Harvest for Calcification rate literature Created 13 Oct 09:34

Harvesting Log

[INFO] [2023-10-13 09:34:58] Created harvest instance #4422
[STOP] [2023-10-13 09:34:58] create_harvest_instance
[START] [2023-10-13 09:34:58] fetch_files
[STOP] [2023-10-13 09:34:58] fetch_files
[START] [2023-10-13 09:34:58] validate_each_file
[INFO] [2023-10-13 09:34:58] Looping over 8 formats...
[INFO] [2023-10-13 09:34:58] ...agents (/app/public/data/Calcification_ra/agents.txt)
[INFO] [2023-10-13 09:34:58] Valid: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_agents_30645.csv (0 lines)
[INFO] [2023-10-13 09:34:58] ...refs (/app/public/data/Calcification_ra/references.txt)
[INFO] [2023-10-13 09:34:58] Valid: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_refs_30644.csv (6 lines)
[INFO] [2023-10-13 09:34:58] ...nodes (/app/public/data/Calcification_ra/taxa.txt)
[INFO] [2023-10-13 09:34:58] Valid: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_nodes_30642.csv (20 lines)
[INFO] [2023-10-13 09:34:58] ...media (/app/public/data/Calcification_ra/media.txt)
[INFO] [2023-10-13 09:34:58] Valid: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_media_30641.csv (0 lines)
[INFO] [2023-10-13 09:34:58] ...vernaculars (/app/public/data/Calcification_ra/common names.txt)
[INFO] [2023-10-13 09:34:58] Valid: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_vernaculars_30643.csv (0 lines)
[INFO] [2023-10-13 09:34:58] ...occurrences (/app/public/data/Calcification_ra/occurrences.txt)
[INFO] [2023-10-13 09:34:58] Valid: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_occurrences_30646.csv (25 lines)
[INFO] [2023-10-13 09:34:58] ...assocs (/app/public/data/Calcification_ra/associations.txt)
[INFO] [2023-10-13 09:34:58] Valid: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_assocs_30648.csv (0 lines)
[INFO] [2023-10-13 09:34:58] ...measurements (/app/public/data/Calcification_ra/measurements or facts.txt)
[INFO] [2023-10-13 09:34:58] Valid: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_measurements_30647.csv (116 lines)
[STOP] [2023-10-13 09:34:58] validate_each_file
[START] [2023-10-13 09:34:58] convert_to_csv
[INFO] [2023-10-13 09:34:58] Looping over 8 formats...
[INFO] [2023-10-13 09:34:58] ...agents (/app/public/data/Calcification_ra/agents.txt)
[CMD] [2023-10-13 09:34:58] /usr/bin/sort /app/public/data/Calcification_ra/converted_csv/Calcification_ra_agents_30645.csv > /app/public/data/Calcification_ra/converted_csv/Calcification_ra_agents_30645.csv_sorted
[INFO] [2023-10-13 09:34:58] Converted: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_agents_30645.csv (0 lines)
[INFO] [2023-10-13 09:34:58] ...refs (/app/public/data/Calcification_ra/references.txt)
[CMD] [2023-10-13 09:34:58] /usr/bin/sort /app/public/data/Calcification_ra/converted_csv/Calcification_ra_refs_30644.csv > /app/public/data/Calcification_ra/converted_csv/Calcification_ra_refs_30644.csv_sorted
[INFO] [2023-10-13 09:34:58] Converted: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_refs_30644.csv (6 lines)
[INFO] [2023-10-13 09:34:58] ...nodes (/app/public/data/Calcification_ra/taxa.txt)
[CMD] [2023-10-13 09:34:58] /usr/bin/sort /app/public/data/Calcification_ra/converted_csv/Calcification_ra_nodes_30642.csv > /app/public/data/Calcification_ra/converted_csv/Calcification_ra_nodes_30642.csv_sorted
[INFO] [2023-10-13 09:34:58] Converted: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_nodes_30642.csv (20 lines)
[INFO] [2023-10-13 09:34:58] ...media (/app/public/data/Calcification_ra/media.txt)
[CMD] [2023-10-13 09:34:58] /usr/bin/sort /app/public/data/Calcification_ra/converted_csv/Calcification_ra_media_30641.csv > /app/public/data/Calcification_ra/converted_csv/Calcification_ra_media_30641.csv_sorted
