(re-)add provenance recording to new data model

docs/adr/hermes-prov-diagram/hermes-prov.drawio.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2026 German Aerospace Center (DLR)
+
+SPDX-License-Identifier: CC-BY-SA-4.0

docs/adr/hermes-prov-diagram/hermes-prov.svg.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2026 German Aerospace Center (DLR)
+
+SPDX-License-Identifier: CC-BY-SA-4.0

hermes.toml

@@ -5,6 +5,9 @@
 [harvest]
 sources = [ "cff", "toml" ] # ordered priority (first one is most important)
 
+[process]
+plugins = [ "invenio", "codemeta" ]
+
 [curate]
 plugin = "pass_curate"
 

pyproject.toml

@@ -75,6 +75,7 @@ codemeta_doi = "hermes.commands.postprocess.invenio:codemeta_doi"
 
 [project.entry-points."hermes.process"]
 codemeta = "hermes.commands.process.standard_merge:CodemetaProcessPlugin"
+invenio = "hermes.commands.process.invenio_merge:InvenioProcessPlugin"
 
 [project.entry-points."hermes.curate"]
 pass_curate = "hermes.commands.curate.pass_curate:DoNothingCuratePlugin"

src/hermes/commands/__init__.py

@@ -17,3 +17,4 @@
 from hermes.commands.process.base import HermesProcessCommand
 from hermes.commands.deposit.base import HermesDepositCommand
 from hermes.commands.postprocess.base import HermesPostprocessCommand
+from hermes.commands.report.base import HermesReportCommand

src/hermes/commands/cli.py

@@ -14,7 +14,7 @@
 from hermes import logger
 from hermes.commands import (
     HermesCurateCommand, HermesCleanCommand, HermesDepositCommand, HermesHarvestCommand, HermesHelpCommand,
-    HermesInitCommand, HermesPostprocessCommand, HermesProcessCommand, HermesVersionCommand
+    HermesInitCommand, HermesPostprocessCommand, HermesProcessCommand, HermesReportCommand, HermesVersionCommand
 )
 from hermes.commands.base import HermesCommand
 from hermes.error import HermesPluginRunError
@@ -46,6 +46,7 @@ def main() -> None:
             HermesInitCommand(parser),
             HermesPostprocessCommand(parser),
             HermesProcessCommand(parser),
+            HermesReportCommand(parser),
             HermesVersionCommand(parser),
     ):
         if command.settings_class is not None:

src/hermes/commands/curate/base.py

@@ -5,6 +5,8 @@
 # SPDX-FileContributor: Michael Meinel
 
 import argparse
+import datetime
+from typing import Optional
 
 from pydantic import BaseModel
 
@@ -13,6 +15,7 @@
 from hermes.model import SoftwareMetadata
 from hermes.model.context_manager import HermesContext
 from hermes.model.error import HermesValidationError
+from hermes.model.provenance.ld_prov import ld_prov_list
 
 
 class HermesCuratePlugin(HermesPlugin):
@@ -35,6 +38,17 @@ class HermesCurateCommand(HermesCommand):
     settings_class = CurateSettings
 
     def __call__(self, args: argparse.Namespace) -> None:
+        self.args = args
+        self.log.info("# Load provenance data from process step")
+        prov_doc = self.load_prov_doc()
+        if prov_doc is not None:
+            prov_doc.add_hermes_settings(self)
+            prov_doc.add_settings_to_command("curate", self)
+            curate_command = prov_doc.get_hermes_command("curate")
+            curate_base_plugin = prov_doc.get_hermes_base_plugin("curate")
+            process_command = prov_doc.get_hermes_command("process")
+            hermes_cache = prov_doc.get_hermes_cache()
+
         self.log.info("# Metadata curation")
         plugin_name = self.settings.plugin
 
@@ -45,7 +59,9 @@ def __call__(self, args: argparse.Namespace) -> None:
         # load processed data
         ctx.prepare_step("process")
         try:
+            begin_load_at_time = datetime.datetime.now()
             metadata = SoftwareMetadata.load_from_cache(ctx, "result")
+            end_load_at_time = datetime.datetime.now()
         except Exception as e:
             self.log.critical(
                 "## The data from the process step could not be loaded or is invalid for some reason.",
@@ -54,6 +70,9 @@ def __call__(self, args: argparse.Namespace) -> None:
             raise HermesValidationError("The results of the process step are invalid.") from e
         ctx.finalize_step("process")
 
+        # save loaded metadata now, because it could be altered in curation
+        loaded_metadata_str = str(metadata.compact())
+
         self.log.info(f"## Load curation plugin {plugin_name}")
         # load plugin
         try:
@@ -66,12 +85,111 @@ def __call__(self, args: argparse.Namespace) -> None:
         # run plugin
         try:
             curated_metadata = plugin_func(self, metadata)
+            end_curation_time = datetime.datetime.now()
         except Exception as e:
             self.log.critical(f"## Unknown error while executing the {plugin_name} plugin.", exc_info=1)
             raise HermesPluginRunError(f"Something went wrong while running the curate plugin {plugin_name}") from e
 
