Harvest for Eick et al 2005 Created 14 Oct 08:25

Harvesting Log

[INFO] [2023-10-14 08:25:21] Created harvest instance #4466
[STOP] [2023-10-14 08:25:21] create_harvest_instance
[START] [2023-10-14 08:25:22] fetch_files
[STOP] [2023-10-14 08:25:22] fetch_files
[START] [2023-10-14 08:25:22] validate_each_file
[INFO] [2023-10-14 08:25:22] Looping over 4 formats...
[INFO] [2023-10-14 08:25:22] ...refs (/app/public/data/eick_et_al_eick_/references.txt)
[INFO] [2023-10-14 08:25:22] Valid: /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__refs_30872.csv (7 lines)
[INFO] [2023-10-14 08:25:22] ...nodes (/app/public/data/eick_et_al_eick_/taxa.txt)
[INFO] [2023-10-14 08:25:22] Valid: /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__nodes_30869.csv (10 lines)
[INFO] [2023-10-14 08:25:22] ...occurrences (/app/public/data/eick_et_al_eick_/occurrences.txt)
[INFO] [2023-10-14 08:25:22] Valid: /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__occurrences_30870.csv (10 lines)
[INFO] [2023-10-14 08:25:22] ...measurements (/app/public/data/eick_et_al_eick_/measurementsorfacts.txt)
[INFO] [2023-10-14 08:25:22] Valid: /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__measurements_30871.csv (30 lines)
[STOP] [2023-10-14 08:25:22] validate_each_file
[START] [2023-10-14 08:25:22] convert_to_csv
[INFO] [2023-10-14 08:25:22] Looping over 4 formats...
[INFO] [2023-10-14 08:25:22] ...refs (/app/public/data/eick_et_al_eick_/references.txt)
[CMD] [2023-10-14 08:25:22] /usr/bin/sort /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__refs_30872.csv > /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__refs_30872.csv_sorted
[INFO] [2023-10-14 08:25:22] Converted: /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__refs_30872.csv (7 lines)
[INFO] [2023-10-14 08:25:22] ...nodes (/app/public/data/eick_et_al_eick_/taxa.txt)
[CMD] [2023-10-14 08:25:22] /usr/bin/sort /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__nodes_30869.csv > /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__nodes_30869.csv_sorted
[INFO] [2023-10-14 08:25:22] Converted: /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__nodes_30869.csv (10 lines)
[INFO] [2023-10-14 08:25:22] ...occurrences (/app/public/data/eick_et_al_eick_/occurrences.txt)
[CMD] [2023-10-14 08:25:22] /usr/bin/sort /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__occurrences_30870.csv > /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__occurrences_30870.csv_sorted
[INFO] [2023-10-14 08:25:22] Converted: /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__occurrences_30870.csv (10 lines)
[INFO] [2023-10-14 08:25:22] ...measurements (/app/public/data/eick_et_al_eick_/measurementsorfacts.txt)
[CMD] [2023-10-14 08:25:22] /usr/bin/sort /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__measurements_30871.csv > /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__measurements_30871.csv_sorted
[INFO] [2023-10-14 08:25:22] Converted: /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__measurements_30871.csv (30 lines)
[STOP] [2023-10-14 08:25:22] convert_to_csv
[START] [2023-10-14 08:25:22] calculate_delta
[INFO] [2023-10-14 08:25:22] Looping over 4 formats...
