Harvest for Marine Planktonic Copepods Created 25 Oct 10:57

Harvesting Log

[INFO] [2023-10-25 10:57:46] Created harvest instance #4491
[STOP] [2023-10-25 10:57:46] create_harvest_instance
[START] [2023-10-25 10:57:46] fetch_files
[STOP] [2023-10-25 10:57:46] fetch_files
[START] [2023-10-25 10:57:46] validate_each_file
[INFO] [2023-10-25 10:57:46] Looping over 4 formats...
[INFO] [2023-10-25 10:57:46] ...refs (/app/public/data/mar_planktonic_c/reference.tab)
[INFO] [2023-10-25 10:57:46] Valid: /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_refs_30964.csv (925 lines)
[INFO] [2023-10-25 10:57:46] ...nodes (/app/public/data/mar_planktonic_c/taxon.tab)
[INFO] [2023-10-25 10:57:46] Valid: /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_nodes_30963.csv (2644 lines)
[INFO] [2023-10-25 10:57:46] ...occurrences (/app/public/data/mar_planktonic_c/occurrence_specific.tab)
[INFO] [2023-10-25 10:57:46] Valid: /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_occurrences_30965.csv (18259 lines)
[INFO] [2023-10-25 10:57:46] ...measurements (/app/public/data/mar_planktonic_c/measurement_or_fact_specific.tab)
[INFO] [2023-10-25 10:57:48] Valid: /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_measurements_30966.csv (21345 lines)
[STOP] [2023-10-25 10:57:48] validate_each_file
[START] [2023-10-25 10:57:48] convert_to_csv
[INFO] [2023-10-25 10:57:48] Looping over 4 formats...
[INFO] [2023-10-25 10:57:48] ...refs (/app/public/data/mar_planktonic_c/reference.tab)
[CMD] [2023-10-25 10:57:48] /usr/bin/sort /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_refs_30964.csv > /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_refs_30964.csv_sorted
[INFO] [2023-10-25 10:57:48] Converted: /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_refs_30964.csv (925 lines)
[INFO] [2023-10-25 10:57:48] ...nodes (/app/public/data/mar_planktonic_c/taxon.tab)
[CMD] [2023-10-25 10:57:48] /usr/bin/sort /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_nodes_30963.csv > /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_nodes_30963.csv_sorted
[INFO] [2023-10-25 10:57:48] Converted: /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_nodes_30963.csv (2644 lines)
[INFO] [2023-10-25 10:57:48] ...occurrences (/app/public/data/mar_planktonic_c/occurrence_specific.tab)
[CMD] [2023-10-25 10:57:48] /usr/bin/sort /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_occurrences_30965.csv > /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_occurrences_30965.csv_sorted
[INFO] [2023-10-25 10:57:48] Converted: /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_occurrences_30965.csv (18259 lines)
[INFO] [2023-10-25 10:57:48] ...measurements (/app/public/data/mar_planktonic_c/measurement_or_fact_specific.tab)
[CMD] [2023-10-25 10:57:48] /usr/bin/sort /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_measurements_30966.csv > /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_measurements_30966.csv_sorted
[INFO] [2023-10-25 10:57:49] Converted: /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_measurements_30966.csv (21345 lines)
[STOP] [2023-10-25 10:57:49] convert_to_csv
[START] [2023-10-25 10:57:49] calculate_delta
[INFO] [2023-10-25 10:57:49] Looping over 4 formats...
