Harvest for Mesquita et al, 2015 Created 13 Oct 11:59

Harvesting Log

[INFO] [2023-10-13 11:59:36] Created harvest instance #4438
[STOP] [2023-10-13 11:59:36] create_harvest_instance
[START] [2023-10-13 11:59:36] fetch_files
[STOP] [2023-10-13 11:59:36] fetch_files
[START] [2023-10-13 11:59:36] validate_each_file
[INFO] [2023-10-13 11:59:36] Looping over 4 formats...
[INFO] [2023-10-13 11:59:36] ...refs (/app/public/data/lhdlw/references.txt)
[INFO] [2023-10-13 11:59:36] Valid: /app/public/data/lhdlw/converted_csv/lhdlw_refs_30730.csv (242 lines)
[INFO] [2023-10-13 11:59:36] ...nodes (/app/public/data/lhdlw/taxa.txt)
[INFO] [2023-10-13 11:59:36] Valid: /app/public/data/lhdlw/converted_csv/lhdlw_nodes_30729.csv (337 lines)
[INFO] [2023-10-13 11:59:36] ...occurrences (/app/public/data/lhdlw/occurrences.tsv)
[INFO] [2023-10-13 11:59:36] Valid: /app/public/data/lhdlw/converted_csv/lhdlw_occurrences_30731.csv (2073 lines)
[INFO] [2023-10-13 11:59:36] ...measurements (/app/public/data/lhdlw/measurements-or-facts.txt)
[INFO] [2023-10-13 11:59:37] Valid: /app/public/data/lhdlw/converted_csv/lhdlw_measurements_30732.csv (7663 lines)
[STOP] [2023-10-13 11:59:37] validate_each_file
[START] [2023-10-13 11:59:37] convert_to_csv
[INFO] [2023-10-13 11:59:37] Looping over 4 formats...
[INFO] [2023-10-13 11:59:37] ...refs (/app/public/data/lhdlw/references.txt)
[CMD] [2023-10-13 11:59:37] /usr/bin/sort /app/public/data/lhdlw/converted_csv/lhdlw_refs_30730.csv > /app/public/data/lhdlw/converted_csv/lhdlw_refs_30730.csv_sorted
[INFO] [2023-10-13 11:59:37] Converted: /app/public/data/lhdlw/converted_csv/lhdlw_refs_30730.csv (242 lines)
[INFO] [2023-10-13 11:59:37] ...nodes (/app/public/data/lhdlw/taxa.txt)
[CMD] [2023-10-13 11:59:37] /usr/bin/sort /app/public/data/lhdlw/converted_csv/lhdlw_nodes_30729.csv > /app/public/data/lhdlw/converted_csv/lhdlw_nodes_30729.csv_sorted
[INFO] [2023-10-13 11:59:37] Converted: /app/public/data/lhdlw/converted_csv/lhdlw_nodes_30729.csv (337 lines)
[INFO] [2023-10-13 11:59:37] ...occurrences (/app/public/data/lhdlw/occurrences.tsv)
[CMD] [2023-10-13 11:59:37] /usr/bin/sort /app/public/data/lhdlw/converted_csv/lhdlw_occurrences_30731.csv > /app/public/data/lhdlw/converted_csv/lhdlw_occurrences_30731.csv_sorted
[INFO] [2023-10-13 11:59:37] Converted: /app/public/data/lhdlw/converted_csv/lhdlw_occurrences_30731.csv (2073 lines)
[INFO] [2023-10-13 11:59:37] ...measurements (/app/public/data/lhdlw/measurements-or-facts.txt)
[CMD] [2023-10-13 11:59:37] /usr/bin/sort /app/public/data/lhdlw/converted_csv/lhdlw_measurements_30732.csv > /app/public/data/lhdlw/converted_csv/lhdlw_measurements_30732.csv_sorted
[INFO] [2023-10-13 11:59:37] Converted: /app/public/data/lhdlw/converted_csv/lhdlw_measurements_30732.csv (7663 lines)
[STOP] [2023-10-13 11:59:37] convert_to_csv
[START] [2023-10-13 11:59:37] calculate_delta
[INFO] [2023-10-13 11:59:37] Looping over 4 formats...