[INFO] [2023-10-14 08:25:22] ...refs (/app/public/data/eick_et_al_eick_/references.txt)
[CMD] [2023-10-14 08:25:22] echo "0a" > /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__refs_30872.diff
[CMD] [2023-10-14 08:25:22] tail -n +1 /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__refs_30872.csv >> /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__refs_30872.diff
[CMD] [2023-10-14 08:25:22] echo "." >> /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__refs_30872.diff
[INFO] [2023-10-14 08:25:22] Created diff: /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__refs_30872.diff (9 lines)
[INFO] [2023-10-14 08:25:22] ...nodes (/app/public/data/eick_et_al_eick_/taxa.txt)
[CMD] [2023-10-14 08:25:22] echo "0a" > /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__nodes_30869.diff
[CMD] [2023-10-14 08:25:22] tail -n +1 /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__nodes_30869.csv >> /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__nodes_30869.diff
[CMD] [2023-10-14 08:25:22] echo "." >> /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__nodes_30869.diff
[INFO] [2023-10-14 08:25:22] Created diff: /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__nodes_30869.diff (12 lines)
[INFO] [2023-10-14 08:25:22] ...occurrences (/app/public/data/eick_et_al_eick_/occurrences.txt)
[CMD] [2023-10-14 08:25:22] echo "0a" > /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__occurrences_30870.diff
[CMD] [2023-10-14 08:25:22] tail -n +1 /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__occurrences_30870.csv >> /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__occurrences_30870.diff
[CMD] [2023-10-14 08:25:23] echo "." >> /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__occurrences_30870.diff
[INFO] [2023-10-14 08:25:23] Created diff: /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__occurrences_30870.diff (12 lines)
[INFO] [2023-10-14 08:25:23] ...measurements (/app/public/data/eick_et_al_eick_/measurementsorfacts.txt)
[CMD] [2023-10-14 08:25:23] echo "0a" > /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__measurements_30871.diff
[CMD] [2023-10-14 08:25:23] tail -n +1 /app/public/data/eick_et_al_eick_/converted_csv/eick_et_al_eick__measurements_30871.csv >> /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__measurements_30871.diff
[CMD] [2023-10-14 08:25:23] echo "." >> /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__measurements_30871.diff
[INFO] [2023-10-14 08:25:23] Created diff: /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__measurements_30871.diff (32 lines)
[STOP] [2023-10-14 08:25:23] calculate_delta
[START] [2023-10-14 08:25:23] parse_diff_and_store
[INFO] [2023-10-14 08:25:23] Handling diff: /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__refs_30872.diff (9 lines)
[INFO] [2023-10-14 08:25:23] Loading refs diff file into memory (9 lines)...
[INFO] [2023-10-14 08:25:23] Storing 7 References (7/7/9)
[INFO] [2023-10-14 08:25:23] Handling diff: /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__nodes_30869.diff (12 lines)
[INFO] [2023-10-14 08:25:23] Loading nodes diff file into memory (12 lines)...
[INFO] [2023-10-14 08:25:23] Storing 10 ScientificNames (20/10/12)
[INFO] [2023-10-14 08:25:23] Storing 10 Nodes (20/10/12)
[INFO] [2023-10-14 08:25:23] Handling diff: /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__occurrences_30870.diff (12 lines)
[INFO] [2023-10-14 08:25:23] Loading occurrences diff file into memory (12 lines)...
[INFO] [2023-10-14 08:25:23] Storing 10 Occurrences (10/10/12)
[INFO] [2023-10-14 08:25:23] Handling diff: /app/public/data/eick_et_al_eick_/diff/eick_et_al_eick__measurements_30871.diff (32 lines)
[INFO] [2023-10-14 08:25:23] Loading measurements diff file into memory (32 lines)...
[INFO] [2023-10-14 08:25:23] Storing 12 TraitsReferences (64/30/32)
[INFO] [2023-10-14 08:25:23] Storing 30 Traits (64/30/32)
[INFO] [2023-10-14 08:25:23] Storing 22 MetaTraits (64/30/32)
[STOP] [2023-10-14 08:25:23] parse_diff_and_store
[START] [2023-10-14 08:25:23] resolve_keys
[2023-10-14 08:25:23] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-14 08:25:31] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-14 08:25:31] traits to occurrences...
[INFO] [2023-10-14 08:25:31] traits to nodes (through occurrences)...
[INFO] [2023-10-14 08:25:31] Traits to sex term...
[INFO] [2023-10-14 08:25:31] Traits to lifestage term...
[INFO] [2023-10-14 08:25:31] MetaTraits to traits...
[INFO] [2023-10-14 08:25:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-14 08:25:31] Assocs to occurrences...
[INFO] [2023-10-14 08:25:31] Assocs to nodes...
[INFO] [2023-10-14 08:25:31] Assoc to sex term...
[INFO] [2023-10-14 08:25:31] Assoc to lifestage term...
[INFO] [2023-10-14 08:25:31] MetaAssoc to assocs...
[STOP] [2023-10-14 08:25:31] resolve_keys
[START] [2023-10-14 08:25:31] hold_for_later_1
[STOP] [2023-10-14 08:25:31] hold_for_later_1
[START] [2023-10-14 08:25:31] hold_for_later_2
[STOP] [2023-10-14 08:25:31] hold_for_later_2
[START] [2023-10-14 08:25:31] resolve_missing_parents
[STOP] [2023-10-14 08:25:31] resolve_missing_parents
[START] [2023-10-14 08:25:31] rebuild_nodes
[START] [2023-10-14 08:25:31] Flattener#flatten
[START] [2023-10-14 08:25:31] Flattener#study_resource
[START] [2023-10-14 08:25:31] Flattener#build_ancestry
[STOP] [2023-10-14 08:25:31] Flattener#build_ancestry
[INFO] [2023-10-14 08:25:31] 10 ancestry keys
[START] [2023-10-14 08:25:31] build_node_ancestors
[INFO] [2023-10-14 08:25:31] old ancestors deleted.
