Merge pull request #469 from softwarepub/feature/454-e2e-deposit

Merged implementation for process and deposit step back into the feature branches base branch.

Author: notactuallyfinn

src/hermes/commands/__init__.py

@@ -8,12 +8,12 @@
 # "unused import" errors.
 # flake8: noqa
 
-# from hermes.commands.base import HermesHelpCommand
-# from hermes.commands.base import HermesVersionCommand
-# from hermes.commands.clean.base import HermesCleanCommand
+from hermes.commands.base import HermesHelpCommand
+from hermes.commands.base import HermesVersionCommand
+from hermes.commands.clean.base import HermesCleanCommand
 # from hermes.commands.init.base import HermesInitCommand
 from hermes.commands.curate.base import HermesCurateCommand
 from hermes.commands.harvest.base import HermesHarvestCommand
-# from hermes.commands.process.base import HermesProcessCommand
-# from hermes.commands.deposit.base import HermesDepositCommand
+from hermes.commands.process.base import HermesProcessCommand
+from hermes.commands.deposit.base import HermesDepositCommand
 # from hermes.commands.postprocess.base import HermesPostprocessCommand

src/hermes/commands/base.py

@@ -175,6 +175,7 @@ def __call__(self, command: HermesCommand) -> None:
 
 
 class HermesHelpSettings(BaseModel):
+    """Intentionally empty settings class for the help command."""
     pass
 
 
@@ -200,3 +201,23 @@ def __call__(self, args: argparse.Namespace) -> None:
             # Otherwise, simply show the general help and exit (cleanly).
             self.parser.print_help()
             self.parser.exit()
+
+
+class HermesVersionSettings(BaseModel):
+    """Intentionally empty settings class for the version command."""
+    pass
+
+
+class HermesVersionCommand(HermesCommand):
+    """Show HERMES version and exit."""
+
+    command_name = "version"
+    settings_class = HermesVersionSettings
+
+    def load_settings(self, args: argparse.Namespace):
+        """Pass loading settings as not necessary for this command."""
+        pass
+
+    def __call__(self, args: argparse.Namespace) -> None:
+        self.log.info(metadata.version("hermes"))
+        self.parser.exit()

src/hermes/commands/cli.py

@@ -16,7 +16,9 @@
 # from hermes.commands import (HermesHelpCommand, HermesVersionCommand, HermesCleanCommand,
 #                              HermesHarvestCommand, HermesProcessCommand, HermesCurateCommand,
 #                              HermesDepositCommand, HermesPostprocessCommand, HermesInitCommand)
-from hermes.commands import HermesCurateCommand, HermesHarvestCommand
+from hermes.commands import (HermesCurateCommand, HermesDepositCommand,
+                             HermesHarvestCommand, HermesHelpCommand,
+                             HermesProcessCommand, HermesVersionCommand)
 from hermes.commands.base import HermesCommand
 
 
@@ -38,15 +40,15 @@ def main() -> None:
     setting_types = {}
 
     for command in (
-            # HermesHelpCommand(parser),
-            # HermesVersionCommand(parser),
-            # HermesInitCommand(parser),
             # HermesCleanCommand(parser),
-            HermesHarvestCommand(parser),
-            # HermesProcessCommand(parser),
             HermesCurateCommand(parser),
-            # HermesDepositCommand(parser),
+            HermesDepositCommand(parser),
+            HermesHarvestCommand(parser),
+            HermesHelpCommand(parser),
+            # HermesInitCommand(parser),
             # HermesPostprocessCommand(parser),
+            HermesProcessCommand(parser),
+            HermesVersionCommand(parser),
     ):
         if command.settings_class is not None:
             setting_types[command.command_name] = command.settings_class

src/hermes/commands/deposit/base.py

@@ -7,15 +7,13 @@
 
 import abc
 import argparse
-import json
-import sys
 
 from pydantic import BaseModel
 
 from hermes.commands.base import HermesCommand, HermesPlugin
-from hermes.model.context import CodeMetaContext
-from hermes.model.path import ContextPath
-from hermes.model.errors import HermesValidationError
+from hermes.model.context_manager import HermesContext
+from hermes.model import SoftwareMetadata
+from hermes.model.error import HermesValidationError
 
 
 class BaseDepositPlugin(HermesPlugin):
@@ -24,26 +22,35 @@ class BaseDepositPlugin(HermesPlugin):
     TODO: describe workflow... needs refactoring to be less stateful!
     """
 
-    def __init__(self, command, ctx):
-        self.command = command
-        self.ctx = ctx
-
     def __call__(self, command: HermesCommand) -> None:
         """Initiate the deposition process.
 