[INFO] [2023-10-25 10:57:49] ...refs (/app/public/data/mar_planktonic_c/reference.tab)
[CMD] [2023-10-25 10:57:49] echo "0a" > /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_refs_30964.diff
[CMD] [2023-10-25 10:57:49] tail -n +1 /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_refs_30964.csv >> /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_refs_30964.diff
[CMD] [2023-10-25 10:57:49] echo "." >> /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_refs_30964.diff
[INFO] [2023-10-25 10:57:49] Created diff: /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_refs_30964.diff (927 lines)
[INFO] [2023-10-25 10:57:49] ...nodes (/app/public/data/mar_planktonic_c/taxon.tab)
[CMD] [2023-10-25 10:57:49] echo "0a" > /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_nodes_30963.diff
[CMD] [2023-10-25 10:57:49] tail -n +1 /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_nodes_30963.csv >> /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_nodes_30963.diff
[CMD] [2023-10-25 10:57:49] echo "." >> /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_nodes_30963.diff
[INFO] [2023-10-25 10:57:49] Created diff: /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_nodes_30963.diff (2646 lines)
[INFO] [2023-10-25 10:57:49] ...occurrences (/app/public/data/mar_planktonic_c/occurrence_specific.tab)
[CMD] [2023-10-25 10:57:49] echo "0a" > /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_occurrences_30965.diff
[CMD] [2023-10-25 10:57:50] tail -n +1 /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_occurrences_30965.csv >> /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_occurrences_30965.diff
[CMD] [2023-10-25 10:57:50] echo "." >> /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_occurrences_30965.diff
[INFO] [2023-10-25 10:57:50] Created diff: /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_occurrences_30965.diff (18261 lines)
[INFO] [2023-10-25 10:57:50] ...measurements (/app/public/data/mar_planktonic_c/measurement_or_fact_specific.tab)
[CMD] [2023-10-25 10:57:50] echo "0a" > /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_measurements_30966.diff
[CMD] [2023-10-25 10:57:50] tail -n +1 /app/public/data/mar_planktonic_c/converted_csv/mar_planktonic_c_measurements_30966.csv >> /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_measurements_30966.diff
[CMD] [2023-10-25 10:57:50] echo "." >> /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_measurements_30966.diff
[INFO] [2023-10-25 10:57:50] Created diff: /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_measurements_30966.diff (21347 lines)
[STOP] [2023-10-25 10:57:50] calculate_delta
[START] [2023-10-25 10:57:50] parse_diff_and_store
[INFO] [2023-10-25 10:57:50] Handling diff: /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_refs_30964.diff (927 lines)
[INFO] [2023-10-25 10:57:50] Loading refs diff file into memory (927 lines)...
[INFO] [2023-10-25 10:57:50] Storing 925 References (925/925/927)
[INFO] [2023-10-25 10:57:51] Handling diff: /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_nodes_30963.diff (2646 lines)
[INFO] [2023-10-25 10:57:51] Loading nodes diff file into memory (2646 lines)...
[WARN] [2023-10-25 10:57:51] Filtered Scientific Name `Gippslandia  estuarina` to `Gippslandia estuarina`
[WARN] [2023-10-25 10:57:51] Filtered Scientific Name `Ryocalanus  brasilianus` to `Ryocalanus brasilianus`
[INFO] [2023-10-25 10:57:52] Storing 3063 ScientificNames (6126/2644/2646)
[INFO] [2023-10-25 10:57:52] Storing 3063 Nodes (6126/2644/2646)
[INFO] [2023-10-25 10:57:53] Handling diff: /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_occurrences_30965.diff (18261 lines)
[INFO] [2023-10-25 10:57:54] Loading occurrences diff file into memory (18261 lines)...
[INFO] [2023-10-25 10:57:55] Storing 9999 Occurrences (14519/10000/18261)
[INFO] [2023-10-25 10:57:56] Storing 4520 OccurrenceMetadata (14519/10000/18261)
[WARN] [2023-10-25 10:57:58] SKIPPED 3678 Occurrence metadata (26457/18259/18261) with resource_pks already be in the database!
[INFO] [2023-10-25 10:57:58] Storing 8260 Occurrences (26457/18259/18261)
[INFO] [2023-10-25 10:58:04] Storing 0 OccurrenceMetadata (26457/18259/18261)
[WARN] [2023-10-25 10:58:04] No models to import, skipping!
[INFO] [2023-10-25 10:58:04] Handling diff: /app/public/data/mar_planktonic_c/diff/mar_planktonic_c_measurements_30966.diff (21347 lines)
[INFO] [2023-10-25 10:58:04] Loading measurements diff file into memory (21347 lines)...