[INFO] [2023-10-13 11:59:37] ...refs (/app/public/data/lhdlw/references.txt)
[CMD] [2023-10-13 11:59:37] echo "0a" > /app/public/data/lhdlw/diff/lhdlw_refs_30730.diff
[CMD] [2023-10-13 11:59:38] tail -n +1 /app/public/data/lhdlw/converted_csv/lhdlw_refs_30730.csv >> /app/public/data/lhdlw/diff/lhdlw_refs_30730.diff
[CMD] [2023-10-13 11:59:38] echo "." >> /app/public/data/lhdlw/diff/lhdlw_refs_30730.diff
[INFO] [2023-10-13 11:59:38] Created diff: /app/public/data/lhdlw/diff/lhdlw_refs_30730.diff (244 lines)
[INFO] [2023-10-13 11:59:38] ...nodes (/app/public/data/lhdlw/taxa.txt)
[CMD] [2023-10-13 11:59:38] echo "0a" > /app/public/data/lhdlw/diff/lhdlw_nodes_30729.diff
[CMD] [2023-10-13 11:59:38] tail -n +1 /app/public/data/lhdlw/converted_csv/lhdlw_nodes_30729.csv >> /app/public/data/lhdlw/diff/lhdlw_nodes_30729.diff
[CMD] [2023-10-13 11:59:38] echo "." >> /app/public/data/lhdlw/diff/lhdlw_nodes_30729.diff
[INFO] [2023-10-13 11:59:38] Created diff: /app/public/data/lhdlw/diff/lhdlw_nodes_30729.diff (339 lines)
[INFO] [2023-10-13 11:59:38] ...occurrences (/app/public/data/lhdlw/occurrences.tsv)
[CMD] [2023-10-13 11:59:38] echo "0a" > /app/public/data/lhdlw/diff/lhdlw_occurrences_30731.diff
[CMD] [2023-10-13 11:59:38] tail -n +1 /app/public/data/lhdlw/converted_csv/lhdlw_occurrences_30731.csv >> /app/public/data/lhdlw/diff/lhdlw_occurrences_30731.diff
[CMD] [2023-10-13 11:59:38] echo "." >> /app/public/data/lhdlw/diff/lhdlw_occurrences_30731.diff
[INFO] [2023-10-13 11:59:38] Created diff: /app/public/data/lhdlw/diff/lhdlw_occurrences_30731.diff (2075 lines)
[INFO] [2023-10-13 11:59:38] ...measurements (/app/public/data/lhdlw/measurements-or-facts.txt)
[CMD] [2023-10-13 11:59:38] echo "0a" > /app/public/data/lhdlw/diff/lhdlw_measurements_30732.diff
[CMD] [2023-10-13 11:59:38] tail -n +1 /app/public/data/lhdlw/converted_csv/lhdlw_measurements_30732.csv >> /app/public/data/lhdlw/diff/lhdlw_measurements_30732.diff
[CMD] [2023-10-13 11:59:38] echo "." >> /app/public/data/lhdlw/diff/lhdlw_measurements_30732.diff
[INFO] [2023-10-13 11:59:38] Created diff: /app/public/data/lhdlw/diff/lhdlw_measurements_30732.diff (7665 lines)
[STOP] [2023-10-13 11:59:38] calculate_delta
[START] [2023-10-13 11:59:38] parse_diff_and_store
[INFO] [2023-10-13 11:59:38] Handling diff: /app/public/data/lhdlw/diff/lhdlw_refs_30730.diff (244 lines)
[INFO] [2023-10-13 11:59:38] Loading refs diff file into memory (244 lines)...
[INFO] [2023-10-13 11:59:38] Storing 242 References (242/242/244)
[INFO] [2023-10-13 11:59:38] Handling diff: /app/public/data/lhdlw/diff/lhdlw_nodes_30729.diff (339 lines)
[INFO] [2023-10-13 11:59:39] Loading nodes diff file into memory (339 lines)...
[INFO] [2023-10-13 11:59:39] Storing 507 ScientificNames (1014/337/339)
[INFO] [2023-10-13 11:59:39] Storing 507 Nodes (1014/337/339)
[INFO] [2023-10-13 11:59:39] Handling diff: /app/public/data/lhdlw/diff/lhdlw_occurrences_30731.diff (2075 lines)
[INFO] [2023-10-13 11:59:39] Loading occurrences diff file into memory (2075 lines)...
