Harvest for Greven 2007 Created 13 Oct 13:51

Harvesting Log

[INFO] [2023-10-13 13:51:56] Created harvest instance #4461
[STOP] [2023-10-13 13:51:56] create_harvest_instance
[START] [2023-10-13 13:51:56] fetch_files
[STOP] [2023-10-13 13:51:56] fetch_files
[START] [2023-10-13 13:51:56] validate_each_file
[INFO] [2023-10-13 13:51:56] Looping over 4 formats...
[INFO] [2023-10-13 13:51:56] ...refs (/app/public/data/greven_greven_20/references.tsv)
[INFO] [2023-10-13 13:51:56] Valid: /app/public/data/greven_greven_20/converted_csv/greven_greven_20_refs_30852.csv (1 lines)
[INFO] [2023-10-13 13:51:56] ...nodes (/app/public/data/greven_greven_20/taxa.txt)
[INFO] [2023-10-13 13:51:56] Valid: /app/public/data/greven_greven_20/converted_csv/greven_greven_20_nodes_30849.csv (4 lines)
[INFO] [2023-10-13 13:51:56] ...occurrences (/app/public/data/greven_greven_20/occurrences.txt)
[INFO] [2023-10-13 13:51:56] Valid: /app/public/data/greven_greven_20/converted_csv/greven_greven_20_occurrences_30850.csv (4 lines)
[INFO] [2023-10-13 13:51:56] ...measurements (/app/public/data/greven_greven_20/measurementsorfacts.txt)
[INFO] [2023-10-13 13:51:56] Valid: /app/public/data/greven_greven_20/converted_csv/greven_greven_20_measurements_30851.csv (10 lines)
[STOP] [2023-10-13 13:51:56] validate_each_file
[START] [2023-10-13 13:51:56] convert_to_csv
[INFO] [2023-10-13 13:51:56] Looping over 4 formats...
[INFO] [2023-10-13 13:51:56] ...refs (/app/public/data/greven_greven_20/references.tsv)
[CMD] [2023-10-13 13:51:56] /usr/bin/sort /app/public/data/greven_greven_20/converted_csv/greven_greven_20_refs_30852.csv > /app/public/data/greven_greven_20/converted_csv/greven_greven_20_refs_30852.csv_sorted
[INFO] [2023-10-13 13:51:56] Converted: /app/public/data/greven_greven_20/converted_csv/greven_greven_20_refs_30852.csv (1 lines)
[INFO] [2023-10-13 13:51:56] ...nodes (/app/public/data/greven_greven_20/taxa.txt)
[CMD] [2023-10-13 13:51:56] /usr/bin/sort /app/public/data/greven_greven_20/converted_csv/greven_greven_20_nodes_30849.csv > /app/public/data/greven_greven_20/converted_csv/greven_greven_20_nodes_30849.csv_sorted
[INFO] [2023-10-13 13:51:56] Converted: /app/public/data/greven_greven_20/converted_csv/greven_greven_20_nodes_30849.csv (4 lines)
[INFO] [2023-10-13 13:51:56] ...occurrences (/app/public/data/greven_greven_20/occurrences.txt)
[CMD] [2023-10-13 13:51:56] /usr/bin/sort /app/public/data/greven_greven_20/converted_csv/greven_greven_20_occurrences_30850.csv > /app/public/data/greven_greven_20/converted_csv/greven_greven_20_occurrences_30850.csv_sorted
[INFO] [2023-10-13 13:51:56] Converted: /app/public/data/greven_greven_20/converted_csv/greven_greven_20_occurrences_30850.csv (4 lines)
[INFO] [2023-10-13 13:51:56] ...measurements (/app/public/data/greven_greven_20/measurementsorfacts.txt)
[CMD] [2023-10-13 13:51:56] /usr/bin/sort /app/public/data/greven_greven_20/converted_csv/greven_greven_20_measurements_30851.csv > /app/public/data/greven_greven_20/converted_csv/greven_greven_20_measurements_30851.csv_sorted
[INFO] [2023-10-13 13:51:56] Converted: /app/public/data/greven_greven_20/converted_csv/greven_greven_20_measurements_30851.csv (10 lines)
[STOP] [2023-10-13 13:51:56] convert_to_csv
[START] [2023-10-13 13:51:56] calculate_delta
[INFO] [2023-10-13 13:51:56] Looping over 4 formats...
