", name=op.f("pk_historyrun")),
+    )
+    op.create_table(
+        "historyunit",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("history_run_id", sa.Integer(), nullable=False),
+        sa.Column(
+            "logfile", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column(
+            "status", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column("zarr_urls", postgresql.ARRAY(sa.String()), nullable=True),
+        sa.ForeignKeyConstraint(
+            ["history_run_id"],
+            ["historyrun.id"],
+            name=op.f("fk_historyunit_history_run_id_historyrun"),
+            ondelete="CASCADE",
+        ),
+        sa.PrimaryKeyConstraint("id", name=op.f("pk_historyunit")),
+    )
+    op.create_table(
+        "historyimagecache",
+        sa.Column(
+            "zarr_url", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column("dataset_id", sa.Integer(), nullable=False),
+        sa.Column("workflowtask_id", sa.Integer(), nullable=False),
+        sa.Column("latest_history_unit_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["dataset_id"],
+            ["datasetv2.id"],
+            name=op.f("fk_historyimagecache_dataset_id_datasetv2"),
+            ondelete="CASCADE",
+        ),
+        sa.ForeignKeyConstraint(
+            ["latest_history_unit_id"],
+            ["historyunit.id"],
+            name=op.f(
+                "fk_historyimagecache_latest_history_unit_id_historyunit"
+            ),
+            ondelete="CASCADE",
+        ),
+        sa.ForeignKeyConstraint(
+            ["workflowtask_id"],
+            ["workflowtaskv2.id"],
+            name=op.f("fk_historyimagecache_workflowtask_id_workflowtaskv2"),
+            ondelete="CASCADE",
+        ),
+        sa.PrimaryKeyConstraint(
+            "zarr_url",
+            "dataset_id",
+            "workflowtask_id",
+            name=op.f("pk_historyimagecache"),
+        ),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table("historyimagecache")
+    op.drop_table("historyunit")
+    op.drop_table("historyrun")
+    # ### end Alembic commands ###

fractal_server/tasks/v2/templates/2_pip_install.sh

@@ -25,7 +25,7 @@ echo
 
 # Install package
 write_log "START install ${INSTALL_STRING}"
-"$VENVPYTHON" -m pip install --no-cache-dir "$INSTALL_STRING"
+"$VENVPYTHON" -m pip install ${FRACTAL_PIP_CACHE_DIR_ARG} "$INSTALL_STRING"
 write_log "END   install ${INSTALL_STRING}"
 echo
 

fractal_server/tasks/v2/utils_templates.py

@@ -2,12 +2,15 @@ from pathlib import Path
 
 from fractal_server.app.models.v2 import TaskGroupV2
 from fractal_server.config import get_settings
+from fractal_server.logger import set_logger
 from fractal_server.syringe import Inject
 
 TEMPLATES_DIR = Path(__file__).parent / "templates"
 
 SCRIPTS_SUBFOLDER = "scripts"
 
+logger = set_logger(__name__)
+
 
 def customize_template(
     *,
@@ -87,4 +90,7 @@ def get_collection_replacements(
             task_group.pinned_package_versions_string,
         ),
     ]
+    logger.info(
+        f"Cache-dir argument for `pip install`: {settings.PIP_CACHE_DIR_ARG}"
+    )
     return replacements

{fractal_server-2.14.0a3.dist-info → fractal_server-2.14.0a4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.14.0a3
+Version: 2.14.0a4
 Summary: Backend component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