[INFO] [2023-10-25 10:58:11] Storing 9999 Traits (38763/10000/21347)
[INFO] [2023-10-25 10:58:14] Storing 26680 MetaTraits (38763/10000/21347)
[INFO] [2023-10-25 10:58:18] Storing 2084 TraitsReferences (38763/10000/21347)
[INFO] [2023-10-25 10:58:24] Storing 10000 Traits (77499/20000/21347)
[INFO] [2023-10-25 10:58:27] Storing 26603 MetaTraits (77499/20000/21347)
[INFO] [2023-10-25 10:58:31] Storing 2133 TraitsReferences (77499/20000/21347)
[INFO] [2023-10-25 10:58:32] Storing 1346 Traits (82678/21345/21347)
[INFO] [2023-10-25 10:58:33] Storing 3555 MetaTraits (82678/21345/21347)
[INFO] [2023-10-25 10:58:33] Storing 278 TraitsReferences (82678/21345/21347)
[STOP] [2023-10-25 10:58:33] parse_diff_and_store
[START] [2023-10-25 10:58:33] resolve_keys
[2023-10-25 10:58:34] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-25 10:58:42] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-25 10:58:43] traits to occurrences...
[INFO] [2023-10-25 10:58:44] traits to nodes (through occurrences)...
[INFO] [2023-10-25 10:58:47] Traits to sex term...
[INFO] [2023-10-25 10:58:48] Traits to lifestage term...
[INFO] [2023-10-25 10:58:48] MetaTraits to traits...
[INFO] [2023-10-25 10:58:52] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-25 10:58:52] Assocs to occurrences...
[INFO] [2023-10-25 10:58:52] Assocs to nodes...
[INFO] [2023-10-25 10:58:52] Assoc to sex term...
[INFO] [2023-10-25 10:58:52] Assoc to lifestage term...
[INFO] [2023-10-25 10:58:52] MetaAssoc to assocs...
[STOP] [2023-10-25 10:58:52] resolve_keys
[START] [2023-10-25 10:58:52] hold_for_later_1
[STOP] [2023-10-25 10:58:52] hold_for_later_1
[START] [2023-10-25 10:58:52] hold_for_later_2
[STOP] [2023-10-25 10:58:52] hold_for_later_2
[START] [2023-10-25 10:58:52] resolve_missing_parents
[STOP] [2023-10-25 10:58:52] resolve_missing_parents
[START] [2023-10-25 10:58:52] rebuild_nodes
[START] [2023-10-25 10:58:52] Flattener#flatten
[START] [2023-10-25 10:58:52] Flattener#study_resource
[START] [2023-10-25 10:58:52] Flattener#build_ancestry
[STOP] [2023-10-25 10:58:53] Flattener#build_ancestry
[INFO] [2023-10-25 10:58:53] 3063 ancestry keys
[START] [2023-10-25 10:58:53] build_node_ancestors
[INFO] [2023-10-25 10:58:53] old ancestors deleted.
[STOP] [2023-10-25 10:58:53] build_node_ancestors
[START] [2023-10-25 10:58:53] Flattener#propagate_ancestor_ids
[STOP] [2023-10-25 10:58:54] Flattener#propagate_ancestor_ids
[STOP] [2023-10-25 10:58:54] Flattener#flatten
[STOP] [2023-10-25 10:58:54] rebuild_nodes
[START] [2023-10-25 10:58:54] resolve_missing_media_owners
[STOP] [2023-10-25 10:58:54] resolve_missing_media_owners
[START] [2023-10-25 10:58:54] sanitize_media_verbatims
[STOP] [2023-10-25 10:58:54] sanitize_media_verbatims
[START] [2023-10-25 10:58:54] queue_downloads
[STOP] [2023-10-25 10:58:54] queue_downloads
[START] [2023-10-25 10:58:54] parse_names
[WARN] [2023-10-25 10:58:54] I see 3063 names which still need to be parsed.
