Harvest for Gymnodiniales Traits Created 13 Oct 11:30

Harvesting Log

[INFO] [2023-10-13 11:30:12] Created harvest instance #4434
[STOP] [2023-10-13 11:30:12] create_harvest_instance
[START] [2023-10-13 11:30:12] fetch_files
[STOP] [2023-10-13 11:30:12] fetch_files
[START] [2023-10-13 11:30:12] validate_each_file
[INFO] [2023-10-13 11:30:12] Looping over 4 formats...
[INFO] [2023-10-13 11:30:12] ...refs (/app/public/data/gymnodiniales_tr/references.txt)
[INFO] [2023-10-13 11:30:12] Valid: /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_refs_30708.csv (162 lines)
[INFO] [2023-10-13 11:30:12] ...nodes (/app/public/data/gymnodiniales_tr/taxon.txt)
[INFO] [2023-10-13 11:30:12] Valid: /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_nodes_30705.csv (298 lines)
[INFO] [2023-10-13 11:30:12] ...occurrences (/app/public/data/gymnodiniales_tr/occurrences.tsv)
[INFO] [2023-10-13 11:30:12] Valid: /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_occurrences_30707.csv (457 lines)
[INFO] [2023-10-13 11:30:12] ...measurements (/app/public/data/gymnodiniales_tr/measurements.txt)
[INFO] [2023-10-13 11:30:12] Valid: /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_measurements_30706.csv (7982 lines)
[STOP] [2023-10-13 11:30:12] validate_each_file
[START] [2023-10-13 11:30:12] convert_to_csv
[INFO] [2023-10-13 11:30:12] Looping over 4 formats...
[INFO] [2023-10-13 11:30:12] ...refs (/app/public/data/gymnodiniales_tr/references.txt)
[CMD] [2023-10-13 11:30:12] /usr/bin/sort /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_refs_30708.csv > /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_refs_30708.csv_sorted
[INFO] [2023-10-13 11:30:12] Converted: /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_refs_30708.csv (162 lines)
[INFO] [2023-10-13 11:30:12] ...nodes (/app/public/data/gymnodiniales_tr/taxon.txt)
[CMD] [2023-10-13 11:30:12] /usr/bin/sort /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_nodes_30705.csv > /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_nodes_30705.csv_sorted
[INFO] [2023-10-13 11:30:12] Converted: /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_nodes_30705.csv (298 lines)
[INFO] [2023-10-13 11:30:12] ...occurrences (/app/public/data/gymnodiniales_tr/occurrences.tsv)
[CMD] [2023-10-13 11:30:12] /usr/bin/sort /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_occurrences_30707.csv > /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_occurrences_30707.csv_sorted
[INFO] [2023-10-13 11:30:12] Converted: /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_occurrences_30707.csv (457 lines)
[INFO] [2023-10-13 11:30:12] ...measurements (/app/public/data/gymnodiniales_tr/measurements.txt)
[CMD] [2023-10-13 11:30:12] /usr/bin/sort /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_measurements_30706.csv > /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_measurements_30706.csv_sorted
[INFO] [2023-10-13 11:30:12] Converted: /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_measurements_30706.csv (7982 lines)
[STOP] [2023-10-13 11:30:12] convert_to_csv
[START] [2023-10-13 11:30:12] calculate_delta
[INFO] [2023-10-13 11:30:12] Looping over 4 formats...