         This calls a list of additional methods on the class, none of which need to be implemented.
         """
         self.command = command
+        self.ctx = HermesContext()
+
+        self.ctx.prepare_step("curate")
+        self.metadata = SoftwareMetadata.load_from_cache(self.ctx, "result")
+        self.ctx.finalize_step("curate")
 
         self.prepare()
-        self.map_metadata()
+        deposit = self.map_metadata()
+        self.ctx.prepare_step("deposit")
+        with self.ctx[command.settings.target] as cache:
+            cache["deposit"] = deposit
+        self.ctx.finalize_step("deposit")
 
         if self.is_initial_publication():
             self.create_initial_version()
         else:
             self.create_new_version()
 
-        self.update_metadata()
+        deposit = self.update_metadata()
+        self.ctx.prepare_step("deposit")
+        with self.ctx["deposit"] as cache:
+            cache["result"] = deposit
+        self.ctx.finalize_step("deposit")
         self.delete_artifacts()
         self.upload_artifacts()
         self.publish()
@@ -58,8 +65,8 @@ def prepare(self) -> None:
         pass
 
     @abc.abstractmethod
-    def map_metadata(self) -> None:
-        """Map the given metadata to the target schema of the deposition platform.
+    def map_metadata(self) -> dict:
+        """Map the given metadata to the target schema of the deposition platform and return it.
 
         When mapping metadata, make sure to add traces to the HERMES software, e.g. via
         DataCite's ``relatedIdentifier`` using the ``isCompiledBy`` relation. Ideally, the value
@@ -88,8 +95,9 @@ def create_new_version(self) -> None:
         """Create a new version of an existing publication on the target platform."""
         pass
 
-    def update_metadata(self) -> None:
-        """Update the metadata of the newly created version."""
+    @abc.abstractmethod
+    def update_metadata(self) -> dict:
+        """Update the metadata of the newly created version and return it even if it hasn't changed."""
         pass
 
     def delete_artifacts(self) -> None:
@@ -106,7 +114,7 @@ def publish(self) -> None:
         pass
 
 
-class _DepositSettings(BaseModel):
+class DepositSettings(BaseModel):
     """Generic deposition settings."""
 
     target: str = ""
@@ -116,7 +124,7 @@ class HermesDepositCommand(HermesCommand):
     """ Deposit the curated metadata to repositories. """
 
     command_name = "deposit"
-    settings_class = _DepositSettings
+    settings_class = DepositSettings
 
     def init_command_parser(self, command_parser: argparse.ArgumentParser) -> None:
         command_parser.add_argument('--file', '-f', nargs=1, action='append',
@@ -128,26 +136,13 @@ def __call__(self, args: argparse.Namespace) -> None:
         self.args = args
         plugin_name = self.settings.target
 
-        ctx = CodeMetaContext()
-        codemeta_file = ctx.get_cache("curate", ctx.hermes_name)
-        if not codemeta_file.exists():
-            self.log.error("You must run the 'curate' command before deposit")
-            sys.exit(1)
-
-        codemeta_path = ContextPath("codemeta")
-        with open(codemeta_file) as codemeta_fh:
-            ctx.update(codemeta_path, json.load(codemeta_fh))
-
         try:
-            plugin_func = self.plugins[plugin_name](self, ctx)
-
+            plugin_func = self.plugins[plugin_name]()
         except KeyError as e:
             self.log.error("Plugin '%s' not found.", plugin_name)
             self.errors.append(e)
-
         try:
             plugin_func(self)
-
         except HermesValidationError as e:
             self.log.error("Error while executing %s: %s", plugin_name, e)
             self.errors.append(e)

src/hermes/commands/deposit/file.py

@@ -11,22 +11,23 @@
 from pydantic import BaseModel
 
 from hermes.commands.deposit.base import BaseDepositPlugin
-from hermes.model.path import ContextPath
 
 
 class FileDepositSettings(BaseModel):
-    filename: str = 'hermes.json'
+    filename: str = 'codemeta.json'
 
 
 class FileDepositPlugin(BaseDepositPlugin):
     settings_class = FileDepositSettings
 
-    def map_metadata(self) -> None:
-        self.ctx.update(ContextPath.parse('deposit.file'), self.ctx['codemeta'])
+    def map_metadata(self) -> dict:
+        return self.metadata.compact()
+
+    def update_metadata(self) -> dict:
+        return self.metadata.compact()
 
     def publish(self) -> None:
         file_config = self.command.settings.file
-        output_data = self.ctx['deposit.file']
 
         with open(file_config.filename, 'w') as deposition_file:
-            json.dump(output_data, deposition_file, indent=2)
+            json.dump(self.metadata.compact(), deposition_file, indent=2)