Harvest for Kanzaki et al, 2017 Created 31 Jan 12:38

Harvesting Log

[INFO] [2023-01-31 12:38:57] Created harvest instance #4292
[STOP] [2023-01-31 12:38:57] create_harvest_instance
[START] [2023-01-31 12:38:57] fetch_files
[STOP] [2023-01-31 12:38:57] fetch_files
[START] [2023-01-31 12:38:57] validate_each_file
[INFO] [2023-01-31 12:38:57] Looping over 3 formats...
[INFO] [2023-01-31 12:38:57] ...nodes (/app/public/data/kanzaki_et_al_ka/taxa.tsv)
[INFO] [2023-01-31 12:38:57] Valid: /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_nodes_30179.csv (1 lines)
[INFO] [2023-01-31 12:38:57] ...occurrences (/app/public/data/kanzaki_et_al_ka/occurrences.tsv)
[INFO] [2023-01-31 12:38:57] Valid: /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_occurrences_30180.csv (1 lines)
[INFO] [2023-01-31 12:38:57] ...measurements (/app/public/data/kanzaki_et_al_ka/measurementOrFact.tsv)
[INFO] [2023-01-31 12:38:57] Valid: /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_measurements_30181.csv (2 lines)
[STOP] [2023-01-31 12:38:57] validate_each_file
[START] [2023-01-31 12:38:57] convert_to_csv
[INFO] [2023-01-31 12:38:57] Looping over 3 formats...
[INFO] [2023-01-31 12:38:57] ...nodes (/app/public/data/kanzaki_et_al_ka/taxa.tsv)
[CMD] [2023-01-31 12:38:57] /usr/bin/sort /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_nodes_30179.csv > /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_nodes_30179.csv_sorted
[INFO] [2023-01-31 12:38:57] Converted: /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_nodes_30179.csv (1 lines)
[INFO] [2023-01-31 12:38:57] ...occurrences (/app/public/data/kanzaki_et_al_ka/occurrences.tsv)
[CMD] [2023-01-31 12:38:57] /usr/bin/sort /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_occurrences_30180.csv > /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_occurrences_30180.csv_sorted
[INFO] [2023-01-31 12:38:57] Converted: /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_occurrences_30180.csv (1 lines)
[INFO] [2023-01-31 12:38:57] ...measurements (/app/public/data/kanzaki_et_al_ka/measurementOrFact.tsv)
[CMD] [2023-01-31 12:38:57] /usr/bin/sort /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_measurements_30181.csv > /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_measurements_30181.csv_sorted
[INFO] [2023-01-31 12:38:57] Converted: /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_measurements_30181.csv (2 lines)
[STOP] [2023-01-31 12:38:57] convert_to_csv
[START] [2023-01-31 12:38:57] calculate_delta
[INFO] [2023-01-31 12:38:57] Looping over 3 formats...
[INFO] [2023-01-31 12:38:57] ...nodes (/app/public/data/kanzaki_et_al_ka/taxa.tsv)
[CMD] [2023-01-31 12:38:58] echo "0a" > /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_nodes_30179.diff
[CMD] [2023-01-31 12:38:58] tail -n +1 /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_nodes_30179.csv >> /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_nodes_30179.diff
[CMD] [2023-01-31 12:38:58] echo "." >> /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_nodes_30179.diff
[INFO] [2023-01-31 12:38:58] Created diff: /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_nodes_30179.diff (3 lines)
[INFO] [2023-01-31 12:38:58] ...occurrences (/app/public/data/kanzaki_et_al_ka/occurrences.tsv)
[CMD] [2023-01-31 12:38:58] echo "0a" > /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_occurrences_30180.diff
[CMD] [2023-01-31 12:38:58] tail -n +1 /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_occurrences_30180.csv >> /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_occurrences_30180.diff
[CMD] [2023-01-31 12:38:58] echo "." >> /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_occurrences_30180.diff
[INFO] [2023-01-31 12:38:58] Created diff: /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_occurrences_30180.diff (3 lines)
[INFO] [2023-01-31 12:38:58] ...measurements (/app/public/data/kanzaki_et_al_ka/measurementOrFact.tsv)
[CMD] [2023-01-31 12:38:58] echo "0a" > /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_measurements_30181.diff
[CMD] [2023-01-31 12:38:58] tail -n +1 /app/public/data/kanzaki_et_al_ka/converted_csv/kanzaki_et_al_ka_measurements_30181.csv >> /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_measurements_30181.diff
[CMD] [2023-01-31 12:38:58] echo "." >> /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_measurements_30181.diff
[INFO] [2023-01-31 12:38:58] Created diff: /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_measurements_30181.diff (4 lines)
[STOP] [2023-01-31 12:38:58] calculate_delta
[START] [2023-01-31 12:38:58] parse_diff_and_store
[INFO] [2023-01-31 12:38:58] Handling diff: /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_nodes_30179.diff (3 lines)
[INFO] [2023-01-31 12:38:58] Loading nodes diff file into memory (3 lines)...
