Harvest for Sting Pain literature Created 13 Oct 11:33

Harvesting Log

[INFO] [2023-10-13 11:33:18] Created harvest instance #4436
[STOP] [2023-10-13 11:33:18] create_harvest_instance
[START] [2023-10-13 11:33:18] fetch_files
[STOP] [2023-10-13 11:33:18] fetch_files
[START] [2023-10-13 11:33:18] validate_each_file
[INFO] [2023-10-13 11:33:18] Looping over 4 formats...
[INFO] [2023-10-13 11:33:18] ...refs (/app/public/data/sting_pain/references.txt)
[INFO] [2023-10-13 11:33:20] Valid: /app/public/data/sting_pain/converted_csv/sting_pain_refs_30718.csv (5 lines)
[INFO] [2023-10-13 11:33:20] ...nodes (/app/public/data/sting_pain/taxa.txt)
[INFO] [2023-10-13 11:33:20] Valid: /app/public/data/sting_pain/converted_csv/sting_pain_nodes_30717.csv (129 lines)
[INFO] [2023-10-13 11:33:20] ...occurrences (/app/public/data/sting_pain/occurrences.txt)
[INFO] [2023-10-13 11:33:20] Valid: /app/public/data/sting_pain/converted_csv/sting_pain_occurrences_30719.csv (148 lines)
[INFO] [2023-10-13 11:33:20] ...measurements (/app/public/data/sting_pain/measurements-or-facts.tsv)
[INFO] [2023-10-13 11:33:20] Valid: /app/public/data/sting_pain/converted_csv/sting_pain_measurements_30720.csv (345 lines)
[STOP] [2023-10-13 11:33:20] validate_each_file
[START] [2023-10-13 11:33:20] convert_to_csv
[INFO] [2023-10-13 11:33:20] Looping over 4 formats...
[INFO] [2023-10-13 11:33:20] ...refs (/app/public/data/sting_pain/references.txt)
[CMD] [2023-10-13 11:33:20] /usr/bin/sort /app/public/data/sting_pain/converted_csv/sting_pain_refs_30718.csv > /app/public/data/sting_pain/converted_csv/sting_pain_refs_30718.csv_sorted
[INFO] [2023-10-13 11:33:20] Converted: /app/public/data/sting_pain/converted_csv/sting_pain_refs_30718.csv (5 lines)
[INFO] [2023-10-13 11:33:20] ...nodes (/app/public/data/sting_pain/taxa.txt)
[CMD] [2023-10-13 11:33:20] /usr/bin/sort /app/public/data/sting_pain/converted_csv/sting_pain_nodes_30717.csv > /app/public/data/sting_pain/converted_csv/sting_pain_nodes_30717.csv_sorted
[INFO] [2023-10-13 11:33:20] Converted: /app/public/data/sting_pain/converted_csv/sting_pain_nodes_30717.csv (129 lines)
[INFO] [2023-10-13 11:33:20] ...occurrences (/app/public/data/sting_pain/occurrences.txt)
[CMD] [2023-10-13 11:33:20] /usr/bin/sort /app/public/data/sting_pain/converted_csv/sting_pain_occurrences_30719.csv > /app/public/data/sting_pain/converted_csv/sting_pain_occurrences_30719.csv_sorted
[INFO] [2023-10-13 11:33:20] Converted: /app/public/data/sting_pain/converted_csv/sting_pain_occurrences_30719.csv (148 lines)
[INFO] [2023-10-13 11:33:20] ...measurements (/app/public/data/sting_pain/measurements-or-facts.tsv)
[CMD] [2023-10-13 11:33:20] /usr/bin/sort /app/public/data/sting_pain/converted_csv/sting_pain_measurements_30720.csv > /app/public/data/sting_pain/converted_csv/sting_pain_measurements_30720.csv_sorted
[INFO] [2023-10-13 11:33:20] Converted: /app/public/data/sting_pain/converted_csv/sting_pain_measurements_30720.csv (345 lines)
[STOP] [2023-10-13 11:33:20] convert_to_csv
[START] [2023-10-13 11:33:20] calculate_delta
[INFO] [2023-10-13 11:33:20] Looping over 4 formats...
