Harvest for Garm and Nilsson 2014 Created 13 Oct 13:46

Harvesting Log

[INFO] [2023-10-13 13:46:57] Created harvest instance #4456
[STOP] [2023-10-13 13:46:57] create_harvest_instance
[START] [2023-10-13 13:46:57] fetch_files
[STOP] [2023-10-13 13:46:57] fetch_files
[START] [2023-10-13 13:46:57] validate_each_file
[INFO] [2023-10-13 13:46:57] Looping over 4 formats...
[INFO] [2023-10-13 13:46:57] ...refs (/app/public/data/garm_nilsson_gar/references.tsv)
[INFO] [2023-10-13 13:46:58] Valid: /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_refs_30832.csv (1 lines)
[INFO] [2023-10-13 13:46:58] ...nodes (/app/public/data/garm_nilsson_gar/taxa.txt)
[INFO] [2023-10-13 13:46:58] Valid: /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_nodes_30829.csv (2 lines)
[INFO] [2023-10-13 13:46:58] ...occurrences (/app/public/data/garm_nilsson_gar/occurrences.txt)
[INFO] [2023-10-13 13:46:58] Valid: /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_occurrences_30830.csv (2 lines)
[INFO] [2023-10-13 13:46:58] ...measurements (/app/public/data/garm_nilsson_gar/measurementsorfacts.txt)
[INFO] [2023-10-13 13:46:58] Valid: /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_measurements_30831.csv (4 lines)
[STOP] [2023-10-13 13:46:58] validate_each_file
[START] [2023-10-13 13:46:58] convert_to_csv
[INFO] [2023-10-13 13:46:58] Looping over 4 formats...
[INFO] [2023-10-13 13:46:58] ...refs (/app/public/data/garm_nilsson_gar/references.tsv)
[CMD] [2023-10-13 13:46:58] /usr/bin/sort /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_refs_30832.csv > /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_refs_30832.csv_sorted
[INFO] [2023-10-13 13:46:58] Converted: /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_refs_30832.csv (1 lines)
[INFO] [2023-10-13 13:46:58] ...nodes (/app/public/data/garm_nilsson_gar/taxa.txt)
[CMD] [2023-10-13 13:46:58] /usr/bin/sort /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_nodes_30829.csv > /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_nodes_30829.csv_sorted
[INFO] [2023-10-13 13:46:58] Converted: /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_nodes_30829.csv (2 lines)
[INFO] [2023-10-13 13:46:58] ...occurrences (/app/public/data/garm_nilsson_gar/occurrences.txt)
[CMD] [2023-10-13 13:46:58] /usr/bin/sort /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_occurrences_30830.csv > /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_occurrences_30830.csv_sorted
[INFO] [2023-10-13 13:46:58] Converted: /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_occurrences_30830.csv (2 lines)
[INFO] [2023-10-13 13:46:58] ...measurements (/app/public/data/garm_nilsson_gar/measurementsorfacts.txt)
[CMD] [2023-10-13 13:46:58] /usr/bin/sort /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_measurements_30831.csv > /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_measurements_30831.csv_sorted
[INFO] [2023-10-13 13:46:58] Converted: /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_measurements_30831.csv (4 lines)
[STOP] [2023-10-13 13:46:58] convert_to_csv
[START] [2023-10-13 13:46:58] calculate_delta
[INFO] [2023-10-13 13:46:58] Looping over 4 formats...
