Harvest for Panganiban et al 1997 Created 03 Aug 16:35

Stage: completed
Fetched: 03 Aug 16:35
Validated: 03 Aug 16:35
Deltas Created 03 Aug 16:35
Units Normalized: 03 Aug 16:35
Ancestry Built: 03 Aug 16:35
Nodes Matched: 03 Aug 16:35
Names Parsed: 03 Aug 16:35
New Models Stored: 03 Aug 16:35
Indexed: 03 Aug 16:35
Completed: 03 Aug 16:37
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:35:28] Created harvest instance #4174
[STOP] [2022-08-03 16:35:28] create_harvest_instance
[START] [2022-08-03 16:35:28] fetch_files
[STOP] [2022-08-03 16:35:28] fetch_files
[START] [2022-08-03 16:35:28] validate_each_file
[INFO] [2022-08-03 16:35:28] Looping over 3 formats...
[INFO] [2022-08-03 16:35:28] ...nodes (/app/public/data/panganiban_et_al/taxa.txt)
[INFO] [2022-08-03 16:35:28] Valid: /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_nodes_29585.csv (1 lines)
[INFO] [2022-08-03 16:35:28] ...occurrences (/app/public/data/panganiban_et_al/occurrences.txt)
[INFO] [2022-08-03 16:35:28] Valid: /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_occurrences_29586.csv (1 lines)
[INFO] [2022-08-03 16:35:28] ...measurements (/app/public/data/panganiban_et_al/measurementOrFact.txt)
[INFO] [2022-08-03 16:35:28] Valid: /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_measurements_29587.csv (2 lines)
[STOP] [2022-08-03 16:35:28] validate_each_file
[START] [2022-08-03 16:35:28] convert_to_csv
[INFO] [2022-08-03 16:35:28] Looping over 3 formats...
[INFO] [2022-08-03 16:35:28] ...nodes (/app/public/data/panganiban_et_al/taxa.txt)
[CMD] [2022-08-03 16:35:28] /usr/bin/sort /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_nodes_29585.csv > /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_nodes_29585.csv_sorted
[INFO] [2022-08-03 16:35:28] Converted: /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_nodes_29585.csv (1 lines)
[INFO] [2022-08-03 16:35:28] ...occurrences (/app/public/data/panganiban_et_al/occurrences.txt)
[CMD] [2022-08-03 16:35:28] /usr/bin/sort /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_occurrences_29586.csv > /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_occurrences_29586.csv_sorted
[INFO] [2022-08-03 16:35:28] Converted: /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_occurrences_29586.csv (1 lines)
[INFO] [2022-08-03 16:35:28] ...measurements (/app/public/data/panganiban_et_al/measurementOrFact.txt)
[CMD] [2022-08-03 16:35:28] /usr/bin/sort /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_measurements_29587.csv > /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_measurements_29587.csv_sorted
[INFO] [2022-08-03 16:35:28] Converted: /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_measurements_29587.csv (2 lines)
[STOP] [2022-08-03 16:35:28] convert_to_csv
[START] [2022-08-03 16:35:28] calculate_delta
[INFO] [2022-08-03 16:35:28] Looping over 3 formats...
