Harvest for Faubel and Kolasa 1978 Created 13 Oct 09:25

Harvesting Log

[INFO] [2023-10-13 09:25:53] Created harvest instance #4420
[STOP] [2023-10-13 09:25:53] create_harvest_instance
[START] [2023-10-13 09:25:53] fetch_files
[STOP] [2023-10-13 09:25:53] fetch_files
[START] [2023-10-13 09:25:53] validate_each_file
[INFO] [2023-10-13 09:25:53] Looping over 4 formats...
[INFO] [2023-10-13 09:25:53] ...refs (/app/public/data/faubel_kolasa_fa/references.txt)
[INFO] [2023-10-13 09:25:53] Valid: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_refs_30630.csv (17 lines)
[INFO] [2023-10-13 09:25:53] ...nodes (/app/public/data/faubel_kolasa_fa/taxa.tsv)
[INFO] [2023-10-13 09:25:53] Valid: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_nodes_30629.csv (12 lines)
[INFO] [2023-10-13 09:25:53] ...occurrences (/app/public/data/faubel_kolasa_fa/occurrences.tsv)
[INFO] [2023-10-13 09:25:53] Valid: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_occurrences_30631.csv (12 lines)
[INFO] [2023-10-13 09:25:53] ...measurements (/app/public/data/faubel_kolasa_fa/measurementOrFact.tsv)
[INFO] [2023-10-13 09:25:53] Valid: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_measurements_30632.csv (13 lines)
[STOP] [2023-10-13 09:25:53] validate_each_file
[START] [2023-10-13 09:25:53] convert_to_csv
[INFO] [2023-10-13 09:25:53] Looping over 4 formats...
[INFO] [2023-10-13 09:25:53] ...refs (/app/public/data/faubel_kolasa_fa/references.txt)
[CMD] [2023-10-13 09:25:53] /usr/bin/sort /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_refs_30630.csv > /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_refs_30630.csv_sorted
[INFO] [2023-10-13 09:25:54] Converted: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_refs_30630.csv (17 lines)
[INFO] [2023-10-13 09:25:54] ...nodes (/app/public/data/faubel_kolasa_fa/taxa.tsv)
[CMD] [2023-10-13 09:25:54] /usr/bin/sort /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_nodes_30629.csv > /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_nodes_30629.csv_sorted
[INFO] [2023-10-13 09:25:54] Converted: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_nodes_30629.csv (12 lines)
[INFO] [2023-10-13 09:25:54] ...occurrences (/app/public/data/faubel_kolasa_fa/occurrences.tsv)
[CMD] [2023-10-13 09:25:54] /usr/bin/sort /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_occurrences_30631.csv > /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_occurrences_30631.csv_sorted
[INFO] [2023-10-13 09:25:54] Converted: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_occurrences_30631.csv (12 lines)
[INFO] [2023-10-13 09:25:54] ...measurements (/app/public/data/faubel_kolasa_fa/measurementOrFact.tsv)
[CMD] [2023-10-13 09:25:54] /usr/bin/sort /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_measurements_30632.csv > /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_measurements_30632.csv_sorted
[INFO] [2023-10-13 09:25:54] Converted: /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_measurements_30632.csv (13 lines)
[STOP] [2023-10-13 09:25:54] convert_to_csv
[START] [2023-10-13 09:25:54] calculate_delta
[INFO] [2023-10-13 09:25:54] Looping over 4 formats...
