Harvest for Cartwright 2003 Created 09 Sep 15:36

Stage: completed
Fetched: 09 Sep 15:36
Validated: 09 Sep 15:36
Deltas Created 09 Sep 15:36
Units Normalized: 09 Sep 15:36
Ancestry Built: 09 Sep 15:36
Nodes Matched: 09 Sep 15:36
Names Parsed: 09 Sep 15:36
New Models Stored: 09 Sep 15:36
Indexed: 09 Sep 15:36
Completed: 09 Sep 15:41
Time to Harvest: less than a minute
Harvesting Log

(141 lines)
[INFO] [2022-09-09 15:36:18] Created harvest instance #4212
[STOP] [2022-09-09 15:36:18] create_harvest_instance
[START] [2022-09-09 15:36:18] fetch_files
[STOP] [2022-09-09 15:36:18] fetch_files
[START] [2022-09-09 15:36:18] validate_each_file
[INFO] [2022-09-09 15:36:18] Looping over 3 formats...
[INFO] [2022-09-09 15:36:18] ...nodes (/app/public/data/cartwright_cartw/taxa.txt)
[INFO] [2022-09-09 15:36:18] Valid: /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_nodes_29697.csv (1 lines)
[INFO] [2022-09-09 15:36:18] ...occurrences (/app/public/data/cartwright_cartw/occurrences.txt)
[INFO] [2022-09-09 15:36:18] Valid: /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_occurrences_29698.csv (1 lines)
[INFO] [2022-09-09 15:36:18] ...measurements (/app/public/data/cartwright_cartw/measurementOrFact.txt)
[INFO] [2022-09-09 15:36:18] Valid: /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_measurements_29699.csv (5 lines)
[STOP] [2022-09-09 15:36:18] validate_each_file
[START] [2022-09-09 15:36:18] convert_to_csv
[INFO] [2022-09-09 15:36:18] Looping over 3 formats...
[INFO] [2022-09-09 15:36:18] ...nodes (/app/public/data/cartwright_cartw/taxa.txt)
[CMD] [2022-09-09 15:36:18] /usr/bin/sort /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_nodes_29697.csv > /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_nodes_29697.csv_sorted
[INFO] [2022-09-09 15:36:18] Converted: /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_nodes_29697.csv (1 lines)
[INFO] [2022-09-09 15:36:18] ...occurrences (/app/public/data/cartwright_cartw/occurrences.txt)
[CMD] [2022-09-09 15:36:18] /usr/bin/sort /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_occurrences_29698.csv > /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_occurrences_29698.csv_sorted
[INFO] [2022-09-09 15:36:18] Converted: /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_occurrences_29698.csv (1 lines)
[INFO] [2022-09-09 15:36:18] ...measurements (/app/public/data/cartwright_cartw/measurementOrFact.txt)
[CMD] [2022-09-09 15:36:18] /usr/bin/sort /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_measurements_29699.csv > /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_measurements_29699.csv_sorted
[INFO] [2022-09-09 15:36:18] Converted: /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_measurements_29699.csv (5 lines)
[STOP] [2022-09-09 15:36:18] convert_to_csv
[START] [2022-09-09 15:36:18] calculate_delta
[INFO] [2022-09-09 15:36:18] Looping over 3 formats...