[INFO] [2023-10-13 13:51:56] ...refs (/app/public/data/greven_greven_20/references.tsv)
[CMD] [2023-10-13 13:51:56] echo "0a" > /app/public/data/greven_greven_20/diff/greven_greven_20_refs_30852.diff
[CMD] [2023-10-13 13:51:57] tail -n +1 /app/public/data/greven_greven_20/converted_csv/greven_greven_20_refs_30852.csv >> /app/public/data/greven_greven_20/diff/greven_greven_20_refs_30852.diff
[CMD] [2023-10-13 13:51:57] echo "." >> /app/public/data/greven_greven_20/diff/greven_greven_20_refs_30852.diff
[INFO] [2023-10-13 13:51:57] Created diff: /app/public/data/greven_greven_20/diff/greven_greven_20_refs_30852.diff (3 lines)
[INFO] [2023-10-13 13:51:57] ...nodes (/app/public/data/greven_greven_20/taxa.txt)
[CMD] [2023-10-13 13:51:57] echo "0a" > /app/public/data/greven_greven_20/diff/greven_greven_20_nodes_30849.diff
[CMD] [2023-10-13 13:51:57] tail -n +1 /app/public/data/greven_greven_20/converted_csv/greven_greven_20_nodes_30849.csv >> /app/public/data/greven_greven_20/diff/greven_greven_20_nodes_30849.diff
[CMD] [2023-10-13 13:51:57] echo "." >> /app/public/data/greven_greven_20/diff/greven_greven_20_nodes_30849.diff
[INFO] [2023-10-13 13:51:57] Created diff: /app/public/data/greven_greven_20/diff/greven_greven_20_nodes_30849.diff (6 lines)
[INFO] [2023-10-13 13:51:57] ...occurrences (/app/public/data/greven_greven_20/occurrences.txt)
[CMD] [2023-10-13 13:51:57] echo "0a" > /app/public/data/greven_greven_20/diff/greven_greven_20_occurrences_30850.diff
[CMD] [2023-10-13 13:51:57] tail -n +1 /app/public/data/greven_greven_20/converted_csv/greven_greven_20_occurrences_30850.csv >> /app/public/data/greven_greven_20/diff/greven_greven_20_occurrences_30850.diff
[CMD] [2023-10-13 13:51:57] echo "." >> /app/public/data/greven_greven_20/diff/greven_greven_20_occurrences_30850.diff
[INFO] [2023-10-13 13:51:57] Created diff: /app/public/data/greven_greven_20/diff/greven_greven_20_occurrences_30850.diff (6 lines)
[INFO] [2023-10-13 13:51:57] ...measurements (/app/public/data/greven_greven_20/measurementsorfacts.txt)
[CMD] [2023-10-13 13:51:57] echo "0a" > /app/public/data/greven_greven_20/diff/greven_greven_20_measurements_30851.diff
[CMD] [2023-10-13 13:51:57] tail -n +1 /app/public/data/greven_greven_20/converted_csv/greven_greven_20_measurements_30851.csv >> /app/public/data/greven_greven_20/diff/greven_greven_20_measurements_30851.diff
[CMD] [2023-10-13 13:51:57] echo "." >> /app/public/data/greven_greven_20/diff/greven_greven_20_measurements_30851.diff
[INFO] [2023-10-13 13:51:57] Created diff: /app/public/data/greven_greven_20/diff/greven_greven_20_measurements_30851.diff (12 lines)
[STOP] [2023-10-13 13:51:57] calculate_delta
[START] [2023-10-13 13:51:57] parse_diff_and_store
[INFO] [2023-10-13 13:51:57] Handling diff: /app/public/data/greven_greven_20/diff/greven_greven_20_refs_30852.diff (3 lines)
[INFO] [2023-10-13 13:51:57] Loading refs diff file into memory (3 lines)...
[INFO] [2023-10-13 13:51:57] Storing 1 References (1/1/3)
[INFO] [2023-10-13 13:51:57] Handling diff: /app/public/data/greven_greven_20/diff/greven_greven_20_nodes_30849.diff (6 lines)
[INFO] [2023-10-13 13:51:58] Loading nodes diff file into memory (6 lines)...
[INFO] [2023-10-13 13:51:58] Storing 4 ScientificNames (8/4/6)
[INFO] [2023-10-13 13:51:58] Storing 4 Nodes (8/4/6)
[INFO] [2023-10-13 13:51:58] Handling diff: /app/public/data/greven_greven_20/diff/greven_greven_20_occurrences_30850.diff (6 lines)
[INFO] [2023-10-13 13:51:58] Loading occurrences diff file into memory (6 lines)...
[INFO] [2023-10-13 13:51:58] Storing 4 Occurrences (4/4/6)
[INFO] [2023-10-13 13:51:58] Handling diff: /app/public/data/greven_greven_20/diff/greven_greven_20_measurements_30851.diff (12 lines)
[INFO] [2023-10-13 13:51:58] Loading measurements diff file into memory (12 lines)...
[INFO] [2023-10-13 13:51:58] Storing 10 Traits (19/10/12)
[INFO] [2023-10-13 13:51:58] Storing 7 MetaTraits (19/10/12)
[INFO] [2023-10-13 13:51:58] Storing 2 TraitsReferences (19/10/12)
[STOP] [2023-10-13 13:51:58] parse_diff_and_store
[START] [2023-10-13 13:51:58] resolve_keys
[2023-10-13 13:51:58] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:52:05] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:52:05] traits to occurrences...
[INFO] [2023-10-13 13:52:05] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:52:05] Traits to sex term...
[INFO] [2023-10-13 13:52:05] Traits to lifestage term...
[INFO] [2023-10-13 13:52:05] MetaTraits to traits...
[INFO] [2023-10-13 13:52:05] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:52:05] Assocs to occurrences...
[INFO] [2023-10-13 13:52:05] Assocs to nodes...
[INFO] [2023-10-13 13:52:05] Assoc to sex term...