[INFO] [2023-10-13 11:30:12] ...refs (/app/public/data/gymnodiniales_tr/references.txt)
[CMD] [2023-10-13 11:30:12] echo "0a" > /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_refs_30708.diff
[CMD] [2023-10-13 11:30:12] cat /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_refs_30708.csv >> /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_refs_30708.diff
[CMD] [2023-10-13 11:30:13] echo "." >> /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_refs_30708.diff
[INFO] [2023-10-13 11:30:13] Created diff: /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_refs_30708.diff (164 lines)
[INFO] [2023-10-13 11:30:13] ...nodes (/app/public/data/gymnodiniales_tr/taxon.txt)
[CMD] [2023-10-13 11:30:13] echo "0a" > /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_nodes_30705.diff
[CMD] [2023-10-13 11:30:13] cat /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_nodes_30705.csv >> /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_nodes_30705.diff
[CMD] [2023-10-13 11:30:13] echo "." >> /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_nodes_30705.diff
[INFO] [2023-10-13 11:30:13] Created diff: /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_nodes_30705.diff (300 lines)
[INFO] [2023-10-13 11:30:13] ...occurrences (/app/public/data/gymnodiniales_tr/occurrences.tsv)
[CMD] [2023-10-13 11:30:13] echo "0a" > /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_occurrences_30707.diff
[CMD] [2023-10-13 11:30:13] cat /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_occurrences_30707.csv >> /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_occurrences_30707.diff
[CMD] [2023-10-13 11:30:13] echo "." >> /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_occurrences_30707.diff
[INFO] [2023-10-13 11:30:13] Created diff: /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_occurrences_30707.diff (459 lines)
[INFO] [2023-10-13 11:30:13] ...measurements (/app/public/data/gymnodiniales_tr/measurements.txt)
[CMD] [2023-10-13 11:30:13] echo "0a" > /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_measurements_30706.diff
[CMD] [2023-10-13 11:30:13] cat /app/public/data/gymnodiniales_tr/converted_csv/gymnodiniales_tr_measurements_30706.csv >> /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_measurements_30706.diff
[CMD] [2023-10-13 11:30:13] echo "." >> /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_measurements_30706.diff
[INFO] [2023-10-13 11:30:13] Created diff: /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_measurements_30706.diff (7984 lines)
[STOP] [2023-10-13 11:30:13] calculate_delta
[START] [2023-10-13 11:30:13] parse_diff_and_store
[INFO] [2023-10-13 11:30:13] Handling diff: /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_refs_30708.diff (164 lines)
[INFO] [2023-10-13 11:30:13] Loading refs diff file into memory (164 lines)...
[INFO] [2023-10-13 11:30:13] Storing 162 References (162/162/164)
[INFO] [2023-10-13 11:30:14] Handling diff: /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_nodes_30705.diff (300 lines)
[INFO] [2023-10-13 11:30:14] Loading nodes diff file into memory (300 lines)...
[INFO] [2023-10-13 11:30:14] Storing 298 ScientificNames (596/298/300)
[INFO] [2023-10-13 11:30:14] Storing 298 Nodes (596/298/300)
[INFO] [2023-10-13 11:30:14] Handling diff: /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_occurrences_30707.diff (459 lines)
[INFO] [2023-10-13 11:30:14] Loading occurrences diff file into memory (459 lines)...
[INFO] [2023-10-13 11:30:14] Storing 457 Occurrences (821/457/459)
[INFO] [2023-10-13 11:30:14] Storing 364 OccurrenceMetadata (821/457/459)
[INFO] [2023-10-13 11:30:14] Handling diff: /app/public/data/gymnodiniales_tr/diff/gymnodiniales_tr_measurements_30706.diff (7984 lines)
[INFO] [2023-10-13 11:30:14] Loading measurements diff file into memory (7984 lines)...
[INFO] [2023-10-13 11:30:17] Storing 7759 Traits (17481/7982/7984)
[INFO] [2023-10-13 11:30:20] Storing 7872 TraitsReferences (17481/7982/7984)
[INFO] [2023-10-13 11:30:21] Storing 255 OccurrenceMetadata (17481/7982/7984)
[INFO] [2023-10-13 11:30:21] Storing 1595 MetaTraits (17481/7982/7984)
[STOP] [2023-10-13 11:30:21] parse_diff_and_store
[START] [2023-10-13 11:30:21] resolve_keys
[2023-10-13 11:30:21] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 11:30:29] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 11:30:29] traits to occurrences...
[INFO] [2023-10-13 11:30:29] traits to nodes (through occurrences)...
[INFO] [2023-10-13 11:30:29] Traits to sex term...
[INFO] [2023-10-13 11:30:29] Traits to lifestage term...
[INFO] [2023-10-13 11:30:29] MetaTraits to traits...
[INFO] [2023-10-13 11:30:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 11:30:30] Assocs to occurrences...
[INFO] [2023-10-13 11:30:30] Assocs to nodes...
