Harvest for Swain et al 2016 Created 13 Oct 09:14

Harvesting Log

[INFO] [2023-10-13 09:14:06] Created harvest instance #4416
[STOP] [2023-10-13 09:14:06] create_harvest_instance
[START] [2023-10-13 09:14:06] fetch_files
[STOP] [2023-10-13 09:14:06] fetch_files
[START] [2023-10-13 09:14:06] validate_each_file
[INFO] [2023-10-13 09:14:06] Looping over 4 formats...
[INFO] [2023-10-13 09:14:06] ...refs (/app/public/data/swain_et_al_swai/references.txt)
[INFO] [2023-10-13 09:14:06] Valid: /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_refs_30613.csv (46 lines)
[INFO] [2023-10-13 09:14:06] ...nodes (/app/public/data/swain_et_al_swai/taxa.txt)
[INFO] [2023-10-13 09:14:06] Valid: /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_nodes_30612.csv (60 lines)
[INFO] [2023-10-13 09:14:06] ...occurrences (/app/public/data/swain_et_al_swai/occurrences.txt)
[INFO] [2023-10-13 09:14:06] Valid: /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_occurrences_30614.csv (69 lines)
[INFO] [2023-10-13 09:14:06] ...measurements (/app/public/data/swain_et_al_swai/measurement_or_fact.txt)
[INFO] [2023-10-13 09:14:06] Valid: /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_measurements_30615.csv (559 lines)
[STOP] [2023-10-13 09:14:06] validate_each_file
[START] [2023-10-13 09:14:06] convert_to_csv
[INFO] [2023-10-13 09:14:06] Looping over 4 formats...
[INFO] [2023-10-13 09:14:06] ...refs (/app/public/data/swain_et_al_swai/references.txt)
[CMD] [2023-10-13 09:14:06] /usr/bin/sort /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_refs_30613.csv > /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_refs_30613.csv_sorted
[INFO] [2023-10-13 09:14:06] Converted: /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_refs_30613.csv (46 lines)
[INFO] [2023-10-13 09:14:06] ...nodes (/app/public/data/swain_et_al_swai/taxa.txt)
[CMD] [2023-10-13 09:14:06] /usr/bin/sort /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_nodes_30612.csv > /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_nodes_30612.csv_sorted
[INFO] [2023-10-13 09:14:07] Converted: /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_nodes_30612.csv (60 lines)
[INFO] [2023-10-13 09:14:07] ...occurrences (/app/public/data/swain_et_al_swai/occurrences.txt)
[CMD] [2023-10-13 09:14:07] /usr/bin/sort /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_occurrences_30614.csv > /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_occurrences_30614.csv_sorted
[INFO] [2023-10-13 09:14:07] Converted: /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_occurrences_30614.csv (69 lines)
[INFO] [2023-10-13 09:14:07] ...measurements (/app/public/data/swain_et_al_swai/measurement_or_fact.txt)
[CMD] [2023-10-13 09:14:07] /usr/bin/sort /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_measurements_30615.csv > /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_measurements_30615.csv_sorted
[INFO] [2023-10-13 09:14:07] Converted: /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_measurements_30615.csv (559 lines)
[STOP] [2023-10-13 09:14:07] convert_to_csv
[START] [2023-10-13 09:14:07] calculate_delta
[INFO] [2023-10-13 09:14:07] Looping over 4 formats...