[INFO] [2023-10-13 09:34:58] Converted: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_media_30641.csv (0 lines)
[INFO] [2023-10-13 09:34:58] ...vernaculars (/app/public/data/Calcification_ra/common names.txt)
[CMD] [2023-10-13 09:34:58] /usr/bin/sort /app/public/data/Calcification_ra/converted_csv/Calcification_ra_vernaculars_30643.csv > /app/public/data/Calcification_ra/converted_csv/Calcification_ra_vernaculars_30643.csv_sorted
[INFO] [2023-10-13 09:34:58] Converted: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_vernaculars_30643.csv (0 lines)
[INFO] [2023-10-13 09:34:58] ...occurrences (/app/public/data/Calcification_ra/occurrences.txt)
[CMD] [2023-10-13 09:34:58] /usr/bin/sort /app/public/data/Calcification_ra/converted_csv/Calcification_ra_occurrences_30646.csv > /app/public/data/Calcification_ra/converted_csv/Calcification_ra_occurrences_30646.csv_sorted
[INFO] [2023-10-13 09:34:58] Converted: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_occurrences_30646.csv (25 lines)
[INFO] [2023-10-13 09:34:58] ...assocs (/app/public/data/Calcification_ra/associations.txt)
[CMD] [2023-10-13 09:34:58] /usr/bin/sort /app/public/data/Calcification_ra/converted_csv/Calcification_ra_assocs_30648.csv > /app/public/data/Calcification_ra/converted_csv/Calcification_ra_assocs_30648.csv_sorted
[INFO] [2023-10-13 09:34:58] Converted: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_assocs_30648.csv (0 lines)
[INFO] [2023-10-13 09:34:58] ...measurements (/app/public/data/Calcification_ra/measurements or facts.txt)
[CMD] [2023-10-13 09:34:58] /usr/bin/sort /app/public/data/Calcification_ra/converted_csv/Calcification_ra_measurements_30647.csv > /app/public/data/Calcification_ra/converted_csv/Calcification_ra_measurements_30647.csv_sorted
[INFO] [2023-10-13 09:34:58] Converted: /app/public/data/Calcification_ra/converted_csv/Calcification_ra_measurements_30647.csv (116 lines)
[STOP] [2023-10-13 09:34:58] convert_to_csv
[START] [2023-10-13 09:34:58] calculate_delta
[INFO] [2023-10-13 09:34:58] Looping over 8 formats...
[INFO] [2023-10-13 09:34:58] ...agents (/app/public/data/Calcification_ra/agents.txt)
[CMD] [2023-10-13 09:34:58] echo "0a" > /app/public/data/Calcification_ra/diff/Calcification_ra_agents_30645.diff
[CMD] [2023-10-13 09:34:59] tail -n +1 /app/public/data/Calcification_ra/converted_csv/Calcification_ra_agents_30645.csv >> /app/public/data/Calcification_ra/diff/Calcification_ra_agents_30645.diff
[CMD] [2023-10-13 09:34:59] echo "." >> /app/public/data/Calcification_ra/diff/Calcification_ra_agents_30645.diff
[INFO] [2023-10-13 09:34:59] Created diff: /app/public/data/Calcification_ra/diff/Calcification_ra_agents_30645.diff (2 lines)
[INFO] [2023-10-13 09:34:59] ...refs (/app/public/data/Calcification_ra/references.txt)
[CMD] [2023-10-13 09:34:59] echo "0a" > /app/public/data/Calcification_ra/diff/Calcification_ra_refs_30644.diff
[CMD] [2023-10-13 09:34:59] tail -n +1 /app/public/data/Calcification_ra/converted_csv/Calcification_ra_refs_30644.csv >> /app/public/data/Calcification_ra/diff/Calcification_ra_refs_30644.diff
[CMD] [2023-10-13 09:34:59] echo "." >> /app/public/data/Calcification_ra/diff/Calcification_ra_refs_30644.diff
[INFO] [2023-10-13 09:34:59] Created diff: /app/public/data/Calcification_ra/diff/Calcification_ra_refs_30644.diff (8 lines)
[INFO] [2023-10-13 09:34:59] ...nodes (/app/public/data/Calcification_ra/taxa.txt)
[CMD] [2023-10-13 09:34:59] echo "0a" > /app/public/data/Calcification_ra/diff/Calcification_ra_nodes_30642.diff
[CMD] [2023-10-13 09:34:59] tail -n +1 /app/public/data/Calcification_ra/converted_csv/Calcification_ra_nodes_30642.csv >> /app/public/data/Calcification_ra/diff/Calcification_ra_nodes_30642.diff
[CMD] [2023-10-13 09:34:59] echo "." >> /app/public/data/Calcification_ra/diff/Calcification_ra_nodes_30642.diff