{fractal_server-2.14.0a3.dist-info → fractal_server-2.14.0a4.dist-info}/RECORD

@@ -1,20 +1,20 @@
-fractal_server/__init__.py,sha256=hpk2FCu0xXoEuH8cDYFItQE2071uD_KsQqreoRWpt4A,25
-fractal_server/__main__.py,sha256=igfS2XL3e8JycuhASl2vsYuIPma0MG0cfPPFRuQfh14,6906
+fractal_server/__init__.py,sha256=7tAxXkNvimqYIX0U_oeIYOmpP_2NjEN3fI6It2ac4-s,25
+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
 fractal_server/app/db/__init__.py,sha256=wup2wcOkyOh8Vd0Xm76PZn_naxeMqaL4eF8DHHXTGlI,2889
-fractal_server/app/history/__init__.py,sha256=bisQpsMCFmtQGhIsf9ES0HdEuH4DYkPxVO7SlvxaWTY,239
-fractal_server/app/history/image_updates.py,sha256=YqoOwPW97LQk9-o04zB1lSU0yQ90V0AcuhFIhTVUxos,3959
-fractal_server/app/history/status_enum.py,sha256=xBBLHQY2Z105b2_HVU9DVRgdEVbbjLm6l4kkcV0Q1Sk,275
+fractal_server/app/history/__init__.py,sha256=ZF-5wb_NH_7SJkUiVkYq2X0MJAy1fFnYBRpgPfEirjo,234
+fractal_server/app/history/image_updates.py,sha256=ToY3yENMM6OdWUuFPG5F7qsLefrsaPqyRDFHaimsaHI,4188
+fractal_server/app/history/status_enum.py,sha256=umznsG4-ZunCLz2ks3Gb-K_s1irwd4ibOJ8vJ2Z0C-M,235
 fractal_server/app/models/__init__.py,sha256=xJWiGAwpXmCpnFMC4c_HTqoUCzMOXrakoGLUH_uMvdA,415
 fractal_server/app/models/linkusergroup.py,sha256=LWTUfhH2uAnn_4moK7QdRUIHWtpw-hPZuW-5jClv_OE,610
 fractal_server/app/models/linkuserproject.py,sha256=hvaxh3Lkiy2uUCwB8gvn8RorCpvxSSdzWdCS_U1GL7g,315
 fractal_server/app/models/security.py,sha256=mMb_HiwWY74QZrs9xuyno0CVSmk4GYQWk5FxGixr8SU,3860
 fractal_server/app/models/user_settings.py,sha256=Y-ZV-uZAFLZqXxy8c5_Qeh_F7zQuZDWOgLpU6Zs6iqU,1316
-fractal_server/app/models/v2/__init__.py,sha256=VNoK2OUB8_IPvZoItLOxup84ZMNslO7j30jojNS2lI0,774
+fractal_server/app/models/v2/__init__.py,sha256=vjHwek7-IXmaZZL9VF0nD30YL9ca4wNc8P4RXJK_kDc,832
 fractal_server/app/models/v2/accounting.py,sha256=f2ALxfKKBNxFLJTtC2-YqRepVK253x68y7zkD2V_Nls,1115
 fractal_server/app/models/v2/dataset.py,sha256=O5_6YfNeX6JM7PUcEZhbeV4JCvuAhFCQbOOuefpVnqc,1544
-fractal_server/app/models/v2/history.py,sha256=SqD6Va7h7LUzSzf_yz_iTcDQpivxif6hy--Rls_yekw,1538
+fractal_server/app/models/v2/history.py,sha256=C0pqn_S5yqc8PjayoyRNcsk5Mt_SxvHitdQznuxJvGM,2044
 fractal_server/app/models/v2/job.py,sha256=L0P1mrztMqqb-6qdPEbuHXhCsf2mxVUct_ehcXrREGg,1844
 fractal_server/app/models/v2/project.py,sha256=rAHoh5KfYwIaW7rTX0_O0jvWmxEvfo1BafvmcXuSSRk,786
 fractal_server/app/models/v2/task.py,sha256=8KEROaadgccXRZIP7EriBp2j1FgzYkgiirOi5_fG79M,1494
@@ -31,31 +31,33 @@ fractal_server/app/routes/admin/v2/project.py,sha256=luy-yiGX1JYTdPm1hpIdDUUqPm8
 fractal_server/app/routes/admin/v2/task.py,sha256=QOwgyDU9m7T_wLMwkdgfFaoMjNxcDg6zMVpngxhUvqk,4374
 fractal_server/app/routes/admin/v2/task_group.py,sha256=XTjdqgABXZcx9EenaoqSmHh12BXSentUus3SV0oxBMs,7929
 fractal_server/app/routes/admin/v2/task_group_lifecycle.py,sha256=0e0ZJ_k75TVHaT2o8Xk33DPDSgh-eBhZf-y4y7t-Adg,9429
-fractal_server/app/routes/api/__init__.py,sha256=2IDheFi0OFdsUg7nbUiyahqybvpgXqeHUXIL2QtWrQQ,641
-fractal_server/app/routes/api/v2/__init__.py,sha256=S7zOeoLkD6Sss1JLRQxeQWPSXKMX2yaIVhLQUw0PDh0,2176
+fractal_server/app/routes/api/__init__.py,sha256=B8l6PSAhR10iZqHEiyTat-_0tkeKdrCigIE6DJGP5b8,638