[INFO] [2023-10-13 11:33:20] ...refs (/app/public/data/sting_pain/references.txt)
[CMD] [2023-10-13 11:33:20] echo "0a" > /app/public/data/sting_pain/diff/sting_pain_refs_30718.diff
[CMD] [2023-10-13 11:33:20] tail -n +1 /app/public/data/sting_pain/converted_csv/sting_pain_refs_30718.csv >> /app/public/data/sting_pain/diff/sting_pain_refs_30718.diff
[CMD] [2023-10-13 11:33:20] echo "." >> /app/public/data/sting_pain/diff/sting_pain_refs_30718.diff
[INFO] [2023-10-13 11:33:20] Created diff: /app/public/data/sting_pain/diff/sting_pain_refs_30718.diff (7 lines)
[INFO] [2023-10-13 11:33:20] ...nodes (/app/public/data/sting_pain/taxa.txt)
[CMD] [2023-10-13 11:33:20] echo "0a" > /app/public/data/sting_pain/diff/sting_pain_nodes_30717.diff
[CMD] [2023-10-13 11:33:20] tail -n +1 /app/public/data/sting_pain/converted_csv/sting_pain_nodes_30717.csv >> /app/public/data/sting_pain/diff/sting_pain_nodes_30717.diff
[CMD] [2023-10-13 11:33:20] echo "." >> /app/public/data/sting_pain/diff/sting_pain_nodes_30717.diff
[INFO] [2023-10-13 11:33:21] Created diff: /app/public/data/sting_pain/diff/sting_pain_nodes_30717.diff (131 lines)
[INFO] [2023-10-13 11:33:21] ...occurrences (/app/public/data/sting_pain/occurrences.txt)
[CMD] [2023-10-13 11:33:21] echo "0a" > /app/public/data/sting_pain/diff/sting_pain_occurrences_30719.diff
[CMD] [2023-10-13 11:33:21] tail -n +1 /app/public/data/sting_pain/converted_csv/sting_pain_occurrences_30719.csv >> /app/public/data/sting_pain/diff/sting_pain_occurrences_30719.diff
[CMD] [2023-10-13 11:33:21] echo "." >> /app/public/data/sting_pain/diff/sting_pain_occurrences_30719.diff
[INFO] [2023-10-13 11:33:21] Created diff: /app/public/data/sting_pain/diff/sting_pain_occurrences_30719.diff (150 lines)
[INFO] [2023-10-13 11:33:21] ...measurements (/app/public/data/sting_pain/measurements-or-facts.tsv)
[CMD] [2023-10-13 11:33:21] echo "0a" > /app/public/data/sting_pain/diff/sting_pain_measurements_30720.diff
[CMD] [2023-10-13 11:33:21] tail -n +1 /app/public/data/sting_pain/converted_csv/sting_pain_measurements_30720.csv >> /app/public/data/sting_pain/diff/sting_pain_measurements_30720.diff
[CMD] [2023-10-13 11:33:21] echo "." >> /app/public/data/sting_pain/diff/sting_pain_measurements_30720.diff
[INFO] [2023-10-13 11:33:21] Created diff: /app/public/data/sting_pain/diff/sting_pain_measurements_30720.diff (347 lines)
[STOP] [2023-10-13 11:33:21] calculate_delta
[START] [2023-10-13 11:33:21] parse_diff_and_store
[INFO] [2023-10-13 11:33:21] Handling diff: /app/public/data/sting_pain/diff/sting_pain_refs_30718.diff (7 lines)
[INFO] [2023-10-13 11:33:21] Loading refs diff file into memory (7 lines)...
[INFO] [2023-10-13 11:33:21] Storing 5 References (5/5/7)
[INFO] [2023-10-13 11:33:21] Handling diff: /app/public/data/sting_pain/diff/sting_pain_nodes_30717.diff (131 lines)
[INFO] [2023-10-13 11:33:21] Loading nodes diff file into memory (131 lines)...
