Harvest for Altman 1965 Created 03 Aug 16:13

Harvesting Log

[INFO] [2022-08-03 16:13:41] Created harvest instance #4165
[STOP] [2022-08-03 16:13:41] create_harvest_instance
[START] [2022-08-03 16:13:41] fetch_files
[STOP] [2022-08-03 16:13:41] fetch_files
[START] [2022-08-03 16:13:41] validate_each_file
[INFO] [2022-08-03 16:13:41] Looping over 3 formats...
[INFO] [2022-08-03 16:13:41] ...nodes (/app/public/data/altman_altman_19/taxa.txt)
[INFO] [2022-08-03 16:13:42] Valid: /app/public/data/altman_altman_19/converted_csv/altman_altman_19_nodes_29558.csv (1 lines)
[INFO] [2022-08-03 16:13:42] ...occurrences (/app/public/data/altman_altman_19/occurrences.txt)
[INFO] [2022-08-03 16:13:42] Valid: /app/public/data/altman_altman_19/converted_csv/altman_altman_19_occurrences_29559.csv (1 lines)
[INFO] [2022-08-03 16:13:42] ...measurements (/app/public/data/altman_altman_19/measurementOrFact.txt)
[INFO] [2022-08-03 16:13:42] Valid: /app/public/data/altman_altman_19/converted_csv/altman_altman_19_measurements_29560.csv (2 lines)
[STOP] [2022-08-03 16:13:42] validate_each_file
[START] [2022-08-03 16:13:42] convert_to_csv
[INFO] [2022-08-03 16:13:42] Looping over 3 formats...
[INFO] [2022-08-03 16:13:42] ...nodes (/app/public/data/altman_altman_19/taxa.txt)
[CMD] [2022-08-03 16:13:42] /usr/bin/sort /app/public/data/altman_altman_19/converted_csv/altman_altman_19_nodes_29558.csv > /app/public/data/altman_altman_19/converted_csv/altman_altman_19_nodes_29558.csv_sorted
[INFO] [2022-08-03 16:13:42] Converted: /app/public/data/altman_altman_19/converted_csv/altman_altman_19_nodes_29558.csv (1 lines)
[INFO] [2022-08-03 16:13:42] ...occurrences (/app/public/data/altman_altman_19/occurrences.txt)
[CMD] [2022-08-03 16:13:42] /usr/bin/sort /app/public/data/altman_altman_19/converted_csv/altman_altman_19_occurrences_29559.csv > /app/public/data/altman_altman_19/converted_csv/altman_altman_19_occurrences_29559.csv_sorted
[INFO] [2022-08-03 16:13:42] Converted: /app/public/data/altman_altman_19/converted_csv/altman_altman_19_occurrences_29559.csv (1 lines)
[INFO] [2022-08-03 16:13:42] ...measurements (/app/public/data/altman_altman_19/measurementOrFact.txt)
[CMD] [2022-08-03 16:13:42] /usr/bin/sort /app/public/data/altman_altman_19/converted_csv/altman_altman_19_measurements_29560.csv > /app/public/data/altman_altman_19/converted_csv/altman_altman_19_measurements_29560.csv_sorted
[INFO] [2022-08-03 16:13:42] Converted: /app/public/data/altman_altman_19/converted_csv/altman_altman_19_measurements_29560.csv (2 lines)
[STOP] [2022-08-03 16:13:42] convert_to_csv
[START] [2022-08-03 16:13:42] calculate_delta
[INFO] [2022-08-03 16:13:42] Looping over 3 formats...
