Harvest for Herranz et al 2021 Created 03 Aug 16:08

Stage: completed
Fetched: 03 Aug 16:08
Validated: 03 Aug 16:08
Deltas Created 03 Aug 16:08
Units Normalized: 03 Aug 16:08
Ancestry Built: 03 Aug 16:08
Nodes Matched: 03 Aug 16:08
Names Parsed: 03 Aug 16:08
New Models Stored: 03 Aug 16:08
Indexed: 03 Aug 16:08
Completed: 03 Aug 16:11
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:08:39] Created harvest instance #4163
[STOP] [2022-08-03 16:08:39] create_harvest_instance
[START] [2022-08-03 16:08:39] fetch_files
[STOP] [2022-08-03 16:08:39] fetch_files
[START] [2022-08-03 16:08:39] validate_each_file
[INFO] [2022-08-03 16:08:39] Looping over 3 formats...
[INFO] [2022-08-03 16:08:39] ...nodes (/app/public/data/herranz_et_al_he/taxa.txt)
[INFO] [2022-08-03 16:08:39] Valid: /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_nodes_29552.csv (3 lines)
[INFO] [2022-08-03 16:08:39] ...occurrences (/app/public/data/herranz_et_al_he/occurrences.txt)
[INFO] [2022-08-03 16:08:39] Valid: /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_occurrences_29553.csv (3 lines)
[INFO] [2022-08-03 16:08:39] ...measurements (/app/public/data/herranz_et_al_he/measurementOrFact.txt)
[INFO] [2022-08-03 16:08:39] Valid: /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_measurements_29554.csv (3 lines)
[STOP] [2022-08-03 16:08:39] validate_each_file
[START] [2022-08-03 16:08:39] convert_to_csv
[INFO] [2022-08-03 16:08:39] Looping over 3 formats...
[INFO] [2022-08-03 16:08:39] ...nodes (/app/public/data/herranz_et_al_he/taxa.txt)
[CMD] [2022-08-03 16:08:39] /usr/bin/sort /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_nodes_29552.csv > /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_nodes_29552.csv_sorted
[INFO] [2022-08-03 16:08:40] Converted: /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_nodes_29552.csv (3 lines)
[INFO] [2022-08-03 16:08:40] ...occurrences (/app/public/data/herranz_et_al_he/occurrences.txt)
[CMD] [2022-08-03 16:08:40] /usr/bin/sort /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_occurrences_29553.csv > /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_occurrences_29553.csv_sorted
[INFO] [2022-08-03 16:08:40] Converted: /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_occurrences_29553.csv (3 lines)
[INFO] [2022-08-03 16:08:40] ...measurements (/app/public/data/herranz_et_al_he/measurementOrFact.txt)
[CMD] [2022-08-03 16:08:40] /usr/bin/sort /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_measurements_29554.csv > /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_measurements_29554.csv_sorted
[INFO] [2022-08-03 16:08:40] Converted: /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_measurements_29554.csv (3 lines)
[STOP] [2022-08-03 16:08:40] convert_to_csv
[START] [2022-08-03 16:08:40] calculate_delta
[INFO] [2022-08-03 16:08:40] Looping over 3 formats...
