Harvest for Namigai et al 2014 Created 03 Aug 17:23

Harvesting Log

[INFO] [2022-08-03 17:23:05] Created harvest instance #4197
[STOP] [2022-08-03 17:23:05] create_harvest_instance
[START] [2022-08-03 17:23:05] fetch_files
[STOP] [2022-08-03 17:23:05] fetch_files
[START] [2022-08-03 17:23:05] validate_each_file
[INFO] [2022-08-03 17:23:05] Looping over 3 formats...
[INFO] [2022-08-03 17:23:05] ...nodes (/app/public/data/namigai_et_al_na/taxa.txt)
[INFO] [2022-08-03 17:23:05] Valid: /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_nodes_29653.csv (21 lines)
[INFO] [2022-08-03 17:23:05] ...occurrences (/app/public/data/namigai_et_al_na/occurrences.txt)
[INFO] [2022-08-03 17:23:05] Valid: /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_occurrences_29654.csv (21 lines)
[INFO] [2022-08-03 17:23:05] ...measurements (/app/public/data/namigai_et_al_na/measurementOrFact.txt)
[INFO] [2022-08-03 17:23:05] Valid: /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_measurements_29655.csv (134 lines)
[STOP] [2022-08-03 17:23:05] validate_each_file
[START] [2022-08-03 17:23:05] convert_to_csv
[INFO] [2022-08-03 17:23:05] Looping over 3 formats...
[INFO] [2022-08-03 17:23:05] ...nodes (/app/public/data/namigai_et_al_na/taxa.txt)
[CMD] [2022-08-03 17:23:05] /usr/bin/sort /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_nodes_29653.csv > /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_nodes_29653.csv_sorted
[INFO] [2022-08-03 17:23:05] Converted: /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_nodes_29653.csv (21 lines)
[INFO] [2022-08-03 17:23:05] ...occurrences (/app/public/data/namigai_et_al_na/occurrences.txt)
[CMD] [2022-08-03 17:23:05] /usr/bin/sort /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_occurrences_29654.csv > /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_occurrences_29654.csv_sorted
[INFO] [2022-08-03 17:23:05] Converted: /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_occurrences_29654.csv (21 lines)
[INFO] [2022-08-03 17:23:05] ...measurements (/app/public/data/namigai_et_al_na/measurementOrFact.txt)
[CMD] [2022-08-03 17:23:05] /usr/bin/sort /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_measurements_29655.csv > /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_measurements_29655.csv_sorted
[INFO] [2022-08-03 17:23:05] Converted: /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_measurements_29655.csv (134 lines)
[STOP] [2022-08-03 17:23:05] convert_to_csv
[START] [2022-08-03 17:23:05] calculate_delta
[INFO] [2022-08-03 17:23:05] Looping over 3 formats...
[INFO] [2022-08-03 17:23:05] ...nodes (/app/public/data/namigai_et_al_na/taxa.txt)
[CMD] [2022-08-03 17:23:05] echo "0a" > /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_nodes_29653.diff
[CMD] [2022-08-03 17:23:05] tail -n +1 /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_nodes_29653.csv >> /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_nodes_29653.diff
[CMD] [2022-08-03 17:23:05] echo "." >> /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_nodes_29653.diff
[INFO] [2022-08-03 17:23:05] Created diff: /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_nodes_29653.diff (23 lines)
[INFO] [2022-08-03 17:23:05] ...occurrences (/app/public/data/namigai_et_al_na/occurrences.txt)
[CMD] [2022-08-03 17:23:05] echo "0a" > /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_occurrences_29654.diff
[CMD] [2022-08-03 17:23:05] tail -n +1 /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_occurrences_29654.csv >> /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_occurrences_29654.diff
[CMD] [2022-08-03 17:23:05] echo "." >> /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_occurrences_29654.diff
[INFO] [2022-08-03 17:23:05] Created diff: /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_occurrences_29654.diff (23 lines)
[INFO] [2022-08-03 17:23:05] ...measurements (/app/public/data/namigai_et_al_na/measurementOrFact.txt)
[CMD] [2022-08-03 17:23:05] echo "0a" > /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_measurements_29655.diff
[CMD] [2022-08-03 17:23:05] tail -n +1 /app/public/data/namigai_et_al_na/converted_csv/namigai_et_al_na_measurements_29655.csv >> /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_measurements_29655.diff
[CMD] [2022-08-03 17:23:05] echo "." >> /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_measurements_29655.diff
[INFO] [2022-08-03 17:23:05] Created diff: /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_measurements_29655.diff (136 lines)
[STOP] [2022-08-03 17:23:05] calculate_delta
[START] [2022-08-03 17:23:05] parse_diff_and_store
[INFO] [2022-08-03 17:23:05] Handling diff: /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_nodes_29653.diff (23 lines)
[INFO] [2022-08-03 17:23:05] Loading nodes diff file into memory (23 lines)...