[INFO] [2023-10-13 09:34:59] Created diff: /app/public/data/Calcification_ra/diff/Calcification_ra_nodes_30642.diff (22 lines)
[INFO] [2023-10-13 09:34:59] ...media (/app/public/data/Calcification_ra/media.txt)
[CMD] [2023-10-13 09:34:59] echo "0a" > /app/public/data/Calcification_ra/diff/Calcification_ra_media_30641.diff
[CMD] [2023-10-13 09:34:59] tail -n +1 /app/public/data/Calcification_ra/converted_csv/Calcification_ra_media_30641.csv >> /app/public/data/Calcification_ra/diff/Calcification_ra_media_30641.diff
[CMD] [2023-10-13 09:34:59] echo "." >> /app/public/data/Calcification_ra/diff/Calcification_ra_media_30641.diff
[INFO] [2023-10-13 09:34:59] Created diff: /app/public/data/Calcification_ra/diff/Calcification_ra_media_30641.diff (2 lines)
[INFO] [2023-10-13 09:34:59] ...vernaculars (/app/public/data/Calcification_ra/common names.txt)
[CMD] [2023-10-13 09:34:59] echo "0a" > /app/public/data/Calcification_ra/diff/Calcification_ra_vernaculars_30643.diff
[CMD] [2023-10-13 09:34:59] tail -n +1 /app/public/data/Calcification_ra/converted_csv/Calcification_ra_vernaculars_30643.csv >> /app/public/data/Calcification_ra/diff/Calcification_ra_vernaculars_30643.diff
[CMD] [2023-10-13 09:35:00] echo "." >> /app/public/data/Calcification_ra/diff/Calcification_ra_vernaculars_30643.diff
[INFO] [2023-10-13 09:35:00] Created diff: /app/public/data/Calcification_ra/diff/Calcification_ra_vernaculars_30643.diff (2 lines)
[INFO] [2023-10-13 09:35:00] ...occurrences (/app/public/data/Calcification_ra/occurrences.txt)
[CMD] [2023-10-13 09:35:00] echo "0a" > /app/public/data/Calcification_ra/diff/Calcification_ra_occurrences_30646.diff
[CMD] [2023-10-13 09:35:00] tail -n +1 /app/public/data/Calcification_ra/converted_csv/Calcification_ra_occurrences_30646.csv >> /app/public/data/Calcification_ra/diff/Calcification_ra_occurrences_30646.diff
[CMD] [2023-10-13 09:35:00] echo "." >> /app/public/data/Calcification_ra/diff/Calcification_ra_occurrences_30646.diff
[INFO] [2023-10-13 09:35:00] Created diff: /app/public/data/Calcification_ra/diff/Calcification_ra_occurrences_30646.diff (27 lines)
[INFO] [2023-10-13 09:35:00] ...assocs (/app/public/data/Calcification_ra/associations.txt)
[CMD] [2023-10-13 09:35:00] echo "0a" > /app/public/data/Calcification_ra/diff/Calcification_ra_assocs_30648.diff
[CMD] [2023-10-13 09:35:00] tail -n +1 /app/public/data/Calcification_ra/converted_csv/Calcification_ra_assocs_30648.csv >> /app/public/data/Calcification_ra/diff/Calcification_ra_assocs_30648.diff
[CMD] [2023-10-13 09:35:00] echo "." >> /app/public/data/Calcification_ra/diff/Calcification_ra_assocs_30648.diff
[INFO] [2023-10-13 09:35:00] Created diff: /app/public/data/Calcification_ra/diff/Calcification_ra_assocs_30648.diff (2 lines)
[INFO] [2023-10-13 09:35:00] ...measurements (/app/public/data/Calcification_ra/measurements or facts.txt)
[CMD] [2023-10-13 09:35:00] echo "0a" > /app/public/data/Calcification_ra/diff/Calcification_ra_measurements_30647.diff
[CMD] [2023-10-13 09:35:00] tail -n +1 /app/public/data/Calcification_ra/converted_csv/Calcification_ra_measurements_30647.csv >> /app/public/data/Calcification_ra/diff/Calcification_ra_measurements_30647.diff
[CMD] [2023-10-13 09:35:00] echo "." >> /app/public/data/Calcification_ra/diff/Calcification_ra_measurements_30647.diff
[INFO] [2023-10-13 09:35:00] Created diff: /app/public/data/Calcification_ra/diff/Calcification_ra_measurements_30647.diff (118 lines)
[STOP] [2023-10-13 09:35:00] calculate_delta
[START] [2023-10-13 09:35:00] parse_diff_and_store
[INFO] [2023-10-13 09:35:00] Handling diff: /app/public/data/Calcification_ra/diff/Calcification_ra_agents_30645.diff (2 lines)
[INFO] [2023-10-13 09:35:00] Loading agents diff file into memory (2 lines)...