[INFO] [2023-10-13 09:25:54] ...refs (/app/public/data/faubel_kolasa_fa/references.txt)
[CMD] [2023-10-13 09:25:54] echo "0a" > /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_refs_30630.diff
[CMD] [2023-10-13 09:25:55] tail -n +1 /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_refs_30630.csv >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_refs_30630.diff
[CMD] [2023-10-13 09:25:55] echo "." >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_refs_30630.diff
[INFO] [2023-10-13 09:25:55] Created diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_refs_30630.diff (19 lines)
[INFO] [2023-10-13 09:25:55] ...nodes (/app/public/data/faubel_kolasa_fa/taxa.tsv)
[CMD] [2023-10-13 09:25:55] echo "0a" > /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_nodes_30629.diff
[CMD] [2023-10-13 09:25:55] tail -n +1 /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_nodes_30629.csv >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_nodes_30629.diff
[CMD] [2023-10-13 09:25:55] echo "." >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_nodes_30629.diff
[INFO] [2023-10-13 09:25:55] Created diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_nodes_30629.diff (14 lines)
[INFO] [2023-10-13 09:25:55] ...occurrences (/app/public/data/faubel_kolasa_fa/occurrences.tsv)
[CMD] [2023-10-13 09:25:55] echo "0a" > /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_occurrences_30631.diff
[CMD] [2023-10-13 09:25:55] tail -n +1 /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_occurrences_30631.csv >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_occurrences_30631.diff
[CMD] [2023-10-13 09:25:55] echo "." >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_occurrences_30631.diff
[INFO] [2023-10-13 09:25:55] Created diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_occurrences_30631.diff (14 lines)
[INFO] [2023-10-13 09:25:55] ...measurements (/app/public/data/faubel_kolasa_fa/measurementOrFact.tsv)
[CMD] [2023-10-13 09:25:55] echo "0a" > /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_measurements_30632.diff
[CMD] [2023-10-13 09:25:55] tail -n +1 /app/public/data/faubel_kolasa_fa/converted_csv/faubel_kolasa_fa_measurements_30632.csv >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_measurements_30632.diff
[CMD] [2023-10-13 09:25:56] echo "." >> /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_measurements_30632.diff
[INFO] [2023-10-13 09:25:56] Created diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_measurements_30632.diff (15 lines)
[STOP] [2023-10-13 09:25:56] calculate_delta
[START] [2023-10-13 09:25:56] parse_diff_and_store
[INFO] [2023-10-13 09:25:56] Handling diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_refs_30630.diff (19 lines)
[INFO] [2023-10-13 09:25:56] Loading refs diff file into memory (19 lines)...
[INFO] [2023-10-13 09:25:56] Storing 17 References (17/17/19)
[INFO] [2023-10-13 09:25:56] Handling diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_nodes_30629.diff (14 lines)
[INFO] [2023-10-13 09:25:56] Loading nodes diff file into memory (14 lines)...
[INFO] [2023-10-13 09:25:56] Storing 12 ScientificNames (24/12/14)
[INFO] [2023-10-13 09:25:56] Storing 12 Nodes (24/12/14)
[INFO] [2023-10-13 09:25:56] Handling diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_occurrences_30631.diff (14 lines)
[INFO] [2023-10-13 09:25:56] Loading occurrences diff file into memory (14 lines)...
[INFO] [2023-10-13 09:25:56] Storing 12 Occurrences (12/12/14)
[INFO] [2023-10-13 09:25:56] Handling diff: /app/public/data/faubel_kolasa_fa/diff/faubel_kolasa_fa_measurements_30632.diff (15 lines)
[INFO] [2023-10-13 09:25:56] Loading measurements diff file into memory (15 lines)...
[INFO] [2023-10-13 09:25:56] Storing 13 Traits (59/13/15)
[INFO] [2023-10-13 09:25:56] Storing 13 MetaTraits (59/13/15)
[INFO] [2023-10-13 09:25:56] Storing 33 TraitsReferences (59/13/15)
[STOP] [2023-10-13 09:25:56] parse_diff_and_store
[START] [2023-10-13 09:25:56] resolve_keys
[2023-10-13 09:25:56] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 09:26:04] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 09:26:04] traits to occurrences...
[INFO] [2023-10-13 09:26:04] traits to nodes (through occurrences)...
[INFO] [2023-10-13 09:26:04] Traits to sex term...
[INFO] [2023-10-13 09:26:04] Traits to lifestage term...
[INFO] [2023-10-13 09:26:04] MetaTraits to traits...
[INFO] [2023-10-13 09:26:04] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 09:26:04] Assocs to occurrences...
[INFO] [2023-10-13 09:26:04] Assocs to nodes...
[INFO] [2023-10-13 09:26:04] Assoc to sex term...
[INFO] [2023-10-13 09:26:04] Assoc to lifestage term...
[INFO] [2023-10-13 09:26:04] MetaAssoc to assocs...
[STOP] [2023-10-13 09:26:04] resolve_keys
[START] [2023-10-13 09:26:04] hold_for_later_1
[STOP] [2023-10-13 09:26:04] hold_for_later_1
[START] [2023-10-13 09:26:04] hold_for_later_2
[STOP] [2023-10-13 09:26:04] hold_for_later_2
[START] [2023-10-13 09:26:04] resolve_missing_parents
[STOP] [2023-10-13 09:26:04] resolve_missing_parents
[START] [2023-10-13 09:26:04] rebuild_nodes
[START] [2023-10-13 09:26:04] Flattener#flatten
[START] [2023-10-13 09:26:04] Flattener#study_resource
[START] [2023-10-13 09:26:04] Flattener#build_ancestry
[STOP] [2023-10-13 09:26:04] Flattener#build_ancestry
[INFO] [2023-10-13 09:26:04] 12 ancestry keys
[START] [2023-10-13 09:26:04] build_node_ancestors
[INFO] [2023-10-13 09:26:04] old ancestors deleted.
