Harvest for Kubitzki et al Created 17 Jan 10:55

Harvesting Log

[INFO] [2023-01-17 10:55:58] Created harvest instance #4255
[STOP] [2023-01-17 10:55:58] create_harvest_instance
[START] [2023-01-17 10:55:58] fetch_files
[STOP] [2023-01-17 10:55:58] fetch_files
[START] [2023-01-17 10:55:58] validate_each_file
[INFO] [2023-01-17 10:55:58] Looping over 4 formats...
[INFO] [2023-01-17 10:55:58] ...refs (/app/public/data/kubitzki_et_al/references.txt)
[INFO] [2023-01-17 10:55:58] Valid: /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_refs_30015.csv (1 lines)
[INFO] [2023-01-17 10:55:58] ...nodes (/app/public/data/kubitzki_et_al/taxa.tsv)
[INFO] [2023-01-17 10:55:59] Valid: /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_nodes_30012.csv (9648 lines)
[INFO] [2023-01-17 10:55:59] ...occurrences (/app/public/data/kubitzki_et_al/occurrences.tsv)
[INFO] [2023-01-17 10:55:59] Valid: /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_occurrences_30013.csv (9387 lines)
[INFO] [2023-01-17 10:55:59] ...measurements (/app/public/data/kubitzki_et_al/measurementsorfacts.txt)
[INFO] [2023-01-17 10:56:02] Valid: /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_measurements_30014.csv (45397 lines)
[STOP] [2023-01-17 10:56:02] validate_each_file
[START] [2023-01-17 10:56:02] convert_to_csv
[INFO] [2023-01-17 10:56:02] Looping over 4 formats...
[INFO] [2023-01-17 10:56:02] ...refs (/app/public/data/kubitzki_et_al/references.txt)
[CMD] [2023-01-17 10:56:02] /usr/bin/sort /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_refs_30015.csv > /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_refs_30015.csv_sorted
[INFO] [2023-01-17 10:56:02] Converted: /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_refs_30015.csv (1 lines)
[INFO] [2023-01-17 10:56:02] ...nodes (/app/public/data/kubitzki_et_al/taxa.tsv)
[CMD] [2023-01-17 10:56:02] /usr/bin/sort /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_nodes_30012.csv > /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_nodes_30012.csv_sorted
[INFO] [2023-01-17 10:56:02] Converted: /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_nodes_30012.csv (9648 lines)
[INFO] [2023-01-17 10:56:02] ...occurrences (/app/public/data/kubitzki_et_al/occurrences.tsv)
[CMD] [2023-01-17 10:56:02] /usr/bin/sort /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_occurrences_30013.csv > /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_occurrences_30013.csv_sorted
[INFO] [2023-01-17 10:56:02] Converted: /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_occurrences_30013.csv (9387 lines)
[INFO] [2023-01-17 10:56:02] ...measurements (/app/public/data/kubitzki_et_al/measurementsorfacts.txt)
[CMD] [2023-01-17 10:56:02] /usr/bin/sort /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_measurements_30014.csv > /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_measurements_30014.csv_sorted
[INFO] [2023-01-17 10:56:02] Converted: /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_measurements_30014.csv (45397 lines)
[STOP] [2023-01-17 10:56:02] convert_to_csv
[START] [2023-01-17 10:56:02] calculate_delta
[INFO] [2023-01-17 10:56:02] Looping over 4 formats...
[INFO] [2023-01-17 10:56:02] ...refs (/app/public/data/kubitzki_et_al/references.txt)
[CMD] [2023-01-17 10:56:02] echo "0a" > /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_refs_30015.diff
[CMD] [2023-01-17 10:56:02] tail -n +1 /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_refs_30015.csv >> /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_refs_30015.diff
[CMD] [2023-01-17 10:56:02] echo "." >> /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_refs_30015.diff
[INFO] [2023-01-17 10:56:02] Created diff: /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_refs_30015.diff (3 lines)
[INFO] [2023-01-17 10:56:02] ...nodes (/app/public/data/kubitzki_et_al/taxa.tsv)
[CMD] [2023-01-17 10:56:02] echo "0a" > /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_nodes_30012.diff
[CMD] [2023-01-17 10:56:02] tail -n +1 /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_nodes_30012.csv >> /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_nodes_30012.diff
[CMD] [2023-01-17 10:56:02] echo "." >> /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_nodes_30012.diff
[INFO] [2023-01-17 10:56:02] Created diff: /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_nodes_30012.diff (9650 lines)
[INFO] [2023-01-17 10:56:02] ...occurrences (/app/public/data/kubitzki_et_al/occurrences.tsv)
[CMD] [2023-01-17 10:56:02] echo "0a" > /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_occurrences_30013.diff
[CMD] [2023-01-17 10:56:02] tail -n +1 /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_occurrences_30013.csv >> /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_occurrences_30013.diff
[CMD] [2023-01-17 10:56:02] echo "." >> /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_occurrences_30013.diff
[INFO] [2023-01-17 10:56:03] Created diff: /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_occurrences_30013.diff (9389 lines)
[INFO] [2023-01-17 10:56:03] ...measurements (/app/public/data/kubitzki_et_al/measurementsorfacts.txt)
[CMD] [2023-01-17 10:56:03] echo "0a" > /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_measurements_30014.diff
[CMD] [2023-01-17 10:56:03] tail -n +1 /app/public/data/kubitzki_et_al/converted_csv/kubitzki_et_al_measurements_30014.csv >> /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_measurements_30014.diff
[CMD] [2023-01-17 10:56:03] echo "." >> /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_measurements_30014.diff
[INFO] [2023-01-17 10:56:03] Created diff: /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_measurements_30014.diff (45399 lines)
[STOP] [2023-01-17 10:56:03] calculate_delta
[START] [2023-01-17 10:56:03] parse_diff_and_store
[INFO] [2023-01-17 10:56:03] Handling diff: /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_refs_30015.diff (3 lines)
[INFO] [2023-01-17 10:56:03] Loading refs diff file into memory (3 lines)...