[INFO] [2022-08-03 16:35:28] ...nodes (/app/public/data/panganiban_et_al/taxa.txt)
[CMD] [2022-08-03 16:35:28] echo "0a" > /app/public/data/panganiban_et_al/diff/panganiban_et_al_nodes_29585.diff
[CMD] [2022-08-03 16:35:28] tail -n +1 /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_nodes_29585.csv >> /app/public/data/panganiban_et_al/diff/panganiban_et_al_nodes_29585.diff
[CMD] [2022-08-03 16:35:28] echo "." >> /app/public/data/panganiban_et_al/diff/panganiban_et_al_nodes_29585.diff
[INFO] [2022-08-03 16:35:28] Created diff: /app/public/data/panganiban_et_al/diff/panganiban_et_al_nodes_29585.diff (3 lines)
[INFO] [2022-08-03 16:35:28] ...occurrences (/app/public/data/panganiban_et_al/occurrences.txt)
[CMD] [2022-08-03 16:35:28] echo "0a" > /app/public/data/panganiban_et_al/diff/panganiban_et_al_occurrences_29586.diff
[CMD] [2022-08-03 16:35:28] tail -n +1 /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_occurrences_29586.csv >> /app/public/data/panganiban_et_al/diff/panganiban_et_al_occurrences_29586.diff
[CMD] [2022-08-03 16:35:28] echo "." >> /app/public/data/panganiban_et_al/diff/panganiban_et_al_occurrences_29586.diff
[INFO] [2022-08-03 16:35:29] Created diff: /app/public/data/panganiban_et_al/diff/panganiban_et_al_occurrences_29586.diff (3 lines)
[INFO] [2022-08-03 16:35:29] ...measurements (/app/public/data/panganiban_et_al/measurementOrFact.txt)
[CMD] [2022-08-03 16:35:29] echo "0a" > /app/public/data/panganiban_et_al/diff/panganiban_et_al_measurements_29587.diff
[CMD] [2022-08-03 16:35:29] tail -n +1 /app/public/data/panganiban_et_al/converted_csv/panganiban_et_al_measurements_29587.csv >> /app/public/data/panganiban_et_al/diff/panganiban_et_al_measurements_29587.diff
[CMD] [2022-08-03 16:35:29] echo "." >> /app/public/data/panganiban_et_al/diff/panganiban_et_al_measurements_29587.diff
[INFO] [2022-08-03 16:35:29] Created diff: /app/public/data/panganiban_et_al/diff/panganiban_et_al_measurements_29587.diff (4 lines)
[STOP] [2022-08-03 16:35:29] calculate_delta
[START] [2022-08-03 16:35:29] parse_diff_and_store
[INFO] [2022-08-03 16:35:29] Handling diff: /app/public/data/panganiban_et_al/diff/panganiban_et_al_nodes_29585.diff (3 lines)
[INFO] [2022-08-03 16:35:29] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:35:29] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:35:29] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:35:29] Handling diff: /app/public/data/panganiban_et_al/diff/panganiban_et_al_occurrences_29586.diff (3 lines)
[INFO] [2022-08-03 16:35:29] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:35:29] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:35:29] Handling diff: /app/public/data/panganiban_et_al/diff/panganiban_et_al_measurements_29587.diff (4 lines)
[INFO] [2022-08-03 16:35:29] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 16:35:29] Storing 2 Traits (4/2/4)
[INFO] [2022-08-03 16:35:29] Storing 2 MetaTraits (4/2/4)
[STOP] [2022-08-03 16:35:29] parse_diff_and_store
[START] [2022-08-03 16:35:29] resolve_keys
[2022-08-03 16:35:29] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:35:36] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:35:36] traits to occurrences...
[INFO] [2022-08-03 16:35:36] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:35:36] Traits to sex term...
[INFO] [2022-08-03 16:35:36] Traits to lifestage term...
[INFO] [2022-08-03 16:35:36] MetaTraits to traits...
[INFO] [2022-08-03 16:35:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:35:36] Assocs to occurrences...
[INFO] [2022-08-03 16:35:36] Assocs to nodes...
[INFO] [2022-08-03 16:35:36] Assoc to sex term...
[INFO] [2022-08-03 16:35:36] Assoc to lifestage term...
[INFO] [2022-08-03 16:35:36] MetaAssoc to assocs...
[STOP] [2022-08-03 16:35:36] resolve_keys
[START] [2022-08-03 16:35:36] hold_for_later_1
[STOP] [2022-08-03 16:35:36] hold_for_later_1
[START] [2022-08-03 16:35:36] hold_for_later_2
[STOP] [2022-08-03 16:35:36] hold_for_later_2
[START] [2022-08-03 16:35:36] resolve_missing_parents
[STOP] [2022-08-03 16:35:36] resolve_missing_parents
[START] [2022-08-03 16:35:36] rebuild_nodes
[START] [2022-08-03 16:35:36] Flattener#flatten
[START] [2022-08-03 16:35:36] Flattener#study_resource
[START] [2022-08-03 16:35:36] Flattener#build_ancestry
[STOP] [2022-08-03 16:35:36] Flattener#build_ancestry
[INFO] [2022-08-03 16:35:36] 1 ancestry keys
[START] [2022-08-03 16:35:36] build_node_ancestors
[INFO] [2022-08-03 16:35:36] old ancestors deleted.