[INFO] [2023-10-13 09:14:07] ...refs (/app/public/data/swain_et_al_swai/references.txt)
[CMD] [2023-10-13 09:14:07] echo "0a" > /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_refs_30613.diff
[CMD] [2023-10-13 09:14:07] tail -n +1 /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_refs_30613.csv >> /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_refs_30613.diff
[CMD] [2023-10-13 09:14:07] echo "." >> /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_refs_30613.diff
[INFO] [2023-10-13 09:14:07] Created diff: /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_refs_30613.diff (48 lines)
[INFO] [2023-10-13 09:14:07] ...nodes (/app/public/data/swain_et_al_swai/taxa.txt)
[CMD] [2023-10-13 09:14:07] echo "0a" > /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_nodes_30612.diff
[CMD] [2023-10-13 09:14:07] tail -n +1 /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_nodes_30612.csv >> /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_nodes_30612.diff
[CMD] [2023-10-13 09:14:07] echo "." >> /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_nodes_30612.diff
[INFO] [2023-10-13 09:14:07] Created diff: /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_nodes_30612.diff (62 lines)
[INFO] [2023-10-13 09:14:07] ...occurrences (/app/public/data/swain_et_al_swai/occurrences.txt)
[CMD] [2023-10-13 09:14:07] echo "0a" > /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_occurrences_30614.diff
[CMD] [2023-10-13 09:14:07] tail -n +1 /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_occurrences_30614.csv >> /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_occurrences_30614.diff
[CMD] [2023-10-13 09:14:07] echo "." >> /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_occurrences_30614.diff
[INFO] [2023-10-13 09:14:07] Created diff: /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_occurrences_30614.diff (71 lines)
[INFO] [2023-10-13 09:14:07] ...measurements (/app/public/data/swain_et_al_swai/measurement_or_fact.txt)
[CMD] [2023-10-13 09:14:07] echo "0a" > /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_measurements_30615.diff
[CMD] [2023-10-13 09:14:07] tail -n +1 /app/public/data/swain_et_al_swai/converted_csv/swain_et_al_swai_measurements_30615.csv >> /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_measurements_30615.diff
[CMD] [2023-10-13 09:14:08] echo "." >> /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_measurements_30615.diff
[INFO] [2023-10-13 09:14:08] Created diff: /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_measurements_30615.diff (561 lines)
[STOP] [2023-10-13 09:14:08] calculate_delta
[START] [2023-10-13 09:14:08] parse_diff_and_store
[INFO] [2023-10-13 09:14:08] Handling diff: /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_refs_30613.diff (48 lines)
[INFO] [2023-10-13 09:14:08] Loading refs diff file into memory (48 lines)...
[INFO] [2023-10-13 09:14:08] Storing 46 References (46/46/48)
[INFO] [2023-10-13 09:14:08] Handling diff: /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_nodes_30612.diff (62 lines)
[INFO] [2023-10-13 09:14:08] Loading nodes diff file into memory (62 lines)...
[INFO] [2023-10-13 09:14:08] Storing 63 ScientificNames (126/60/62)
[INFO] [2023-10-13 09:14:08] Storing 63 Nodes (126/60/62)
[INFO] [2023-10-13 09:14:08] Handling diff: /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_occurrences_30614.diff (71 lines)
[INFO] [2023-10-13 09:14:08] Loading occurrences diff file into memory (71 lines)...
[INFO] [2023-10-13 09:14:08] Storing 69 Occurrences (69/69/71)
[INFO] [2023-10-13 09:14:08] Handling diff: /app/public/data/swain_et_al_swai/diff/swain_et_al_swai_measurements_30615.diff (561 lines)
[INFO] [2023-10-13 09:14:08] Loading measurements diff file into memory (561 lines)...
[INFO] [2023-10-13 09:14:08] Storing 559 Traits (1258/559/561)
[INFO] [2023-10-13 09:14:09] Storing 322 TraitsReferences (1258/559/561)
[INFO] [2023-10-13 09:14:09] Storing 377 MetaTraits (1258/559/561)
[STOP] [2023-10-13 09:14:09] parse_diff_and_store
[START] [2023-10-13 09:14:09] resolve_keys
[2023-10-13 09:14:09] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 09:14:16] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 09:14:16] traits to occurrences...
[INFO] [2023-10-13 09:14:17] traits to nodes (through occurrences)...
[INFO] [2023-10-13 09:14:17] Traits to sex term...
[INFO] [2023-10-13 09:14:17] Traits to lifestage term...
[INFO] [2023-10-13 09:14:17] MetaTraits to traits...
[INFO] [2023-10-13 09:14:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 09:14:17] Assocs to occurrences...
[INFO] [2023-10-13 09:14:17] Assocs to nodes...
[INFO] [2023-10-13 09:14:17] Assoc to sex term...
[INFO] [2023-10-13 09:14:17] Assoc to lifestage term...
[INFO] [2023-10-13 09:14:17] MetaAssoc to assocs...
[STOP] [2023-10-13 09:14:17] resolve_keys
[START] [2023-10-13 09:14:17] hold_for_later_1
[STOP] [2023-10-13 09:14:17] hold_for_later_1
[START] [2023-10-13 09:14:17] hold_for_later_2
[STOP] [2023-10-13 09:14:17] hold_for_later_2
[START] [2023-10-13 09:14:17] resolve_missing_parents
[STOP] [2023-10-13 09:14:17] resolve_missing_parents
[START] [2023-10-13 09:14:17] rebuild_nodes
[START] [2023-10-13 09:14:17] Flattener#flatten
[START] [2023-10-13 09:14:17] Flattener#study_resource
[START] [2023-10-13 09:14:17] Flattener#build_ancestry
[STOP] [2023-10-13 09:14:17] Flattener#build_ancestry
[INFO] [2023-10-13 09:14:17] 63 ancestry keys
[START] [2023-10-13 09:14:17] build_node_ancestors
[INFO] [2023-10-13 09:14:17] old ancestors deleted.