[INFO] [2023-01-17 10:56:03] Storing 1 References (1/1/3)
[INFO] [2023-01-17 10:56:03] Handling diff: /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_nodes_30012.diff (9650 lines)
[INFO] [2023-01-17 10:56:03] Loading nodes diff file into memory (9650 lines)...
[WARN] [2023-01-17 10:56:05] Filtered Scientific Name `Cane/la` to `Canela`
[INFO] [2023-01-17 10:56:05] Storing 9648 ScientificNames (19296/9648/9650)
[INFO] [2023-01-17 10:56:08] Storing 9648 Nodes (19296/9648/9650)
[INFO] [2023-01-17 10:56:11] Handling diff: /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_occurrences_30013.diff (9389 lines)
[INFO] [2023-01-17 10:56:11] Loading occurrences diff file into memory (9389 lines)...
[INFO] [2023-01-17 10:56:11] Storing 9387 Occurrences (9387/9387/9389)
[INFO] [2023-01-17 10:56:12] Handling diff: /app/public/data/kubitzki_et_al/diff/kubitzki_et_al_measurements_30014.diff (45399 lines)
[INFO] [2023-01-17 10:56:13] Loading measurements diff file into memory (45399 lines)...
[INFO] [2023-01-17 10:56:15] Storing 9999 Traits (10018/10000/45399)
[INFO] [2023-01-17 10:56:18] Storing 19 MetaTraits (10018/10000/45399)
[INFO] [2023-01-17 10:56:20] Storing 10000 Traits (20036/20000/45399)
[INFO] [2023-01-17 10:56:23] Storing 18 MetaTraits (20036/20000/45399)
[INFO] [2023-01-17 10:56:27] Storing 10000 Traits (38502/30000/45399)
[INFO] [2023-01-17 10:56:30] Storing 8466 MetaTraits (38502/30000/45399)
[INFO] [2023-01-17 10:56:36] Storing 10000 Traits (58502/40000/45399)
[INFO] [2023-01-17 10:56:39] Storing 10000 MetaTraits (58502/40000/45399)
[INFO] [2023-01-17 10:56:42] Storing 5398 Traits (68362/45397/45399)
[INFO] [2023-01-17 10:56:44] Storing 4462 MetaTraits (68362/45397/45399)
[STOP] [2023-01-17 10:56:44] parse_diff_and_store
[START] [2023-01-17 10:56:44] resolve_keys
[2023-01-17 10:56:46] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-17 10:56:56] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-17 10:56:56] traits to occurrences...
[INFO] [2023-01-17 10:56:57] traits to nodes (through occurrences)...
[INFO] [2023-01-17 10:56:58] Traits to sex term...
[INFO] [2023-01-17 10:56:58] Traits to lifestage term...
[INFO] [2023-01-17 10:56:58] MetaTraits to traits...
[INFO] [2023-01-17 10:56:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-17 10:56:59] Assocs to occurrences...
[INFO] [2023-01-17 10:56:59] Assocs to nodes...
[INFO] [2023-01-17 10:56:59] Assoc to sex term...
[INFO] [2023-01-17 10:56:59] Assoc to lifestage term...
[INFO] [2023-01-17 10:56:59] MetaAssoc to assocs...
[STOP] [2023-01-17 10:56:59] resolve_keys
[START] [2023-01-17 10:56:59] hold_for_later_1
[STOP] [2023-01-17 10:56:59] hold_for_later_1
[START] [2023-01-17 10:56:59] hold_for_later_2
[STOP] [2023-01-17 10:56:59] hold_for_later_2
[START] [2023-01-17 10:56:59] resolve_missing_parents
[STOP] [2023-01-17 10:57:00] resolve_missing_parents
[START] [2023-01-17 10:57:00] rebuild_nodes
[START] [2023-01-17 10:57:00] Flattener#flatten
[START] [2023-01-17 10:57:00] Flattener#study_resource
[START] [2023-01-17 10:57:00] Flattener#build_ancestry
[STOP] [2023-01-17 10:57:00] Flattener#build_ancestry
[INFO] [2023-01-17 10:57:00] 9648 ancestry keys
[START] [2023-01-17 10:57:00] build_node_ancestors
[INFO] [2023-01-17 10:57:00] old ancestors deleted.