[INFO] [2022-09-09 15:36:18] ...nodes (/app/public/data/cartwright_cartw/taxa.txt)
[CMD] [2022-09-09 15:36:18] echo "0a" > /app/public/data/cartwright_cartw/diff/cartwright_cartw_nodes_29697.diff
[CMD] [2022-09-09 15:36:18] tail -n +1 /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_nodes_29697.csv >> /app/public/data/cartwright_cartw/diff/cartwright_cartw_nodes_29697.diff
[CMD] [2022-09-09 15:36:18] echo "." >> /app/public/data/cartwright_cartw/diff/cartwright_cartw_nodes_29697.diff
[INFO] [2022-09-09 15:36:18] Created diff: /app/public/data/cartwright_cartw/diff/cartwright_cartw_nodes_29697.diff (3 lines)
[INFO] [2022-09-09 15:36:18] ...occurrences (/app/public/data/cartwright_cartw/occurrences.txt)
[CMD] [2022-09-09 15:36:18] echo "0a" > /app/public/data/cartwright_cartw/diff/cartwright_cartw_occurrences_29698.diff
[CMD] [2022-09-09 15:36:18] tail -n +1 /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_occurrences_29698.csv >> /app/public/data/cartwright_cartw/diff/cartwright_cartw_occurrences_29698.diff
[CMD] [2022-09-09 15:36:18] echo "." >> /app/public/data/cartwright_cartw/diff/cartwright_cartw_occurrences_29698.diff
[INFO] [2022-09-09 15:36:18] Created diff: /app/public/data/cartwright_cartw/diff/cartwright_cartw_occurrences_29698.diff (3 lines)
[INFO] [2022-09-09 15:36:18] ...measurements (/app/public/data/cartwright_cartw/measurementOrFact.txt)
[CMD] [2022-09-09 15:36:18] echo "0a" > /app/public/data/cartwright_cartw/diff/cartwright_cartw_measurements_29699.diff
[CMD] [2022-09-09 15:36:18] tail -n +1 /app/public/data/cartwright_cartw/converted_csv/cartwright_cartw_measurements_29699.csv >> /app/public/data/cartwright_cartw/diff/cartwright_cartw_measurements_29699.diff
[CMD] [2022-09-09 15:36:18] echo "." >> /app/public/data/cartwright_cartw/diff/cartwright_cartw_measurements_29699.diff
[INFO] [2022-09-09 15:36:18] Created diff: /app/public/data/cartwright_cartw/diff/cartwright_cartw_measurements_29699.diff (7 lines)
[STOP] [2022-09-09 15:36:18] calculate_delta
[START] [2022-09-09 15:36:18] parse_diff_and_store
[INFO] [2022-09-09 15:36:18] Handling diff: /app/public/data/cartwright_cartw/diff/cartwright_cartw_nodes_29697.diff (3 lines)
[INFO] [2022-09-09 15:36:18] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-09-09 15:36:19] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-09-09 15:36:19] Storing 1 Nodes (2/1/3)
[INFO] [2022-09-09 15:36:19] Handling diff: /app/public/data/cartwright_cartw/diff/cartwright_cartw_occurrences_29698.diff (3 lines)
[INFO] [2022-09-09 15:36:19] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-09-09 15:36:20] Storing 1 Occurrences (2/1/3)
[INFO] [2022-09-09 15:36:20] Storing 1 OccurrenceMetadata (2/1/3)
[INFO] [2022-09-09 15:36:20] Handling diff: /app/public/data/cartwright_cartw/diff/cartwright_cartw_measurements_29699.diff (7 lines)
[INFO] [2022-09-09 15:36:20] Loading measurements diff file into memory (7 lines)...
[INFO] [2022-09-09 15:36:20] Storing 5 Traits (6/5/7)
[INFO] [2022-09-09 15:36:20] Storing 1 MetaTraits (6/5/7)
[STOP] [2022-09-09 15:36:20] parse_diff_and_store
[START] [2022-09-09 15:36:20] resolve_keys
[2022-09-09 15:36:20] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-09-09 15:36:27] Occurrences to nodes (through scientific_names)...
[INFO] [2022-09-09 15:36:27] traits to occurrences...
[INFO] [2022-09-09 15:36:27] traits to nodes (through occurrences)...
[INFO] [2022-09-09 15:36:27] Traits to sex term...
[INFO] [2022-09-09 15:36:27] Traits to lifestage term...
[INFO] [2022-09-09 15:36:27] MetaTraits to traits...
[INFO] [2022-09-09 15:36:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-09-09 15:36:27] Assocs to occurrences...
[INFO] [2022-09-09 15:36:27] Assocs to nodes...
[INFO] [2022-09-09 15:36:27] Assoc to sex term...
[INFO] [2022-09-09 15:36:27] Assoc to lifestage term...
[INFO] [2022-09-09 15:36:27] MetaAssoc to assocs...
[STOP] [2022-09-09 15:36:27] resolve_keys
[START] [2022-09-09 15:36:27] hold_for_later_1
[STOP] [2022-09-09 15:36:27] hold_for_later_1
[START] [2022-09-09 15:36:27] hold_for_later_2
[STOP] [2022-09-09 15:36:27] hold_for_later_2
[START] [2022-09-09 15:36:27] resolve_missing_parents
[STOP] [2022-09-09 15:36:27] resolve_missing_parents
[START] [2022-09-09 15:36:27] rebuild_nodes
[START] [2022-09-09 15:36:27] Flattener#flatten
[START] [2022-09-09 15:36:27] Flattener#study_resource
[START] [2022-09-09 15:36:27] Flattener#build_ancestry
[STOP] [2022-09-09 15:36:27] Flattener#build_ancestry
[INFO] [2022-09-09 15:36:27] 1 ancestry keys
[START] [2022-09-09 15:36:27] build_node_ancestors
[INFO] [2022-09-09 15:36:27] old ancestors deleted.