[INFO] [2023-10-13 09:35:00] Handling diff: /app/public/data/Calcification_ra/diff/Calcification_ra_refs_30644.diff (8 lines)
[INFO] [2023-10-13 09:35:00] Loading refs diff file into memory (8 lines)...
[INFO] [2023-10-13 09:35:01] Storing 6 References (6/6/8)
[INFO] [2023-10-13 09:35:01] Handling diff: /app/public/data/Calcification_ra/diff/Calcification_ra_nodes_30642.diff (22 lines)
[INFO] [2023-10-13 09:35:01] Loading nodes diff file into memory (22 lines)...
[INFO] [2023-10-13 09:35:01] Storing 24 ScientificNames (48/20/22)
[INFO] [2023-10-13 09:35:01] Storing 24 Nodes (48/20/22)
[INFO] [2023-10-13 09:35:01] Handling diff: /app/public/data/Calcification_ra/diff/Calcification_ra_media_30641.diff (2 lines)
[INFO] [2023-10-13 09:35:01] Loading media diff file into memory (2 lines)...
[INFO] [2023-10-13 09:35:01] Handling diff: /app/public/data/Calcification_ra/diff/Calcification_ra_vernaculars_30643.diff (2 lines)
[INFO] [2023-10-13 09:35:01] Loading vernaculars diff file into memory (2 lines)...
[INFO] [2023-10-13 09:35:01] Handling diff: /app/public/data/Calcification_ra/diff/Calcification_ra_occurrences_30646.diff (27 lines)
[INFO] [2023-10-13 09:35:01] Loading occurrences diff file into memory (27 lines)...
[INFO] [2023-10-13 09:35:01] Storing 25 Occurrences (48/25/27)
[INFO] [2023-10-13 09:35:01] Storing 23 OccurrenceMetadata (48/25/27)
[INFO] [2023-10-13 09:35:01] Handling diff: /app/public/data/Calcification_ra/diff/Calcification_ra_assocs_30648.diff (2 lines)
[INFO] [2023-10-13 09:35:01] Loading assocs diff file into memory (2 lines)...
[INFO] [2023-10-13 09:35:01] Handling diff: /app/public/data/Calcification_ra/diff/Calcification_ra_measurements_30647.diff (118 lines)
[INFO] [2023-10-13 09:35:01] Loading measurements diff file into memory (118 lines)...
[INFO] [2023-10-13 09:35:01] Storing 8 TraitsReferences (175/116/118)
[INFO] [2023-10-13 09:35:01] Storing 26 Traits (175/116/118)
[INFO] [2023-10-13 09:35:01] Storing 51 MetaTraits (175/116/118)
[INFO] [2023-10-13 09:35:01] Storing 90 OccurrenceMetadata (175/116/118)
[STOP] [2023-10-13 09:35:01] parse_diff_and_store
[START] [2023-10-13 09:35:01] resolve_keys
[2023-10-13 09:35:01] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 09:35:09] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 09:35:09] traits to occurrences...
[INFO] [2023-10-13 09:35:09] traits to nodes (through occurrences)...
[INFO] [2023-10-13 09:35:09] Traits to sex term...
[INFO] [2023-10-13 09:35:09] Traits to lifestage term...
[INFO] [2023-10-13 09:35:09] MetaTraits to traits...
[INFO] [2023-10-13 09:35:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 09:35:09] Assocs to occurrences...
[INFO] [2023-10-13 09:35:09] Assocs to nodes...
[INFO] [2023-10-13 09:35:09] Assoc to sex term...
[INFO] [2023-10-13 09:35:09] Assoc to lifestage term...
[INFO] [2023-10-13 09:35:09] MetaAssoc to assocs...
[STOP] [2023-10-13 09:35:09] resolve_keys
[START] [2023-10-13 09:35:09] hold_for_later_1
[STOP] [2023-10-13 09:35:09] hold_for_later_1
[START] [2023-10-13 09:35:09] hold_for_later_2
[STOP] [2023-10-13 09:35:09] hold_for_later_2
[START] [2023-10-13 09:35:09] resolve_missing_parents
[STOP] [2023-10-13 09:35:09] resolve_missing_parents
[START] [2023-10-13 09:35:09] rebuild_nodes
[START] [2023-10-13 09:35:09] Flattener#flatten
[START] [2023-10-13 09:35:09] Flattener#study_resource
[START] [2023-10-13 09:35:09] Flattener#build_ancestry
[STOP] [2023-10-13 09:35:09] Flattener#build_ancestry
[INFO] [2023-10-13 09:35:09] 24 ancestry keys
[START] [2023-10-13 09:35:09] build_node_ancestors
[INFO] [2023-10-13 09:35:09] old ancestors deleted.
