Harvest for Sorensen et al 2008 Created 03 Aug 15:52

Stage: completed
Fetched: 03 Aug 15:52
Validated: 03 Aug 15:52
Deltas Created 03 Aug 15:52
Units Normalized: 03 Aug 15:52
Ancestry Built: 03 Aug 15:52
Nodes Matched: 03 Aug 15:52
Names Parsed: 03 Aug 15:52
New Models Stored: 03 Aug 15:52
Indexed: 03 Aug 15:52
Completed: 03 Aug 15:54
Time to Harvest: less than a minute
Harvesting Log

(143 lines)
[INFO] [2022-08-03 15:52:00] Created harvest instance #4157
[STOP] [2022-08-03 15:52:00] create_harvest_instance
[START] [2022-08-03 15:52:00] fetch_files
[STOP] [2022-08-03 15:52:00] fetch_files
[START] [2022-08-03 15:52:00] validate_each_file
[INFO] [2022-08-03 15:52:00] Looping over 3 formats...
[INFO] [2022-08-03 15:52:00] ...nodes (/app/public/data/sorensen_et_al_s/taxa.txt)
[INFO] [2022-08-03 15:52:00] Valid: /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_nodes_29534.csv (1 lines)
[INFO] [2022-08-03 15:52:00] ...occurrences (/app/public/data/sorensen_et_al_s/occurrences.txt)
[INFO] [2022-08-03 15:52:00] Valid: /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_occurrences_29535.csv (1 lines)
[INFO] [2022-08-03 15:52:00] ...measurements (/app/public/data/sorensen_et_al_s/measurementOrFact.txt)
[INFO] [2022-08-03 15:52:00] Valid: /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_measurements_29536.csv (2 lines)
[STOP] [2022-08-03 15:52:00] validate_each_file
[START] [2022-08-03 15:52:00] convert_to_csv
[INFO] [2022-08-03 15:52:00] Looping over 3 formats...
[INFO] [2022-08-03 15:52:00] ...nodes (/app/public/data/sorensen_et_al_s/taxa.txt)
[CMD] [2022-08-03 15:52:00] /usr/bin/sort /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_nodes_29534.csv > /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_nodes_29534.csv_sorted
[INFO] [2022-08-03 15:52:00] Converted: /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_nodes_29534.csv (1 lines)
[INFO] [2022-08-03 15:52:00] ...occurrences (/app/public/data/sorensen_et_al_s/occurrences.txt)
[CMD] [2022-08-03 15:52:00] /usr/bin/sort /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_occurrences_29535.csv > /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_occurrences_29535.csv_sorted
[INFO] [2022-08-03 15:52:00] Converted: /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_occurrences_29535.csv (1 lines)
[INFO] [2022-08-03 15:52:00] ...measurements (/app/public/data/sorensen_et_al_s/measurementOrFact.txt)
[CMD] [2022-08-03 15:52:00] /usr/bin/sort /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_measurements_29536.csv > /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_measurements_29536.csv_sorted
[INFO] [2022-08-03 15:52:00] Converted: /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_measurements_29536.csv (2 lines)
[STOP] [2022-08-03 15:52:00] convert_to_csv
[START] [2022-08-03 15:52:00] calculate_delta
[INFO] [2022-08-03 15:52:00] Looping over 3 formats...