[INFO] [2023-10-13 11:30:30] Assoc to sex term...
[INFO] [2023-10-13 11:30:30] Assoc to lifestage term...
[INFO] [2023-10-13 11:30:30] MetaAssoc to assocs...
[STOP] [2023-10-13 11:30:30] resolve_keys
[START] [2023-10-13 11:30:30] hold_for_later_1
[STOP] [2023-10-13 11:30:30] hold_for_later_1
[START] [2023-10-13 11:30:30] hold_for_later_2
[STOP] [2023-10-13 11:30:30] hold_for_later_2
[START] [2023-10-13 11:30:30] resolve_missing_parents
[STOP] [2023-10-13 11:30:30] resolve_missing_parents
[START] [2023-10-13 11:30:30] rebuild_nodes
[START] [2023-10-13 11:30:30] Flattener#flatten
[START] [2023-10-13 11:30:30] Flattener#study_resource
[START] [2023-10-13 11:30:30] Flattener#build_ancestry
[STOP] [2023-10-13 11:30:30] Flattener#build_ancestry
[INFO] [2023-10-13 11:30:30] 298 ancestry keys
[START] [2023-10-13 11:30:30] build_node_ancestors
[INFO] [2023-10-13 11:30:30] old ancestors deleted.
[STOP] [2023-10-13 11:30:30] build_node_ancestors
[START] [2023-10-13 11:30:30] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:30:30] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:30:30] Flattener#flatten
[STOP] [2023-10-13 11:30:30] rebuild_nodes
[START] [2023-10-13 11:30:30] resolve_missing_media_owners
[STOP] [2023-10-13 11:30:30] resolve_missing_media_owners
[START] [2023-10-13 11:30:30] sanitize_media_verbatims
[STOP] [2023-10-13 11:30:30] sanitize_media_verbatims
[START] [2023-10-13 11:30:30] queue_downloads
[STOP] [2023-10-13 11:30:30] queue_downloads
[START] [2023-10-13 11:30:30] parse_names
[WARN] [2023-10-13 11:30:30] I see 298 names which still need to be parsed.
[WARN] [2023-10-13 11:30:30] Names to parse: 298 formatted: 298 learned: 295 parsed: 298
[STOP] [2023-10-13 11:30:31] parse_names
[START] [2023-10-13 11:30:32] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 11:30:32] denormalize_canonical_names_to_nodes
[START] [2023-10-13 11:30:32] match_nodes
[START] [2023-10-13 11:30:32] map_all_nodes_to_pages
[STOP] [2023-10-13 11:30:35] map_all_nodes_to_pages
[INFO] [2023-10-13 11:30:35] 64 Unmatched nodes (of 298)! That's too many to output. Full list in /app/public/data/gymnodiniales_tr/unmatched_nodes.txt ; First 10: Canonical: Gymnodinium absumens; Node#137157948; ResourceID: T001; Canonical: Gymnodinium aesculum; Node#137157953; ResourceID: T006; Canonical: Gymnodinium affine; Node#137157954; ResourceID: T007; Canonical: Gymnodinium alaskensis; Node#137157957; ResourceID: T010; Canonical: Gymnodinium arenicolus; Node#137157966; ResourceID: T019; Canonical: Gymnodinium autumnale; Node#137158091; ResourceID: T144; Canonical: Gymnodinium titubens; Node#137158093; ResourceID: T146; Canonical: Gymnodinium cruciatum; Node#137158094; ResourceID: T147; Canonical: Gymnodinium autumnale; Node#137157977; ResourceID: T030; Canonical: Gymnodinium caerulescens; Node#137157989; ResourceID: T042
[START] [2023-10-13 11:30:35] update_nodes
[STOP] [2023-10-13 11:30:35] update_nodes
[STOP] [2023-10-13 11:30:35] match_nodes
[START] [2023-10-13 11:30:35] reindex_search
[STOP] [2023-10-13 11:30:35] reindex_search
[START] [2023-10-13 11:30:35] normalize_units
[STOP] [2023-10-13 11:30:40] normalize_units
[START] [2023-10-13 11:30:40] calculate_statistics
[INFO] [2023-10-13 11:30:40] Duplicate page_id count: 0
[2023-10-13 11:30:40] WARNING: 19 trait(s) without source found! Please confirm that this is intentional.
