Harvest for Palmer et al 2017 Created 13 Oct 13:47

Harvesting Log

[INFO] [2023-10-13 13:47:57] Created harvest instance #4457
[STOP] [2023-10-13 13:47:57] create_harvest_instance
[START] [2023-10-13 13:47:57] fetch_files
[STOP] [2023-10-13 13:47:57] fetch_files
[START] [2023-10-13 13:47:57] validate_each_file
[INFO] [2023-10-13 13:47:57] Looping over 4 formats...
[INFO] [2023-10-13 13:47:57] ...refs (/app/public/data/palmer_et_al_pal/references.tsv)
[INFO] [2023-10-13 13:47:57] Valid: /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_refs_30836.csv (4 lines)
[INFO] [2023-10-13 13:47:57] ...nodes (/app/public/data/palmer_et_al_pal/taxa.txt)
[INFO] [2023-10-13 13:47:57] Valid: /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_nodes_30833.csv (4 lines)
[INFO] [2023-10-13 13:47:57] ...occurrences (/app/public/data/palmer_et_al_pal/occurrences.txt)
[INFO] [2023-10-13 13:47:57] Valid: /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_occurrences_30834.csv (4 lines)
[INFO] [2023-10-13 13:47:57] ...measurements (/app/public/data/palmer_et_al_pal/measurementsorfacts.txt)
[INFO] [2023-10-13 13:47:57] Valid: /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_measurements_30835.csv (4 lines)
[STOP] [2023-10-13 13:47:57] validate_each_file
[START] [2023-10-13 13:47:57] convert_to_csv
[INFO] [2023-10-13 13:47:57] Looping over 4 formats...
[INFO] [2023-10-13 13:47:57] ...refs (/app/public/data/palmer_et_al_pal/references.tsv)
[CMD] [2023-10-13 13:47:57] /usr/bin/sort /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_refs_30836.csv > /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_refs_30836.csv_sorted
[INFO] [2023-10-13 13:47:58] Converted: /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_refs_30836.csv (4 lines)
[INFO] [2023-10-13 13:47:58] ...nodes (/app/public/data/palmer_et_al_pal/taxa.txt)
[CMD] [2023-10-13 13:47:58] /usr/bin/sort /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_nodes_30833.csv > /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_nodes_30833.csv_sorted
[INFO] [2023-10-13 13:47:58] Converted: /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_nodes_30833.csv (4 lines)
[INFO] [2023-10-13 13:47:58] ...occurrences (/app/public/data/palmer_et_al_pal/occurrences.txt)
[CMD] [2023-10-13 13:47:58] /usr/bin/sort /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_occurrences_30834.csv > /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_occurrences_30834.csv_sorted
[INFO] [2023-10-13 13:47:58] Converted: /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_occurrences_30834.csv (4 lines)
[INFO] [2023-10-13 13:47:58] ...measurements (/app/public/data/palmer_et_al_pal/measurementsorfacts.txt)
[CMD] [2023-10-13 13:47:58] /usr/bin/sort /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_measurements_30835.csv > /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_measurements_30835.csv_sorted
[INFO] [2023-10-13 13:47:58] Converted: /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_measurements_30835.csv (4 lines)
[STOP] [2023-10-13 13:47:58] convert_to_csv
[START] [2023-10-13 13:47:58] calculate_delta
[INFO] [2023-10-13 13:47:58] Looping over 4 formats...
