Harvest for Gamble et al 2015 Created 13 Oct 09:05

Harvesting Log

[INFO] [2023-10-13 09:05:27] Created harvest instance #4413
[STOP] [2023-10-13 09:05:27] create_harvest_instance
[START] [2023-10-13 09:05:27] fetch_files
[STOP] [2023-10-13 09:05:27] fetch_files
[START] [2023-10-13 09:05:27] validate_each_file
[INFO] [2023-10-13 09:05:27] Looping over 4 formats...
[INFO] [2023-10-13 09:05:27] ...refs (/app/public/data/gamble_et_al_gam/references.txt)
[INFO] [2023-10-13 09:05:27] Valid: /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_refs_30602.csv (90 lines)
[INFO] [2023-10-13 09:05:27] ...nodes (/app/public/data/gamble_et_al_gam/taxa.txt)
[INFO] [2023-10-13 09:05:27] Valid: /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_nodes_30600.csv (111 lines)
[INFO] [2023-10-13 09:05:27] ...occurrences (/app/public/data/gamble_et_al_gam/occurrences.txt)
[INFO] [2023-10-13 09:05:27] Valid: /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_occurrences_30601.csv (111 lines)
[INFO] [2023-10-13 09:05:27] ...measurements (/app/public/data/gamble_et_al_gam/measurementsorfacts.txt)
[INFO] [2023-10-13 09:05:27] Valid: /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_measurements_30603.csv (224 lines)
[STOP] [2023-10-13 09:05:27] validate_each_file
[START] [2023-10-13 09:05:27] convert_to_csv
[INFO] [2023-10-13 09:05:27] Looping over 4 formats...
[INFO] [2023-10-13 09:05:27] ...refs (/app/public/data/gamble_et_al_gam/references.txt)
[CMD] [2023-10-13 09:05:27] /usr/bin/sort /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_refs_30602.csv > /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_refs_30602.csv_sorted
[INFO] [2023-10-13 09:05:27] Converted: /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_refs_30602.csv (90 lines)
[INFO] [2023-10-13 09:05:27] ...nodes (/app/public/data/gamble_et_al_gam/taxa.txt)
[CMD] [2023-10-13 09:05:27] /usr/bin/sort /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_nodes_30600.csv > /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_nodes_30600.csv_sorted
[INFO] [2023-10-13 09:05:27] Converted: /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_nodes_30600.csv (111 lines)
[INFO] [2023-10-13 09:05:27] ...occurrences (/app/public/data/gamble_et_al_gam/occurrences.txt)
[CMD] [2023-10-13 09:05:27] /usr/bin/sort /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_occurrences_30601.csv > /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_occurrences_30601.csv_sorted
[INFO] [2023-10-13 09:05:27] Converted: /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_occurrences_30601.csv (111 lines)
[INFO] [2023-10-13 09:05:27] ...measurements (/app/public/data/gamble_et_al_gam/measurementsorfacts.txt)
[CMD] [2023-10-13 09:05:27] /usr/bin/sort /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_measurements_30603.csv > /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_measurements_30603.csv_sorted
[INFO] [2023-10-13 09:05:27] Converted: /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_measurements_30603.csv (224 lines)
[STOP] [2023-10-13 09:05:27] convert_to_csv
[START] [2023-10-13 09:05:27] calculate_delta
[INFO] [2023-10-13 09:05:27] Looping over 4 formats...
