Harvest for Faubel and Kolasa 1978 Created 17 Jul 08:43

Stage: completed
Fetched: 17 Jul 08:43
Validated: 17 Jul 08:43
Deltas Created 17 Jul 08:43
Units Normalized: 17 Jul 08:44
Ancestry Built: 17 Jul 08:43
Nodes Matched: 17 Jul 08:44
Names Parsed: 17 Jul 08:43
New Models Stored: 17 Jul 08:43
Indexed: 17 Jul 08:44
Completed: 17 Jul 08:46
Time to Harvest: less than a minute
Harvesting Log

(158 lines)
[INFO] [2024-07-17 08:43:35] Created harvest instance #4553
[STOP] [2024-07-17 08:43:35] create_harvest_instance
[START] [2024-07-17 08:43:35] fetch_files
[STOP] [2024-07-17 08:43:35] fetch_files
[START] [2024-07-17 08:43:35] validate_each_file
[INFO] [2024-07-17 08:43:35] Created new folder: /app/public/converted_csv
[INFO] [2024-07-17 08:43:35] Looping over 4 formats...
[INFO] [2024-07-17 08:43:35] ...refs (/app/public/data/faubel_kolasa_fa/references.txt)
[INFO] [2024-07-17 08:43:35] Valid: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_refs_31177.csv (17 lines)
[INFO] [2024-07-17 08:43:35] ...nodes (/app/public/data/faubel_kolasa_fa/taxa.tsv)
[INFO] [2024-07-17 08:43:35] Valid: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_nodes_31176.csv (13 lines)
[INFO] [2024-07-17 08:43:35] ...occurrences (/app/public/data/faubel_kolasa_fa/occurrences.tsv)
[INFO] [2024-07-17 08:43:35] Valid: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_occurrences_31178.csv (13 lines)
[INFO] [2024-07-17 08:43:35] ...measurements (/app/public/data/faubel_kolasa_fa/measurementOrFact.tsv)
[INFO] [2024-07-17 08:43:35] Valid: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_measurements_31179.csv (13 lines)
[STOP] [2024-07-17 08:43:35] validate_each_file
[START] [2024-07-17 08:43:35] convert_to_csv
[INFO] [2024-07-17 08:43:35] Looping over 4 formats...
[INFO] [2024-07-17 08:43:35] ...refs (/app/public/data/faubel_kolasa_fa/references.txt)
[CMD] [2024-07-17 08:43:35] /usr/bin/sort /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_refs_31177.csv > /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_refs_31177.csv_sorted
[INFO] [2024-07-17 08:43:35] Converted: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_refs_31177.csv (17 lines)
[INFO] [2024-07-17 08:43:35] ...nodes (/app/public/data/faubel_kolasa_fa/taxa.tsv)
[CMD] [2024-07-17 08:43:35] /usr/bin/sort /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_nodes_31176.csv > /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_nodes_31176.csv_sorted
[INFO] [2024-07-17 08:43:35] Converted: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_nodes_31176.csv (13 lines)
[INFO] [2024-07-17 08:43:35] ...occurrences (/app/public/data/faubel_kolasa_fa/occurrences.tsv)
[CMD] [2024-07-17 08:43:35] /usr/bin/sort /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_occurrences_31178.csv > /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_occurrences_31178.csv_sorted
[INFO] [2024-07-17 08:43:35] Converted: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_occurrences_31178.csv (13 lines)
[INFO] [2024-07-17 08:43:35] ...measurements (/app/public/data/faubel_kolasa_fa/measurementOrFact.tsv)
[CMD] [2024-07-17 08:43:35] /usr/bin/sort /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_measurements_31179.csv > /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_measurements_31179.csv_sorted
[INFO] [2024-07-17 08:43:35] Converted: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_measurements_31179.csv (13 lines)
[STOP] [2024-07-17 08:43:35] convert_to_csv
[START] [2024-07-17 08:43:35] calculate_delta
[INFO] [2024-07-17 08:43:35] Created diff dir: /app/public/diff
[INFO] [2024-07-17 08:43:35] Looping over 4 formats...
