refactor: introduce subgraphs to organize stages

This abstracts the different sections better

docs/single_xml.mmd

@@ -1,15 +1,93 @@
-flowchart TD
+flowchart LR
 
-  %% Old Logic
-  gs([GATHER STARTED])
-  ge([GATHER ENDED])
-  fs([FETCH STARTED])
-  fe([FETCH ENDED])
-  is([IMPORT STARTED])
-  ie([IMPORT ENDED])
+  %% Algorithm
+  gather_stage ==> fetch_stage
+  fetch_stage ==> import_stage
+
+  subgraph gather_stage [Gather Stage]
+    direction TB
+    gs([GATHER STARTED])
+    ge([GATHER ENDED])
+    gs ==> _get_content_as_unicode
+    _get_content_as_unicode ==> is_existing_object
+    is_existing_object == Yes ==> get_existing_object
+    is_existing_object == No ==> create_object
+    get_existing_object ==> change_object
+    change_object ==> guess_standard
+    create_object ==> guess_standard
+    guess_standard ==> is_iso
+    is_iso == Yes ==> save_content
+    is_iso == No ==> save_original_document
+    save_content ==> ge
+    save_original_document ==> ge
+    _get_content_as_unicode-. Exception .-> error
+  end
+  subgraph fetch_stage [Fetch Stage]
+    direction TB
+    fs([FETCH STARTED])
+    fe([FETCH ENDED])
+    fs ==> do_nothing
+    do_nothing ==> fe
+  end
+  subgraph import_stage [Import Stage]
+    direction TB
+    is([IMPORT STARTED])
+    ie([IMPORT ENDED])
+    is ==> is_object_empty
+    is_object_empty == No ==> is_force_import
+    is_force_import == Yes ==> change_object_2
+    is_force_import == No ==> check_status_from_gather
+    change_object_2 ==> get_existing_object_2
+    check_status_from_gather ==> get_existing_object_2
+    get_existing_object_2 ==> is_delete
+    is_delete == Yes ==> delete
+    is_delete == No ==> is_iso_2
+    is_iso_2 == No ==> transform_to_iso
+    transform_to_iso == Success ==> save_content_2
+    save_content_2 == tranform ==> parse_iso
+    is_iso_2 == Yes ==> is_object_content_empty
+    is_object_content_empty == No ==> _validate_document
+    _validate_document == valid ==> parse_iso
+    _validate_document == not valid ==> continue_on_validation_errors
+    continue_on_validation_errors == Yes ==> parse_iso
+    continue_on_validation_errors == No ==> ie
+    parse_iso ==> update_object_reference
+    update_object_reference ==> is_guid_current
+    is_guid_current == No ==> update_guid
+    update_guid ==> is_guid_present
+    is_guid_present == No ==> generate_guid
+    is_guid_present == Yes ==> get_modified_date
+    generate_guid ==> get_modified_date
+    get_modified_date ==> spatial_package_create
+    spatial_package_create ==> is_source_private
+    is_source_private == Yes ==> mark_object_private
+    %% BUG: if source marked as private --> harvest --> changed to public --> harvest --> datasets remain private
+    is_source_private == No ==> is_source_part_of_topic
+    mark_object_private ==> is_source_part_of_topic
+    is_source_part_of_topic == Yes ==> mark_object_part_of_topic
+    is_source_part_of_topic == No ==> mark_as_geospatial
+    mark_object_part_of_topic ==> mark_as_geospatial
+    mark_as_geospatial ==> update_object_reference_2
+    update_object_reference_2 ==> is_status_new
+    is_status_new == Yes ==> create
+    is_status_new == No ==> is_modified_newer
+    is_modified_newer == No ==> transfer_job_history
+    transfer_job_history ==> delete_old_object
+    delete_old_object ==> reindex_package
+    is_modified_newer == Yes ==> update
+    create ==> ie
+    update ==> ie
+    is_object_content_empty-. Yes .-> error_2
+    parse_iso-. exception .-> error_2
+    is_guid_current-. Yes .-> error_2
+    get_modified_date-. exception .-> error_2
+    is_object_empty-. Yes .-> skip
+    reindex_package -.-> skip
+  end
 
   %% Data
   error[\Error/]
+  error_2[\Error/]
   skip[/Skip\]
 
   %% Functons
@@ -59,72 +137,3 @@ flowchart TD
   is_source_private{Is the Harvest Source Private?}
   is_source_part_of_topic{Is the Harvest Source part of a Topic?}
   is_status_new{Is the Status new?}
-
-  %% Algorithm
-  gs ==> _get_content_as_unicode
-  _get_content_as_unicode-. Exception .-> error
-  _get_content_as_unicode ==> is_existing_object
-  is_existing_object == Yes ==> get_existing_object
-  is_existing_object == No ==> create_object
-  get_existing_object ==> change_object
-  change_object ==> guess_standard
-  create_object ==> guess_standard
-  guess_standard ==> is_iso
-  is_iso == Yes ==> save_content
-  is_iso == No ==> save_original_document
-  save_content ==> ge
-  save_original_document ==> ge
-  ge ==> fs
-  fs ==> do_nothing
-  do_nothing ==> fe
-  fe ==> is
-  is ==> is_object_empty
-  is_object_empty-. Yes .-> skip
-  is_object_empty == No ==> is_force_import
-  is_force_import == Yes ==> change_object_2
-  is_force_import == No ==> check_status_from_gather
-  change_object_2 ==> get_existing_object_2
-  check_status_from_gather ==> get_existing_object_2
-  get_existing_object_2 ==> is_delete
-  is_delete == Yes ==> delete
-  is_delete == No ==> is_iso_2
-  is_iso_2 == No ==> transform_to_iso
-  transform_to_iso == Success ==> save_content_2
-  save_content_2 == tranform ==> parse_iso
-  is_iso_2 == Yes ==> is_object_content_empty
-  is_object_content_empty-. Yes .-> error
-  is_object_content_empty == No ==> _validate_document
-  _validate_document == valid ==> parse_iso
-  _validate_document == not valid ==> continue_on_validation_errors
-  continue_on_validation_errors == Yes ==> parse_iso
-  continue_on_validation_errors == No ==> ie
-  parse_iso-. exception .-> error
-  parse_iso ==> update_object_reference
-  update_object_reference ==> is_guid_current
-  is_guid_current-. Yes .-> error
-  is_guid_current == No ==> update_guid
-  update_guid ==> is_guid_present
-  is_guid_present == No ==> generate_guid
-  is_guid_present == Yes ==> get_modified_date
-  generate_guid ==> get_modified_date
-  get_modified_date-. exception .-> error
-  get_modified_date ==> spatial_package_create
-  spatial_package_create ==> is_source_private
-  is_source_private == Yes ==> mark_object_private
-  %% BUG: if source marked as private --> harvest --> changed to public --> harvest --> datasets remain private
-  is_source_private == No ==> is_source_part_of_topic
-  mark_object_private ==> is_source_part_of_topic
-  is_source_part_of_topic == Yes ==> mark_object_part_of_topic
-  is_source_part_of_topic == No ==> mark_as_geospatial
-  mark_object_part_of_topic ==> mark_as_geospatial
-  mark_as_geospatial ==> update_object_reference_2
-  update_object_reference_2 ==> is_status_new
-  is_status_new == Yes ==> create
-  is_status_new == No ==> is_modified_newer
-  is_modified_newer == No ==> transfer_job_history
-  transfer_job_history ==> delete_old_object
-  delete_old_object ==> reindex_package
-  reindex_package -.-> skip
-  is_modified_newer == Yes ==> update
-  create ==> ie
-  update ==> ie