[INFO] [2023-10-13 09:05:27] ...refs (/app/public/data/gamble_et_al_gam/references.txt)
[CMD] [2023-10-13 09:05:27] echo "0a" > /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_refs_30602.diff
[CMD] [2023-10-13 09:05:27] tail -n +1 /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_refs_30602.csv >> /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_refs_30602.diff
[CMD] [2023-10-13 09:05:27] echo "." >> /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_refs_30602.diff
[INFO] [2023-10-13 09:05:27] Created diff: /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_refs_30602.diff (92 lines)
[INFO] [2023-10-13 09:05:27] ...nodes (/app/public/data/gamble_et_al_gam/taxa.txt)
[CMD] [2023-10-13 09:05:27] echo "0a" > /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_nodes_30600.diff
[CMD] [2023-10-13 09:05:28] tail -n +1 /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_nodes_30600.csv >> /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_nodes_30600.diff
[CMD] [2023-10-13 09:05:28] echo "." >> /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_nodes_30600.diff
[INFO] [2023-10-13 09:05:28] Created diff: /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_nodes_30600.diff (113 lines)
[INFO] [2023-10-13 09:05:28] ...occurrences (/app/public/data/gamble_et_al_gam/occurrences.txt)
[CMD] [2023-10-13 09:05:28] echo "0a" > /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_occurrences_30601.diff
[CMD] [2023-10-13 09:05:28] tail -n +1 /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_occurrences_30601.csv >> /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_occurrences_30601.diff
[CMD] [2023-10-13 09:05:28] echo "." >> /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_occurrences_30601.diff
[INFO] [2023-10-13 09:05:28] Created diff: /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_occurrences_30601.diff (113 lines)
[INFO] [2023-10-13 09:05:28] ...measurements (/app/public/data/gamble_et_al_gam/measurementsorfacts.txt)
[CMD] [2023-10-13 09:05:28] echo "0a" > /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_measurements_30603.diff
[CMD] [2023-10-13 09:05:28] tail -n +1 /app/public/data/gamble_et_al_gam/converted_csv/gamble_et_al_gam_measurements_30603.csv >> /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_measurements_30603.diff
[CMD] [2023-10-13 09:05:28] echo "." >> /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_measurements_30603.diff
[INFO] [2023-10-13 09:05:28] Created diff: /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_measurements_30603.diff (226 lines)
[STOP] [2023-10-13 09:05:28] calculate_delta
[START] [2023-10-13 09:05:28] parse_diff_and_store
[INFO] [2023-10-13 09:05:28] Handling diff: /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_refs_30602.diff (92 lines)
[INFO] [2023-10-13 09:05:28] Loading refs diff file into memory (92 lines)...
[INFO] [2023-10-13 09:05:28] Storing 90 References (90/90/92)
[INFO] [2023-10-13 09:05:28] Handling diff: /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_nodes_30600.diff (113 lines)
[INFO] [2023-10-13 09:05:28] Loading nodes diff file into memory (113 lines)...
[INFO] [2023-10-13 09:05:28] Storing 111 ScientificNames (222/111/113)
[INFO] [2023-10-13 09:05:28] Storing 111 Nodes (222/111/113)
[INFO] [2023-10-13 09:05:29] Handling diff: /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_occurrences_30601.diff (113 lines)
[INFO] [2023-10-13 09:05:29] Loading occurrences diff file into memory (113 lines)...
[INFO] [2023-10-13 09:05:29] Storing 111 Occurrences (111/111/113)
[INFO] [2023-10-13 09:05:29] Handling diff: /app/public/data/gamble_et_al_gam/diff/gamble_et_al_gam_measurements_30603.diff (226 lines)
[INFO] [2023-10-13 09:05:29] Loading measurements diff file into memory (226 lines)...
[INFO] [2023-10-13 09:05:29] Storing 215 TraitsReferences (550/224/226)
[INFO] [2023-10-13 09:05:29] Storing 224 Traits (550/224/226)
[INFO] [2023-10-13 09:05:29] Storing 111 MetaTraits (550/224/226)
[STOP] [2023-10-13 09:05:29] parse_diff_and_store
[START] [2023-10-13 09:05:29] resolve_keys
[2023-10-13 09:05:29] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 09:05:37] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 09:05:37] traits to occurrences...
[INFO] [2023-10-13 09:05:37] traits to nodes (through occurrences)...
[INFO] [2023-10-13 09:05:37] Traits to sex term...
[INFO] [2023-10-13 09:05:37] Traits to lifestage term...
[INFO] [2023-10-13 09:05:37] MetaTraits to traits...
[INFO] [2023-10-13 09:05:37] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 09:05:37] Assocs to occurrences...
[INFO] [2023-10-13 09:05:37] Assocs to nodes...
[INFO] [2023-10-13 09:05:37] Assoc to sex term...
[INFO] [2023-10-13 09:05:37] Assoc to lifestage term...
[INFO] [2023-10-13 09:05:37] MetaAssoc to assocs...
[STOP] [2023-10-13 09:05:37] resolve_keys
[START] [2023-10-13 09:05:37] hold_for_later_1
[STOP] [2023-10-13 09:05:37] hold_for_later_1
[START] [2023-10-13 09:05:37] hold_for_later_2
[STOP] [2023-10-13 09:05:37] hold_for_later_2
[START] [2023-10-13 09:05:37] resolve_missing_parents
[STOP] [2023-10-13 09:05:37] resolve_missing_parents
[START] [2023-10-13 09:05:37] rebuild_nodes
[START] [2023-10-13 09:05:37] Flattener#flatten
[START] [2023-10-13 09:05:37] Flattener#study_resource
[START] [2023-10-13 09:05:37] Flattener#build_ancestry
[STOP] [2023-10-13 09:05:37] Flattener#build_ancestry
[INFO] [2023-10-13 09:05:37] 111 ancestry keys
[START] [2023-10-13 09:05:37] build_node_ancestors
[INFO] [2023-10-13 09:05:37] old ancestors deleted.