[INFO] [2022-08-03 15:52:00] ...nodes (/app/public/data/sorensen_et_al_s/taxa.txt)
[CMD] [2022-08-03 15:52:00] echo "0a" > /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_nodes_29534.diff
[CMD] [2022-08-03 15:52:00] tail -n +1 /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_nodes_29534.csv >> /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_nodes_29534.diff
[CMD] [2022-08-03 15:52:00] echo "." >> /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_nodes_29534.diff
[INFO] [2022-08-03 15:52:00] Created diff: /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_nodes_29534.diff (3 lines)
[INFO] [2022-08-03 15:52:00] ...occurrences (/app/public/data/sorensen_et_al_s/occurrences.txt)
[CMD] [2022-08-03 15:52:00] echo "0a" > /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_occurrences_29535.diff
[CMD] [2022-08-03 15:52:00] tail -n +1 /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_occurrences_29535.csv >> /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_occurrences_29535.diff
[CMD] [2022-08-03 15:52:00] echo "." >> /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_occurrences_29535.diff
[INFO] [2022-08-03 15:52:00] Created diff: /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_occurrences_29535.diff (3 lines)
[INFO] [2022-08-03 15:52:00] ...measurements (/app/public/data/sorensen_et_al_s/measurementOrFact.txt)
[CMD] [2022-08-03 15:52:00] echo "0a" > /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_measurements_29536.diff
[CMD] [2022-08-03 15:52:00] tail -n +1 /app/public/data/sorensen_et_al_s/converted_csv/sorensen_et_al_s_measurements_29536.csv >> /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_measurements_29536.diff
[CMD] [2022-08-03 15:52:00] echo "." >> /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_measurements_29536.diff
[INFO] [2022-08-03 15:52:00] Created diff: /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_measurements_29536.diff (4 lines)
[STOP] [2022-08-03 15:52:00] calculate_delta
[START] [2022-08-03 15:52:00] parse_diff_and_store
[INFO] [2022-08-03 15:52:00] Handling diff: /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_nodes_29534.diff (3 lines)
[INFO] [2022-08-03 15:52:00] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 15:52:00] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 15:52:00] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 15:52:00] Handling diff: /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_occurrences_29535.diff (3 lines)
[INFO] [2022-08-03 15:52:00] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 15:52:00] Storing 1 Occurrences (2/1/3)
[INFO] [2022-08-03 15:52:00] Storing 1 OccurrenceMetadata (2/1/3)
[INFO] [2022-08-03 15:52:00] Handling diff: /app/public/data/sorensen_et_al_s/diff/sorensen_et_al_s_measurements_29536.diff (4 lines)
[INFO] [2022-08-03 15:52:00] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 15:52:00] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 15:52:00] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 15:52:00] parse_diff_and_store
[START] [2022-08-03 15:52:00] resolve_keys
[2022-08-03 15:52:00] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 15:52:07] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 15:52:07] traits to occurrences...
[INFO] [2022-08-03 15:52:07] traits to nodes (through occurrences)...
[INFO] [2022-08-03 15:52:07] Traits to sex term...
[INFO] [2022-08-03 15:52:07] Traits to lifestage term...
[INFO] [2022-08-03 15:52:07] MetaTraits to traits...
[INFO] [2022-08-03 15:52:07] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 15:52:07] Assocs to occurrences...
[INFO] [2022-08-03 15:52:07] Assocs to nodes...
[INFO] [2022-08-03 15:52:07] Assoc to sex term...
[INFO] [2022-08-03 15:52:07] Assoc to lifestage term...
[INFO] [2022-08-03 15:52:07] MetaAssoc to assocs...
[STOP] [2022-08-03 15:52:07] resolve_keys
[START] [2022-08-03 15:52:07] hold_for_later_1
[STOP] [2022-08-03 15:52:07] hold_for_later_1
[START] [2022-08-03 15:52:07] hold_for_later_2
[STOP] [2022-08-03 15:52:07] hold_for_later_2
[START] [2022-08-03 15:52:07] resolve_missing_parents
[STOP] [2022-08-03 15:52:07] resolve_missing_parents
[START] [2022-08-03 15:52:07] rebuild_nodes
[START] [2022-08-03 15:52:07] Flattener#flatten
[START] [2022-08-03 15:52:07] Flattener#study_resource
[START] [2022-08-03 15:52:07] Flattener#build_ancestry
[STOP] [2022-08-03 15:52:07] Flattener#build_ancestry
[INFO] [2022-08-03 15:52:07] 1 ancestry keys
[START] [2022-08-03 15:52:07] build_node_ancestors
[INFO] [2022-08-03 15:52:07] old ancestors deleted.