[INFO] [2023-10-13 11:33:21] Storing 218 ScientificNames (436/129/131)
[INFO] [2023-10-13 11:33:21] Storing 218 Nodes (436/129/131)
[INFO] [2023-10-13 11:33:21] Handling diff: /app/public/data/sting_pain/diff/sting_pain_occurrences_30719.diff (150 lines)
[INFO] [2023-10-13 11:33:21] Loading occurrences diff file into memory (150 lines)...
[INFO] [2023-10-13 11:33:21] Storing 148 Occurrences (148/148/150)
[INFO] [2023-10-13 11:33:22] Handling diff: /app/public/data/sting_pain/diff/sting_pain_measurements_30720.diff (347 lines)
[INFO] [2023-10-13 11:33:22] Loading measurements diff file into memory (347 lines)...
[INFO] [2023-10-13 11:33:22] Storing 116 TraitsReferences (954/345/347)
[INFO] [2023-10-13 11:33:22] Storing 345 Traits (954/345/347)
[INFO] [2023-10-13 11:33:22] Storing 493 MetaTraits (954/345/347)
[STOP] [2023-10-13 11:33:22] parse_diff_and_store
[START] [2023-10-13 11:33:22] resolve_keys
[2023-10-13 11:33:23] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 11:33:30] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 11:33:30] traits to occurrences...
[INFO] [2023-10-13 11:33:30] traits to nodes (through occurrences)...
[INFO] [2023-10-13 11:33:30] Traits to sex term...
[INFO] [2023-10-13 11:33:30] Traits to lifestage term...
[INFO] [2023-10-13 11:33:30] MetaTraits to traits...
[INFO] [2023-10-13 11:33:30] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 11:33:30] Assocs to occurrences...
[INFO] [2023-10-13 11:33:30] Assocs to nodes...
[INFO] [2023-10-13 11:33:30] Assoc to sex term...
[INFO] [2023-10-13 11:33:30] Assoc to lifestage term...
[INFO] [2023-10-13 11:33:30] MetaAssoc to assocs...
[STOP] [2023-10-13 11:33:30] resolve_keys
[START] [2023-10-13 11:33:30] hold_for_later_1
[STOP] [2023-10-13 11:33:30] hold_for_later_1
[START] [2023-10-13 11:33:30] hold_for_later_2
[STOP] [2023-10-13 11:33:30] hold_for_later_2
[START] [2023-10-13 11:33:31] resolve_missing_parents
[STOP] [2023-10-13 11:33:31] resolve_missing_parents
[START] [2023-10-13 11:33:31] rebuild_nodes
[START] [2023-10-13 11:33:31] Flattener#flatten
[START] [2023-10-13 11:33:31] Flattener#study_resource
[START] [2023-10-13 11:33:31] Flattener#build_ancestry
[STOP] [2023-10-13 11:33:31] Flattener#build_ancestry
[INFO] [2023-10-13 11:33:31] 218 ancestry keys
[START] [2023-10-13 11:33:31] build_node_ancestors
[INFO] [2023-10-13 11:33:31] old ancestors deleted.
[STOP] [2023-10-13 11:33:31] build_node_ancestors
[START] [2023-10-13 11:33:31] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:33:31] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:33:31] Flattener#flatten
[STOP] [2023-10-13 11:33:31] rebuild_nodes
[START] [2023-10-13 11:33:31] resolve_missing_media_owners
[STOP] [2023-10-13 11:33:31] resolve_missing_media_owners
[START] [2023-10-13 11:33:31] sanitize_media_verbatims
[STOP] [2023-10-13 11:33:31] sanitize_media_verbatims
[START] [2023-10-13 11:33:31] queue_downloads
[STOP] [2023-10-13 11:33:31] queue_downloads
[START] [2023-10-13 11:33:31] parse_names
[WARN] [2023-10-13 11:33:31] I see 218 names which still need to be parsed.