+fractal_server/app/routes/api/v2/__init__.py,sha256=Q65mxJOfuexzj53m6IB5fNl9PDec-Asu97W0bBxrRMM,2324
 fractal_server/app/routes/api/v2/_aux_functions.py,sha256=pmYbsHjJexb5-zMCJQLNStmU_95ZfeEIBpoCJx4GFIY,13480
+fractal_server/app/routes/api/v2/_aux_functions_history.py,sha256=dGr9mhuE1kJPx8RNDwFplCWBunV1Zh0QxNQbssGAqMI,1341
 fractal_server/app/routes/api/v2/_aux_functions_task_lifecycle.py,sha256=qdXCb6IP8-qPEAxGZKljtjIqNzIAyRaAsQSRi5VqFHM,6773
 fractal_server/app/routes/api/v2/_aux_functions_tasks.py,sha256=uhNSs-jcS7ndIUFKiOC1yrDiViw3uvKEXi9UL04BMks,11642
-fractal_server/app/routes/api/v2/dataset.py,sha256=gS5169eJRGHBQNUnkDB75Bv3Kg8Ql-tMVw5_FAxUEKc,9664
-fractal_server/app/routes/api/v2/history.py,sha256=C_V_u2ab4i8v4bM-uQ0SV3Olyor_5olQRDYFsLco2Ac,9801
+fractal_server/app/routes/api/v2/dataset.py,sha256=osoWJIA5SZH4aAr-0TG6Uc3877wzsgCLB_Oek59hRjk,9230
+fractal_server/app/routes/api/v2/history.py,sha256=GPok8bYnagGPjNmoHvdLm2h-lirsd2ROUlMt2OjIoKM,12911
 fractal_server/app/routes/api/v2/images.py,sha256=wUhYomNLGtJTtu_pD2oQorcH2LISxo64Wxo6ogc4IXc,8185
 fractal_server/app/routes/api/v2/job.py,sha256=m89FTh9Px25oXCeWj2k2NdGWQaO2oxMh-6lZppcsJOY,5551
-fractal_server/app/routes/api/v2/project.py,sha256=apWQNOdj2FIZmBl6Cjtr2tK-jUclEsw-ikKg6PMT8sU,7828
+fractal_server/app/routes/api/v2/project.py,sha256=hMvL9QLPUcAAiPGy6ta2LBLTVRozJsfvBPl5D06_MHg,6666
+fractal_server/app/routes/api/v2/status_legacy.py,sha256=sJLHGGHI9so_Sa4-8JuhMGBPeE6n4K2DmDuiw6IB4XY,6317
 fractal_server/app/routes/api/v2/submit.py,sha256=K4OjcSg476JXIeeMUaYdTDk8Qpj5IO5UULvfErI7Y5Y,8624
 fractal_server/app/routes/api/v2/task.py,sha256=z3_SxsXoKsbM9GGNJUdIiZisQwAJSBqvCc7thaJIOTU,7191
 fractal_server/app/routes/api/v2/task_collection.py,sha256=IDNF6sjDuU37HIQ0TuQA-TZIuf7nfHAQXUUNmkrlhLM,12706
 fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=cctW61-C2QYF2KXluS15lLhZJS_kt30Ca6UGLFO32z0,6207
 fractal_server/app/routes/api/v2/task_group.py,sha256=j3zDvVZizB7NWEgVgZU42JCXETkaVkk2ImJPr0jS7BQ,8164
 fractal_server/app/routes/api/v2/task_group_lifecycle.py,sha256=3o9bCC8ubMwffQPPaxQZy-CjH9IB2RkIReIecI6L2_w,9300
-fractal_server/app/routes/api/v2/workflow.py,sha256=R-wnT9tWTSbaNobGcfgLdk-4pbfbxoBwKZd1JRZXsSU,12223
+fractal_server/app/routes/api/v2/workflow.py,sha256=U3iZX5IiFAJ20-R8IjlYToOdm9gXsmtr1lW7ASEH9P8,11689
 fractal_server/app/routes/api/v2/workflow_import.py,sha256=INmnhlMEBJp-vHPR0f940DANPmIidts3OfcooeM_aNA,11205
-fractal_server/app/routes/api/v2/workflowtask.py,sha256=89yLpSzdr7Mv3wRmdMt71CSC3hclrVUP56UVtfTQHOQ,12152
+fractal_server/app/routes/api/v2/workflowtask.py,sha256=pi4oxWszNgWkDm6oQavanmq4_P5kpcgN3Dfjz9XAuV8,11063
 fractal_server/app/routes/auth/__init__.py,sha256=fao6CS0WiAjHDTvBzgBVV_bSXFpEAeDBF6Z6q7rRkPc,1658
 fractal_server/app/routes/auth/_aux_auth.py,sha256=UZgauY0V6mSqjte_sYI1cBl2h8bcbLaeWzgpl1jdJlk,4883
 fractal_server/app/routes/auth/current_user.py,sha256=FUegTahlxT3BdPVCQYir0-ogg2YAaZ1DYuLcE_5NC9Y,5906
 fractal_server/app/routes/auth/group.py,sha256=EblxNVNTiPQj82eMaxNxf3OqoAbRLOExxCnm1-8C-k0,8364
 fractal_server/app/routes/auth/login.py,sha256=tSu6OBLOieoBtMZB4JkBAdEgH2Y8KqPGSbwy7NIypIo,566