[INFO] [2022-08-03 16:13:42] ...nodes (/app/public/data/altman_altman_19/taxa.txt)
[CMD] [2022-08-03 16:13:42] echo "0a" > /app/public/data/altman_altman_19/diff/altman_altman_19_nodes_29558.diff
[CMD] [2022-08-03 16:13:42] tail -n +1 /app/public/data/altman_altman_19/converted_csv/altman_altman_19_nodes_29558.csv >> /app/public/data/altman_altman_19/diff/altman_altman_19_nodes_29558.diff
[CMD] [2022-08-03 16:13:42] echo "." >> /app/public/data/altman_altman_19/diff/altman_altman_19_nodes_29558.diff
[INFO] [2022-08-03 16:13:42] Created diff: /app/public/data/altman_altman_19/diff/altman_altman_19_nodes_29558.diff (3 lines)
[INFO] [2022-08-03 16:13:42] ...occurrences (/app/public/data/altman_altman_19/occurrences.txt)
[CMD] [2022-08-03 16:13:42] echo "0a" > /app/public/data/altman_altman_19/diff/altman_altman_19_occurrences_29559.diff
[CMD] [2022-08-03 16:13:42] tail -n +1 /app/public/data/altman_altman_19/converted_csv/altman_altman_19_occurrences_29559.csv >> /app/public/data/altman_altman_19/diff/altman_altman_19_occurrences_29559.diff
[CMD] [2022-08-03 16:13:42] echo "." >> /app/public/data/altman_altman_19/diff/altman_altman_19_occurrences_29559.diff
[INFO] [2022-08-03 16:13:42] Created diff: /app/public/data/altman_altman_19/diff/altman_altman_19_occurrences_29559.diff (3 lines)
[INFO] [2022-08-03 16:13:42] ...measurements (/app/public/data/altman_altman_19/measurementOrFact.txt)
[CMD] [2022-08-03 16:13:42] echo "0a" > /app/public/data/altman_altman_19/diff/altman_altman_19_measurements_29560.diff
[CMD] [2022-08-03 16:13:42] tail -n +1 /app/public/data/altman_altman_19/converted_csv/altman_altman_19_measurements_29560.csv >> /app/public/data/altman_altman_19/diff/altman_altman_19_measurements_29560.diff
[CMD] [2022-08-03 16:13:42] echo "." >> /app/public/data/altman_altman_19/diff/altman_altman_19_measurements_29560.diff
[INFO] [2022-08-03 16:13:42] Created diff: /app/public/data/altman_altman_19/diff/altman_altman_19_measurements_29560.diff (4 lines)
[STOP] [2022-08-03 16:13:42] calculate_delta
[START] [2022-08-03 16:13:42] parse_diff_and_store
[INFO] [2022-08-03 16:13:42] Handling diff: /app/public/data/altman_altman_19/diff/altman_altman_19_nodes_29558.diff (3 lines)
[INFO] [2022-08-03 16:13:42] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:13:42] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:13:42] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:13:42] Handling diff: /app/public/data/altman_altman_19/diff/altman_altman_19_occurrences_29559.diff (3 lines)
[INFO] [2022-08-03 16:13:43] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:13:43] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:13:43] Handling diff: /app/public/data/altman_altman_19/diff/altman_altman_19_measurements_29560.diff (4 lines)
[INFO] [2022-08-03 16:13:43] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 16:13:43] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 16:13:43] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 16:13:43] parse_diff_and_store
[START] [2022-08-03 16:13:43] resolve_keys
[2022-08-03 16:13:43] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:13:50] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:13:50] traits to occurrences...
[INFO] [2022-08-03 16:13:50] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:13:50] Traits to sex term...
[INFO] [2022-08-03 16:13:50] Traits to lifestage term...
[INFO] [2022-08-03 16:13:50] MetaTraits to traits...
[INFO] [2022-08-03 16:13:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:13:50] Assocs to occurrences...
[INFO] [2022-08-03 16:13:50] Assocs to nodes...
[INFO] [2022-08-03 16:13:50] Assoc to sex term...
[INFO] [2022-08-03 16:13:50] Assoc to lifestage term...
[INFO] [2022-08-03 16:13:50] MetaAssoc to assocs...