[INFO] [2023-10-13 11:59:40] Storing 2073 Occurrences (10964/2073/2075)
[INFO] [2023-10-13 11:59:40] Storing 8891 OccurrenceMetadata (10964/2073/2075)
[INFO] [2023-10-13 11:59:41] Handling diff: /app/public/data/lhdlw/diff/lhdlw_measurements_30732.diff (7665 lines)
[INFO] [2023-10-13 11:59:41] Loading measurements diff file into memory (7665 lines)...
[INFO] [2023-10-13 11:59:45] Storing 7663 Traits (23296/7663/7665)
[INFO] [2023-10-13 11:59:48] Storing 11561 MetaTraits (23296/7663/7665)
[INFO] [2023-10-13 11:59:49] Storing 4072 TraitsReferences (23296/7663/7665)
[STOP] [2023-10-13 11:59:50] parse_diff_and_store
[START] [2023-10-13 11:59:50] resolve_keys
[2023-10-13 11:59:50] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 11:59:58] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 11:59:58] traits to occurrences...
[INFO] [2023-10-13 11:59:58] traits to nodes (through occurrences)...
[INFO] [2023-10-13 11:59:58] Traits to sex term...
[INFO] [2023-10-13 11:59:58] Traits to lifestage term...
[INFO] [2023-10-13 11:59:58] MetaTraits to traits...
[INFO] [2023-10-13 11:59:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 11:59:59] Assocs to occurrences...
[INFO] [2023-10-13 11:59:59] Assocs to nodes...
[INFO] [2023-10-13 11:59:59] Assoc to sex term...
[INFO] [2023-10-13 11:59:59] Assoc to lifestage term...
[INFO] [2023-10-13 11:59:59] MetaAssoc to assocs...
[STOP] [2023-10-13 11:59:59] resolve_keys
[START] [2023-10-13 11:59:59] hold_for_later_1
[STOP] [2023-10-13 11:59:59] hold_for_later_1
[START] [2023-10-13 11:59:59] hold_for_later_2
[STOP] [2023-10-13 11:59:59] hold_for_later_2
[START] [2023-10-13 11:59:59] resolve_missing_parents
[STOP] [2023-10-13 11:59:59] resolve_missing_parents
[START] [2023-10-13 11:59:59] rebuild_nodes
[START] [2023-10-13 11:59:59] Flattener#flatten
[START] [2023-10-13 11:59:59] Flattener#study_resource
[START] [2023-10-13 11:59:59] Flattener#build_ancestry
[STOP] [2023-10-13 11:59:59] Flattener#build_ancestry
[INFO] [2023-10-13 11:59:59] 507 ancestry keys
[START] [2023-10-13 11:59:59] build_node_ancestors
[INFO] [2023-10-13 11:59:59] old ancestors deleted.
[STOP] [2023-10-13 11:59:59] build_node_ancestors
[START] [2023-10-13 11:59:59] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:59:59] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:59:59] Flattener#flatten
[STOP] [2023-10-13 11:59:59] rebuild_nodes
[START] [2023-10-13 11:59:59] resolve_missing_media_owners
[STOP] [2023-10-13 11:59:59] resolve_missing_media_owners
[START] [2023-10-13 11:59:59] sanitize_media_verbatims
[STOP] [2023-10-13 11:59:59] sanitize_media_verbatims
[START] [2023-10-13 11:59:59] queue_downloads
[STOP] [2023-10-13 11:59:59] queue_downloads
[START] [2023-10-13 11:59:59] parse_names
[WARN] [2023-10-13 11:59:59] I see 507 names which still need to be parsed.