-fractal_server/app/routes/auth/oauth.py,sha256=AnFHbjqL2AgBX3eksI931xD6RTtmbciHBEuGf9YJLjU,1895
+fractal_server/app/routes/auth/oauth.py,sha256=KCtJHSzemC4S8AfX9bLLdVhlF1nU4DOyox-sNQtcWew,1978
 fractal_server/app/routes/auth/register.py,sha256=DlHq79iOvGd_gt2v9uwtsqIKeO6i_GKaW59VIkllPqY,587
 fractal_server/app/routes/auth/router.py,sha256=tzJrygXFZlmV_uWelVqTOJMEH-3Fr7ydwlgx1LxRjxY,527
 fractal_server/app/routes/auth/users.py,sha256=Zr1Bsa7Hpricb_1uFwKPCtgt3PzGnP0TaMLMdpbQDNs,7825
@@ -73,7 +75,7 @@ fractal_server/app/runner/executors/base_runner.py,sha256=0E3gbSndXdEAxZwFCiZXrU
 fractal_server/app/runner/executors/local/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/local/_local_config.py,sha256=8dyg2Gh8L2FlG_jJRYLMkcMgVHGEY2w7DME9aaKXFFo,3688
 fractal_server/app/runner/executors/local/_submit_setup.py,sha256=pDc9Q6axXL8_5JAV0byXzGOLOB0bZF88_L9LZykOgwM,1220
-fractal_server/app/runner/executors/local/runner.py,sha256=tEI3qe9UQKgqNoY6gkP1b2O1yRw3VGTiPTDKztrCt2I,7577
+fractal_server/app/runner/executors/local/runner.py,sha256=Iy5Pc8rdkj7IGcwUbkO_UgZNDytXtfMysYtMSu_dlY0,5498
 fractal_server/app/runner/executors/slurm_common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm_common/_batching.py,sha256=ZY020JZlDS5mfpgpWTChQkyHU7iLE5kx2HVd57_C6XA,8850
 fractal_server/app/runner/executors/slurm_common/_job_states.py,sha256=nuV-Zba38kDrRESOVB3gaGbrSPZc4q7YGichQaeqTW0,238
@@ -88,50 +90,48 @@ fractal_server/app/runner/executors/slurm_ssh/_slurm_job.py,sha256=IL1C52dezEiin
 fractal_server/app/runner/executors/slurm_ssh/executor.py,sha256=JW6zguEy9XsHebSPt_JTK4Kw78r5rlbDEipSOxOqoHk,53660
 fractal_server/app/runner/executors/slurm_sudo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm_sudo/_check_jobs_status.py,sha256=eZd9lxbObsqc1M3B96IGMJ-1oC0jo8lBOX4Nto97VvE,2036
-fractal_server/app/runner/executors/slurm_sudo/_executor_wait_thread.py,sha256=7CaMarvaKFCq3RcyqW5CABng_3b3QaS2pmTzVRDgm3I,4077
 fractal_server/app/runner/executors/slurm_sudo/_subprocess_run_as_user.py,sha256=O1bNg1DiSDJmQE0RmOk2Ii47DagiXp5ryd0R6KxO2OM,3177
-fractal_server/app/runner/executors/slurm_sudo/runner.py,sha256=JFVGb0K7w0l6kuy4QjIey_3M4indQUwvqbflzdW9Gi8,21256
+fractal_server/app/runner/executors/slurm_sudo/runner.py,sha256=VOWd8bYzCU8C6TziZN7VUurX52lbvNDWLZ2Ht3uvnGc,24057
 fractal_server/app/runner/extract_archive.py,sha256=tLpjDrX47OjTNhhoWvm6iNukg8KoieWyTb7ZfvE9eWU,2483
 fractal_server/app/runner/filenames.py,sha256=lPnxKHtdRizr6FqG3zOdjDPyWA7GoaJGTtiuJV0gA8E,70
 fractal_server/app/runner/run_subprocess.py,sha256=c3JbYXq3hX2aaflQU19qJ5Xs6J6oXGNvnTEoAfv2bxc,959
 fractal_server/app/runner/set_start_and_last_task_index.py,sha256=-q4zVybAj8ek2XlbENKlfOAJ39hT_zoJoZkqzDqiAMY,1254
 fractal_server/app/runner/shutdown.py,sha256=9pfSKHDNdIcm0eY-opgRTi7y0HmvfPmYiu9JR6Idark,2082
 fractal_server/app/runner/task_files.py,sha256=5enzBqiQct1AUGwrGX-rxFCxnhW3SPYIUylMYwyVfrE,2482
-fractal_server/app/runner/v2/__init__.py,sha256=llVnhgNGsSuP_eZ_ilQixQTmwst79LWrgjILpC2Xn9o,14247
+fractal_server/app/runner/v2/__init__.py,sha256=ro5C4ro7gXuV-H7p8SrV90vBsS52IfukWn-b2FxJ9F4,13293
 fractal_server/app/runner/v2/_local.py,sha256=Zas2RS_f9mfdkXszBpzISHylLX1bX8pFuoLA1fHLFqQ,2945