[INFO] [2024-07-17 08:43:35] ...refs (/app/public/data/faubel_kolasa_fa/references.txt)
[CMD] [2024-07-17 08:43:37] echo "0a" > /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_refs_31177.diff
[CMD] [2024-07-17 08:43:37] tail -n +1 /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_refs_31177.csv >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_refs_31177.diff
[CMD] [2024-07-17 08:43:37] echo "." >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_refs_31177.diff
[INFO] [2024-07-17 08:43:37] Created diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_refs_31177.diff (19 lines)
[INFO] [2024-07-17 08:43:37] ...nodes (/app/public/data/faubel_kolasa_fa/taxa.tsv)
[CMD] [2024-07-17 08:43:37] echo "0a" > /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_nodes_31176.diff
[CMD] [2024-07-17 08:43:37] tail -n +1 /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_nodes_31176.csv >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_nodes_31176.diff
[CMD] [2024-07-17 08:43:37] echo "." >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_nodes_31176.diff
[INFO] [2024-07-17 08:43:37] Created diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_nodes_31176.diff (15 lines)
[INFO] [2024-07-17 08:43:37] ...occurrences (/app/public/data/faubel_kolasa_fa/occurrences.tsv)
[CMD] [2024-07-17 08:43:37] echo "0a" > /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_occurrences_31178.diff
[CMD] [2024-07-17 08:43:37] tail -n +1 /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_occurrences_31178.csv >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_occurrences_31178.diff
[CMD] [2024-07-17 08:43:37] echo "." >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_occurrences_31178.diff
[INFO] [2024-07-17 08:43:37] Created diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_occurrences_31178.diff (15 lines)
[INFO] [2024-07-17 08:43:37] ...measurements (/app/public/data/faubel_kolasa_fa/measurementOrFact.tsv)
[CMD] [2024-07-17 08:43:37] echo "0a" > /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_measurements_31179.diff
[CMD] [2024-07-17 08:43:37] tail -n +1 /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_measurements_31179.csv >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_measurements_31179.diff
[CMD] [2024-07-17 08:43:37] echo "." >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_measurements_31179.diff
[INFO] [2024-07-17 08:43:37] Created diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_measurements_31179.diff (15 lines)
[STOP] [2024-07-17 08:43:37] calculate_delta
[START] [2024-07-17 08:43:37] parse_diff_and_store
[INFO] [2024-07-17 08:43:37] Handling diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_refs_31177.diff (19 lines)
[INFO] [2024-07-17 08:43:37] Loading refs diff file into memory (19 lines)...
[INFO] [2024-07-17 08:43:37] Storing 17 References (17/17/19)
[INFO] [2024-07-17 08:43:38] Handling diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_nodes_31176.diff (15 lines)
[INFO] [2024-07-17 08:43:38] Loading nodes diff file into memory (15 lines)...
[INFO] [2024-07-17 08:43:38] Storing 13 ScientificNames (26/13/15)
[INFO] [2024-07-17 08:43:38] Storing 13 Nodes (26/13/15)
[INFO] [2024-07-17 08:43:38] Handling diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_occurrences_31178.diff (15 lines)
[INFO] [2024-07-17 08:43:38] Loading occurrences diff file into memory (15 lines)...
[INFO] [2024-07-17 08:43:38] Storing 13 Occurrences (13/13/15)
[INFO] [2024-07-17 08:43:38] Handling diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_measurements_31179.diff (15 lines)
[INFO] [2024-07-17 08:43:38] Loading measurements diff file into memory (15 lines)...
[INFO] [2024-07-17 08:43:39] Storing 13 Traits (59/13/15)
[INFO] [2024-07-17 08:43:39] Storing 13 MetaTraits (59/13/15)
[INFO] [2024-07-17 08:43:39] Storing 33 TraitsReferences (59/13/15)
[STOP] [2024-07-17 08:43:39] parse_diff_and_store
[START] [2024-07-17 08:43:39] resolve_keys
[2024-07-17 08:43:39] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2024-07-17 08:43:53] Occurrences to nodes (through scientific_names)...
[INFO] [2024-07-17 08:43:53] traits to occurrences...
[INFO] [2024-07-17 08:43:53] traits to nodes (through occurrences)...
[INFO] [2024-07-17 08:43:53] Traits to sex term...
[INFO] [2024-07-17 08:43:53] Traits to lifestage term...
[INFO] [2024-07-17 08:43:53] MetaTraits to traits...
[INFO] [2024-07-17 08:43:53] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2024-07-17 08:43:53] Assocs to occurrences...
[INFO] [2024-07-17 08:43:53] Assocs to nodes...
[INFO] [2024-07-17 08:43:53] Assoc to sex term...
[INFO] [2024-07-17 08:43:53] Assoc to lifestage term...
[INFO] [2024-07-17 08:43:53] MetaAssoc to assocs...
[STOP] [2024-07-17 08:43:53] resolve_keys
[START] [2024-07-17 08:43:53] hold_for_later_1
[STOP] [2024-07-17 08:43:53] hold_for_later_1
[START] [2024-07-17 08:43:53] hold_for_later_2
[STOP] [2024-07-17 08:43:53] hold_for_later_2
[START] [2024-07-17 08:43:53] resolve_missing_parents
[STOP] [2024-07-17 08:43:53] resolve_missing_parents
[START] [2024-07-17 08:43:53] rebuild_nodes
[START] [2024-07-17 08:43:53] Flattener#flatten
[START] [2024-07-17 08:43:53] Flattener#study_resource
[START] [2024-07-17 08:43:53] Flattener#build_ancestry
[STOP] [2024-07-17 08:43:53] Flattener#build_ancestry
[INFO] [2024-07-17 08:43:53] 13 ancestry keys
[START] [2024-07-17 08:43:53] build_node_ancestors
[INFO] [2024-07-17 08:43:53] old ancestors deleted.