[WARN] [2023-10-13 11:33:31] Names to parse: 218 formatted: 218 learned: 202 parsed: 218
[STOP] [2023-10-13 11:33:32] parse_names
[START] [2023-10-13 11:33:32] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 11:33:32] denormalize_canonical_names_to_nodes
[START] [2023-10-13 11:33:32] match_nodes
[START] [2023-10-13 11:33:32] map_all_nodes_to_pages
[STOP] [2023-10-13 11:33:40] map_all_nodes_to_pages
[INFO] [2023-10-13 11:33:40] 55 Unmatched nodes (of 218)! That's too many to output. Full list in /app/public/data/sting_pain/unmatched_nodes.txt ; First 10: Canonical: Megapolistes; Node#137158552; ResourceID: Megapolistes; Canonical: Polistes erythrocephalis; Node#137158617; ResourceID: Polistes_erythrocephalis; Canonical: Polistes exclamens; Node#137158618; ResourceID: Polistes_exclamens; Canonical: Polistes fuscatis; Node#137158619; ResourceID: Polistes_fuscatis; Canonical: Metapholybia; Node#137158555; ResourceID: Animalia/Arthropoda/Insecta/Hymenoptera/Vespidae/Metapholybia; Canonical: Metapholybia docilis; Node#137158556; ResourceID: Metapholybia_docilis; Canonical: Mischocyttarus; Node#137158558; ResourceID: Mischocyttarus; Canonical: Provespa; Node#137158631; ResourceID: Provespa; Canonical: Ropalidia; Node#137158642; ResourceID: Ropalidia; Canonical: Stelopybia; Node#137158659; ResourceID: Animalia/Arthropoda/Insecta/Hymenoptera/Vespidae/Stelopybia
[START] [2023-10-13 11:33:40] update_nodes
[STOP] [2023-10-13 11:33:40] update_nodes
[STOP] [2023-10-13 11:33:40] match_nodes
[START] [2023-10-13 11:33:40] reindex_search
[STOP] [2023-10-13 11:33:41] reindex_search
[START] [2023-10-13 11:33:41] normalize_units
[STOP] [2023-10-13 11:33:41] normalize_units
[START] [2023-10-13 11:33:41] calculate_statistics
[INFO] [2023-10-13 11:33:41] Duplicate page_id count: 0
[STOP] [2023-10-13 11:33:41] calculate_statistics
[START] [2023-10-13 11:33:41] complete_harvest_instance
[START] [2023-10-13 11:33:41] overall_tsv_creation
[INFO] [2023-10-13 11:33:41] Exporting 218 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 11:33:41] Processing group of 218 in 1 batches of 10000
[INFO] [2023-10-13 11:33:42] 191 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 11:33:42] Building Traits map for 218 nodes (this can take a while)...
[INFO] [2023-10-13 11:33:42] Mapped 191 traits (468 meta) for 218 nodes.
[INFO] [2023-10-13 11:33:42] Building Associations map (this can take a while)...
[INFO] [2023-10-13 11:33:42] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 11:33:42] Adding 191 traits...
[INFO] [2023-10-13 11:33:42] 270 metadata added.
[INFO] [2023-10-13 11:33:42] Adding 0 assocs...
[INFO] [2023-10-13 11:33:42] 0 metadata added.
[INFO] [2023-10-13 11:34:26] Processed 218/218 nodes
[INFO] [2023-10-13 11:34:26] Average Time: 45.0
[INFO] [2023-10-13 11:34:26] Total Time: 46s
[STOP] [2023-10-13 11:34:26] overall_tsv_creation
[INFO] [2023-10-13 11:34:26] Done. Check your files:
[INFO] [2023-10-13 11:34:27] (218 lines) /app/public/data/sting_pain/publish_nodes.tsv
[INFO] [2023-10-13 11:34:27] (1189 lines) /app/public/data/sting_pain/publish_node_ancestors.tsv
[INFO] [2023-10-13 11:34:27] (218 lines) /app/public/data/sting_pain/publish_scientific_names.tsv
[INFO] [2023-10-13 11:34:27] (192 lines) /app/public/data/sting_pain/publish_traits.tsv
[INFO] [2023-10-13 11:34:27] (271 lines) /app/public/data/sting_pain/publish_metadata.tsv
[STOP] [2023-10-13 11:34:27] complete_harvest_instance
[START] [2023-10-13 11:34:27] completed
[STOP] [2023-10-13 11:34:27] completed
[STOP] [2023-10-13 11:34:27] logged process, took 68.81

Latest Process

13 Oct 11:33 EXITED currently processing 0