Use CumulativeAnalysisReport.generation.activity when registering in …

…Nexus (#6)

Other changes:

- Remove EnsuredList because not needed anymore
- Remove analysis entities already moved to entity-management
- Upgrade requirements.txt, needing entity-management>=1.5.0

CHANGELOG.rst

@@ -1,6 +1,27 @@
 Changelog
 =========
 
+Version 4.1.0 (2024-08-28)
+--------------------------
+
+Breaking changes
+~~~~~~~~~~~~~~~~
+
+- Use CumulativeAnalysisReport.generation.activity when registering custom analyses in Nexus.
+
+Improvements
+~~~~~~~~~~~~
+
+- Upgrade requirements.txt.
+
+Version 4.0.2 (2024-08-23)
+--------------------------
+
+Improvements
+~~~~~~~~~~~~
+
+- Add generatorName in VariantTaskConfig to obey schema.
+
 Version 4.0.1 (2024-08-15)
 --------------------------
 

bbp_workflow/sbo/analysis/common/task.py

@@ -10,8 +10,14 @@
 from functools import cached_property
 from pathlib import Path
 
+from entity_management.analysis import (
+    AnalysisReportGeneration,
+    AnalysisReportGenerationActivity,
+    AnalysisSoftwareSourceCode,
+    CumulativeAnalysisReport,
+    MultiCumulativeAnalysisReport,
+)
 from entity_management.base import Derivation
-from entity_management.core import Contribution
 from luigi import (
     BoolParameter,
     Config,
@@ -28,11 +34,6 @@
 from luigi.parameter import ParameterVisibility
 
 from bbp_workflow.luigi import CompleteTask, RemoteTarget, inherits
-from bbp_workflow.sbo.entity import (
-    AnalysisSoftwareSourceCode,
-    CumulativeAnalysisReport,
-    MultiCumulativeAnalysisReport,
-)
 from bbp_workflow.sbo.task import BaseTask, MetaTask
 from bbp_workflow.settings import DEFAULT_HOST, L
 from bbp_workflow.slurm import _run_cmd, _run_sbatch, _sbatch
@@ -534,21 +535,22 @@ def pre_publish_resource(self, activity):
             assert isinstance(task, AnalyseGeneric)
             if task.source_code_url:
                 agent = AnalysisSoftwareSourceCode.from_url(task.source_code_url)
-                contributions = [Contribution(agent=agent)]
+                generation_activity = AnalysisReportGenerationActivity(wasAssociatedWith=agent)
+                generations = [AnalysisReportGeneration(activity=generation_activity)]
             else:
                 L.warning(
                     "The source code url for analysis %s is missing, the relation won't be created",
                     index,
                 )
-                contributions = None
+                generations = None
             sub_resource = CumulativeAnalysisReport(
                 name=task.report_name,
                 description=task.report_description,
                 categories=list(task.categories),
                 types=list(task.types),
                 derivation=Derivation(entity=analysed_entity),
                 index=index,
-                contribution=contributions,
+                generation=generations,
             )
             sub_resource = self.publish(sub_resource, activity=activity)
             parts.append(sub_resource)

bbp_workflow/sbo/analysis/emodel/task.py

@@ -7,6 +7,7 @@
 from pathlib import Path
 
 from blue_cwl.me_model.staging import stage_emodel
+from entity_management.analysis import AnalysisReport, MultiEModelAnalysis
 from entity_management.base import Derivation
 from entity_management.emodel import EModel
 from luigi import DictParameter, ListParameter, Parameter, PathParameter
@@ -18,7 +19,6 @@
     MultiAnalyseGenericMeta,
     get_analysis_config_schema,
 )
-from bbp_workflow.sbo.entity import AnalysisReport, MultiEModelAnalysis
 from bbp_workflow.sbo.task import BaseTask
 from bbp_workflow.settings import DEFAULT_HOST
 from bbp_workflow.task import KgCfg

bbp_workflow/sbo/analysis/sim/task.py

@@ -6,6 +6,11 @@
 from functools import cached_property
 from pathlib import Path
 
+from entity_management.analysis import (
+    AnalysisReport,
+    Derivation,
+    MultiCumulativeSimulationCampaignAnalysis,
+)
 from entity_management.simulation import Simulation
 from luigi import DictParameter, ListParameter, Parameter
 
@@ -15,11 +20,6 @@
     MultiAnalyseGenericMeta,
     get_analysis_config_schema,
 )
-from bbp_workflow.sbo.entity import (
-    AnalysisReport,
-    Derivation,
-    MultiCumulativeSimulationCampaignAnalysis,
-)
 from bbp_workflow.sbo.sim.task import RunSimCampaign, RunSimCampaignMeta
 from bbp_workflow.settings import L
 from bbp_workflow.simulation.util import read_config

bbp_workflow/sbo/emodel/task.py

@@ -13,9 +13,9 @@
 from bluepyemodel.emodel_pipeline.emodel_settings import EModelPipelineSettings
 from bluepyemodel.model.model_configurator import ModelConfigurator
 from entity_management.core import Entity
+from entity_management.workflow import BbpWorkflowActivity
 from luigi import Parameter
 
-from bbp_workflow.sbo.entity import BbpWorkflowActivity
 from bbp_workflow.sbo.task import BaseTask, MetaTask
 