[STOP] [2024-07-17 08:43:53] build_node_ancestors
[WARN] [2024-07-17 08:43:53] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2024-07-17 08:43:53] Flattener#flatten
[STOP] [2024-07-17 08:43:53] rebuild_nodes
[START] [2024-07-17 08:43:53] resolve_missing_media_owners
[STOP] [2024-07-17 08:43:53] resolve_missing_media_owners
[START] [2024-07-17 08:43:53] sanitize_media_verbatims
[STOP] [2024-07-17 08:43:53] sanitize_media_verbatims
[START] [2024-07-17 08:43:53] queue_downloads
[STOP] [2024-07-17 08:43:53] queue_downloads
[START] [2024-07-17 08:43:53] parse_names
[WARN] [2024-07-17 08:43:53] I see 13 names which still need to be parsed.
[WARN] [2024-07-17 08:43:58] Names to parse: 13 formatted: 13 learned: 13 parsed: 13
[STOP] [2024-07-17 08:43:59] parse_names
[START] [2024-07-17 08:43:59] denormalize_canonical_names_to_nodes
[STOP] [2024-07-17 08:43:59] denormalize_canonical_names_to_nodes
[START] [2024-07-17 08:43:59] match_nodes
[START] [2024-07-17 08:43:59] map_all_nodes_to_pages
[STOP] [2024-07-17 08:44:15] map_all_nodes_to_pages
[INFO] [2024-07-17 08:44:15] Unmatched nodes (2 of 13): Canonical: Parviplana californica; Node#159688896; ResourceID: Parviplana californica; Canonical: Stulochoplana challengeri; Node#159688901; ResourceID: Stulochoplana challengeri
[START] [2024-07-17 08:44:15] update_nodes
[STOP] [2024-07-17 08:44:15] update_nodes
[STOP] [2024-07-17 08:44:15] match_nodes
[START] [2024-07-17 08:44:15] reindex_search
[STOP] [2024-07-17 08:44:17] reindex_search
[START] [2024-07-17 08:44:17] normalize_units
[STOP] [2024-07-17 08:44:17] normalize_units
[START] [2024-07-17 08:44:17] calculate_statistics
[2024-07-17 08:44:17] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2024-07-17 08:44:18] Duplicate page_id count: 0
[STOP] [2024-07-17 08:44:18] calculate_statistics
[START] [2024-07-17 08:44:18] complete_harvest_instance
[START] [2024-07-17 08:44:18] overall_tsv_creation
[INFO] [2024-07-17 08:44:18] Exporting 13 nodes as TSV in batches of 10000...
[INFO] [2024-07-17 08:44:18] Processing group of 13 in 1 batches of 10000
[INFO] [2024-07-17 08:44:18] 13 Traits (unfiltered) and 0 associations...
[INFO] [2024-07-17 08:44:18] Building Traits map for 13 nodes (this can take a while)...
[INFO] [2024-07-17 08:44:18] Mapped 13 traits (13 meta) for 13 nodes.
[INFO] [2024-07-17 08:44:18] Building Associations map (this can take a while)...
[INFO] [2024-07-17 08:44:18] Done. 0 assocs mapped (0 meta).
[INFO] [2024-07-17 08:44:18] Adding 13 traits...
[INFO] [2024-07-17 08:44:18] 33 metadata added.
[INFO] [2024-07-17 08:44:18] Adding 0 assocs...
[INFO] [2024-07-17 08:44:18] 0 metadata added.
[INFO] [2024-07-17 08:46:20] Processed 13/13 nodes
[INFO] [2024-07-17 08:46:20] Average Time: 121.71
[INFO] [2024-07-17 08:46:20] Total Time: 2m2s
[STOP] [2024-07-17 08:46:20] overall_tsv_creation
[INFO] [2024-07-17 08:46:20] Done. Check your files:
[INFO] [2024-07-17 08:46:20] (13 lines) /app/public/data/faubel_kolasa_fa/publish_nodes.tsv
[INFO] [2024-07-17 08:46:20] (13 lines) /app/public/data/faubel_kolasa_fa/publish_scientific_names.tsv
[INFO] [2024-07-17 08:46:20] (14 lines) /app/public/data/faubel_kolasa_fa/publish_traits.tsv
[INFO] [2024-07-17 08:46:20] (34 lines) /app/public/data/faubel_kolasa_fa/publish_metadata.tsv
[STOP] [2024-07-17 08:46:20] complete_harvest_instance
[START] [2024-07-17 08:46:20] completed
[STOP] [2024-07-17 08:46:20] completed
[STOP] [2024-07-17 08:46:20] logged process, took 165.62
Latest Process

17 Jul 08:43 EXITED currently processing 0