[STOP] [2023-10-13 09:05:37] build_node_ancestors
[WARN] [2023-10-13 09:05:37] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 09:05:37] Flattener#flatten
[STOP] [2023-10-13 09:05:37] rebuild_nodes
[START] [2023-10-13 09:05:37] resolve_missing_media_owners
[STOP] [2023-10-13 09:05:37] resolve_missing_media_owners
[START] [2023-10-13 09:05:37] sanitize_media_verbatims
[STOP] [2023-10-13 09:05:37] sanitize_media_verbatims
[START] [2023-10-13 09:05:37] queue_downloads
[STOP] [2023-10-13 09:05:37] queue_downloads
[START] [2023-10-13 09:05:37] parse_names
[WARN] [2023-10-13 09:05:37] I see 111 names which still need to be parsed.
[WARN] [2023-10-13 09:05:37] Names to parse: 111 formatted: 111 learned: 111 parsed: 111
[STOP] [2023-10-13 09:05:38] parse_names
[START] [2023-10-13 09:05:38] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 09:05:38] denormalize_canonical_names_to_nodes
[START] [2023-10-13 09:05:38] match_nodes
[START] [2023-10-13 09:05:38] map_all_nodes_to_pages
[STOP] [2023-10-13 09:05:38] map_all_nodes_to_pages
[INFO] [2023-10-13 09:05:38] ZERO unmatched nodes (of 111)! Nicely done.
[START] [2023-10-13 09:05:38] update_nodes
[STOP] [2023-10-13 09:05:38] update_nodes
[STOP] [2023-10-13 09:05:38] match_nodes
[START] [2023-10-13 09:05:38] reindex_search
[STOP] [2023-10-13 09:05:39] reindex_search
[START] [2023-10-13 09:05:39] normalize_units
[STOP] [2023-10-13 09:05:39] normalize_units
[START] [2023-10-13 09:05:39] calculate_statistics
[2023-10-13 09:05:39] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 09:05:39] Duplicate page_id count: 0
[STOP] [2023-10-13 09:05:39] calculate_statistics
[START] [2023-10-13 09:05:39] complete_harvest_instance
[START] [2023-10-13 09:05:39] overall_tsv_creation
[INFO] [2023-10-13 09:05:39] Exporting 111 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 09:05:39] Processing group of 111 in 1 batches of 10000
[INFO] [2023-10-13 09:05:40] 111 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 09:05:40] Building Traits map for 111 nodes (this can take a while)...
[INFO] [2023-10-13 09:05:40] Mapped 111 traits (111 meta) for 111 nodes.
[INFO] [2023-10-13 09:05:40] Building Associations map (this can take a while)...
[INFO] [2023-10-13 09:05:40] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 09:05:40] Adding 111 traits...
[INFO] [2023-10-13 09:05:40] 328 metadata added.
[INFO] [2023-10-13 09:05:40] Adding 0 assocs...
[INFO] [2023-10-13 09:05:40] 0 metadata added.
[INFO] [2023-10-13 09:06:24] Processed 111/111 nodes
[INFO] [2023-10-13 09:06:24] Average Time: 44.76
[INFO] [2023-10-13 09:06:24] Total Time: 45s
[STOP] [2023-10-13 09:06:24] overall_tsv_creation
[INFO] [2023-10-13 09:06:24] Done. Check your files:
[INFO] [2023-10-13 09:06:24] (111 lines) /app/public/data/gamble_et_al_gam/publish_nodes.tsv
[INFO] [2023-10-13 09:06:24] (111 lines) /app/public/data/gamble_et_al_gam/publish_scientific_names.tsv
[INFO] [2023-10-13 09:06:24] (112 lines) /app/public/data/gamble_et_al_gam/publish_traits.tsv
[INFO] [2023-10-13 09:06:24] (329 lines) /app/public/data/gamble_et_al_gam/publish_metadata.tsv
[STOP] [2023-10-13 09:06:24] complete_harvest_instance
[START] [2023-10-13 09:06:24] completed
[STOP] [2023-10-13 09:06:24] completed
[STOP] [2023-10-13 09:06:24] logged process, took 57.79

Latest Process

13 Oct 09:05 EXITED currently processing 0