 fractal_server/app/runner/v2/_slurm_ssh.py,sha256=5w_lwQzySx-R3kVg2Bf-21n5JpWjJAgMtYP2BROvWJo,3227
 fractal_server/app/runner/v2/_slurm_sudo.py,sha256=CzWUeC6at_Sj-wU1myjA68ZRKMiLZYBTLv9I9odUxBU,2914
 fractal_server/app/runner/v2/deduplicate_list.py,sha256=IVTE4abBU1bUprFTkxrTfYKnvkNTanWQ-KWh_etiT08,645
 fractal_server/app/runner/v2/merge_outputs.py,sha256=D1L4Taieq9i71SPQyNc1kMokgHh-sV_MqF3bv7QMDBc,907
-fractal_server/app/runner/v2/runner.py,sha256=qtxmnrgMdlB3CA5Ayg7BXUv1yETR6H7kMLp70R1faSM,14456
-fractal_server/app/runner/v2/runner_functions.py,sha256=Zvi6sC5krltygLO-fC0K21VJEhmX1XQCm9IzVqf_cB0,9583
+fractal_server/app/runner/v2/runner.py,sha256=25kOKm4B7_BhUlg7Dh0yzIcJ2izugA_WFNhVf06O0Y4,13970
+fractal_server/app/runner/v2/runner_functions.py,sha256=PQC5wsi-o3AlFZbk3EeIZ_9KMBLQxYleMDi7CYcXySE,14473
 fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=dvvRK7od8iQ8vdPf80uGUxs3i5i0buGjCodBxSjZ7PQ,3671
 fractal_server/app/runner/v2/task_interface.py,sha256=e1GGQSYd0MyBj1EZvEVzqv-HpVE4YffXOq82WLrCaOc,1866
 fractal_server/app/runner/versions.py,sha256=dSaPRWqmFPHjg20kTCHmi_dmGNcCETflDtDLronNanU,852
 fractal_server/app/schemas/__init__.py,sha256=stURAU_t3AOBaH0HSUbV-GKhlPKngnnIMoqWc3orFyI,135
 fractal_server/app/schemas/_filter_validators.py,sha256=Gkf2USrkuxZx1TWeeMRmhgfmG60AAIDQfbaWslLsvJQ,1572
-fractal_server/app/schemas/_validators.py,sha256=ap0VWJzOfPcq_tbH3sglZClkuinNvMjRq9fhTIdn-zk,3029
-fractal_server/app/schemas/user.py,sha256=vLijVyPIQJdpFc36S6qK2XtSKMzfkhULN1nBsb9tV18,2407
+fractal_server/app/schemas/_validators.py,sha256=ZzTlTTzRATzf9Snx4Xp67aDmG77GaM2ewssFtlxQaaY,2680
+fractal_server/app/schemas/user.py,sha256=oCftAKeHdFFowpLyh1G-RiylR8cIO7fTn0PkT5xjs0E,2494
 fractal_server/app/schemas/user_group.py,sha256=Uao1igRYflBu7Dg6Zs0kaFU3zBFJzIwDLrkFfaJk6z8,2176
-fractal_server/app/schemas/user_settings.py,sha256=4XeXQ3rnDS1UvLPd9hvh-WVSbzBGcMDjChfiZ_WGi-w,3134
+fractal_server/app/schemas/user_settings.py,sha256=z7hx54yTrWfjo98oX_1lkeRh1UGrC1dSRH6yIOpnCsY,2772
 fractal_server/app/schemas/v2/__init__.py,sha256=pjRUOJwZGzsDbBbxfnCgQgShs5V8SaHRqwIQDW3STpY,2676
 fractal_server/app/schemas/v2/accounting.py,sha256=Wylt7uWTiDIFlHJOh4XEtYitk2FjFlmnodDrJDxcr0E,397
-fractal_server/app/schemas/v2/dataset.py,sha256=xo7Y3fq5ThMVBp6xDVypdG-EmGfBX_vWVRs66u2pC34,5157
+fractal_server/app/schemas/v2/dataset.py,sha256=9yc-tte70yPPk4CSfy2imykYVbCW8-23K499pi9z2e0,5206
 fractal_server/app/schemas/v2/dumps.py,sha256=2GUjoqeblUvrSoojBz5odoUUf53IABtbY_5GvFZoMVc,1782
-fractal_server/app/schemas/v2/history.py,sha256=OHwRIbOIjBiiTYUNZYsHTdEXJHff17JRizQ8pf1e0vk,601
-fractal_server/app/schemas/v2/job.py,sha256=Dp_RRiC5uvJqq1fAJlBXztAFA-tS5FWuRnUbTnLtL6M,4226
-fractal_server/app/schemas/v2/manifest.py,sha256=tcCvT4PbdtpdC5eU54MKUne6puXpnPlIExZYwLGHEAo,7133
-fractal_server/app/schemas/v2/project.py,sha256=uqBreoS0UAkbVEJJS2HkSdjCCWfFIkv6N70TWk9HgxA,868
+fractal_server/app/schemas/v2/job.py,sha256=KhxQOfncpE_SAu7Wed8CXS2G6onh0v875GkotBvKBTY,4304
+fractal_server/app/schemas/v2/manifest.py,sha256=tMNKtwVUBhVyAmBHK6f2agzvdKuYhuTP-e2cG9t66y0,7045
+fractal_server/app/schemas/v2/project.py,sha256=ulgCmUnX0w-0jrSjVYIT7sxeK95CSNGh2msXydhsgYI,885