[2023-10-13 11:30:40] traits w/o source (up to 100):
[2023-10-13 11:30:40] (resource_pk: M2028, id: 291496180)
[2023-10-13 11:30:40] (resource_pk: M2029, id: 291496181)
[2023-10-13 11:30:40] (resource_pk: M2975, id: 291497079)
[2023-10-13 11:30:40] (resource_pk: M2976, id: 291497080)
[2023-10-13 11:30:40] (resource_pk: M2977, id: 291497081)
[2023-10-13 11:30:40] (resource_pk: M3234, id: 291497321)
[2023-10-13 11:30:40] (resource_pk: M3235, id: 291497322)
[2023-10-13 11:30:40] (resource_pk: M3236, id: 291497323)
[2023-10-13 11:30:40] (resource_pk: M3237, id: 291497324)
[2023-10-13 11:30:40] (resource_pk: M3238, id: 291497325)
[2023-10-13 11:30:40] (resource_pk: M3239, id: 291497326)
[2023-10-13 11:30:40] (resource_pk: M3240, id: 291497327)
[2023-10-13 11:30:40] (resource_pk: M3241, id: 291497328)
[2023-10-13 11:30:40] (resource_pk: M3242, id: 291497329)
[2023-10-13 11:30:40] (resource_pk: M5125, id: 291499116)
[2023-10-13 11:30:40] (resource_pk: M5126, id: 291499117)
[2023-10-13 11:30:40] (resource_pk: M5264, id: 291499248)
[2023-10-13 11:30:40] (resource_pk: M5265, id: 291499249)
[2023-10-13 11:30:40] (resource_pk: M5270, id: 291499252)
[STOP] [2023-10-13 11:30:40] calculate_statistics
[START] [2023-10-13 11:30:40] complete_harvest_instance
[START] [2023-10-13 11:30:40] overall_tsv_creation
[INFO] [2023-10-13 11:30:40] Exporting 298 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 11:30:40] Processing group of 298 in 1 batches of 10000
[INFO] [2023-10-13 11:30:40] 7666 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 11:30:40] Building Traits map for 298 nodes (this can take a while)...
[INFO] [2023-10-13 11:30:42] Mapped 7666 traits (1595 meta) for 298 nodes.
[INFO] [2023-10-13 11:30:42] Building Associations map (this can take a while)...
[INFO] [2023-10-13 11:30:42] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 11:30:42] Adding 7666 traits...
[INFO] [2023-10-13 11:30:44] 18592 metadata added.
[INFO] [2023-10-13 11:30:44] Adding 0 assocs...
[INFO] [2023-10-13 11:30:44] 0 metadata added.
[INFO] [2023-10-13 11:31:29] Processed 298/298 nodes
[INFO] [2023-10-13 11:31:29] Average Time: 49.19
[INFO] [2023-10-13 11:31:29] Total Time: 50s
[STOP] [2023-10-13 11:31:29] overall_tsv_creation
[INFO] [2023-10-13 11:31:29] Done. Check your files:
[INFO] [2023-10-13 11:31:29] (298 lines) /app/public/data/gymnodiniales_tr/publish_nodes.tsv
[INFO] [2023-10-13 11:31:30] (633 lines) /app/public/data/gymnodiniales_tr/publish_node_ancestors.tsv
[INFO] [2023-10-13 11:31:30] (298 lines) /app/public/data/gymnodiniales_tr/publish_scientific_names.tsv
[INFO] [2023-10-13 11:31:30] (7667 lines) /app/public/data/gymnodiniales_tr/publish_traits.tsv
[INFO] [2023-10-13 11:31:30] (18593 lines) /app/public/data/gymnodiniales_tr/publish_metadata.tsv
[STOP] [2023-10-13 11:31:30] complete_harvest_instance
[START] [2023-10-13 11:31:30] completed
[STOP] [2023-10-13 11:31:30] completed
[STOP] [2023-10-13 11:31:30] logged process, took 78.35

Latest Process

13 Oct 11:30 EXITED currently processing 0