[INFO] [2023-10-13 13:47:58] ...refs (/app/public/data/palmer_et_al_pal/references.tsv)
[CMD] [2023-10-13 13:47:58] echo "0a" > /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_refs_30836.diff
[CMD] [2023-10-13 13:47:58] tail -n +1 /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_refs_30836.csv >> /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_refs_30836.diff
[CMD] [2023-10-13 13:47:58] echo "." >> /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_refs_30836.diff
[INFO] [2023-10-13 13:47:58] Created diff: /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_refs_30836.diff (6 lines)
[INFO] [2023-10-13 13:47:58] ...nodes (/app/public/data/palmer_et_al_pal/taxa.txt)
[CMD] [2023-10-13 13:47:58] echo "0a" > /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_nodes_30833.diff
[CMD] [2023-10-13 13:47:58] tail -n +1 /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_nodes_30833.csv >> /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_nodes_30833.diff
[CMD] [2023-10-13 13:47:58] echo "." >> /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_nodes_30833.diff
[INFO] [2023-10-13 13:47:58] Created diff: /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_nodes_30833.diff (6 lines)
[INFO] [2023-10-13 13:47:58] ...occurrences (/app/public/data/palmer_et_al_pal/occurrences.txt)
[CMD] [2023-10-13 13:47:58] echo "0a" > /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_occurrences_30834.diff
[CMD] [2023-10-13 13:47:58] tail -n +1 /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_occurrences_30834.csv >> /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_occurrences_30834.diff
[CMD] [2023-10-13 13:47:58] echo "." >> /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_occurrences_30834.diff
[INFO] [2023-10-13 13:47:58] Created diff: /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_occurrences_30834.diff (6 lines)
[INFO] [2023-10-13 13:47:58] ...measurements (/app/public/data/palmer_et_al_pal/measurementsorfacts.txt)
[CMD] [2023-10-13 13:47:58] echo "0a" > /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_measurements_30835.diff
[CMD] [2023-10-13 13:47:59] tail -n +1 /app/public/data/palmer_et_al_pal/converted_csv/palmer_et_al_pal_measurements_30835.csv >> /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_measurements_30835.diff
[CMD] [2023-10-13 13:47:59] echo "." >> /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_measurements_30835.diff
[INFO] [2023-10-13 13:47:59] Created diff: /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_measurements_30835.diff (6 lines)
[STOP] [2023-10-13 13:47:59] calculate_delta
[START] [2023-10-13 13:47:59] parse_diff_and_store
[INFO] [2023-10-13 13:47:59] Handling diff: /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_refs_30836.diff (6 lines)
[INFO] [2023-10-13 13:47:59] Loading refs diff file into memory (6 lines)...
[INFO] [2023-10-13 13:47:59] Storing 4 References (4/4/6)
[INFO] [2023-10-13 13:47:59] Handling diff: /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_nodes_30833.diff (6 lines)
[INFO] [2023-10-13 13:47:59] Loading nodes diff file into memory (6 lines)...
[INFO] [2023-10-13 13:47:59] Storing 4 ScientificNames (8/4/6)
[INFO] [2023-10-13 13:47:59] Storing 4 Nodes (8/4/6)
[INFO] [2023-10-13 13:47:59] Handling diff: /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_occurrences_30834.diff (6 lines)
[INFO] [2023-10-13 13:47:59] Loading occurrences diff file into memory (6 lines)...
[INFO] [2023-10-13 13:47:59] Storing 4 Occurrences (4/4/6)
[INFO] [2023-10-13 13:47:59] Handling diff: /app/public/data/palmer_et_al_pal/diff/palmer_et_al_pal_measurements_30835.diff (6 lines)
[INFO] [2023-10-13 13:47:59] Loading measurements diff file into memory (6 lines)...
[INFO] [2023-10-13 13:47:59] Storing 4 TraitsReferences (16/4/6)
[INFO] [2023-10-13 13:47:59] Storing 4 Traits (16/4/6)
[INFO] [2023-10-13 13:47:59] Storing 8 MetaTraits (16/4/6)
[STOP] [2023-10-13 13:47:59] parse_diff_and_store
[START] [2023-10-13 13:47:59] resolve_keys
[2023-10-13 13:47:59] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:48:07] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:48:07] traits to occurrences...
[INFO] [2023-10-13 13:48:07] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:48:07] Traits to sex term...
[INFO] [2023-10-13 13:48:07] Traits to lifestage term...
[INFO] [2023-10-13 13:48:07] MetaTraits to traits...
[INFO] [2023-10-13 13:48:07] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:48:07] Assocs to occurrences...
[INFO] [2023-10-13 13:48:07] Assocs to nodes...
[INFO] [2023-10-13 13:48:07] Assoc to sex term...
[INFO] [2023-10-13 13:48:07] Assoc to lifestage term...
[INFO] [2023-10-13 13:48:07] MetaAssoc to assocs...
[STOP] [2023-10-13 13:48:07] resolve_keys
[START] [2023-10-13 13:48:07] hold_for_later_1
[STOP] [2023-10-13 13:48:07] hold_for_later_1
[START] [2023-10-13 13:48:07] hold_for_later_2
[STOP] [2023-10-13 13:48:07] hold_for_later_2
[START] [2023-10-13 13:48:07] resolve_missing_parents
[STOP] [2023-10-13 13:48:07] resolve_missing_parents
[START] [2023-10-13 13:48:07] rebuild_nodes
[START] [2023-10-13 13:48:07] Flattener#flatten
[START] [2023-10-13 13:48:07] Flattener#study_resource
[START] [2023-10-13 13:48:07] Flattener#build_ancestry
[STOP] [2023-10-13 13:48:07] Flattener#build_ancestry
[INFO] [2023-10-13 13:48:07] 4 ancestry keys
[START] [2023-10-13 13:48:07] build_node_ancestors
[INFO] [2023-10-13 13:48:07] old ancestors deleted.