[INFO] [2023-10-13 13:46:58] ...refs (/app/public/data/garm_nilsson_gar/references.tsv)
[CMD] [2023-10-13 13:46:58] echo "0a" > /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_refs_30832.diff
[CMD] [2023-10-13 13:46:58] tail -n +1 /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_refs_30832.csv >> /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_refs_30832.diff
[CMD] [2023-10-13 13:46:58] echo "." >> /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_refs_30832.diff
[INFO] [2023-10-13 13:46:58] Created diff: /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_refs_30832.diff (3 lines)
[INFO] [2023-10-13 13:46:58] ...nodes (/app/public/data/garm_nilsson_gar/taxa.txt)
[CMD] [2023-10-13 13:46:58] echo "0a" > /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_nodes_30829.diff
[CMD] [2023-10-13 13:46:58] tail -n +1 /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_nodes_30829.csv >> /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_nodes_30829.diff
[CMD] [2023-10-13 13:46:58] echo "." >> /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_nodes_30829.diff
[INFO] [2023-10-13 13:46:58] Created diff: /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_nodes_30829.diff (4 lines)
[INFO] [2023-10-13 13:46:58] ...occurrences (/app/public/data/garm_nilsson_gar/occurrences.txt)
[CMD] [2023-10-13 13:46:58] echo "0a" > /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_occurrences_30830.diff
[CMD] [2023-10-13 13:46:59] tail -n +1 /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_occurrences_30830.csv >> /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_occurrences_30830.diff
[CMD] [2023-10-13 13:46:59] echo "." >> /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_occurrences_30830.diff
[INFO] [2023-10-13 13:46:59] Created diff: /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_occurrences_30830.diff (4 lines)
[INFO] [2023-10-13 13:46:59] ...measurements (/app/public/data/garm_nilsson_gar/measurementsorfacts.txt)
[CMD] [2023-10-13 13:46:59] echo "0a" > /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_measurements_30831.diff
[CMD] [2023-10-13 13:46:59] tail -n +1 /app/public/data/garm_nilsson_gar/converted_csv/garm_nilsson_gar_measurements_30831.csv >> /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_measurements_30831.diff
[CMD] [2023-10-13 13:46:59] echo "." >> /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_measurements_30831.diff
[INFO] [2023-10-13 13:46:59] Created diff: /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_measurements_30831.diff (6 lines)
[STOP] [2023-10-13 13:46:59] calculate_delta
[START] [2023-10-13 13:46:59] parse_diff_and_store
[INFO] [2023-10-13 13:46:59] Handling diff: /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_refs_30832.diff (3 lines)
[INFO] [2023-10-13 13:46:59] Loading refs diff file into memory (3 lines)...
[INFO] [2023-10-13 13:46:59] Storing 1 References (1/1/3)
[INFO] [2023-10-13 13:46:59] Handling diff: /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_nodes_30829.diff (4 lines)
[INFO] [2023-10-13 13:46:59] Loading nodes diff file into memory (4 lines)...
[INFO] [2023-10-13 13:46:59] Storing 2 ScientificNames (4/2/4)
[INFO] [2023-10-13 13:46:59] Storing 2 Nodes (4/2/4)
[INFO] [2023-10-13 13:46:59] Handling diff: /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_occurrences_30830.diff (4 lines)
[INFO] [2023-10-13 13:46:59] Loading occurrences diff file into memory (4 lines)...
[INFO] [2023-10-13 13:46:59] Storing 2 Occurrences (2/2/4)
[INFO] [2023-10-13 13:46:59] Handling diff: /app/public/data/garm_nilsson_gar/diff/garm_nilsson_gar_measurements_30831.diff (6 lines)
[INFO] [2023-10-13 13:46:59] Loading measurements diff file into memory (6 lines)...
[INFO] [2023-10-13 13:46:59] Storing 4 Traits (8/4/6)
[INFO] [2023-10-13 13:46:59] Storing 3 MetaTraits (8/4/6)
[INFO] [2023-10-13 13:46:59] Storing 1 TraitsReferences (8/4/6)
[STOP] [2023-10-13 13:46:59] parse_diff_and_store
[START] [2023-10-13 13:46:59] resolve_keys
[2023-10-13 13:46:59] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:47:07] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:47:07] traits to occurrences...
[INFO] [2023-10-13 13:47:07] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:47:07] Traits to sex term...
[INFO] [2023-10-13 13:47:07] Traits to lifestage term...
[INFO] [2023-10-13 13:47:07] MetaTraits to traits...
[INFO] [2023-10-13 13:47:07] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:47:07] Assocs to occurrences...
[INFO] [2023-10-13 13:47:07] Assocs to nodes...
[INFO] [2023-10-13 13:47:07] Assoc to sex term...
[INFO] [2023-10-13 13:47:07] Assoc to lifestage term...
[INFO] [2023-10-13 13:47:07] MetaAssoc to assocs...
[STOP] [2023-10-13 13:47:07] resolve_keys
[START] [2023-10-13 13:47:07] hold_for_later_1
[STOP] [2023-10-13 13:47:07] hold_for_later_1
[START] [2023-10-13 13:47:07] hold_for_later_2
[STOP] [2023-10-13 13:47:07] hold_for_later_2
[START] [2023-10-13 13:47:07] resolve_missing_parents
[STOP] [2023-10-13 13:47:07] resolve_missing_parents
[START] [2023-10-13 13:47:07] rebuild_nodes
[START] [2023-10-13 13:47:07] Flattener#flatten
[START] [2023-10-13 13:47:07] Flattener#study_resource
[START] [2023-10-13 13:47:07] Flattener#build_ancestry
[STOP] [2023-10-13 13:47:07] Flattener#build_ancestry
[INFO] [2023-10-13 13:47:07] 2 ancestry keys
[START] [2023-10-13 13:47:07] build_node_ancestors
[INFO] [2023-10-13 13:47:07] old ancestors deleted.