[STOP] [2023-10-13 09:14:17] build_node_ancestors
[START] [2023-10-13 09:14:17] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 09:14:17] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 09:14:17] Flattener#flatten
[STOP] [2023-10-13 09:14:17] rebuild_nodes
[START] [2023-10-13 09:14:17] resolve_missing_media_owners
[STOP] [2023-10-13 09:14:17] resolve_missing_media_owners
[START] [2023-10-13 09:14:17] sanitize_media_verbatims
[STOP] [2023-10-13 09:14:17] sanitize_media_verbatims
[START] [2023-10-13 09:14:17] queue_downloads
[STOP] [2023-10-13 09:14:17] queue_downloads
[START] [2023-10-13 09:14:17] parse_names
[WARN] [2023-10-13 09:14:17] I see 63 names which still need to be parsed.
[WARN] [2023-10-13 09:14:17] Names to parse: 63 formatted: 63 learned: 63 parsed: 63
[STOP] [2023-10-13 09:14:18] parse_names
[START] [2023-10-13 09:14:18] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 09:14:18] denormalize_canonical_names_to_nodes
[START] [2023-10-13 09:14:18] match_nodes
[START] [2023-10-13 09:14:18] map_all_nodes_to_pages
[STOP] [2023-10-13 09:14:19] map_all_nodes_to_pages
[INFO] [2023-10-13 09:14:19] Unmatched nodes (2 of 63): Canonical: Palythoa sakurajimensis; Node#136982701; ResourceID: Palythoa sakurajimensis; Canonical: Protopalythoa; Node#136982713; ResourceID: Protopalythoa 
[START] [2023-10-13 09:14:19] update_nodes
[STOP] [2023-10-13 09:14:19] update_nodes
[STOP] [2023-10-13 09:14:19] match_nodes
[START] [2023-10-13 09:14:19] reindex_search
[STOP] [2023-10-13 09:14:19] reindex_search
[START] [2023-10-13 09:14:19] normalize_units
[STOP] [2023-10-13 09:14:19] normalize_units
[START] [2023-10-13 09:14:19] calculate_statistics
[INFO] [2023-10-13 09:14:19] Duplicate page_id count: 0
[STOP] [2023-10-13 09:14:19] calculate_statistics
[START] [2023-10-13 09:14:19] complete_harvest_instance
[START] [2023-10-13 09:14:19] overall_tsv_creation
[INFO] [2023-10-13 09:14:19] Exporting 63 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 09:14:19] Processing group of 63 in 1 batches of 10000
[INFO] [2023-10-13 09:14:19] 282 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 09:14:19] Building Traits map for 63 nodes (this can take a while)...
[INFO] [2023-10-13 09:14:19] Mapped 282 traits (377 meta) for 63 nodes.
[INFO] [2023-10-13 09:14:19] Building Associations map (this can take a while)...
[INFO] [2023-10-13 09:14:19] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 09:14:19] Adding 282 traits...
[INFO] [2023-10-13 09:14:19] 595 metadata added.
[INFO] [2023-10-13 09:14:19] Adding 0 assocs...
[INFO] [2023-10-13 09:14:19] 0 metadata added.
[INFO] [2023-10-13 09:15:04] Processed 63/63 nodes
[INFO] [2023-10-13 09:15:04] Average Time: 44.67
[INFO] [2023-10-13 09:15:04] Total Time: 45s
[STOP] [2023-10-13 09:15:04] overall_tsv_creation
[INFO] [2023-10-13 09:15:04] Done. Check your files:
[INFO] [2023-10-13 09:15:04] (63 lines) /app/public/data/swain_et_al_swai/publish_nodes.tsv
[INFO] [2023-10-13 09:15:04] (183 lines) /app/public/data/swain_et_al_swai/publish_node_ancestors.tsv
[INFO] [2023-10-13 09:15:04] (63 lines) /app/public/data/swain_et_al_swai/publish_scientific_names.tsv
[INFO] [2023-10-13 09:15:04] (283 lines) /app/public/data/swain_et_al_swai/publish_traits.tsv
[INFO] [2023-10-13 09:15:04] (596 lines) /app/public/data/swain_et_al_swai/publish_metadata.tsv
[STOP] [2023-10-13 09:15:04] complete_harvest_instance
[START] [2023-10-13 09:15:04] completed
[STOP] [2023-10-13 09:15:04] completed
[STOP] [2023-10-13 09:15:04] logged process, took 58.1

Latest Process

13 Oct 09:14 EXITED currently processing 0