[STOP] [2022-08-03 16:35:36] build_node_ancestors
[WARN] [2022-08-03 16:35:36] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:35:36] Flattener#flatten
[STOP] [2022-08-03 16:35:36] rebuild_nodes
[START] [2022-08-03 16:35:36] resolve_missing_media_owners
[STOP] [2022-08-03 16:35:36] resolve_missing_media_owners
[START] [2022-08-03 16:35:36] sanitize_media_verbatims
[STOP] [2022-08-03 16:35:36] sanitize_media_verbatims
[START] [2022-08-03 16:35:36] queue_downloads
[STOP] [2022-08-03 16:35:36] queue_downloads
[START] [2022-08-03 16:35:36] parse_names
[WARN] [2022-08-03 16:35:36] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:35:36] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:35:37] parse_names
[START] [2022-08-03 16:35:37] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:35:37] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:35:37] match_nodes
[START] [2022-08-03 16:35:37] map_all_nodes_to_pages
[STOP] [2022-08-03 16:35:37] map_all_nodes_to_pages
[INFO] [2022-08-03 16:35:37] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:35:37] update_nodes
[STOP] [2022-08-03 16:35:37] update_nodes
[STOP] [2022-08-03 16:35:37] match_nodes
[START] [2022-08-03 16:35:37] reindex_search
[STOP] [2022-08-03 16:35:37] reindex_search
[START] [2022-08-03 16:35:37] normalize_units
[STOP] [2022-08-03 16:35:37] normalize_units
[START] [2022-08-03 16:35:37] calculate_statistics
[2022-08-03 16:35:37] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:35:37] Duplicate page_id count: 0
[STOP] [2022-08-03 16:35:37] calculate_statistics
[START] [2022-08-03 16:35:38] complete_harvest_instance
[START] [2022-08-03 16:35:38] overall_tsv_creation
[INFO] [2022-08-03 16:35:38] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:35:38] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:36:19] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:36:19] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:37:10] Mapped 1 traits (2 meta) for 1 nodes.
[INFO] [2022-08-03 16:37:10] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:37:10] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:37:11] Adding 1 traits...
[INFO] [2022-08-03 16:37:11] 1 metadata added.
[INFO] [2022-08-03 16:37:11] Adding 0 assocs...
[INFO] [2022-08-03 16:37:11] 0 metadata added.
[INFO] [2022-08-03 16:37:53] Processed 1/1 nodes
[INFO] [2022-08-03 16:37:53] Average Time: 110.62
[INFO] [2022-08-03 16:37:53] Total Time: 2m16s
[STOP] [2022-08-03 16:37:53] overall_tsv_creation
[INFO] [2022-08-03 16:37:53] Done. Check your files:
[INFO] [2022-08-03 16:37:53] (1 lines) /app/public/data/panganiban_et_al/publish_nodes.tsv
[INFO] [2022-08-03 16:37:53] (1 lines) /app/public/data/panganiban_et_al/publish_scientific_names.tsv
[INFO] [2022-08-03 16:37:53] (2 lines) /app/public/data/panganiban_et_al/publish_traits.tsv
[INFO] [2022-08-03 16:37:53] (2 lines) /app/public/data/panganiban_et_al/publish_metadata.tsv
[STOP] [2022-08-03 16:37:53] complete_harvest_instance
[START] [2022-08-03 16:37:53] completed
[STOP] [2022-08-03 16:37:53] completed
[STOP] [2022-08-03 16:37:53] logged process, took 144.92
Latest Process

03 Aug 16:35 EXITED currently processing 0