[STOP] [2023-10-13 13:47:07] build_node_ancestors
[WARN] [2023-10-13 13:47:07] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:47:07] Flattener#flatten
[STOP] [2023-10-13 13:47:07] rebuild_nodes
[START] [2023-10-13 13:47:07] resolve_missing_media_owners
[STOP] [2023-10-13 13:47:07] resolve_missing_media_owners
[START] [2023-10-13 13:47:07] sanitize_media_verbatims
[STOP] [2023-10-13 13:47:07] sanitize_media_verbatims
[START] [2023-10-13 13:47:07] queue_downloads
[STOP] [2023-10-13 13:47:07] queue_downloads
[START] [2023-10-13 13:47:07] parse_names
[WARN] [2023-10-13 13:47:07] I see 2 names which still need to be parsed.
[WARN] [2023-10-13 13:47:07] Names to parse: 2 formatted: 2 learned: 2 parsed: 2
[STOP] [2023-10-13 13:47:08] parse_names
[START] [2023-10-13 13:47:08] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:47:08] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:47:08] match_nodes
[START] [2023-10-13 13:47:08] map_all_nodes_to_pages
[STOP] [2023-10-13 13:47:08] map_all_nodes_to_pages
[INFO] [2023-10-13 13:47:08] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2023-10-13 13:47:08] update_nodes
[STOP] [2023-10-13 13:47:08] update_nodes
[STOP] [2023-10-13 13:47:08] match_nodes
[START] [2023-10-13 13:47:08] reindex_search
[STOP] [2023-10-13 13:47:08] reindex_search
[START] [2023-10-13 13:47:08] normalize_units
[STOP] [2023-10-13 13:47:08] normalize_units
[START] [2023-10-13 13:47:08] calculate_statistics
[2023-10-13 13:47:08] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:47:08] Duplicate page_id count: 0
[STOP] [2023-10-13 13:47:08] calculate_statistics
[START] [2023-10-13 13:47:08] complete_harvest_instance
[START] [2023-10-13 13:47:08] overall_tsv_creation
[INFO] [2023-10-13 13:47:08] Exporting 2 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:47:08] Processing group of 2 in 1 batches of 10000
[INFO] [2023-10-13 13:47:08] 2 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:47:08] Building Traits map for 2 nodes (this can take a while)...
[INFO] [2023-10-13 13:47:08] Mapped 2 traits (3 meta) for 2 nodes.
[INFO] [2023-10-13 13:47:08] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:47:08] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:47:08] Adding 2 traits...
[INFO] [2023-10-13 13:47:08] 3 metadata added.
[INFO] [2023-10-13 13:47:08] Adding 0 assocs...
[INFO] [2023-10-13 13:47:08] 0 metadata added.
[INFO] [2023-10-13 13:47:52] Processed 2/2 nodes
[INFO] [2023-10-13 13:47:52] Average Time: 43.88
[INFO] [2023-10-13 13:47:52] Total Time: 44s
[STOP] [2023-10-13 13:47:52] overall_tsv_creation
[INFO] [2023-10-13 13:47:52] Done. Check your files:
[INFO] [2023-10-13 13:47:52] (2 lines) /app/public/data/garm_nilsson_gar/publish_nodes.tsv
[INFO] [2023-10-13 13:47:53] (2 lines) /app/public/data/garm_nilsson_gar/publish_scientific_names.tsv
[INFO] [2023-10-13 13:47:53] (3 lines) /app/public/data/garm_nilsson_gar/publish_traits.tsv
[INFO] [2023-10-13 13:47:53] (4 lines) /app/public/data/garm_nilsson_gar/publish_metadata.tsv
[STOP] [2023-10-13 13:47:53] complete_harvest_instance
[START] [2023-10-13 13:47:53] completed
[STOP] [2023-10-13 13:47:53] completed
[STOP] [2023-10-13 13:47:53] logged process, took 55.32

Latest Process

13 Oct 13:46 EXITED currently processing 0