Merge branch 'feature/ssh-into-sessions' of github.com:SwissDataScien…

…ceCenter/renku-python into feature/ssh-into-sessions

renku/command/checks/__init__.py

@@ -17,7 +17,7 @@
 # limitations under the License.
 """Define repository checks for :program:`renku doctor`."""
 
-from .activities import check_migrated_activity_ids
+from .activities import check_activity_dates, check_migrated_activity_ids
 from .datasets import (
     check_dataset_files_outside_datadir,
     check_dataset_old_metadata_location,
@@ -30,7 +30,7 @@
 from .project import check_project_id_group
 from .storage import check_lfs_info
 from .validate_shacl import check_datasets_structure, check_project_structure
-from .workflow import check_activity_catalog, check_modification_date
+from .workflow import check_activity_catalog, check_plan_modification_date
 
 # Checks will be executed in the order as they are listed in __all__. They are mostly used in ``doctor`` command to
 # inspect broken things. The order of operations matters when fixing issues, so, don't sort this list.
@@ -48,5 +48,6 @@
     "check_missing_files",
     "check_project_id_group",
     "check_project_structure",
-    "check_modification_date",
+    "check_plan_modification_date",
+    "check_activity_dates",
 )

renku/command/checks/activities.py

@@ -71,3 +71,61 @@ def check_migrated_activity_ids(fix, activity_gateway: IActivityGateway, **_):
     )
 
     return False, problems
+
+
+@inject.autoparams("activity_gateway")
+def check_activity_dates(fix, activity_gateway: IActivityGateway, **_):
+    """Check activities have correct start/end/delete dates.
+
+    Args:
+        fix(bool): Whether to fix found issues.
+        activity_gateway(IActivityGateway): Injected ActivityGateway.
+        _: keyword arguments.
+
+    Returns:
+        Tuple[bool, Optional[str]]: Tuple of whether there are activities with invalid dates a string of the problem.
+    """
+    invalid_activities = []
+
+    for activity in activity_gateway.get_all_activities(include_deleted=True):
+        plan = activity.association.plan
+        if (
+            activity.started_at_time < plan.date_created
+            or activity.ended_at_time < activity.started_at_time
+            or (activity.invalidated_at and activity.invalidated_at < activity.ended_at_time)
+        ):
+            invalid_activities.append(activity)
+
+    if not invalid_activities:
+        return True, None
+    if not fix:
+        ids = [a.id for a in invalid_activities]
+        message = (
+            WARNING
+            + "The following activity have incorrect start, end, or delete date (use 'renku doctor --fix' to fix them):"
+            + "\n\t"
+            + "\n\t".join(ids)
+        )
+        return False, message
+
+    fix_activity_dates(activities=invalid_activities)
+    project_context.database.commit()
+    communication.info("Activity dates were fixed")
+
+    return True, None
+
+
+def fix_activity_dates(activities):
+    """Fix activities' start/end/delete dates."""
+    for activity in activities:
+        plan = activity.association.plan
+        activity.unfreeze()
+        if activity.started_at_time < plan.date_created:
+            activity.started_at_time = plan.date_created
+
+        if activity.ended_at_time < activity.started_at_time:
+            activity.ended_at_time = activity.started_at_time
+
+        if activity.invalidated_at and activity.invalidated_at < activity.ended_at_time:
+            activity.invalidated_at = activity.ended_at_time
+        activity.freeze()

renku/command/checks/workflow.py

@@ -16,7 +16,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Checks needed to determine integrity of workflows."""
-
+from datetime import timedelta
 from typing import List, Optional, Tuple, cast
 
 from renku.command.command_builder import inject
@@ -64,7 +64,7 @@ def check_activity_catalog(fix, force, **_) -> Tuple[bool, Optional[str]]:
 
 
 @inject.autoparams("plan_gateway")
-def check_modification_date(fix, plan_gateway: IPlanGateway, **_) -> Tuple[bool, Optional[str]]:
+def check_plan_modification_date(fix, plan_gateway: IPlanGateway, **_) -> Tuple[bool, Optional[str]]:
     """Check if all plans have modification date set for them.
 