[INFO] [2023-01-31 12:38:58] Storing 1 ScientificNames (2/1/3)
[INFO] [2023-01-31 12:38:58] Storing 1 Nodes (2/1/3)
[INFO] [2023-01-31 12:38:58] Handling diff: /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_occurrences_30180.diff (3 lines)
[INFO] [2023-01-31 12:38:58] Loading occurrences diff file into memory (3 lines)...
[INFO] [2023-01-31 12:38:58] Storing 1 Occurrences (1/1/3)
[INFO] [2023-01-31 12:38:58] Handling diff: /app/public/data/kanzaki_et_al_ka/diff/kanzaki_et_al_ka_measurements_30181.diff (4 lines)
[INFO] [2023-01-31 12:38:58] Loading measurements diff file into memory (4 lines)...
[INFO] [2023-01-31 12:38:58] Storing 2 Traits (3/2/4)
[INFO] [2023-01-31 12:38:58] Storing 1 MetaTraits (3/2/4)
[STOP] [2023-01-31 12:38:58] parse_diff_and_store
[START] [2023-01-31 12:38:58] resolve_keys
[2023-01-31 12:38:58] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-31 12:39:06] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-31 12:39:06] traits to occurrences...
[INFO] [2023-01-31 12:39:06] traits to nodes (through occurrences)...
[INFO] [2023-01-31 12:39:06] Traits to sex term...
[INFO] [2023-01-31 12:39:06] Traits to lifestage term...
[INFO] [2023-01-31 12:39:06] MetaTraits to traits...
[INFO] [2023-01-31 12:39:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-31 12:39:06] Assocs to occurrences...
[INFO] [2023-01-31 12:39:06] Assocs to nodes...
[INFO] [2023-01-31 12:39:06] Assoc to sex term...
[INFO] [2023-01-31 12:39:06] Assoc to lifestage term...
[INFO] [2023-01-31 12:39:06] MetaAssoc to assocs...
[STOP] [2023-01-31 12:39:06] resolve_keys
[START] [2023-01-31 12:39:06] hold_for_later_1
[STOP] [2023-01-31 12:39:06] hold_for_later_1
[START] [2023-01-31 12:39:06] hold_for_later_2
[STOP] [2023-01-31 12:39:06] hold_for_later_2
[START] [2023-01-31 12:39:06] resolve_missing_parents
[STOP] [2023-01-31 12:39:06] resolve_missing_parents
[START] [2023-01-31 12:39:06] rebuild_nodes
[START] [2023-01-31 12:39:06] Flattener#flatten
[START] [2023-01-31 12:39:06] Flattener#study_resource
[START] [2023-01-31 12:39:06] Flattener#build_ancestry
[STOP] [2023-01-31 12:39:06] Flattener#build_ancestry
[INFO] [2023-01-31 12:39:06] 1 ancestry keys
[START] [2023-01-31 12:39:06] build_node_ancestors
[INFO] [2023-01-31 12:39:06] old ancestors deleted.
