Harvest for Dooling et al 2000 Created 14 Oct 08:27

Stage: completed
Fetched: 14 Oct 08:27
Validated: 14 Oct 08:27
Deltas Created 14 Oct 08:27
Units Normalized: 14 Oct 08:27
Ancestry Built: 14 Oct 08:27
Nodes Matched: 14 Oct 08:27
Names Parsed: 14 Oct 08:27
New Models Stored: 14 Oct 08:27
Indexed: 14 Oct 08:27
Completed: 14 Oct 08:28
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
[INFO] [2023-10-14 08:27:23] Created harvest instance #4468
[STOP] [2023-10-14 08:27:23] create_harvest_instance
[START] [2023-10-14 08:27:23] fetch_files
[STOP] [2023-10-14 08:27:23] fetch_files
[START] [2023-10-14 08:27:23] validate_each_file
[INFO] [2023-10-14 08:27:23] Looping over 4 formats...
[INFO] [2023-10-14 08:27:23] ...refs (/app/public/data/dooling_et_al_do/references.txt)
[INFO] [2023-10-14 08:27:23] Valid: /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_refs_30880.csv (19 lines)
[INFO] [2023-10-14 08:27:23] ...nodes (/app/public/data/dooling_et_al_do/taxa.txt)
[INFO] [2023-10-14 08:27:23] Valid: /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_nodes_30877.csv (19 lines)
[INFO] [2023-10-14 08:27:23] ...occurrences (/app/public/data/dooling_et_al_do/occurrences.txt)
[INFO] [2023-10-14 08:27:23] Valid: /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_occurrences_30878.csv (19 lines)
[INFO] [2023-10-14 08:27:23] ...measurements (/app/public/data/dooling_et_al_do/measurementsorfacts.txt)
[INFO] [2023-10-14 08:27:23] Valid: /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_measurements_30879.csv (206 lines)
[STOP] [2023-10-14 08:27:23] validate_each_file
[START] [2023-10-14 08:27:23] convert_to_csv
[INFO] [2023-10-14 08:27:23] Looping over 4 formats...
[INFO] [2023-10-14 08:27:23] ...refs (/app/public/data/dooling_et_al_do/references.txt)
[CMD] [2023-10-14 08:27:23] /usr/bin/sort /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_refs_30880.csv > /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_refs_30880.csv_sorted
[INFO] [2023-10-14 08:27:24] Converted: /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_refs_30880.csv (19 lines)
[INFO] [2023-10-14 08:27:24] ...nodes (/app/public/data/dooling_et_al_do/taxa.txt)
[CMD] [2023-10-14 08:27:24] /usr/bin/sort /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_nodes_30877.csv > /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_nodes_30877.csv_sorted
[INFO] [2023-10-14 08:27:24] Converted: /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_nodes_30877.csv (19 lines)
[INFO] [2023-10-14 08:27:24] ...occurrences (/app/public/data/dooling_et_al_do/occurrences.txt)
[CMD] [2023-10-14 08:27:24] /usr/bin/sort /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_occurrences_30878.csv > /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_occurrences_30878.csv_sorted
[INFO] [2023-10-14 08:27:24] Converted: /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_occurrences_30878.csv (19 lines)
[INFO] [2023-10-14 08:27:24] ...measurements (/app/public/data/dooling_et_al_do/measurementsorfacts.txt)
[CMD] [2023-10-14 08:27:24] /usr/bin/sort /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_measurements_30879.csv > /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_measurements_30879.csv_sorted
[INFO] [2023-10-14 08:27:24] Converted: /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_measurements_30879.csv (206 lines)
[STOP] [2023-10-14 08:27:24] convert_to_csv
[START] [2023-10-14 08:27:24] calculate_delta
[INFO] [2023-10-14 08:27:24] Looping over 4 formats...