[STOP] [2022-08-03 16:13:50] resolve_keys
[START] [2022-08-03 16:13:50] hold_for_later_1
[STOP] [2022-08-03 16:13:50] hold_for_later_1
[START] [2022-08-03 16:13:50] hold_for_later_2
[STOP] [2022-08-03 16:13:50] hold_for_later_2
[START] [2022-08-03 16:13:50] resolve_missing_parents
[STOP] [2022-08-03 16:13:50] resolve_missing_parents
[START] [2022-08-03 16:13:50] rebuild_nodes
[START] [2022-08-03 16:13:50] Flattener#flatten
[START] [2022-08-03 16:13:50] Flattener#study_resource
[START] [2022-08-03 16:13:50] Flattener#build_ancestry
[STOP] [2022-08-03 16:13:50] Flattener#build_ancestry
[INFO] [2022-08-03 16:13:50] 1 ancestry keys
[START] [2022-08-03 16:13:50] build_node_ancestors
[INFO] [2022-08-03 16:13:50] old ancestors deleted.
[STOP] [2022-08-03 16:13:50] build_node_ancestors
[WARN] [2022-08-03 16:13:50] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:13:50] Flattener#flatten
[STOP] [2022-08-03 16:13:50] rebuild_nodes
[START] [2022-08-03 16:13:50] resolve_missing_media_owners
[STOP] [2022-08-03 16:13:50] resolve_missing_media_owners
[START] [2022-08-03 16:13:50] sanitize_media_verbatims
[STOP] [2022-08-03 16:13:50] sanitize_media_verbatims
[START] [2022-08-03 16:13:50] queue_downloads
[STOP] [2022-08-03 16:13:50] queue_downloads
[START] [2022-08-03 16:13:50] parse_names
[WARN] [2022-08-03 16:13:50] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:13:50] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:13:51] parse_names
[START] [2022-08-03 16:13:51] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:13:51] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:13:51] match_nodes
[START] [2022-08-03 16:13:51] map_all_nodes_to_pages
[STOP] [2022-08-03 16:13:51] map_all_nodes_to_pages
[INFO] [2022-08-03 16:13:51] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:13:51] update_nodes
[STOP] [2022-08-03 16:13:51] update_nodes
[STOP] [2022-08-03 16:13:51] match_nodes
[START] [2022-08-03 16:13:51] reindex_search
[STOP] [2022-08-03 16:13:52] reindex_search
[START] [2022-08-03 16:13:52] normalize_units
[STOP] [2022-08-03 16:13:52] normalize_units
[START] [2022-08-03 16:13:52] calculate_statistics
[2022-08-03 16:13:52] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:13:52] Duplicate page_id count: 0
[STOP] [2022-08-03 16:13:52] calculate_statistics
[START] [2022-08-03 16:13:52] complete_harvest_instance
[START] [2022-08-03 16:13:52] overall_tsv_creation
[INFO] [2022-08-03 16:13:52] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:13:52] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:14:33] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:14:33] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:15:25] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 16:15:25] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:15:25] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:15:26] Adding 1 traits...
[INFO] [2022-08-03 16:15:26] 1 metadata added.
[INFO] [2022-08-03 16:15:26] Adding 0 assocs...
[INFO] [2022-08-03 16:15:26] 0 metadata added.
[INFO] [2022-08-03 16:16:08] Processed 1/1 nodes
[INFO] [2022-08-03 16:16:08] Average Time: 110.42
[INFO] [2022-08-03 16:16:08] Total Time: 2m16s
[STOP] [2022-08-03 16:16:08] overall_tsv_creation
[INFO] [2022-08-03 16:16:08] Done. Check your files:
[INFO] [2022-08-03 16:16:08] (1 lines) /app/public/data/altman_altman_19/publish_nodes.tsv
[INFO] [2022-08-03 16:16:08] (1 lines) /app/public/data/altman_altman_19/publish_scientific_names.tsv
[INFO] [2022-08-03 16:16:08] (2 lines) /app/public/data/altman_altman_19/publish_traits.tsv
[INFO] [2022-08-03 16:16:08] (2 lines) /app/public/data/altman_altman_19/publish_metadata.tsv
[STOP] [2022-08-03 16:16:08] complete_harvest_instance
[START] [2022-08-03 16:16:08] completed
[STOP] [2022-08-03 16:16:08] completed
[STOP] [2022-08-03 16:16:08] logged process, took 147.01

Latest Process

03 Aug 16:13 EXITED currently processing 0