[STOP] [2023-01-31 12:39:06] build_node_ancestors
[WARN] [2023-01-31 12:39:06] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-31 12:39:06] Flattener#flatten
[STOP] [2023-01-31 12:39:06] rebuild_nodes
[START] [2023-01-31 12:39:06] resolve_missing_media_owners
[STOP] [2023-01-31 12:39:06] resolve_missing_media_owners
[START] [2023-01-31 12:39:06] sanitize_media_verbatims
[STOP] [2023-01-31 12:39:06] sanitize_media_verbatims
[START] [2023-01-31 12:39:06] queue_downloads
[STOP] [2023-01-31 12:39:06] queue_downloads
[START] [2023-01-31 12:39:06] parse_names
[WARN] [2023-01-31 12:39:06] I see 1 names which still need to be parsed.
[WARN] [2023-01-31 12:39:06] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2023-01-31 12:39:07] parse_names
[START] [2023-01-31 12:39:07] denormalize_canonical_names_to_nodes
[STOP] [2023-01-31 12:39:07] denormalize_canonical_names_to_nodes
[START] [2023-01-31 12:39:07] match_nodes
[START] [2023-01-31 12:39:07] map_all_nodes_to_pages
[STOP] [2023-01-31 12:39:07] map_all_nodes_to_pages
[INFO] [2023-01-31 12:39:07] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2023-01-31 12:39:07] update_nodes
[STOP] [2023-01-31 12:39:07] update_nodes
[STOP] [2023-01-31 12:39:07] match_nodes
[START] [2023-01-31 12:39:07] reindex_search
[STOP] [2023-01-31 12:39:07] reindex_search
[START] [2023-01-31 12:39:07] normalize_units
[STOP] [2023-01-31 12:39:07] normalize_units
[START] [2023-01-31 12:39:07] calculate_statistics
[2023-01-31 12:39:07] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-31 12:39:07] Duplicate page_id count: 0
[STOP] [2023-01-31 12:39:07] calculate_statistics
[START] [2023-01-31 12:39:07] complete_harvest_instance
[START] [2023-01-31 12:39:07] overall_tsv_creation
[INFO] [2023-01-31 12:39:07] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2023-01-31 12:39:07] Processing group of 1 in 1 batches of 10000
[INFO] [2023-01-31 12:39:07] 1 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-31 12:39:07] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2023-01-31 12:39:07] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2023-01-31 12:39:07] Building Associations map (this can take a while)...
[INFO] [2023-01-31 12:39:07] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-31 12:39:07] Adding 1 traits...
[INFO] [2023-01-31 12:39:07] 1 metadata added.
[INFO] [2023-01-31 12:39:07] Adding 0 assocs...
[INFO] [2023-01-31 12:39:07] 0 metadata added.
[INFO] [2023-01-31 12:39:52] Processed 1/1 nodes
[INFO] [2023-01-31 12:39:52] Average Time: 44.87
[INFO] [2023-01-31 12:39:52] Total Time: 45s
[STOP] [2023-01-31 12:39:52] overall_tsv_creation
[INFO] [2023-01-31 12:39:52] Done. Check your files:
[INFO] [2023-01-31 12:39:52] (1 lines) /app/public/data/kanzaki_et_al_ka/publish_nodes.tsv
[INFO] [2023-01-31 12:39:52] (1 lines) /app/public/data/kanzaki_et_al_ka/publish_scientific_names.tsv
[INFO] [2023-01-31 12:39:52] (2 lines) /app/public/data/kanzaki_et_al_ka/publish_traits.tsv
[INFO] [2023-01-31 12:39:52] (2 lines) /app/public/data/kanzaki_et_al_ka/publish_metadata.tsv
[STOP] [2023-01-31 12:39:52] complete_harvest_instance
[START] [2023-01-31 12:39:52] completed
[STOP] [2023-01-31 12:39:52] completed
[STOP] [2023-01-31 12:39:52] logged process, took 55.47

Latest Process

31 Jan 12:38 EXITED currently processing 0