Merge branch 'develop' into feature/2810-minimum-renku-version-property

docs/conf.py

@@ -349,9 +349,11 @@
     ("py:class", "CommandResult"),
     ("py:class", "CommunicationCallback"),
     ("py:class", "DynamicProxy"),
+    ("py:class", "IActivityGateway"),
     ("py:class", "IClientDispatcher"),
     ("py:class", "IDatabaseDispatcher"),
     ("py:class", "IDatasetGateway"),
+    ("py:class", "IPlanGateway"),
     ("py:class", "LocalClient"),
     ("py:class", "OID_TYPE"),
     ("py:class", "Path"),

helm-chart/renku-core/templates/deployment.yaml

@@ -47,11 +47,15 @@ spec:
         {{- include "certificates.volumes" $ | nindent 8 }}
       initContainers:
         {{- include "certificates.initContainer" $ | nindent 8 }}
+      securityContext:
+        {{- toYaml $.Values.podSecurityContext | nindent 8 }}
       containers:
       {{ if $.Values.metrics.enabled }}
         - name: {{ $.Chart.Name}}-rqmetrics
           image: "{{ $.Values.metrics.image.repository }}:{{ $.Values.metrics.image.tag }}"
           imagePullPolicy: {{ $.Values.metrics.image.pullPolicy }}
+          securityContext:
+            {{- toYaml $.Values.securityContext | nindent 12 }}
           env:
             - name: RQ_REDIS_HOST
               value: {{ $.Values.global.redis.host | quote }}
@@ -74,9 +78,7 @@ spec:
           image: "{{ $version.image.repository }}:{{ $version.image.tag }}"
           imagePullPolicy: {{ $version.image.pullPolicy }}
           securityContext:
-            runAsUser: 1000
-            runAsGroup: 1000
-            allowPrivilegeEscalation: false
+            {{- toYaml $.Values.securityContext | nindent 12 }}
           args: ["service", "api"]
           env:
             - name: REDIS_HOST
@@ -152,6 +154,8 @@ spec:
         - name: {{ $.Chart.Name }}-datasets-workers
           image: "{{ $version.image.repository }}:{{ $version.image.tag }}"
           imagePullPolicy: {{ $version.image.pullPolicy }}
+          securityContext:
+            {{- toYaml $.Values.securityContext | nindent 12 }}
           args: ["service", "worker"]
           env:
             - name: REDIS_HOST
@@ -206,6 +210,8 @@ spec:
         - name: {{ $.Chart.Name }}-management-workers
           image: "{{ $version.image.repository }}:{{ $version.image.tag }}"
           imagePullPolicy: {{ $version.image.pullPolicy }}
+          securityContext:
+            {{- toYaml $.Values.securityContext | nindent 12 }}
           args: ["service", "worker"]
           env:
             - name: REDIS_HOST
@@ -258,6 +264,8 @@ spec:
         - name: {{ $.Chart.Name }}-scheduler
           image: "{{ $version.image.repository }}:{{ $version.image.tag }}"
           imagePullPolicy: {{ $version.image.pullPolicy }}
+          securityContext:
+            {{- toYaml $.Values.securityContext | nindent 12 }}
           args: ["service", "scheduler"]
           env:
             - name: REDIS_HOST

helm-chart/renku-core/values.yaml

@@ -120,3 +120,11 @@ versions:
       repository: renku/renku-core
       tag: "v0.16.7"
       pullPolicy: IfNotPresent
+
+podSecurityContext:
+  runAsUser: 1000
+  runAsGroup: 1000
+  fsGroup: 100
+
+securityContext:
+  allowPrivilegeEscalation: false

renku/command/status.py

@@ -18,95 +18,74 @@
 """Renku ``status`` command."""
 