[INFO] [2022-08-03 16:08:40] ...nodes (/app/public/data/herranz_et_al_he/taxa.txt)
[CMD] [2022-08-03 16:08:40] echo "0a" > /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_nodes_29552.diff
[CMD] [2022-08-03 16:08:40] tail -n +1 /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_nodes_29552.csv >> /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_nodes_29552.diff
[CMD] [2022-08-03 16:08:40] echo "." >> /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_nodes_29552.diff
[INFO] [2022-08-03 16:08:40] Created diff: /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_nodes_29552.diff (5 lines)
[INFO] [2022-08-03 16:08:40] ...occurrences (/app/public/data/herranz_et_al_he/occurrences.txt)
[CMD] [2022-08-03 16:08:40] echo "0a" > /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_occurrences_29553.diff
[CMD] [2022-08-03 16:08:40] tail -n +1 /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_occurrences_29553.csv >> /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_occurrences_29553.diff
[CMD] [2022-08-03 16:08:40] echo "." >> /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_occurrences_29553.diff
[INFO] [2022-08-03 16:08:40] Created diff: /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_occurrences_29553.diff (5 lines)
[INFO] [2022-08-03 16:08:40] ...measurements (/app/public/data/herranz_et_al_he/measurementOrFact.txt)
[CMD] [2022-08-03 16:08:40] echo "0a" > /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_measurements_29554.diff
[CMD] [2022-08-03 16:08:40] tail -n +1 /app/public/data/herranz_et_al_he/converted_csv/herranz_et_al_he_measurements_29554.csv >> /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_measurements_29554.diff
[CMD] [2022-08-03 16:08:40] echo "." >> /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_measurements_29554.diff
[INFO] [2022-08-03 16:08:40] Created diff: /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_measurements_29554.diff (5 lines)
[STOP] [2022-08-03 16:08:40] calculate_delta
[START] [2022-08-03 16:08:40] parse_diff_and_store
[INFO] [2022-08-03 16:08:40] Handling diff: /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_nodes_29552.diff (5 lines)
[INFO] [2022-08-03 16:08:40] Loading nodes diff file into memory (5 lines)...
[INFO] [2022-08-03 16:08:40] Storing 3 ScientificNames (6/3/5)
[INFO] [2022-08-03 16:08:40] Storing 3 Nodes (6/3/5)
[INFO] [2022-08-03 16:08:40] Handling diff: /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_occurrences_29553.diff (5 lines)
[INFO] [2022-08-03 16:08:40] Loading occurrences diff file into memory (5 lines)...
[INFO] [2022-08-03 16:08:40] Storing 3 Occurrences (3/3/5)
[INFO] [2022-08-03 16:08:40] Handling diff: /app/public/data/herranz_et_al_he/diff/herranz_et_al_he_measurements_29554.diff (5 lines)
[INFO] [2022-08-03 16:08:40] Loading measurements diff file into memory (5 lines)...
[INFO] [2022-08-03 16:08:40] Storing 3 Traits (6/3/5)
[INFO] [2022-08-03 16:08:40] Storing 3 MetaTraits (6/3/5)
[STOP] [2022-08-03 16:08:40] parse_diff_and_store
[START] [2022-08-03 16:08:40] resolve_keys
[2022-08-03 16:08:40] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:08:47] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:08:47] traits to occurrences...
[INFO] [2022-08-03 16:08:47] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:08:47] Traits to sex term...
[INFO] [2022-08-03 16:08:47] Traits to lifestage term...
[INFO] [2022-08-03 16:08:47] MetaTraits to traits...
[INFO] [2022-08-03 16:08:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:08:47] Assocs to occurrences...
[INFO] [2022-08-03 16:08:47] Assocs to nodes...
[INFO] [2022-08-03 16:08:47] Assoc to sex term...
[INFO] [2022-08-03 16:08:47] Assoc to lifestage term...
[INFO] [2022-08-03 16:08:47] MetaAssoc to assocs...
[STOP] [2022-08-03 16:08:47] resolve_keys
[START] [2022-08-03 16:08:47] hold_for_later_1
[STOP] [2022-08-03 16:08:47] hold_for_later_1
[START] [2022-08-03 16:08:47] hold_for_later_2
[STOP] [2022-08-03 16:08:47] hold_for_later_2
[START] [2022-08-03 16:08:47] resolve_missing_parents
[STOP] [2022-08-03 16:08:47] resolve_missing_parents
[START] [2022-08-03 16:08:47] rebuild_nodes
[START] [2022-08-03 16:08:47] Flattener#flatten
[START] [2022-08-03 16:08:47] Flattener#study_resource
[START] [2022-08-03 16:08:47] Flattener#build_ancestry
[STOP] [2022-08-03 16:08:47] Flattener#build_ancestry
[INFO] [2022-08-03 16:08:47] 3 ancestry keys
[START] [2022-08-03 16:08:47] build_node_ancestors
[INFO] [2022-08-03 16:08:47] old ancestors deleted.