[INFO] [2023-10-14 08:27:24] ...refs (/app/public/data/dooling_et_al_do/references.txt)
[CMD] [2023-10-14 08:27:25] echo "0a" > /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_refs_30880.diff
[CMD] [2023-10-14 08:27:25] tail -n +1 /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_refs_30880.csv >> /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_refs_30880.diff
[CMD] [2023-10-14 08:27:25] echo "." >> /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_refs_30880.diff
[INFO] [2023-10-14 08:27:25] Created diff: /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_refs_30880.diff (21 lines)
[INFO] [2023-10-14 08:27:25] ...nodes (/app/public/data/dooling_et_al_do/taxa.txt)
[CMD] [2023-10-14 08:27:25] echo "0a" > /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_nodes_30877.diff
[CMD] [2023-10-14 08:27:25] tail -n +1 /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_nodes_30877.csv >> /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_nodes_30877.diff
[CMD] [2023-10-14 08:27:25] echo "." >> /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_nodes_30877.diff
[INFO] [2023-10-14 08:27:25] Created diff: /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_nodes_30877.diff (21 lines)
[INFO] [2023-10-14 08:27:25] ...occurrences (/app/public/data/dooling_et_al_do/occurrences.txt)
[CMD] [2023-10-14 08:27:25] echo "0a" > /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_occurrences_30878.diff
[CMD] [2023-10-14 08:27:25] tail -n +1 /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_occurrences_30878.csv >> /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_occurrences_30878.diff
[CMD] [2023-10-14 08:27:25] echo "." >> /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_occurrences_30878.diff
[INFO] [2023-10-14 08:27:26] Created diff: /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_occurrences_30878.diff (21 lines)
[INFO] [2023-10-14 08:27:26] ...measurements (/app/public/data/dooling_et_al_do/measurementsorfacts.txt)
[CMD] [2023-10-14 08:27:26] echo "0a" > /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_measurements_30879.diff
[CMD] [2023-10-14 08:27:26] tail -n +1 /app/public/data/dooling_et_al_do/converted_csv/dooling_et_al_do_measurements_30879.csv >> /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_measurements_30879.diff
[CMD] [2023-10-14 08:27:26] echo "." >> /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_measurements_30879.diff
[INFO] [2023-10-14 08:27:26] Created diff: /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_measurements_30879.diff (208 lines)
[STOP] [2023-10-14 08:27:26] calculate_delta
[START] [2023-10-14 08:27:26] parse_diff_and_store
[INFO] [2023-10-14 08:27:26] Handling diff: /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_refs_30880.diff (21 lines)
[INFO] [2023-10-14 08:27:26] Loading refs diff file into memory (21 lines)...
[INFO] [2023-10-14 08:27:26] Storing 19 References (19/19/21)
[INFO] [2023-10-14 08:27:26] Handling diff: /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_nodes_30877.diff (21 lines)
[INFO] [2023-10-14 08:27:26] Loading nodes diff file into memory (21 lines)...
[INFO] [2023-10-14 08:27:26] Storing 19 ScientificNames (38/19/21)
[INFO] [2023-10-14 08:27:26] Storing 19 Nodes (38/19/21)
[INFO] [2023-10-14 08:27:26] Handling diff: /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_occurrences_30878.diff (21 lines)
[INFO] [2023-10-14 08:27:26] Loading occurrences diff file into memory (21 lines)...
[INFO] [2023-10-14 08:27:26] Storing 19 Occurrences (19/19/21)
[INFO] [2023-10-14 08:27:26] Handling diff: /app/public/data/dooling_et_al_do/diff/dooling_et_al_do_measurements_30879.diff (208 lines)
[INFO] [2023-10-14 08:27:26] Loading measurements diff file into memory (208 lines)...
[INFO] [2023-10-14 08:27:26] Storing 147 TraitsReferences (502/206/208)
[INFO] [2023-10-14 08:27:26] Storing 206 Traits (502/206/208)
[INFO] [2023-10-14 08:27:26] Storing 149 MetaTraits (502/206/208)
[STOP] [2023-10-14 08:27:26] parse_diff_and_store
[START] [2023-10-14 08:27:26] resolve_keys
[2023-10-14 08:27:26] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-14 08:27:34] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-14 08:27:34] traits to occurrences...
[INFO] [2023-10-14 08:27:34] traits to nodes (through occurrences)...
[INFO] [2023-10-14 08:27:34] Traits to sex term...
[INFO] [2023-10-14 08:27:34] Traits to lifestage term...
[INFO] [2023-10-14 08:27:34] MetaTraits to traits...
[INFO] [2023-10-14 08:27:34] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-14 08:27:34] Assocs to occurrences...
[INFO] [2023-10-14 08:27:34] Assocs to nodes...
[INFO] [2023-10-14 08:27:34] Assoc to sex term...
[INFO] [2023-10-14 08:27:34] Assoc to lifestage term...
[INFO] [2023-10-14 08:27:34] MetaAssoc to assocs...
[STOP] [2023-10-14 08:27:34] resolve_keys
[START] [2023-10-14 08:27:34] hold_for_later_1
[STOP] [2023-10-14 08:27:34] hold_for_later_1
[START] [2023-10-14 08:27:34] hold_for_later_2
[STOP] [2023-10-14 08:27:34] hold_for_later_2
[START] [2023-10-14 08:27:34] resolve_missing_parents
[STOP] [2023-10-14 08:27:34] resolve_missing_parents
[START] [2023-10-14 08:27:34] rebuild_nodes
[START] [2023-10-14 08:27:34] Flattener#flatten
[START] [2023-10-14 08:27:34] Flattener#study_resource
[START] [2023-10-14 08:27:34] Flattener#build_ancestry
[STOP] [2023-10-14 08:27:34] Flattener#build_ancestry
[INFO] [2023-10-14 08:27:34] 19 ancestry keys
[START] [2023-10-14 08:27:34] build_node_ancestors
[INFO] [2023-10-14 08:27:34] old ancestors deleted.