 from collections import defaultdict
-from typing import Dict, Set, Tuple
+from pathlib import Path
+from typing import Dict, Set
 
 from renku.command.command_builder import inject
 from renku.command.command_builder.command import Command
-from renku.core.interface.activity_gateway import IActivityGateway
 from renku.core.interface.client_dispatcher import IClientDispatcher
-from renku.core.util.metadata import filter_overridden_activities, get_modified_activities
 from renku.core.util.os import get_relative_path_to_cwd, get_relative_paths
-from renku.domain_model.entity import Entity
-from renku.domain_model.provenance.activity import Activity
+from renku.core.workflow.activity import (
+    get_all_modified_and_deleted_activities_and_entities,
+    get_downstream_generating_activities,
+    is_activity_valid,
+)
 
 
 def get_status_command():
     """Show a status of the repository."""
-    return Command().command(_get_status).require_migration().require_clean().with_database(write=False)
+    return Command().command(_get_status).require_migration().with_database(write=False)
 
 
 @inject.autoparams()
-def _get_status(client_dispatcher: IClientDispatcher, activity_gateway: IActivityGateway, paths=None):
-    def get_dependant_activities_from(start_activity):
-        """Return a set of activity and all its downstream activities.
-
-        Args:
-            start_activity: Root activity to start from.
-
-        Returns:
-            Root activity and all its downstream activities.
-        """
-        all_activities = activity_gateway.get_downstream_activities(start_activity)
-        all_activities.add(start_activity)
-        return all_activities
-
+def _get_status(ignore_deleted: bool, client_dispatcher: IClientDispatcher, paths=None):
     def mark_generations_as_stale(activity):
         for generation in activity.generations:
             generation_path = get_relative_path_to_cwd(client.path / generation.entity.path)
             stale_outputs[generation_path].add(usage_path)
 
     client = client_dispatcher.current_client
 
-    paths = paths or []
-    paths = get_relative_paths(base=client.path, paths=paths)
+    ignore_deleted = ignore_deleted or client.get_value("renku", "update_ignore_delete")
+
+    modified, deleted = get_all_modified_and_deleted_activities_and_entities(client.repository)
 
-    modified, deleted = _get_modified_paths(activity_gateway=activity_gateway, repository=client.repository)
+    modified = {(a, e) for a, e in modified if is_activity_valid(a)}
+    deleted = {(a, e) for a, e in deleted if is_activity_valid(a)}
 
     if not modified and not deleted:
         return None, None, None, None
 
+    paths = paths or []
+    paths = get_relative_paths(base=client.path, paths=[Path.cwd() / p for p in paths])
+
     modified_inputs: Set[str] = set()
     stale_outputs: Dict[str, Set[str]] = defaultdict(set)
     stale_activities: Dict[str, Set[str]] = defaultdict(set)
 
     for start_activity, entity in modified:
         usage_path = get_relative_path_to_cwd(client.path / entity.path)
 
-        activities = get_dependant_activities_from(start_activity)
-
-        if not paths or entity.path in paths:  # add all downstream activities
+        # NOTE: Add all downstream activities if the modified entity is in paths; otherwise, add only activities that
+        # chain-generate at least one of the paths
+        generation_paths = [] if not paths or entity.path in paths else paths
+
+        activities = get_downstream_generating_activities(
+            starting_activities={start_activity},
+            paths=generation_paths,
+            ignore_deleted=ignore_deleted,
+            client_path=client.path,
+        )
+        if activities:
             modified_inputs.add(usage_path)
+
             for activity in activities:
                 if len(activity.generations) == 0:
                     stale_activities[activity.id].add(usage_path)
                 else:
                     mark_generations_as_stale(activity)
-        else:
-            for activity in activities:
-                if any(g.entity.path in paths for g in activity.generations):
-                    modified_inputs.add(usage_path)
-                    mark_generations_as_stale(activity)
-
-    deleted = {get_relative_path_to_cwd(client.path / d) for d in deleted if not paths or d in paths}
-
-    return stale_outputs, stale_activities, modified_inputs, deleted
-
-
-def _get_modified_paths(activity_gateway, repository) -> Tuple[Set[Tuple[Activity, Entity]], Set[str]]:
-    """Get modified and deleted usages/inputs of a list of activities.
-
-    Args:
-        activity_gateway: Activity gateway.
-        repository: Current ``Repository``.
-
-    Returns:
-        Tuple[Set[Tuple[Activity, Entity]], Set[str]]: Tuple of Activities with their modified paths
-            and deleted paths.
-    """
-    all_activities = activity_gateway.get_all_activities()
-
-    relevant_activities = filter_overridden_activities(all_activities)
 