     Args:
@@ -88,7 +88,7 @@ def check_modification_date(fix, plan_gateway: IPlanGateway, **_) -> Tuple[bool,
         ids = [plan.id for plan in to_be_processed]
         message = (
             WARNING
-            + "The following workflows have incorrect modification date (use 'renku doctor --fix' to fix them).:\n\t"
+            + "The following workflows have incorrect modification date (use 'renku doctor --fix' to fix them):\n\t"
             + "\n\t".join(ids)
         )
         return False, message
@@ -124,4 +124,6 @@ def fix_plan_dates(plans: List[AbstractPlan], plan_gateway):
             plan.unfreeze()
             plan.date_modified = plan.date_created
             plan.date_created = creation_date
+            if plan.date_removed and plan.date_removed < plan.date_created:
+                plan.date_removed = plan.date_created + timedelta(seconds=1)
             plan.freeze()

renku/core/migration/m_0009__new_metadata_storage.py

@@ -655,19 +655,16 @@ def _process_datasets(
 
     for dataset in datasets:
         dataset, tags = convert_dataset(dataset=dataset, revision=revision)
-        if is_last_commit:
-            datasets_provenance.update_during_migration(
-                dataset,
-                commit_sha=revision,
-                date=date,
-                tags=tags,
-                replace=True,
-                preserve_identifiers=preserve_identifiers,
-            )
-        else:
-            datasets_provenance.update_during_migration(
-                dataset, commit_sha=revision, date=date, tags=tags, preserve_identifiers=preserve_identifiers
-            )
+
+        datasets_provenance.update_during_migration(
+            dataset,
+            commit_sha=revision,
+            date=date,
+            tags=tags,
+            replace=True if is_last_commit else False,
+            preserve_identifiers=preserve_identifiers,
+        )
+
     for dataset in deleted_datasets:
         dataset, _ = convert_dataset(dataset=dataset, revision=revision)
         datasets_provenance.update_during_migration(

renku/core/migration/m_0010__metadata_fixes.py

@@ -16,6 +16,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Various metadata migrations for v10."""
+
 import io
 import json
 import os
@@ -26,6 +27,7 @@
 
 import zstandard as zstd
 
+from renku.command.checks.activities import fix_activity_dates
 from renku.command.checks.workflow import fix_plan_dates
 from renku.command.command_builder import inject
 from renku.core.interface.activity_gateway import IActivityGateway
@@ -53,9 +55,12 @@ def migrate(migration_context: MigrationContext):
     if MigrationType.WORKFLOWS in migration_context.options.type:
         migrate_activity_ids()
         fix_plan_times()
+        fix_activity_times()
 
     migrate_remote_entity_ids()
     fix_dataset_date_modified()
+    fix_dataset_image_ids()
+    fix_removed_plans()
 
     # NOTE: Rebuild all workflow catalogs since ids and times have changed
     communication.echo("Rebuilding workflow metadata")
@@ -76,8 +81,8 @@ def migrate_old_metadata_namespaces():
                 header = int.from_bytes(file.read(4), "little")
                 file.seek(0)
                 if header == zstd.MAGIC_NUMBER:
-                    with decompressor.stream_reader(file) as zfile:
-                        data = json.load(zfile)
+                    with decompressor.stream_reader(file) as compressed_file:
+                        data = json.load(compressed_file)
                         compressed = True
                 else:
                     data = json.load(file)
@@ -99,7 +104,7 @@ def migrate_old_metadata_namespaces():
 
 
 def nested_update(data: Dict[str, Any], target_key: str, transforms: List[Tuple[str, str]]) -> None:
-    """Update a key's value based on tranformations (from, to) in a deeply nested dictionary."""
+    """Update a key's value based on transformations (from, to) in a deeply nested dictionary."""
     for k in list(data.keys()):
         value = data[k]
         if isinstance(value, str) and k == target_key:
@@ -232,19 +237,10 @@ def migrate_project_template_data(project_gateway: IProjectGateway):
     project_context.database.commit()
 