[STOP] [2023-10-14 08:27:34] build_node_ancestors
[WARN] [2023-10-14 08:27:34] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-14 08:27:34] Flattener#flatten
[STOP] [2023-10-14 08:27:34] rebuild_nodes
[START] [2023-10-14 08:27:34] resolve_missing_media_owners
[STOP] [2023-10-14 08:27:34] resolve_missing_media_owners
[START] [2023-10-14 08:27:34] sanitize_media_verbatims
[STOP] [2023-10-14 08:27:34] sanitize_media_verbatims
[START] [2023-10-14 08:27:34] queue_downloads
[STOP] [2023-10-14 08:27:34] queue_downloads
[START] [2023-10-14 08:27:34] parse_names
[WARN] [2023-10-14 08:27:34] I see 19 names which still need to be parsed.
[WARN] [2023-10-14 08:27:34] Names to parse: 19 formatted: 19 learned: 19 parsed: 19
[STOP] [2023-10-14 08:27:36] parse_names
[START] [2023-10-14 08:27:36] denormalize_canonical_names_to_nodes
[STOP] [2023-10-14 08:27:36] denormalize_canonical_names_to_nodes
[START] [2023-10-14 08:27:36] match_nodes
[START] [2023-10-14 08:27:36] map_all_nodes_to_pages
[STOP] [2023-10-14 08:27:36] map_all_nodes_to_pages
[INFO] [2023-10-14 08:27:36] ZERO unmatched nodes (of 19)! Nicely done.
[START] [2023-10-14 08:27:36] update_nodes
[STOP] [2023-10-14 08:27:36] update_nodes
[STOP] [2023-10-14 08:27:36] match_nodes
[START] [2023-10-14 08:27:36] reindex_search
[STOP] [2023-10-14 08:27:36] reindex_search
[START] [2023-10-14 08:27:36] normalize_units
[STOP] [2023-10-14 08:27:36] normalize_units
[START] [2023-10-14 08:27:36] calculate_statistics
[2023-10-14 08:27:36] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-14 08:27:36] Duplicate page_id count: 0
[STOP] [2023-10-14 08:27:36] calculate_statistics
[START] [2023-10-14 08:27:36] complete_harvest_instance
[START] [2023-10-14 08:27:36] overall_tsv_creation
[INFO] [2023-10-14 08:27:36] Exporting 19 nodes as TSV in batches of 10000...
[INFO] [2023-10-14 08:27:36] Processing group of 19 in 1 batches of 10000
[INFO] [2023-10-14 08:27:36] 75 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-14 08:27:36] Building Traits map for 19 nodes (this can take a while)...
[INFO] [2023-10-14 08:27:36] Mapped 75 traits (149 meta) for 19 nodes.
[INFO] [2023-10-14 08:27:36] Building Associations map (this can take a while)...
[INFO] [2023-10-14 08:27:36] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-14 08:27:36] Adding 75 traits...
[INFO] [2023-10-14 08:27:36] 274 metadata added.
[INFO] [2023-10-14 08:27:36] Adding 0 assocs...
[INFO] [2023-10-14 08:27:36] 0 metadata added.
[INFO] [2023-10-14 08:28:20] Processed 19/19 nodes
[INFO] [2023-10-14 08:28:20] Average Time: 43.92
[INFO] [2023-10-14 08:28:20] Total Time: 44s
[STOP] [2023-10-14 08:28:20] overall_tsv_creation
[INFO] [2023-10-14 08:28:20] Done. Check your files:
[INFO] [2023-10-14 08:28:20] (19 lines) /app/public/data/dooling_et_al_do/publish_nodes.tsv
[INFO] [2023-10-14 08:28:20] (19 lines) /app/public/data/dooling_et_al_do/publish_scientific_names.tsv
[INFO] [2023-10-14 08:28:20] (76 lines) /app/public/data/dooling_et_al_do/publish_traits.tsv
[INFO] [2023-10-14 08:28:20] (275 lines) /app/public/data/dooling_et_al_do/publish_metadata.tsv
[STOP] [2023-10-14 08:28:20] complete_harvest_instance
[START] [2023-10-14 08:28:20] completed
[STOP] [2023-10-14 08:28:20] completed
[STOP] [2023-10-14 08:28:20] logged process, took 57.24
Latest Process

14 Oct 08:27 EXITED currently processing 0