[STOP] [2023-10-13 13:48:07] build_node_ancestors
[WARN] [2023-10-13 13:48:07] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:48:07] Flattener#flatten
[STOP] [2023-10-13 13:48:07] rebuild_nodes
[START] [2023-10-13 13:48:07] resolve_missing_media_owners
[STOP] [2023-10-13 13:48:07] resolve_missing_media_owners
[START] [2023-10-13 13:48:07] sanitize_media_verbatims
[STOP] [2023-10-13 13:48:07] sanitize_media_verbatims
[START] [2023-10-13 13:48:07] queue_downloads
[STOP] [2023-10-13 13:48:07] queue_downloads
[START] [2023-10-13 13:48:07] parse_names
[WARN] [2023-10-13 13:48:07] I see 4 names which still need to be parsed.
[WARN] [2023-10-13 13:48:07] Names to parse: 4 formatted: 4 learned: 4 parsed: 4
[STOP] [2023-10-13 13:48:08] parse_names
[START] [2023-10-13 13:48:08] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:48:08] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:48:08] match_nodes
[START] [2023-10-13 13:48:08] map_all_nodes_to_pages
[STOP] [2023-10-13 13:48:08] map_all_nodes_to_pages
[INFO] [2023-10-13 13:48:08] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2023-10-13 13:48:08] update_nodes
[STOP] [2023-10-13 13:48:08] update_nodes
[STOP] [2023-10-13 13:48:08] match_nodes
[START] [2023-10-13 13:48:08] reindex_search
[STOP] [2023-10-13 13:48:08] reindex_search
[START] [2023-10-13 13:48:08] normalize_units
[STOP] [2023-10-13 13:48:08] normalize_units
[START] [2023-10-13 13:48:08] calculate_statistics
[2023-10-13 13:48:08] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:48:08] Duplicate page_id count: 0
[STOP] [2023-10-13 13:48:08] calculate_statistics
[START] [2023-10-13 13:48:08] complete_harvest_instance
[START] [2023-10-13 13:48:08] overall_tsv_creation
[INFO] [2023-10-13 13:48:08] Exporting 4 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:48:08] Processing group of 4 in 1 batches of 10000
[INFO] [2023-10-13 13:48:08] 4 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:48:08] Building Traits map for 4 nodes (this can take a while)...
[INFO] [2023-10-13 13:48:08] Mapped 4 traits (8 meta) for 4 nodes.
[INFO] [2023-10-13 13:48:08] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:48:08] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:48:08] Adding 4 traits...
[INFO] [2023-10-13 13:48:08] 4 metadata added.
[INFO] [2023-10-13 13:48:08] Adding 0 assocs...
[INFO] [2023-10-13 13:48:08] 0 metadata added.
[INFO] [2023-10-13 13:48:52] Processed 4/4 nodes
[INFO] [2023-10-13 13:48:52] Average Time: 43.86
[INFO] [2023-10-13 13:48:52] Total Time: 44s
[STOP] [2023-10-13 13:48:52] overall_tsv_creation
[INFO] [2023-10-13 13:48:52] Done. Check your files:
[INFO] [2023-10-13 13:48:52] (4 lines) /app/public/data/palmer_et_al_pal/publish_nodes.tsv
[INFO] [2023-10-13 13:48:52] (4 lines) /app/public/data/palmer_et_al_pal/publish_scientific_names.tsv
[INFO] [2023-10-13 13:48:52] (5 lines) /app/public/data/palmer_et_al_pal/publish_traits.tsv
[INFO] [2023-10-13 13:48:52] (5 lines) /app/public/data/palmer_et_al_pal/publish_metadata.tsv
[STOP] [2023-10-13 13:48:52] complete_harvest_instance
[START] [2023-10-13 13:48:52] completed
[STOP] [2023-10-13 13:48:52] completed
[STOP] [2023-10-13 13:48:52] logged process, took 55.11

Latest Process

13 Oct 13:47 EXITED currently processing 0