 
-@inject.autoparams("activity_gateway", "plan_gateway")
-def fix_plan_times(activity_gateway: IActivityGateway, plan_gateway: IPlanGateway):
+@inject.autoparams("plan_gateway")
+def fix_plan_times(plan_gateway: IPlanGateway):
     """Add timezone to plan invalidations."""
-    database = project_context.database
-
     plans: List[AbstractPlan] = plan_gateway.get_all_plans()
-    all_activities = activity_gateway.get_all_activities()
-    activity_map: Dict[str, Activity] = {}
-
-    for activity in all_activities:
-        plan_id = activity.association.plan.id
-        if plan_id not in activity_map or activity.started_at_time < activity_map[plan_id].started_at_time:
-            activity_map[plan_id] = activity
 
     for plan in plans:
         plan.unfreeze()
@@ -255,24 +251,41 @@ def fix_plan_times(activity_gateway: IActivityGateway, plan_gateway: IPlanGatewa
             plan.date_removed = None
 
         if plan.date_removed is not None:
-            if plan.date_removed < plan.date_created:
-                # NOTE: Fix invalidation times set before creation date on plans
-                plan.date_removed = plan.date_created
             if plan.date_removed.tzinfo is None:
                 # NOTE: There was a bug that caused date_removed to be set without timezone (as UTC time)
                 # so we patch in the timezone here
                 plan.date_removed = plan.date_removed.replace(microsecond=0).astimezone(timezone.utc)
-        if plan.id in activity_map and plan.date_created > activity_map[plan.id].started_at_time:
-            plan.date_created = activity_map[plan.id].started_at_time
+            if plan.date_removed < plan.date_created:
+                # NOTE: Fix invalidation times set before creation date on plans
+                plan.date_removed = plan.date_created
         plan.freeze()
 
     fix_plan_dates(plans=plans, plan_gateway=plan_gateway)
-    database.commit()
+    project_context.database.commit()
+
+
+@inject.autoparams("activity_gateway")
+def fix_activity_times(activity_gateway: IActivityGateway):
+    """Make sure activities have valid start/end/delete dates."""
+    fix_activity_dates(activities=activity_gateway.get_all_activities(include_deleted=True))
+    project_context.database.commit()
 
 
 @inject.autoparams("dataset_gateway")
 def fix_dataset_date_modified(dataset_gateway: IDatasetGateway):
     """Change date_created and date_modified to have correct semantics."""
+
+    def fix_creation_date(dataset):
+        """Check creation date to make sure that it's after project's creation date."""
+        if dataset.date_created and dataset.date_created < project_context.project.date_created:
+            try:
+                dataset.date_created = min([f.date_added for f in dataset.files])
+            except (ValueError, TypeError):
+                dataset.date_created = project_context.project.date_created
+            else:
+                if dataset.date_created < project_context.project.date_created:
+                    dataset.date_created = project_context.project.date_created
+
     tails = dataset_gateway.get_provenance_tails()
 
     for dataset_tail in tails:
@@ -281,6 +294,7 @@ def fix_dataset_date_modified(dataset_gateway: IDatasetGateway):
         previous_modification_date = local_now()
 
         while dataset.derived_from is not None:
+            fix_creation_date(dataset)
             modification_date = dataset.date_removed or dataset.date_created
 
             if modification_date is not None:
@@ -294,8 +308,9 @@ def fix_dataset_date_modified(dataset_gateway: IDatasetGateway):
             found_datasets.append(dataset)
             dataset = dataset_gateway.get_by_id(dataset.derived_from.value)
 