[WARN] [2023-10-13 11:59:59] Names to parse: 507 formatted: 507 learned: 507 parsed: 507
[STOP] [2023-10-13 12:00:01] parse_names
[START] [2023-10-13 12:00:01] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 12:00:01] denormalize_canonical_names_to_nodes
[START] [2023-10-13 12:00:01] match_nodes
[START] [2023-10-13 12:00:01] map_all_nodes_to_pages
[STOP] [2023-10-13 12:00:17] map_all_nodes_to_pages
[INFO] [2023-10-13 12:00:17] 21 Unmatched nodes (of 507)! That's too many to output. Full list in /app/public/data/lhdlw/unmatched_nodes.txt ; First 10: Canonical: Leposoma oswadoi; Node#137159025; ResourceID: Leposoma_oswadoi; Canonical: Leposoma percarinatum; Node#137159026; ResourceID: Leposoma_percarinatum; Canonical: Leposoma rugiceps; Node#137159027; ResourceID: Leposoma_rugiceps; Canonical: Agama; Node#137158750; ResourceID: Agama_Agama; Canonical: Draco quinquefaciatus; Node#137158925; ResourceID: Draco_quinquefaciatus; Canonical: Cnemidophorus ocellifer; Node#137158846; ResourceID: Cnemidophorus_ocellifer; Canonical: Cnemidophorus; Node#137158847; ResourceID: Cnemidophorus_sp.; Canonical: Lerista bouganvillei; Node#137159030; ResourceID: Lerista_bouganvillei; Canonical: Oligosoma cherrieri; Node#137159101; ResourceID: Oligosoma_cherrieri; Canonical: Sceloporus clarki; Node#137159161; ResourceID: Sceloporus_clarki
[START] [2023-10-13 12:00:17] update_nodes
[STOP] [2023-10-13 12:00:17] update_nodes
[STOP] [2023-10-13 12:00:17] match_nodes
[START] [2023-10-13 12:00:17] reindex_search
[STOP] [2023-10-13 12:00:18] reindex_search
[START] [2023-10-13 12:00:18] normalize_units
[STOP] [2023-10-13 12:00:24] normalize_units
[START] [2023-10-13 12:00:24] calculate_statistics
[INFO] [2023-10-13 12:00:26] Duplicate page_id count: 0
[STOP] [2023-10-13 12:00:26] calculate_statistics
[START] [2023-10-13 12:00:26] complete_harvest_instance
[START] [2023-10-13 12:00:26] overall_tsv_creation
[INFO] [2023-10-13 12:00:26] Exporting 507 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 12:00:26] Processing group of 507 in 1 batches of 10000
[INFO] [2023-10-13 12:00:27] 5629 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 12:00:27] Building Traits map for 507 nodes (this can take a while)...
[INFO] [2023-10-13 12:00:29] Mapped 5629 traits (11561 meta) for 507 nodes.
[INFO] [2023-10-13 12:00:29] Building Associations map (this can take a while)...
[INFO] [2023-10-13 12:00:29] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 12:00:29] Adding 5629 traits...
[INFO] [2023-10-13 12:00:32] 24537 metadata added.
[INFO] [2023-10-13 12:00:32] Adding 0 assocs...
[INFO] [2023-10-13 12:00:32] 0 metadata added.
[INFO] [2023-10-13 12:01:18] Processed 507/507 nodes
[INFO] [2023-10-13 12:01:18] Average Time: 51.52
[INFO] [2023-10-13 12:01:18] Total Time: 52s
[STOP] [2023-10-13 12:01:18] overall_tsv_creation
[INFO] [2023-10-13 12:01:18] Done. Check your files:
[INFO] [2023-10-13 12:01:18] (507 lines) /app/public/data/lhdlw/publish_nodes.tsv
[INFO] [2023-10-13 12:01:18] (1316 lines) /app/public/data/lhdlw/publish_node_ancestors.tsv
[INFO] [2023-10-13 12:01:18] (507 lines) /app/public/data/lhdlw/publish_scientific_names.tsv
[INFO] [2023-10-13 12:01:18] (5630 lines) /app/public/data/lhdlw/publish_traits.tsv
[INFO] [2023-10-13 12:01:18] (24538 lines) /app/public/data/lhdlw/publish_metadata.tsv
[STOP] [2023-10-13 12:01:18] complete_harvest_instance
[START] [2023-10-13 12:01:18] completed
[STOP] [2023-10-13 12:01:18] completed
[STOP] [2023-10-13 12:01:18] logged process, took 101.99

Latest Process

13 Oct 11:59 EXITED currently processing 0