[WARN] [2023-10-25 10:58:54] Names to parse: 3063 formatted: 3063 learned: 3034 parsed: 3063
[STOP] [2023-10-25 10:58:57] parse_names
[START] [2023-10-25 10:58:57] denormalize_canonical_names_to_nodes
[STOP] [2023-10-25 10:58:57] denormalize_canonical_names_to_nodes
[START] [2023-10-25 10:58:57] match_nodes
[START] [2023-10-25 10:58:57] map_all_nodes_to_pages
[STOP] [2023-10-25 10:59:51] map_all_nodes_to_pages
[INFO] [2023-10-25 10:59:51] 216 Unmatched nodes (of 3063)! That's too many to output. Full list in /app/public/data/mar_planktonic_c/unmatched_nodes.txt ; First 10: Canonical: Acartiura; Node#137242736; ResourceID: 35; Canonical: Acartia erythraea; Node#137242836; ResourceID: 44; Canonical: Bradyidius; Node#137240767; ResourceID: 125; Canonical: Bradyidius; Node#137240779; ResourceID: 126; Canonical: Euchirella messinensis; Node#137241372; ResourceID: 173; Canonical: Euchirella rostromagna; Node#137241464; ResourceID: 181; Canonical: Gaetanus kruppii; Node#137241655; ResourceID: 194; Canonical: Gaetanus; Node#137241782; ResourceID: 204; Canonical: Gaetanus; Node#137241919; ResourceID: 215; Canonical: Gaetanus; Node#137241930; ResourceID: 216
[START] [2023-10-25 10:59:51] update_nodes
[STOP] [2023-10-25 10:59:52] update_nodes
[STOP] [2023-10-25 10:59:52] match_nodes
[START] [2023-10-25 10:59:52] reindex_search
[STOP] [2023-10-25 10:59:55] reindex_search
[START] [2023-10-25 10:59:55] normalize_units
[STOP] [2023-10-25 11:00:20] normalize_units
[START] [2023-10-25 11:00:20] calculate_statistics
[INFO] [2023-10-25 11:00:21] Duplicate page_id count: 0
[STOP] [2023-10-25 11:00:21] calculate_statistics
[START] [2023-10-25 11:00:21] complete_harvest_instance
[START] [2023-10-25 11:00:21] overall_tsv_creation
[INFO] [2023-10-25 11:00:21] Exporting 3063 nodes as TSV in batches of 10000...
[INFO] [2023-10-25 11:00:21] Processing group of 3063 in 1 batches of 10000
[INFO] [2023-10-25 11:00:26] 21345 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-25 11:00:26] Building Traits map for 3063 nodes (this can take a while)...
[INFO] [2023-10-25 11:00:37] Mapped 21345 traits (56838 meta) for 3063 nodes.
[INFO] [2023-10-25 11:00:37] Building Associations map (this can take a while)...
[INFO] [2023-10-25 11:00:37] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-25 11:00:37] Adding 21345 traits...
[INFO] [2023-10-25 11:00:41] 11680 metadata added.
[INFO] [2023-10-25 11:00:41] Adding 0 assocs...
[INFO] [2023-10-25 11:00:41] 0 metadata added.
[INFO] [2023-10-25 11:01:27] Processed 3063/3063 nodes
[INFO] [2023-10-25 11:01:27] Average Time: 65.0
[INFO] [2023-10-25 11:01:27] Total Time: 1m7s
[STOP] [2023-10-25 11:01:27] overall_tsv_creation
[INFO] [2023-10-25 11:01:27] Done. Check your files:
[INFO] [2023-10-25 11:01:27] (3063 lines) /app/public/data/mar_planktonic_c/publish_nodes.tsv
[INFO] [2023-10-25 11:01:27] (8681 lines) /app/public/data/mar_planktonic_c/publish_node_ancestors.tsv
[INFO] [2023-10-25 11:01:27] (3063 lines) /app/public/data/mar_planktonic_c/publish_scientific_names.tsv
[INFO] [2023-10-25 11:01:27] (21346 lines) /app/public/data/mar_planktonic_c/publish_traits.tsv
[INFO] [2023-10-25 11:01:28] (11681 lines) /app/public/data/mar_planktonic_c/publish_metadata.tsv
[STOP] [2023-10-25 11:01:28] complete_harvest_instance
[START] [2023-10-25 11:01:28] completed
[STOP] [2023-10-25 11:01:28] completed
[STOP] [2023-10-25 11:01:28] logged process, took 222.33

Latest Process

25 Oct 10:57 EXITED currently processing 0