         self.log.info("## Store curated data")
         # store metadata
+        begin_store_at_time = datetime.datetime.now()
         curated_metadata.write_to_cache(ctx, "result")
+        stored_at_time = datetime.datetime.now()
+
+        if prov_doc is not None:
+            curate_plugin = prov_doc.add_hermes_plugin("curate", plugin_name, plugin_func, self)
+            store_action_of_process = prov_doc.shallow_search(lambda node: (
+                "prov:wasAssociatedWith" in node and
+                node["prov:wasAssociatedWith"] == [process_command.ref, hermes_cache.ref] and
+                "prov:wasInformedBy" in node
+            ))[0]
+            stored_results_of_process = [res.ref for res in prov_doc.shallow_search(lambda node: (
+                "prov:wasGeneratedBy" in node and node["prov:wasGeneratedBy"] == [store_action_of_process.ref]
+            ))]
+            load_action = prov_doc.add_activity(data={
+                "schema:description": "loads the data from process step",
+                "prov:wasAssociatedWith": [process_command.ref, hermes_cache.ref],
+                "prov:used": stored_results_of_process,
+                "prov:startedAtTime": begin_load_at_time,
+                "prov:endedAtTime": end_load_at_time
+            })
+            loaded_data = prov_doc.add_entity(data={
+                "@type": "schema:CreativeWork",
+                "schema:description": "data loaded from process step",
+                "schema:text": loaded_metadata_str,  # TODO: maybe "prov:value" instead?
+                "prov:wasAttributedTo": hermes_cache.ref,
+                "prov:wasGeneratedBy": load_action.ref,
+                "prov:wasDerivedFrom": stored_results_of_process,
+                "prov:generatedAtTime": end_load_at_time
+            })
+            curated_data = prov_doc.add_entity(data={
+                "@type": "schema:CreativeWork",
+                "schema:description": "curated metadata",
+                "schema:text": str(curated_metadata.compact()),  # TODO: maybe "prov:value" instead?
+                "prov:wasAttributedTo": [curate_plugin.ref, curate_base_plugin.ref, curate_command.ref],
+                "prov:wasInfluencedBy": curate_plugin.ref,
+                "prov:wasGeneratedBy": load_action.ref,
+                "prov:wasDerivedFrom": loaded_data.ref,
+                "prov:generatedAtTime": end_curation_time
+            })
+            write = prov_doc.add_activity(data={
+                "schema:description": "Writes the processed metadata into the HERMES cache.",
+                "prov:wasAssociatedWith": [curate_command.ref, hermes_cache.ref],
+                "prov:used": curated_data.ref,
+                "prov:startedAtTime": begin_store_at_time,
+                "prov:endedAtTime": stored_at_time
+            })
+            # TODO: add more info
+            prov_doc.add_entity(data={
+                "@type": "schema:CreativeWork",
+                "schema:description": "The compacted version of the processed metadata.",
+                "schema:text": str(curated_metadata.compact()),  # TODO: maybe "prov:value" instead?
+                "schema:encodingFormat": "application/json",
+                "schema:url": (ctx.cache_dir / "curate" / "result" / "codemeta.json").absolute().as_uri(),
+                "prov:wasGeneratedBy": write.ref,
+                "prov:wasDerivedFrom": curated_data.ref,
+                "prov:wasAttributedTo": hermes_cache.ref,
+                "prov:generatedAtTime": stored_at_time
+            })
+            prov_doc.add_entity(data={
+                "@type": "schema:CreativeWork",
+                "schema:description": "The context of the processed metadata.",
+                "schema:text": str({"@context": curated_metadata.full_context}),  # TODO: maybe "prov:value" instead?
+                "schema:encodingFormat": "application/json",
+                "schema:url": (ctx.cache_dir / "curate" / "result" / "context.json").absolute().as_uri(),
+                "prov:wasGeneratedBy": write.ref,
+                "prov:wasDerivedFrom": curated_data.ref,
+                "prov:wasAttributedTo": hermes_cache.ref,
+                "prov:generatedAtTime": stored_at_time
+            })
+            prov_doc.add_entity(data={
+                "@type": "schema:CreativeWork",
+                "schema:description": "The expanded version of the processed metadata.",
+                "schema:text": str(curated_metadata.ld_value),  # TODO: maybe "prov:value" instead?
+                "schema:encodingFormat": "application/json",
+                "schema:url": (ctx.cache_dir / "curate" / "result" / "expanded.json").absolute().as_uri(),
+                "prov:wasGeneratedBy": write.ref,
+                "prov:wasDerivedFrom": curated_data.ref,
+                "prov:wasAttributedTo": hermes_cache.ref,
+                "prov:generatedAtTime": stored_at_time
+            })
+
+            with ctx["provenance"] as cache:
+                cache["result"] = prov_doc.ld_value
 
         ctx.finalize_step("curate")
+
+    def load_prov_doc(self) -> Optional[ld_prov_list]:
+        ctx = HermesContext()
+        ctx.prepare_step("process")
+        with ctx["provenance"] as cache:
+            try:
+                return ld_prov_list.load_ld_prov_list(cache["result"])
+            except Exception:
+                self.log.warning(
+                    "The provenance data from the process step could not be loaded. "
+                    "Processing will proceed without collecting provenance data.",
+                    exc_info=1
+                )
+            finally:
+                ctx.finalize_step("process")