 fractal_server/app/schemas/v2/status.py,sha256=SQaUpQkjFq5c5k5J4rOjNhuQaDOEg8lksPhkKmPU5VU,332
-fractal_server/app/schemas/v2/task.py,sha256=OUCNQQUULmWSOdPm8Dz8E0ivG1XOcvO4dxz-osSa9R0,7248
-fractal_server/app/schemas/v2/task_collection.py,sha256=NFIcfTAhFN5LMxmyJCat7CKxUXq2CLEuWl5Hs0siZl8,6561
-fractal_server/app/schemas/v2/task_group.py,sha256=vFF850kJRmmcxt2sn7nrhm-OWJHRhYu_XOQP5LNiXyU,3850
-fractal_server/app/schemas/v2/workflow.py,sha256=qmKJZ9xZ6-sN41XdocZ7K6hum_pUfaMuKOJs_TlFCRQ,2211
+fractal_server/app/schemas/v2/task.py,sha256=lPXxhwvPLjXuoZGdVSLZq3wTChfBbP7V-uTEpQa1HoU,5753
+fractal_server/app/schemas/v2/task_collection.py,sha256=dLu4sy-su5k5vDJqCZdJMW8mLT5TX2SV60l_RAvKhwY,5930
+fractal_server/app/schemas/v2/task_group.py,sha256=A3SFHNHLKPJyrnDz-wbnQvycetafKltp6UsH1u-euwA,3850
+fractal_server/app/schemas/v2/workflow.py,sha256=ZpM43zTMyLRnEUtkbr_J5DYP00NwjItaC8gweB7GGAA,2172
 fractal_server/app/schemas/v2/workflowtask.py,sha256=qMvwlnFCsnyD8uv8HJ4cFy2-QMm2ETUFlTIbxIFUWxk,8056
 fractal_server/app/security/__init__.py,sha256=e2cveg5hQpieGD3bSPd5GTOMthvJ-HXH3buSb9WVfEU,14096
-fractal_server/app/security/signup_email.py,sha256=CR1VbsGFNshxsWquLDZPbUAYnGzkCHeJChtncq63RBc,1434
+fractal_server/app/security/signup_email.py,sha256=Xd6QYxcdmg0PHpDwmUE8XQmPcOj3Xjy5oROcIMhmltM,1472
 fractal_server/app/user_settings.py,sha256=OP1yiYKtPadxwM51_Q0hdPk3z90TCN4z1BLpQsXyWiU,1316
-fractal_server/config.py,sha256=eYo-c3Zt4rkC45mewLYOeFZSA_7FF4Wmm6zDvX1dpt4,28549
+fractal_server/config.py,sha256=mdVsXHo3bCBMyTErro2kN2CKV2547XTHWoaAAiawq94,28561
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyMmRbbJl-hAM,572
 fractal_server/gunicorn_fractal.py,sha256=u6U01TLGlXgq1v8QmEpLih3QnsInZD7CqphgJ_GrGzc,1230
@@ -155,11 +155,9 @@ fractal_server/migrations/versions/5bf02391cfef_v2.py,sha256=axhNkr_H6R4rRbY7oGY
 fractal_server/migrations/versions/70e77f1c38b0_add_applyworkflow_first_task_index_and_.py,sha256=Q-DsMzG3IcUV2Ol1dhJWosDvKERamBE6QvA2zzS5zpQ,1632
 fractal_server/migrations/versions/71eefd1dd202_add_slurm_accounts.py,sha256=mbWuCkTpRAdGbRhW7lhXs_e5S6O37UAcCN6JfoY5H8A,1353
 fractal_server/migrations/versions/84bf0fffde30_add_dumps_to_applyworkflow.py,sha256=NSCuhANChsg76vBkShBl-9tQ4VEHubOjtAv1etHhlvY,2684
-fractal_server/migrations/versions/87cd72a537a2_add_historyitem_table.py,sha256=xxAftQYyQ2C_7qiuPcG5FeVmhFQGznxfCglsfk2CjiU,2092
 fractal_server/migrations/versions/8e8f227a3e36_update_taskv2_post_2_7_0.py,sha256=68y9-fpSuKx6KPtM_9n8Ho0I1qwa8IoG-yJqXUYQrGg,1111
 fractal_server/migrations/versions/8f79bd162e35_add_docs_info_and_docs_link_to_task_.py,sha256=6pgODDtyAxevZvAJBj9IJ41inhV1RpwbpZr_qfPPu1A,1115
 fractal_server/migrations/versions/94a47ea2d3ff_remove_cache_dir_slurm_user_and_slurm_.py,sha256=yL3-Hvzw5jBLKj4LFP1z5ofZE9L9W3tLwYtPNW7z4ko,1508
-fractal_server/migrations/versions/954ddc64425a_image_status.py,sha256=cPjuGTztDkjvhVQDO8i41qAmG5O2CgKNUfV_PRK9Pck,1742
 fractal_server/migrations/versions/97f444d47249_add_applyworkflow_project_dump.py,sha256=eKTZm3EgUgapXBxO0RuHkEfTKic-TZG3ADaMpGLuc0k,1057
 fractal_server/migrations/versions/99ea79d9e5d2_add_dataset_history.py,sha256=0im6TxDr53sKKcjiPgeH4ftVRGnRXZSh2lPbRQ1Ir9w,883