-    modified, deleted = get_modified_activities(activities=relevant_activities, repository=repository)
+    deleted_paths = {e.path for _, e in deleted}
+    deleted_paths = {get_relative_path_to_cwd(client.path / d) for d in deleted_paths if not paths or d in paths}
 
-    return modified, {e.path for _, e in deleted}
+    return stale_outputs, stale_activities, modified_inputs, deleted_paths

renku/command/update.py

@@ -17,24 +17,23 @@
 # limitations under the License.
 """Renku ``update`` command."""
 
-from collections import defaultdict
 from pathlib import Path
-from typing import Dict, List, Optional, Set, Tuple
+from typing import Optional
 
 from renku.command.command_builder import inject
 from renku.command.command_builder.command import Command
 from renku.command.workflow import execute_workflow
 from renku.core import errors
 from renku.core.errors import ParameterError
-from renku.core.interface.activity_gateway import IActivityGateway
 from renku.core.interface.client_dispatcher import IClientDispatcher
-from renku.core.interface.plan_gateway import IPlanGateway
-from renku.core.util.metadata import add_activity_if_recent, filter_overridden_activities, get_modified_activities
 from renku.core.util.os import get_relative_paths
-from renku.core.workflow.activity import sort_activities
+from renku.core.workflow.activity import (
+    get_all_modified_and_deleted_activities_and_entities,
+    get_downstream_generating_activities,
+    is_activity_valid,
+    sort_activities,
+)
 from renku.core.workflow.concrete_execution_graph import ExecutionGraph
-from renku.domain_model.provenance.activity import Activity
-from renku.domain_model.workflow.plan import AbstractPlan
 
 
 def update_command():
@@ -44,10 +43,10 @@ def update_command():
 
 @inject.autoparams()
 def _update(
-    update_all,
-    dry_run,
+    update_all: bool,
+    dry_run: bool,
+    ignore_deleted: bool,
     client_dispatcher: IClientDispatcher,
-    activity_gateway: IActivityGateway,
     provider: str,
     config: Optional[str],
     paths=None,
@@ -60,10 +59,18 @@ def _update(
     client = client_dispatcher.current_client
 
     paths = paths or []
-    paths = get_relative_paths(base=client.path, paths=paths)
+    paths = get_relative_paths(base=client.path, paths=[Path.cwd() / p for p in paths])
 
-    modified_activities, modified_paths = _get_modified_activities_and_paths(client.repository, activity_gateway)
-    activities = _get_downstream_activities(modified_activities, activity_gateway, paths)
+    modified, _ = get_all_modified_and_deleted_activities_and_entities(client.repository)
+    modified_activities = {a for a, _ in modified if is_activity_valid(a)}
+    modified_paths = {e.path for _, e in modified}
+
+    activities = get_downstream_generating_activities(
+        starting_activities=modified_activities,
+        paths=paths,
+        ignore_deleted=ignore_deleted,
+        client_path=client.path,
+    )
 
     if len(activities) == 0:
         raise errors.NothingToExecuteError()
@@ -75,110 +82,3 @@ def _update(
 