[STOP] [2023-10-13 09:35:09] build_node_ancestors
[START] [2023-10-13 09:35:09] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 09:35:09] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 09:35:09] Flattener#flatten
[STOP] [2023-10-13 09:35:09] rebuild_nodes
[START] [2023-10-13 09:35:09] resolve_missing_media_owners
[STOP] [2023-10-13 09:35:09] resolve_missing_media_owners
[START] [2023-10-13 09:35:09] sanitize_media_verbatims
[STOP] [2023-10-13 09:35:09] sanitize_media_verbatims
[START] [2023-10-13 09:35:09] queue_downloads
[STOP] [2023-10-13 09:35:09] queue_downloads
[START] [2023-10-13 09:35:09] parse_names
[WARN] [2023-10-13 09:35:09] I see 24 names which still need to be parsed.
[WARN] [2023-10-13 09:35:09] Names to parse: 24 formatted: 24 learned: 23 parsed: 24
[STOP] [2023-10-13 09:35:10] parse_names
[START] [2023-10-13 09:35:10] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 09:35:10] denormalize_canonical_names_to_nodes
[START] [2023-10-13 09:35:10] match_nodes
[START] [2023-10-13 09:35:10] map_all_nodes_to_pages
[STOP] [2023-10-13 09:35:11] map_all_nodes_to_pages
[INFO] [2023-10-13 09:35:11] Unmatched nodes (2 of 24): Canonical: Scleractinia; Node#136994602; ResourceID: Scleractinia; Canonical: Solenastrea hyades; Node#136994605; ResourceID: Solenastrea hyades
[START] [2023-10-13 09:35:11] update_nodes
[STOP] [2023-10-13 09:35:11] update_nodes
[STOP] [2023-10-13 09:35:11] match_nodes
[START] [2023-10-13 09:35:11] reindex_search
[STOP] [2023-10-13 09:35:11] reindex_search
[START] [2023-10-13 09:35:11] normalize_units
[STOP] [2023-10-13 09:35:11] normalize_units
[START] [2023-10-13 09:35:11] calculate_statistics
[INFO] [2023-10-13 09:35:11] Duplicate page_id count: 0
[STOP] [2023-10-13 09:35:11] calculate_statistics
[START] [2023-10-13 09:35:11] complete_harvest_instance
[START] [2023-10-13 09:35:11] overall_tsv_creation
[INFO] [2023-10-13 09:35:11] Exporting 24 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 09:35:11] Processing group of 24 in 1 batches of 10000
[INFO] [2023-10-13 09:35:12] 26 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 09:35:12] Building Traits map for 24 nodes (this can take a while)...
[INFO] [2023-10-13 09:35:12] Mapped 26 traits (51 meta) for 24 nodes.
[INFO] [2023-10-13 09:35:12] Building Associations map (this can take a while)...
[INFO] [2023-10-13 09:35:12] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 09:35:12] Adding 26 traits...
[INFO] [2023-10-13 09:35:12] 112 metadata added.
[INFO] [2023-10-13 09:35:12] Adding 0 assocs...
[INFO] [2023-10-13 09:35:12] 0 metadata added.
[INFO] [2023-10-13 09:35:57] Processed 24/24 nodes
[INFO] [2023-10-13 09:35:57] Average Time: 45.16
[INFO] [2023-10-13 09:35:57] Total Time: 46s
[STOP] [2023-10-13 09:35:57] overall_tsv_creation
[INFO] [2023-10-13 09:35:57] Done. Check your files:
[INFO] [2023-10-13 09:35:57] (24 lines) /app/public/data/Calcification_ra/publish_nodes.tsv
[INFO] [2023-10-13 09:35:57] (86 lines) /app/public/data/Calcification_ra/publish_node_ancestors.tsv
[INFO] [2023-10-13 09:35:57] (24 lines) /app/public/data/Calcification_ra/publish_scientific_names.tsv
[INFO] [2023-10-13 09:35:57] (27 lines) /app/public/data/Calcification_ra/publish_traits.tsv
[INFO] [2023-10-13 09:35:57] (113 lines) /app/public/data/Calcification_ra/publish_metadata.tsv
[STOP] [2023-10-13 09:35:57] complete_harvest_instance
[START] [2023-10-13 09:35:57] completed
[STOP] [2023-10-13 09:35:57] completed
[STOP] [2023-10-13 09:35:57] logged process, took 59.6

Latest Process

13 Oct 09:34 EXITED currently processing 0