 fractal_server/migrations/versions/9c5ae74c9b98_add_user_settings_table.py,sha256=syONdZNf4-OnAcWIsbzXpYwpXPsXZ4SsmjwVvmVG0PU,2256
@@ -174,6 +172,7 @@ fractal_server/migrations/versions/db09233ad13a_split_filters_and_keep_old_colum
 fractal_server/migrations/versions/e75cac726012_make_applyworkflow_start_timestamp_not_.py,sha256=lOggSvzGWqQvnxxFuSM6W50Ui49R918A-uBuiZJ0pNM,963
 fractal_server/migrations/versions/efa89c30e0a4_add_project_timestamp_created.py,sha256=jilQW3QIqYQ4Q6hCnUiG7UtNMpA41ujqrB3tPFiPM1Q,1221
 fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.py,sha256=9BwqUS9Gf7UW_KjrzHbtViC880qhD452KAytkHWWZyk,746
+fractal_server/migrations/versions/fbce16ff4e47_new_history_items.py,sha256=TDWCaIoM0Q4SpRWmR9zr_rdp3lJXhCfBPTMhtrP5xYE,3950
 fractal_server/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/ssh/__init__.py,sha256=sVUmzxf7_DuXG1xoLQ1_00fo5NPhi2LJipSmU5EAkPs,124
 fractal_server/ssh/_fabric.py,sha256=lNy4IX1I4We6VoWa4Bz4fUPuApLMSoejpyE6I3jDZeM,22869
@@ -193,7 +192,7 @@ fractal_server/tasks/v2/ssh/collect.py,sha256=-wqqGMapjD1hQz1vphwXmZaD4qzziMetc6
 fractal_server/tasks/v2/ssh/deactivate.py,sha256=EAVH2HtyvmIFXqUwsGYhlJcAcVh_MvIOaKDY8AyBODw,11400
 fractal_server/tasks/v2/ssh/reactivate.py,sha256=8Rnbbny7TjMEAHhboqfgxBVZZK5UNNmh4Ud-0y3jaVM,7970
 fractal_server/tasks/v2/templates/1_create_venv.sh,sha256=PK0jdHKtQpda1zULebBaVPORt4t6V17wa4N1ohcj5ac,548
-fractal_server/tasks/v2/templates/2_pip_install.sh,sha256=Gpk2io8u9YaflFUlQu2NgkDQw5AA4m4AOVG1sB4yrHQ,1822
+fractal_server/tasks/v2/templates/2_pip_install.sh,sha256=Md2LPt3BJ7IfN0USF2uivl4rP8OwbzJOUepGAr_Cicg,1836
 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
@@ -202,12 +201,12 @@ fractal_server/tasks/v2/utils_background.py,sha256=W_RvihI1aiYPJNsPo8z4wKuA_bPs0
 fractal_server/tasks/v2/utils_database.py,sha256=iLbwkxMxTCgpyKe1JQzdfIR3zBfxohgmLwSdGps1AUo,1274
 fractal_server/tasks/v2/utils_package_names.py,sha256=RDg__xrvQs4ieeVzmVdMcEh95vGQYrv9Hfal-5EDBM8,2393
 fractal_server/tasks/v2/utils_python_interpreter.py,sha256=5_wrlrTqXyo1YuLZvAW9hrSoh5MyLOzdPVUlUwM7uDQ,955
-fractal_server/tasks/v2/utils_templates.py,sha256=07TZpJ0Mh_A4lXVXrrH2o1VLFFGwxeRumA6DdgMgCWk,2947
+fractal_server/tasks/v2/utils_templates.py,sha256=Kc_nSzdlV6KIsO0CQSPs1w70zLyENPqJeTQEFiz4bOg,3124
 fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=PMwrxWFxRTQRl1b9h-NRIbFGPKqpH_hXnkAT3NfZdpY,3571
 fractal_server/zip_tools.py,sha256=GjDgo_sf6V_DDg6wWeBlZu5zypIxycn_l257p_YVKGc,4876
-fractal_server-2.14.0a3.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.14.0a3.dist-info/METADATA,sha256=F2fjhacHy-6hFP43F8JNom4iV9-WNRiO6CiCye5KzLI,4550
-fractal_server-2.14.0a3.dist-info/WHEEL,sha256=RaoafKOydTQ7I_I3JTrPCg6kUmTgtm4BornzOqyEfJ8,88
-fractal_server-2.14.0a3.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.14.0a3.dist-info/RECORD,,
+fractal_server-2.14.0a4.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.14.0a4.dist-info/METADATA,sha256=dnHmj3wrxhQa2uhKzb4A9tJ2sSWtvj6kPEiTSO26NBQ,4550
+fractal_server-2.14.0a4.dist-info/WHEEL,sha256=RaoafKOydTQ7I_I3JTrPCg6kUmTgtm4BornzOqyEfJ8,88
+fractal_server-2.14.0a4.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.14.0a4.dist-info/RECORD,,