[STOP] [2023-01-17 10:57:00] build_node_ancestors
[WARN] [2023-01-17 10:57:00] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-17 10:57:00] Flattener#flatten
[STOP] [2023-01-17 10:57:00] rebuild_nodes
[START] [2023-01-17 10:57:00] resolve_missing_media_owners
[STOP] [2023-01-17 10:57:00] resolve_missing_media_owners
[START] [2023-01-17 10:57:00] sanitize_media_verbatims
[STOP] [2023-01-17 10:57:00] sanitize_media_verbatims
[START] [2023-01-17 10:57:00] queue_downloads
[STOP] [2023-01-17 10:57:00] queue_downloads
[START] [2023-01-17 10:57:00] parse_names
[WARN] [2023-01-17 10:57:00] I see 9648 names which still need to be parsed.
[WARN] [2023-01-17 10:57:01] Names to parse: 9648 formatted: 9648 learned: 9621 parsed: 9648
[STOP] [2023-01-17 10:57:07] parse_names
[START] [2023-01-17 10:57:07] denormalize_canonical_names_to_nodes
[STOP] [2023-01-17 10:57:07] denormalize_canonical_names_to_nodes
[START] [2023-01-17 10:57:07] match_nodes
[START] [2023-01-17 10:57:07] map_all_nodes_to_pages
[STOP] [2023-01-17 10:57:16] map_all_nodes_to_pages
[INFO] [2023-01-17 10:57:16] ZERO unmatched nodes (of 9648)! Nicely done.
[START] [2023-01-17 10:57:16] update_nodes
[STOP] [2023-01-17 10:57:16] update_nodes
[STOP] [2023-01-17 10:57:16] match_nodes
[START] [2023-01-17 10:57:16] reindex_search
[STOP] [2023-01-17 10:57:21] reindex_search
[START] [2023-01-17 10:57:21] normalize_units
[STOP] [2023-01-17 10:57:21] normalize_units
[START] [2023-01-17 10:57:21] calculate_statistics
[2023-01-17 10:57:22] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-17 10:57:34] Duplicate page_id count: 362
[STOP] [2023-01-17 10:57:34] calculate_statistics
[START] [2023-01-17 10:57:34] complete_harvest_instance
[START] [2023-01-17 10:57:34] overall_tsv_creation
[INFO] [2023-01-17 10:57:34] Exporting 9648 nodes as TSV in batches of 10000...
[INFO] [2023-01-17 10:57:34] Processing group of 9648 in 1 batches of 10000
[INFO] [2023-01-17 10:57:48] 22685 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-17 10:57:48] Building Traits map for 9648 nodes (this can take a while)...
[INFO] [2023-01-17 10:58:07] Mapped 22685 traits (22963 meta) for 9648 nodes.
[INFO] [2023-01-17 10:58:07] Building Associations map (this can take a while)...
[INFO] [2023-01-17 10:58:18] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-17 10:58:18] Adding 22685 traits...
[INFO] [2023-01-17 10:58:23] 22679 metadata added.
[INFO] [2023-01-17 10:58:23] Adding 0 assocs...
[INFO] [2023-01-17 10:58:23] 0 metadata added.
[INFO] [2023-01-17 10:59:12] Processed 9648/9648 nodes
[INFO] [2023-01-17 10:59:12] Average Time: 95.39
[INFO] [2023-01-17 10:59:12] Total Time: 1m39s
[STOP] [2023-01-17 10:59:12] overall_tsv_creation
[INFO] [2023-01-17 10:59:12] Done. Check your files:
[INFO] [2023-01-17 10:59:13] (9501 lines) /app/public/data/kubitzki_et_al/publish_nodes.tsv
[INFO] [2023-01-17 10:59:13] (9648 lines) /app/public/data/kubitzki_et_al/publish_scientific_names.tsv
[INFO] [2023-01-17 10:59:13] (22686 lines) /app/public/data/kubitzki_et_al/publish_traits.tsv
[INFO] [2023-01-17 10:59:13] (22680 lines) /app/public/data/kubitzki_et_al/publish_metadata.tsv
[STOP] [2023-01-17 10:59:13] complete_harvest_instance
[START] [2023-01-17 10:59:13] completed
[STOP] [2023-01-17 10:59:13] completed
[STOP] [2023-01-17 10:59:13] logged process, took 194.5

Latest Process

17 Jan 10:55 EXITED currently processing 0