[STOP] [2022-09-09 15:36:27] build_node_ancestors
[WARN] [2022-09-09 15:36:27] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-09-09 15:36:27] Flattener#flatten
[STOP] [2022-09-09 15:36:27] rebuild_nodes
[START] [2022-09-09 15:36:28] resolve_missing_media_owners
[STOP] [2022-09-09 15:36:28] resolve_missing_media_owners
[START] [2022-09-09 15:36:28] sanitize_media_verbatims
[STOP] [2022-09-09 15:36:28] sanitize_media_verbatims
[START] [2022-09-09 15:36:28] queue_downloads
[STOP] [2022-09-09 15:36:28] queue_downloads
[START] [2022-09-09 15:36:28] parse_names
[WARN] [2022-09-09 15:36:28] I see 1 names which still need to be parsed.
[WARN] [2022-09-09 15:36:28] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-09-09 15:36:29] parse_names
[START] [2022-09-09 15:36:29] denormalize_canonical_names_to_nodes
[STOP] [2022-09-09 15:36:29] denormalize_canonical_names_to_nodes
[START] [2022-09-09 15:36:29] match_nodes
[START] [2022-09-09 15:36:29] map_all_nodes_to_pages
[STOP] [2022-09-09 15:36:29] map_all_nodes_to_pages
[INFO] [2022-09-09 15:36:29] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-09-09 15:36:29] update_nodes
[STOP] [2022-09-09 15:36:29] update_nodes
[STOP] [2022-09-09 15:36:29] match_nodes
[START] [2022-09-09 15:36:29] reindex_search
[STOP] [2022-09-09 15:36:29] reindex_search
[START] [2022-09-09 15:36:29] normalize_units
[STOP] [2022-09-09 15:36:29] normalize_units
[START] [2022-09-09 15:36:29] calculate_statistics
[2022-09-09 15:36:29] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-09-09 15:36:29] Duplicate page_id count: 0
[STOP] [2022-09-09 15:36:29] calculate_statistics
[START] [2022-09-09 15:36:29] complete_harvest_instance
[START] [2022-09-09 15:36:29] overall_tsv_creation
[INFO] [2022-09-09 15:36:29] Processing group of 1 in 1 batches of 10000
[INFO] [2022-09-09 15:39:20] 1 Traits (unfiltered)...
[INFO] [2022-09-09 15:39:20] Building Traits map (this can take a while)...
[INFO] [2022-09-09 15:40:22] Done. 1 traits mapped (1 meta).
[INFO] [2022-09-09 15:40:22] Building Associations map (this can take a while)...
[INFO] [2022-09-09 15:40:22] Done. 0 assocs mapped (0 meta).
[INFO] [2022-09-09 15:40:22] Adding 1 traits...
[INFO] [2022-09-09 15:40:22] 4 metadata added.
[INFO] [2022-09-09 15:40:22] Adding 0 assocs...
[INFO] [2022-09-09 15:40:22] 0 metadata added.
[INFO] [2022-09-09 15:41:11] Average Time: 138.84
[INFO] [2022-09-09 15:41:11] Total Time: 4m43s
[STOP] [2022-09-09 15:41:11] overall_tsv_creation
[INFO] [2022-09-09 15:41:11] Done. Check your files:
[INFO] [2022-09-09 15:41:11] (1 lines) /app/public/data/cartwright_cartw/publish_nodes.tsv
[INFO] [2022-09-09 15:41:11] (1 lines) /app/public/data/cartwright_cartw/publish_scientific_names.tsv
[INFO] [2022-09-09 15:41:11] (2 lines) /app/public/data/cartwright_cartw/publish_traits.tsv
[INFO] [2022-09-09 15:41:11] (5 lines) /app/public/data/cartwright_cartw/publish_metadata.tsv
[STOP] [2022-09-09 15:41:11] complete_harvest_instance
[START] [2022-09-09 15:41:11] completed
[STOP] [2022-09-09 15:41:11] completed
[STOP] [2022-09-09 15:41:11] logged process, took 293.13
Latest Process

09 Sep 15:36 EXITED currently processing 0