[INFO] [2022-08-03 17:23:05] Storing 21 ScientificNames (42/21/23)
[INFO] [2022-08-03 17:23:05] Storing 21 Nodes (42/21/23)
[INFO] [2022-08-03 17:23:05] Handling diff: /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_occurrences_29654.diff (23 lines)
[INFO] [2022-08-03 17:23:05] Loading occurrences diff file into memory (23 lines)...
[INFO] [2022-08-03 17:23:05] Storing 21 Occurrences (21/21/23)
[INFO] [2022-08-03 17:23:05] Handling diff: /app/public/data/namigai_et_al_na/diff/namigai_et_al_na_measurements_29655.diff (136 lines)
[INFO] [2022-08-03 17:23:05] Loading measurements diff file into memory (136 lines)...
[INFO] [2022-08-03 17:23:05] Storing 134 Traits (178/134/136)
[INFO] [2022-08-03 17:23:05] Storing 44 MetaTraits (178/134/136)
[STOP] [2022-08-03 17:23:05] parse_diff_and_store
[START] [2022-08-03 17:23:05] resolve_keys
[2022-08-03 17:23:05] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:23:12] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:23:12] traits to occurrences...
[INFO] [2022-08-03 17:23:12] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:23:12] Traits to sex term...
[INFO] [2022-08-03 17:23:12] Traits to lifestage term...
[INFO] [2022-08-03 17:23:12] MetaTraits to traits...
[INFO] [2022-08-03 17:23:12] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:23:12] Assocs to occurrences...
[INFO] [2022-08-03 17:23:12] Assocs to nodes...
[INFO] [2022-08-03 17:23:12] Assoc to sex term...
[INFO] [2022-08-03 17:23:12] Assoc to lifestage term...
[INFO] [2022-08-03 17:23:12] MetaAssoc to assocs...
[STOP] [2022-08-03 17:23:12] resolve_keys
[START] [2022-08-03 17:23:12] hold_for_later_1
[STOP] [2022-08-03 17:23:12] hold_for_later_1
[START] [2022-08-03 17:23:12] hold_for_later_2
[STOP] [2022-08-03 17:23:12] hold_for_later_2
[START] [2022-08-03 17:23:12] resolve_missing_parents
[STOP] [2022-08-03 17:23:12] resolve_missing_parents
[START] [2022-08-03 17:23:12] rebuild_nodes
[START] [2022-08-03 17:23:12] Flattener#flatten
[START] [2022-08-03 17:23:12] Flattener#study_resource
[START] [2022-08-03 17:23:12] Flattener#build_ancestry
[STOP] [2022-08-03 17:23:12] Flattener#build_ancestry
[INFO] [2022-08-03 17:23:12] 21 ancestry keys
[START] [2022-08-03 17:23:12] build_node_ancestors
[INFO] [2022-08-03 17:23:12] old ancestors deleted.