[STOP] [2023-10-14 08:25:31] build_node_ancestors
[WARN] [2023-10-14 08:25:31] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-14 08:25:31] Flattener#flatten
[STOP] [2023-10-14 08:25:31] rebuild_nodes
[START] [2023-10-14 08:25:31] resolve_missing_media_owners
[STOP] [2023-10-14 08:25:31] resolve_missing_media_owners
[START] [2023-10-14 08:25:31] sanitize_media_verbatims
[STOP] [2023-10-14 08:25:31] sanitize_media_verbatims
[START] [2023-10-14 08:25:31] queue_downloads
[STOP] [2023-10-14 08:25:31] queue_downloads
[START] [2023-10-14 08:25:31] parse_names
[WARN] [2023-10-14 08:25:31] I see 10 names which still need to be parsed.
[WARN] [2023-10-14 08:25:31] Names to parse: 10 formatted: 10 learned: 10 parsed: 10
[STOP] [2023-10-14 08:25:32] parse_names
[START] [2023-10-14 08:25:32] denormalize_canonical_names_to_nodes
[STOP] [2023-10-14 08:25:32] denormalize_canonical_names_to_nodes
[START] [2023-10-14 08:25:32] match_nodes
[START] [2023-10-14 08:25:32] map_all_nodes_to_pages
[STOP] [2023-10-14 08:25:32] map_all_nodes_to_pages
[INFO] [2023-10-14 08:25:32] ZERO unmatched nodes (of 10)! Nicely done.
[START] [2023-10-14 08:25:32] update_nodes
[STOP] [2023-10-14 08:25:32] update_nodes
[STOP] [2023-10-14 08:25:32] match_nodes
[START] [2023-10-14 08:25:32] reindex_search
[STOP] [2023-10-14 08:25:33] reindex_search
[START] [2023-10-14 08:25:33] normalize_units
[STOP] [2023-10-14 08:25:33] normalize_units
[START] [2023-10-14 08:25:33] calculate_statistics
[2023-10-14 08:25:33] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-14 08:25:33] Duplicate page_id count: 0
[STOP] [2023-10-14 08:25:33] calculate_statistics
[START] [2023-10-14 08:25:33] complete_harvest_instance
[START] [2023-10-14 08:25:33] overall_tsv_creation
[INFO] [2023-10-14 08:25:33] Exporting 10 nodes as TSV in batches of 10000...
[INFO] [2023-10-14 08:25:33] Processing group of 10 in 1 batches of 10000
[INFO] [2023-10-14 08:25:33] 10 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-14 08:25:33] Building Traits map for 10 nodes (this can take a while)...
[INFO] [2023-10-14 08:25:33] Mapped 10 traits (20 meta) for 10 nodes.
[INFO] [2023-10-14 08:25:33] Building Associations map (this can take a while)...
[INFO] [2023-10-14 08:25:33] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-14 08:25:33] Adding 10 traits...
[INFO] [2023-10-14 08:25:33] 30 metadata added.
[INFO] [2023-10-14 08:25:33] Adding 0 assocs...
[INFO] [2023-10-14 08:25:33] 0 metadata added.
[INFO] [2023-10-14 08:26:17] Processed 10/10 nodes
[INFO] [2023-10-14 08:26:17] Average Time: 43.83
[INFO] [2023-10-14 08:26:17] Total Time: 44s
[STOP] [2023-10-14 08:26:17] overall_tsv_creation
[INFO] [2023-10-14 08:26:17] Done. Check your files:
[INFO] [2023-10-14 08:26:17] (10 lines) /app/public/data/eick_et_al_eick_/publish_nodes.tsv
[INFO] [2023-10-14 08:26:17] (10 lines) /app/public/data/eick_et_al_eick_/publish_scientific_names.tsv
[INFO] [2023-10-14 08:26:17] (11 lines) /app/public/data/eick_et_al_eick_/publish_traits.tsv
[INFO] [2023-10-14 08:26:17] (31 lines) /app/public/data/eick_et_al_eick_/publish_metadata.tsv
[STOP] [2023-10-14 08:26:17] complete_harvest_instance
[START] [2023-10-14 08:26:17] completed
[STOP] [2023-10-14 08:26:17] completed
[STOP] [2023-10-14 08:26:17] logged process, took 55.44

Latest Process

14 Oct 08:25 EXITED currently processing 0