[STOP] [2023-10-13 09:26:04] build_node_ancestors
[WARN] [2023-10-13 09:26:04] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 09:26:04] Flattener#flatten
[STOP] [2023-10-13 09:26:04] rebuild_nodes
[START] [2023-10-13 09:26:04] resolve_missing_media_owners
[STOP] [2023-10-13 09:26:04] resolve_missing_media_owners
[START] [2023-10-13 09:26:04] sanitize_media_verbatims
[STOP] [2023-10-13 09:26:04] sanitize_media_verbatims
[START] [2023-10-13 09:26:04] queue_downloads
[STOP] [2023-10-13 09:26:04] queue_downloads
[START] [2023-10-13 09:26:04] parse_names
[WARN] [2023-10-13 09:26:04] I see 12 names which still need to be parsed.
[WARN] [2023-10-13 09:26:04] Names to parse: 12 formatted: 12 learned: 12 parsed: 12
[STOP] [2023-10-13 09:26:05] parse_names
[START] [2023-10-13 09:26:05] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 09:26:05] denormalize_canonical_names_to_nodes
[START] [2023-10-13 09:26:05] match_nodes
[START] [2023-10-13 09:26:05] map_all_nodes_to_pages
[STOP] [2023-10-13 09:26:05] map_all_nodes_to_pages
[INFO] [2023-10-13 09:26:05] Unmatched nodes (2 of 12): Canonical: Parviplana californica; Node#136983460; ResourceID: Parviplana californica; Canonical: Stulochoplana challengeri; Node#136983465; ResourceID: Stulochoplana challengeri
[START] [2023-10-13 09:26:05] update_nodes
[STOP] [2023-10-13 09:26:05] update_nodes
[STOP] [2023-10-13 09:26:05] match_nodes
[START] [2023-10-13 09:26:05] reindex_search
[STOP] [2023-10-13 09:26:05] reindex_search
[START] [2023-10-13 09:26:05] normalize_units
[STOP] [2023-10-13 09:26:05] normalize_units
[START] [2023-10-13 09:26:05] calculate_statistics
[2023-10-13 09:26:05] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 09:26:05] Duplicate page_id count: 0
[STOP] [2023-10-13 09:26:05] calculate_statistics
[START] [2023-10-13 09:26:05] complete_harvest_instance
[START] [2023-10-13 09:26:05] overall_tsv_creation
[INFO] [2023-10-13 09:26:05] Exporting 12 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 09:26:05] Processing group of 12 in 1 batches of 10000
[INFO] [2023-10-13 09:26:05] 12 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 09:26:05] Building Traits map for 12 nodes (this can take a while)...
[INFO] [2023-10-13 09:26:05] Mapped 12 traits (12 meta) for 12 nodes.
[INFO] [2023-10-13 09:26:05] Building Associations map (this can take a while)...
[INFO] [2023-10-13 09:26:05] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 09:26:05] Adding 12 traits...
[INFO] [2023-10-13 09:26:05] 33 metadata added.
[INFO] [2023-10-13 09:26:05] Adding 0 assocs...
[INFO] [2023-10-13 09:26:05] 0 metadata added.
[INFO] [2023-10-13 09:26:50] Processed 12/12 nodes
[INFO] [2023-10-13 09:26:50] Average Time: 44.98
[INFO] [2023-10-13 09:26:50] Total Time: 46s
[STOP] [2023-10-13 09:26:50] overall_tsv_creation
[INFO] [2023-10-13 09:26:50] Done. Check your files:
[INFO] [2023-10-13 09:26:50] (12 lines) /app/public/data/faubel_kolasa_fa/publish_nodes.tsv
[INFO] [2023-10-13 09:26:50] (12 lines) /app/public/data/faubel_kolasa_fa/publish_scientific_names.tsv
[INFO] [2023-10-13 09:26:51] (13 lines) /app/public/data/faubel_kolasa_fa/publish_traits.tsv
[INFO] [2023-10-13 09:26:51] (34 lines) /app/public/data/faubel_kolasa_fa/publish_metadata.tsv
[STOP] [2023-10-13 09:26:51] complete_harvest_instance
[START] [2023-10-13 09:26:51] completed
[STOP] [2023-10-13 09:26:51] completed
[STOP] [2023-10-13 09:26:51] logged process, took 57.37

Latest Process

13 Oct 09:25 EXITED currently processing 0