[STOP] [2022-08-03 17:23:13] build_node_ancestors
[WARN] [2022-08-03 17:23:13] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:23:13] Flattener#flatten
[STOP] [2022-08-03 17:23:13] rebuild_nodes
[START] [2022-08-03 17:23:13] resolve_missing_media_owners
[STOP] [2022-08-03 17:23:13] resolve_missing_media_owners
[START] [2022-08-03 17:23:13] sanitize_media_verbatims
[STOP] [2022-08-03 17:23:13] sanitize_media_verbatims
[START] [2022-08-03 17:23:13] queue_downloads
[STOP] [2022-08-03 17:23:13] queue_downloads
[START] [2022-08-03 17:23:13] parse_names
[WARN] [2022-08-03 17:23:13] I see 21 names which still need to be parsed.
[WARN] [2022-08-03 17:23:13] Names to parse: 21 formatted: 21 learned: 21 parsed: 21
[STOP] [2022-08-03 17:23:14] parse_names
[START] [2022-08-03 17:23:14] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:23:14] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:23:14] match_nodes
[START] [2022-08-03 17:23:14] map_all_nodes_to_pages
[STOP] [2022-08-03 17:23:14] map_all_nodes_to_pages
[INFO] [2022-08-03 17:23:14] ZERO unmatched nodes (of 21)! Nicely done.
[START] [2022-08-03 17:23:14] update_nodes
[STOP] [2022-08-03 17:23:14] update_nodes
[STOP] [2022-08-03 17:23:14] match_nodes
[START] [2022-08-03 17:23:14] reindex_search
[STOP] [2022-08-03 17:23:14] reindex_search
[START] [2022-08-03 17:23:14] normalize_units
[STOP] [2022-08-03 17:23:15] normalize_units
[START] [2022-08-03 17:23:15] calculate_statistics
[2022-08-03 17:23:15] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:23:15] Duplicate page_id count: 0
[STOP] [2022-08-03 17:23:15] calculate_statistics
[START] [2022-08-03 17:23:15] complete_harvest_instance
[START] [2022-08-03 17:23:15] overall_tsv_creation
[INFO] [2022-08-03 17:23:15] Exporting 21 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:23:15] Processing group of 21 in 1 batches of 10000
[INFO] [2022-08-03 17:23:57] 21 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:23:57] Building Traits map for 21 nodes (this can take a while)...
[INFO] [2022-08-03 17:24:50] Mapped 21 traits (21 meta) for 21 nodes.
[INFO] [2022-08-03 17:24:50] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:24:50] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:24:50] Adding 21 traits...
[INFO] [2022-08-03 17:24:50] 29 metadata added.
[INFO] [2022-08-03 17:24:50] Adding 0 assocs...
[INFO] [2022-08-03 17:24:50] 0 metadata added.
[INFO] [2022-08-03 17:25:32] Processed 21/21 nodes
[INFO] [2022-08-03 17:25:32] Average Time: 112.51
[INFO] [2022-08-03 17:25:32] Total Time: 2m18s
[STOP] [2022-08-03 17:25:32] overall_tsv_creation
[INFO] [2022-08-03 17:25:32] Done. Check your files:
[INFO] [2022-08-03 17:25:32] (21 lines) /app/public/data/namigai_et_al_na/publish_nodes.tsv
[INFO] [2022-08-03 17:25:32] (21 lines) /app/public/data/namigai_et_al_na/publish_scientific_names.tsv
[INFO] [2022-08-03 17:25:32] (22 lines) /app/public/data/namigai_et_al_na/publish_traits.tsv
[INFO] [2022-08-03 17:25:32] (30 lines) /app/public/data/namigai_et_al_na/publish_metadata.tsv
[STOP] [2022-08-03 17:25:32] complete_harvest_instance
[START] [2022-08-03 17:25:32] completed
[STOP] [2022-08-03 17:25:32] completed
[STOP] [2022-08-03 17:25:32] logged process, took 147.87

Latest Process

03 Aug 17:23 EXITED currently processing 0