     graph = ExecutionGraph([a.plan_with_values for a in activities], virtual_links=True)
     execute_workflow(dag=graph.workflow_graph, provider=provider, config=config)
-
-
-@inject.autoparams()
-def _is_activity_valid(activity: Activity, plan_gateway: IPlanGateway, client_dispatcher: IClientDispatcher) -> bool:
-    """Return whether this plan is current and has not been deleted.
-
-    Args:
-        activity(Activity): The Activity whose Plan should be checked.
-        plan_gateway(IPlanGateway): The injected Plan gateway.
-        client_dispatcher(IClientDispatcher): The injected client dispatcher.
-
-    Returns:
-        bool: True if the activities' Plan is still valid, False otherwise.
-
-    """
-    client = client_dispatcher.current_client
-
-    for usage in activity.usages:
-        if not (client.path / usage.entity.path).exists():
-            return False
-
-    plan = activity.association.plan
-
-    if plan.invalidated_at is not None:
-        return False
-
-    # get newest with same name
-    newest_plan = plan_gateway.get_by_name(plan.name)
-
-    if newest_plan is None or newest_plan.invalidated_at is not None:
-        return False
-
-    all_plans = plan_gateway.get_all_plans()
-
-    derived: Optional[AbstractPlan] = plan
-    while derived:
-        plan = derived
-        derived = next((p for p in all_plans if p.derived_from is not None and p.derived_from == plan.id), None)
-
-    return plan.invalidated_at is None
-
-
-def _get_modified_activities_and_paths(repository, activity_gateway) -> Tuple[Set[Activity], Set[str]]:
-    """Return latest activities that one of their inputs is modified.
-
-    Args:
-        repository: The current ``Repository``.
-        activity_gateway: The injected Activity gateway.
-
-    Returns:
-        Tuple[Set[Activity],Set[str]]: Tuple of modified activites and modified paths.
-
-    """
-    all_activities = activity_gateway.get_all_activities()
-    relevant_activities = filter_overridden_activities(all_activities)
-    modified, _ = get_modified_activities(activities=list(relevant_activities), repository=repository)
-    return {a for a, _ in modified if _is_activity_valid(a)}, {e.path for _, e in modified}
-
-
-def _get_downstream_activities(
-    starting_activities: Set[Activity], activity_gateway: IActivityGateway, paths: List[str]
-) -> List[Activity]:
-    """Return activities downstream of passed activities.
-
-    Args:
-        starting_activities(Set[Activity]): Activities to use as starting/upstream nodes.
-        activity_gateway(IActivityGateway): The injected Activity gateway.
-        paths(List[str]): Optional gnerated paths to end downstream chains at.
-
-    Returns:
-        Set[Activity]: All activites and their downstream activities.
-
-    """
-    all_activities: Dict[str, Set[Activity]] = defaultdict(set)
-
-    def include_newest_activity(activity):
-        existing_activities = all_activities[activity.association.plan.id]
-        add_activity_if_recent(activity=activity, activities=existing_activities)
-
-    def does_activity_generate_any_paths(activity):
-        is_same = any(g.entity.path in paths for g in activity.generations)
-        is_parent = any(Path(p) in Path(g.entity.path).parents for p in paths for g in activity.generations)
-
-        return is_same or is_parent
-
-    for activity in starting_activities:
-        downstream_chains = activity_gateway.get_downstream_activity_chains(activity)
-
-        if paths:
-            # NOTE: Add the activity to check if it also matches the condition
-            downstream_chains.append((activity,))
-            downstream_chains = [c for c in downstream_chains if does_activity_generate_any_paths(c[-1])]
-
-            # NOTE: Include activity only if any of its downstream match the condition
-            if downstream_chains:
-                include_newest_activity(activity)
-        else:
-            include_newest_activity(activity)
-
-        for chain in downstream_chains:
-            for activity in chain:
-                if not _is_activity_valid(activity):
-                    # don't process further downstream activities as the plan in question was deleted
-                    break
-                include_newest_activity(activity)
-
-    return list({a for activities in all_activities.values() for a in activities})