[STOP] [2022-08-03 16:08:47] build_node_ancestors
[WARN] [2022-08-03 16:08:47] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:08:47] Flattener#flatten
[STOP] [2022-08-03 16:08:47] rebuild_nodes
[START] [2022-08-03 16:08:47] resolve_missing_media_owners
[STOP] [2022-08-03 16:08:47] resolve_missing_media_owners
[START] [2022-08-03 16:08:47] sanitize_media_verbatims
[STOP] [2022-08-03 16:08:47] sanitize_media_verbatims
[START] [2022-08-03 16:08:47] queue_downloads
[STOP] [2022-08-03 16:08:47] queue_downloads
[START] [2022-08-03 16:08:47] parse_names
[WARN] [2022-08-03 16:08:47] I see 3 names which still need to be parsed.
[WARN] [2022-08-03 16:08:47] Names to parse: 3 formatted: 3 learned: 3 parsed: 3
[STOP] [2022-08-03 16:08:48] parse_names
[START] [2022-08-03 16:08:48] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:08:48] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:08:48] match_nodes
[START] [2022-08-03 16:08:48] map_all_nodes_to_pages
[STOP] [2022-08-03 16:08:48] map_all_nodes_to_pages
[INFO] [2022-08-03 16:08:48] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2022-08-03 16:08:48] update_nodes
[STOP] [2022-08-03 16:08:48] update_nodes
[STOP] [2022-08-03 16:08:48] match_nodes
[START] [2022-08-03 16:08:48] reindex_search
[STOP] [2022-08-03 16:08:48] reindex_search
[START] [2022-08-03 16:08:48] normalize_units
[STOP] [2022-08-03 16:08:48] normalize_units
[START] [2022-08-03 16:08:48] calculate_statistics
[2022-08-03 16:08:48] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:08:48] Duplicate page_id count: 0
[STOP] [2022-08-03 16:08:48] calculate_statistics
[START] [2022-08-03 16:08:48] complete_harvest_instance
[START] [2022-08-03 16:08:48] overall_tsv_creation
[INFO] [2022-08-03 16:08:48] Exporting 3 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:08:48] Processing group of 3 in 1 batches of 10000
[INFO] [2022-08-03 16:09:30] 3 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:09:30] Building Traits map for 3 nodes (this can take a while)...
[INFO] [2022-08-03 16:10:24] Mapped 3 traits (3 meta) for 3 nodes.
[INFO] [2022-08-03 16:10:24] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:10:24] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:10:24] Adding 3 traits...
[INFO] [2022-08-03 16:10:24] 0 metadata added.
[INFO] [2022-08-03 16:10:24] Adding 0 assocs...
[INFO] [2022-08-03 16:10:24] 0 metadata added.
[INFO] [2022-08-03 16:11:06] Processed 3/3 nodes
[INFO] [2022-08-03 16:11:06] Average Time: 112.54
[INFO] [2022-08-03 16:11:06] Total Time: 2m18s
[STOP] [2022-08-03 16:11:06] overall_tsv_creation
[INFO] [2022-08-03 16:11:06] Done. Check your files:
[INFO] [2022-08-03 16:11:06] (3 lines) /app/public/data/herranz_et_al_he/publish_nodes.tsv
[INFO] [2022-08-03 16:11:06] (3 lines) /app/public/data/herranz_et_al_he/publish_scientific_names.tsv
[INFO] [2022-08-03 16:11:06] (4 lines) /app/public/data/herranz_et_al_he/publish_traits.tsv
[INFO] [2022-08-03 16:11:06] (1 lines) /app/public/data/herranz_et_al_he/publish_metadata.tsv
[STOP] [2022-08-03 16:11:06] complete_harvest_instance
[START] [2022-08-03 16:11:06] completed
[STOP] [2022-08-03 16:11:06] completed
[STOP] [2022-08-03 16:11:06] logged process, took 148.51
Latest Process

03 Aug 16:08 EXITED currently processing 0