fractal_server/app/runner/executors/slurm_sudo/_executor_wait_thread.py

@@ -1,130 +0,0 @@
-import os
-import threading
-import time
-import traceback
-from itertools import count
-from typing import Optional
-
-from ._check_jobs_status import get_finished_jobs
-from fractal_server.app.runner.exceptions import JobExecutionError
-from fractal_server.logger import set_logger
-
-logger = set_logger(__name__)
-
-
-class FractalSlurmSudoWaitThread(threading.Thread):
-    """
-    Thread that monitors a pool of SLURM jobs
-
-    This class is a custom re-implementation of the waiting thread class from:
-
-    > clusterfutures <https://github.com/sampsyo/clusterfutures>
-    > Original Copyright
-    > Copyright 2021 Adrian Sampson <asampson@cs.washington.edu>
-    > License: MIT
-
-    Attributes:
-        slurm_user:
-        shutdown_file:
-        shutdown_callback:
-        slurm_poll_interval:
-        waiting:
-        shutdown:
-        lock:
-    """
-
-    slurm_user: str
-    shutdown_file: Optional[str] = None
-    shutdown_callback: callable
-    slurm_poll_interval: int = 30
-    waiting: dict[tuple[str, ...], str]
-    shutdown: bool
-    _lock: threading.Lock
-
-    def __init__(self, callback: callable, interval=1):
-        threading.Thread.__init__(self, daemon=True)
-        self.callback = callback
-        self.interval = interval
-        self.waiting = {}
-        self._lock = threading.Lock()  # To protect the .waiting dict
-        self.shutdown = False
-        self.active_job_ids = []
-
-    def wait(
-        self,
-        *,
-        filenames: tuple[str, ...],
-        jobid: str,
-    ):
-        """
-        Add a a new job to the set of jobs being waited for.
-
-        A job consists of a tuple of filenames and a callback value (i.e. a
-        SLURM job ID).
-
-        Note that (with respect to clusterfutures) we replaced `filename` with
-        `filenames`.
-        """
-        if self.shutdown:
-            error_msg = "Cannot call `wait` method after executor shutdown."
-            logger.warning(error_msg)
-            raise JobExecutionError(info=error_msg)
-        with self._lock:
-            self.waiting[filenames] = jobid
-
-    def check_shutdown(self, i):
-        """
-        Do one shutdown-file-existence check.
-
-        Note: the `i` parameter allows subclasses like `SlurmWaitThread` to do
-        something on every Nth check.
-
-        Changed from clusterfutures:
-        * Do not check for output-pickle-file existence (we rather rely on
-          `cfut.slurm.jobs_finished`);
-        * Check for the existence of shutdown-file.
-        """
-        if self.shutdown_file and os.path.exists(self.shutdown_file):
-            logger.info(
-                f"Detected executor-shutdown file {str(self.shutdown_file)}"
-            )
-            self.shutdown = True
-
-    def run(self):
-        """
-        Overrides the original clusterfutures.FileWaitThread.run, adding a call
-        to self.shutdown_callback.
-
-        Changed from clusterfutures:
-        * We do not rely on output-file-existence checks to verify whether a
-          job is complete.
-
-        Note that `shutdown_callback` only takes care of cleaning up the
-        FractalSlurmExecutor variables, and then the `return` here is enough to
-        fully clean up the `FractalFileWaitThread` object.
-        """
-        for i in count():
-            if self.shutdown:
-                self.shutdown_callback()
-                return
-            with self._lock:
-                self.check(i)
-            time.sleep(self.interval)
-
-    def check(self, i):
-        self.check_shutdown(i)
-        if i % (self.slurm_poll_interval // self.interval) == 0:
-            try:
-                finished_jobs = get_finished_jobs(self.waiting.values())
-            except Exception:
-                # Don't abandon completion checking if jobs_finished errors
-                traceback.print_exc()
-                return
-
-            if not finished_jobs:
-                return
-
-            id_to_filenames = {v: k for (k, v) in self.waiting.items()}
-            for finished_id in finished_jobs:
-                self.callback(finished_id)
-                self.waiting.pop(id_to_filenames[finished_id])