[INFO] [2023-10-13 13:52:05] Assoc to lifestage term...
[INFO] [2023-10-13 13:52:05] MetaAssoc to assocs...
[STOP] [2023-10-13 13:52:06] resolve_keys
[START] [2023-10-13 13:52:06] hold_for_later_1
[STOP] [2023-10-13 13:52:06] hold_for_later_1
[START] [2023-10-13 13:52:06] hold_for_later_2
[STOP] [2023-10-13 13:52:06] hold_for_later_2
[START] [2023-10-13 13:52:06] resolve_missing_parents
[STOP] [2023-10-13 13:52:06] resolve_missing_parents
[START] [2023-10-13 13:52:06] rebuild_nodes
[START] [2023-10-13 13:52:06] Flattener#flatten
[START] [2023-10-13 13:52:06] Flattener#study_resource
[START] [2023-10-13 13:52:06] Flattener#build_ancestry
[STOP] [2023-10-13 13:52:06] Flattener#build_ancestry
[INFO] [2023-10-13 13:52:06] 4 ancestry keys
[START] [2023-10-13 13:52:06] build_node_ancestors
[INFO] [2023-10-13 13:52:06] old ancestors deleted.
[STOP] [2023-10-13 13:52:06] build_node_ancestors
[WARN] [2023-10-13 13:52:06] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:52:06] Flattener#flatten
[STOP] [2023-10-13 13:52:06] rebuild_nodes
[START] [2023-10-13 13:52:06] resolve_missing_media_owners
[STOP] [2023-10-13 13:52:06] resolve_missing_media_owners
[START] [2023-10-13 13:52:06] sanitize_media_verbatims
[STOP] [2023-10-13 13:52:06] sanitize_media_verbatims
[START] [2023-10-13 13:52:06] queue_downloads
[STOP] [2023-10-13 13:52:06] queue_downloads
[START] [2023-10-13 13:52:06] parse_names
[WARN] [2023-10-13 13:52:06] I see 4 names which still need to be parsed.
[WARN] [2023-10-13 13:52:06] Names to parse: 4 formatted: 4 learned: 4 parsed: 4
[STOP] [2023-10-13 13:52:07] parse_names
[START] [2023-10-13 13:52:07] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:52:07] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:52:07] match_nodes
[START] [2023-10-13 13:52:07] map_all_nodes_to_pages
[STOP] [2023-10-13 13:52:07] map_all_nodes_to_pages
[INFO] [2023-10-13 13:52:07] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2023-10-13 13:52:07] update_nodes
[STOP] [2023-10-13 13:52:07] update_nodes
[STOP] [2023-10-13 13:52:07] match_nodes
[START] [2023-10-13 13:52:07] reindex_search
[STOP] [2023-10-13 13:52:07] reindex_search
[START] [2023-10-13 13:52:07] normalize_units
[STOP] [2023-10-13 13:52:07] normalize_units
[START] [2023-10-13 13:52:07] calculate_statistics
[2023-10-13 13:52:07] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:52:07] Duplicate page_id count: 0
[STOP] [2023-10-13 13:52:07] calculate_statistics
[START] [2023-10-13 13:52:07] complete_harvest_instance
[START] [2023-10-13 13:52:07] overall_tsv_creation
[INFO] [2023-10-13 13:52:07] Exporting 4 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:52:07] Processing group of 4 in 1 batches of 10000
[INFO] [2023-10-13 13:52:07] 4 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:52:07] Building Traits map for 4 nodes (this can take a while)...
[INFO] [2023-10-13 13:52:07] Mapped 4 traits (7 meta) for 4 nodes.
[INFO] [2023-10-13 13:52:07] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:52:07] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:52:07] Adding 4 traits...
[INFO] [2023-10-13 13:52:07] 8 metadata added.
[INFO] [2023-10-13 13:52:07] Adding 0 assocs...
[INFO] [2023-10-13 13:52:07] 0 metadata added.
[INFO] [2023-10-13 13:52:51] Processed 4/4 nodes
[INFO] [2023-10-13 13:52:51] Average Time: 43.8
[INFO] [2023-10-13 13:52:51] Total Time: 44s
[STOP] [2023-10-13 13:52:51] overall_tsv_creation
[INFO] [2023-10-13 13:52:51] Done. Check your files:
[INFO] [2023-10-13 13:52:51] (4 lines) /app/public/data/greven_greven_20/publish_nodes.tsv
[INFO] [2023-10-13 13:52:51] (4 lines) /app/public/data/greven_greven_20/publish_scientific_names.tsv
[INFO] [2023-10-13 13:52:51] (5 lines) /app/public/data/greven_greven_20/publish_traits.tsv
[INFO] [2023-10-13 13:52:51] (9 lines) /app/public/data/greven_greven_20/publish_metadata.tsv
[STOP] [2023-10-13 13:52:51] complete_harvest_instance
[START] [2023-10-13 13:52:51] completed
[STOP] [2023-10-13 13:52:51] completed
[STOP] [2023-10-13 13:52:51] logged process, took 55.03

Latest Process

13 Oct 13:51 EXITED currently processing 0