 L = logging.getLogger(__name__)

bbp_workflow/sbo/sim/task.py

@@ -8,6 +8,8 @@
 from threading import Thread
 
 import numpy as np
+from entity_management.analysis import AnalysisReport
+from entity_management.base import Derivation
 from entity_management.simulation import Simulation as SimEntity
 from entity_management.simulation import (
     SimulationCampaign,
@@ -32,7 +34,6 @@
 
 from bbp_workflow.luigi import RemoteTarget, inherits
 from bbp_workflow.sbo.circ.task import FindDetailedCircuit, FindDetailedCircuitMeta
-from bbp_workflow.sbo.entity import AnalysisReport, Derivation
 from bbp_workflow.sbo.task import BaseTask, MetaTask
 from bbp_workflow.settings import (
     BBP_WORKFLOW_SIF,

bbp_workflow/sbo/viz/task.py

@@ -6,6 +6,8 @@
 from pathlib import Path
 
 import brayns
+from entity_management.analysis import AnalysisReport
+from entity_management.base import Derivation
 from entity_management.simulation import Simulation as SimEntity
 from entity_management.simulation import SimulationCampaignAnalysis
 from luigi import (
@@ -23,7 +25,6 @@
 
 from bbp_workflow.luigi import RemoteTarget, inherits
 from bbp_workflow.sbo.analysis.sim.task import MultiAnalyseSimCampaignMeta
-from bbp_workflow.sbo.entity import AnalysisReport, Derivation
 from bbp_workflow.sbo.sim.task import ReportsSimCampaignMeta, RunSimCampaign, RunSimCampaignMeta
 from bbp_workflow.sbo.task import BaseTask, MetaTask
 from bbp_workflow.settings import BBP_WORKFLOW_SIF, BRAYNS_SIF, DEFAULT_HOST, ENVIRONMENT

bbp_workflow/simulation/task.py

@@ -415,7 +415,9 @@ def _handle_post_processors(self, config):
         if self.post_processors:
             sim_indices = _indices_to_ranges(_campaign_sim_indices(config))
             path_prefix_name = Path(config.attrs["path_prefix"]) / config.name
-            cmd = f'python "$POST_PROCESSOR" {path_prefix_name/"config.json"} $SLURM_ARRAY_TASK_ID'
+            cmd = (
+                f'python "$POST_PROCESSOR" {path_prefix_name / "config.json"} $SLURM_ARRAY_TASK_ID'
+            )
             pre_cmd = dedent(
                 f"""\
                 cd {path_prefix_name}/$SLURM_ARRAY_TASK_ID

requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.11
+# This file is autogenerated by pip-compile with Python 3.12
 # by the following command:
 #
 #    pip-compile
@@ -27,15 +27,15 @@ bluepyefe==2.3.34
     # via bluepyemodel
 bluepyemodel==1.0.15
     # via bbp-workflow (setup.py)
-bluepyopt==1.14.13
+bluepyopt==1.14.15
     # via bluepyemodel
 bluepysnap==3.0.1
     # via
     #   bbp-workflow (setup.py)
     #   brainbuilder
 brainbuilder==0.20.1
     # via blue-cwl
-brayns==3.8.3
+brayns==3.9.0
     # via bbp-workflow (setup.py)
 cached-property==1.5.2
     # via
@@ -63,9 +63,9 @@ click==8.1.7
     #   neurom
 comm==0.2.2
     # via ipykernel
-configparser==7.0.0
+configparser==7.1.0
     # via bluepyemodel
-contourpy==1.2.1
+contourpy==1.3.0
     # via matplotlib
 cryptography==43.0.0
     # via jwcrypto
@@ -89,14 +89,14 @@ devtools[pygments]==0.12.2
     # via entity-management
 docutils==0.21.2
     # via python-daemon
-efel==5.7.6
+efel==5.7.8
     # via
     #   bluepyefe
     #   bluepyemodel
     #   bluepyopt
 elephant==1.1.0
     # via bbp-workflow (setup.py)
-entity-management==1.4.1
+entity-management==1.5.0
     # via
     #   bbp-workflow (setup.py)
     #   blue-cwl
@@ -136,16 +136,16 @@ hdmf==3.14.3
     # via pynwb
 httpcore==1.0.5
     # via httpx
-httpx==0.27.0
+httpx==0.27.2
     # via python-keycloak
-idna==3.7
+idna==3.8
     # via
     #   anyio
     #   httpx
     #   requests
 igor2==0.5.8
     # via bluepyefe
-importlib-resources==6.4.2
+importlib-resources==6.4.4
     # via bluepysnap
 ipykernel==6.29.5
     # via ipyparallel
@@ -364,7 +364,7 @@ pynrrd==1.0.0
     # via voxcell
 pynwb==2.8.1
     # via efel
-pyparsing==3.1.2
+pyparsing==3.1.4
     # via
     #   matplotlib
     #   rdflib
@@ -389,12 +389,12 @@ pyyaml==6.0.2
     #   brainbuilder
     #   fz-td-recipe
     #   neurom
-pyzmq==26.1.0
+pyzmq==26.2.0
     # via
     #   ipykernel
     #   ipyparallel
     #   jupyter-client
-quantities==0.15.0
+quantities==0.16.0
     # via
     #   elephant
     #   neo
@@ -422,7 +422,7 @@ ruamel-yaml==0.18.6
     # via hdmf
 ruamel-yaml-clib==0.2.8
     # via ruamel-yaml
-scipy==1.14.0
+scipy==1.14.1
     # via
     #   bluepyefe
     #   bluepyemodel
@@ -480,7 +480,6 @@ typing-extensions==4.12.2
     #   efel
     #   flexcache
     #   flexparser
-    #   ipython
     #   jwcrypto
     #   luigi-tools
     #   pint
@@ -498,7 +497,7 @@ voxcell==3.1.9
     #   brainbuilder
 wcwidth==0.2.13
     # via prompt-toolkit
-websockets==12.0
+websockets==13.0
     # via brayns
 xarray==2024.7.0
     # via