[STOP] [2022-08-03 15:52:07] build_node_ancestors
[WARN] [2022-08-03 15:52:07] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 15:52:07] Flattener#flatten
[STOP] [2022-08-03 15:52:07] rebuild_nodes
[START] [2022-08-03 15:52:07] resolve_missing_media_owners
[STOP] [2022-08-03 15:52:07] resolve_missing_media_owners
[START] [2022-08-03 15:52:07] sanitize_media_verbatims
[STOP] [2022-08-03 15:52:07] sanitize_media_verbatims
[START] [2022-08-03 15:52:07] queue_downloads
[STOP] [2022-08-03 15:52:07] queue_downloads
[START] [2022-08-03 15:52:07] parse_names
[WARN] [2022-08-03 15:52:07] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 15:52:08] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 15:52:09] parse_names
[START] [2022-08-03 15:52:09] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 15:52:09] denormalize_canonical_names_to_nodes
[START] [2022-08-03 15:52:09] match_nodes
[START] [2022-08-03 15:52:09] map_all_nodes_to_pages
[STOP] [2022-08-03 15:52:09] map_all_nodes_to_pages
[INFO] [2022-08-03 15:52:09] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 15:52:09] update_nodes
[STOP] [2022-08-03 15:52:09] update_nodes
[STOP] [2022-08-03 15:52:09] match_nodes
[START] [2022-08-03 15:52:09] reindex_search
[STOP] [2022-08-03 15:52:09] reindex_search
[START] [2022-08-03 15:52:09] normalize_units
[STOP] [2022-08-03 15:52:09] normalize_units
[START] [2022-08-03 15:52:09] calculate_statistics
[2022-08-03 15:52:09] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 15:52:09] Duplicate page_id count: 0
[STOP] [2022-08-03 15:52:09] calculate_statistics
[START] [2022-08-03 15:52:09] complete_harvest_instance
[START] [2022-08-03 15:52:09] overall_tsv_creation
[INFO] [2022-08-03 15:52:09] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 15:52:09] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 15:52:51] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 15:52:51] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 15:53:43] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 15:53:43] Building Associations map (this can take a while)...
[INFO] [2022-08-03 15:53:43] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 15:53:43] Adding 1 traits...
[INFO] [2022-08-03 15:53:43] 1 metadata added.
[INFO] [2022-08-03 15:53:43] Adding 0 assocs...
[INFO] [2022-08-03 15:53:43] 0 metadata added.
[INFO] [2022-08-03 15:54:25] Processed 1/1 nodes
[INFO] [2022-08-03 15:54:25] Average Time: 109.97
[INFO] [2022-08-03 15:54:25] Total Time: 2m16s
[STOP] [2022-08-03 15:54:25] overall_tsv_creation
[INFO] [2022-08-03 15:54:25] Done. Check your files:
[INFO] [2022-08-03 15:54:25] (1 lines) /app/public/data/sorensen_et_al_s/publish_nodes.tsv
[INFO] [2022-08-03 15:54:25] (1 lines) /app/public/data/sorensen_et_al_s/publish_scientific_names.tsv
[INFO] [2022-08-03 15:54:25] (2 lines) /app/public/data/sorensen_et_al_s/publish_traits.tsv
[INFO] [2022-08-03 15:54:25] (2 lines) /app/public/data/sorensen_et_al_s/publish_metadata.tsv
[STOP] [2022-08-03 15:54:25] complete_harvest_instance
[START] [2022-08-03 15:54:25] completed
[STOP] [2022-08-03 15:54:25] completed
[STOP] [2022-08-03 15:54:25] logged process, took 145.43
Latest Process

03 Aug 15:51 EXITED currently processing 0