+        fix_creation_date(dataset)
         # NOTE: first dataset in chain
-        modification_date = dataset.date_created or dataset.date_published
+        modification_date = dataset.date_published or dataset.date_created
         if modification_date is not None:
             dataset.unfreeze()
             dataset.date_modified = modification_date
@@ -308,3 +323,41 @@ def fix_dataset_date_modified(dataset_gateway: IDatasetGateway):
             child.freeze()
 
     project_context.database.commit()
+
+
+@inject.autoparams("dataset_gateway")
+def fix_dataset_image_ids(dataset_gateway: IDatasetGateway):
+    """Remove dashes from dataset image IDs."""
+    for dataset in dataset_gateway.get_provenance_tails():
+        while True:
+            if dataset.images:
+                for image in dataset.images:
+                    image.id = image.id.replace("-", "")
+
+                dataset._p_changed = True
+
+            if not dataset.derived_from:
+                break
+
+            dataset = dataset_gateway.get_by_id(dataset.derived_from.value)
+
+    project_context.database.commit()
+
+
+@inject.autoparams("plan_gateway")
+def fix_removed_plans(plan_gateway: IPlanGateway):
+    """Create a derivative if a removed plan doesn't have one."""
+    plans: List[AbstractPlan] = plan_gateway.get_all_plans()
+
+    for plan in plans:
+        if plan.date_removed and plan.derived_from is None:
+            derived_plan = plan.derive()
+            derived_plan.date_modified = plan.date_modified
+            derived_plan.delete(when=plan.date_removed)
+            plan_gateway.add(derived_plan)
+
+            plan.unfreeze()
+            plan.date_removed = None
+            plan.freeze()
+
+    project_context.database.commit()

renku/core/util/datetime8601.py

@@ -75,6 +75,7 @@ def _set_to_local_timezone(value):
     return value.replace(tzinfo=local_tz)
 
 
-def local_now() -> datetime:
+def local_now(remove_microseconds: bool = True) -> datetime:
     """Return current datetime in local timezone."""
-    return datetime.now(timezone.utc).replace(microsecond=0).astimezone()
+    now = datetime.now(timezone.utc).astimezone()
+    return now.replace(microsecond=0) if remove_microseconds else now

renku/core/util/git.py

@@ -379,7 +379,7 @@ def get_entity_from_revision(
         Entity: The Entity for the given path and revision.
 
     """
-    from renku.domain_model.entity import Collection, Entity
+    from renku.domain_model.entity import NON_EXISTING_ENTITY_CHECKSUM, Collection, Entity
 
     def get_directory_members(absolute_path: Path) -> List[Entity]:
         """Return first-level files/directories in a directory."""
@@ -410,7 +410,9 @@ def get_directory_members(absolute_path: Path) -> List[Entity]:
     checksum = repository.get_object_hash(revision=revision, path=path)
     # NOTE: If object was not found at a revision it's either removed or exists in a different revision; keep the
     # entity and use revision as checksum
-    checksum = checksum or revision or "HEAD"
+    if isinstance(revision, str) and revision == "HEAD":
+        revision = repository.head.commit.hexsha
+    checksum = checksum or revision or NON_EXISTING_ENTITY_CHECKSUM
     id = Entity.generate_id(checksum=checksum, path=path)
 
     absolute_path = repository.path / path

renku/data/shacl_shape.json

@@ -1635,7 +1635,6 @@
                "datatype": {
                   "@id": "xsd:string"
                },
-               "minCount": 1,
                "maxCount": 1
             },
             {

renku/domain_model/workflow/plan.py

@@ -153,14 +153,14 @@ def is_derivation(self) -> bool:
         """Return if an ``AbstractPlan`` has correct derived_from."""
         raise NotImplementedError()
 
-    def delete(self):
+    def delete(self, when: datetime = local_now()):
         """Mark a plan as deleted.
 
         NOTE: Don't call this function for deleting plans since it doesn't delete the whole plan derivatives chain. Use
         renku.core.workflow.plan::remove_plan instead.
         """
         self.unfreeze()
-        self.date_removed = local_now()
+        self.date_removed = when
         self.freeze()
 
 
@@ -323,6 +323,7 @@ def derive(self, creator: Optional[Person] = None) -> "Plan":
         derived.keywords = copy.deepcopy(self.keywords)
         derived.outputs = self.outputs.copy()
         derived.success_codes = self.success_codes.copy()
+        derived.creators = self.creators.copy()
         derived.assign_new_id()
 
         if creator and hasattr(creator, "email") and not any(c for c in self.creators if c.email == creator.email):