Harvest for Borges et al 2016 Created 13 Oct 09:02

Stage: completed
Fetched: 13 Oct 09:02
Validated: 13 Oct 09:02
Deltas Created 13 Oct 09:02
Units Normalized: 13 Oct 09:02
Ancestry Built: 13 Oct 09:02
Nodes Matched: 13 Oct 09:02
Names Parsed: 13 Oct 09:02
New Models Stored: 13 Oct 09:02
Indexed: 13 Oct 09:02
Completed: 13 Oct 09:03
Time to Harvest: less than a minute
Harvesting Log

(157 lines)
[INFO] [2023-10-13 09:02:36] Created harvest instance #4412
[STOP] [2023-10-13 09:02:36] create_harvest_instance
[START] [2023-10-13 09:02:36] fetch_files
[STOP] [2023-10-13 09:02:36] fetch_files
[START] [2023-10-13 09:02:36] validate_each_file
[INFO] [2023-10-13 09:02:36] Looping over 4 formats...
[INFO] [2023-10-13 09:02:36] ...refs (/app/public/data/borges_et_al_bor/references.txt)
[INFO] [2023-10-13 09:02:36] Valid: /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_refs_30597.csv (2 lines)
[INFO] [2023-10-13 09:02:36] ...nodes (/app/public/data/borges_et_al_bor/taxa.txt)
[INFO] [2023-10-13 09:02:36] Valid: /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_nodes_30596.csv (9 lines)
[INFO] [2023-10-13 09:02:36] ...occurrences (/app/public/data/borges_et_al_bor/occurrences.txt)
[INFO] [2023-10-13 09:02:36] Valid: /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_occurrences_30598.csv (9 lines)
[INFO] [2023-10-13 09:02:36] ...measurements (/app/public/data/borges_et_al_bor/measurementsorfacts.txt)
[INFO] [2023-10-13 09:02:36] Valid: /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_measurements_30599.csv (10 lines)
[STOP] [2023-10-13 09:02:36] validate_each_file
[START] [2023-10-13 09:02:36] convert_to_csv
[INFO] [2023-10-13 09:02:36] Looping over 4 formats...
[INFO] [2023-10-13 09:02:36] ...refs (/app/public/data/borges_et_al_bor/references.txt)
[CMD] [2023-10-13 09:02:36] /usr/bin/sort /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_refs_30597.csv > /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_refs_30597.csv_sorted
[INFO] [2023-10-13 09:02:36] Converted: /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_refs_30597.csv (2 lines)
[INFO] [2023-10-13 09:02:36] ...nodes (/app/public/data/borges_et_al_bor/taxa.txt)
[CMD] [2023-10-13 09:02:36] /usr/bin/sort /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_nodes_30596.csv > /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_nodes_30596.csv_sorted
[INFO] [2023-10-13 09:02:36] Converted: /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_nodes_30596.csv (9 lines)
[INFO] [2023-10-13 09:02:36] ...occurrences (/app/public/data/borges_et_al_bor/occurrences.txt)
[CMD] [2023-10-13 09:02:36] /usr/bin/sort /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_occurrences_30598.csv > /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_occurrences_30598.csv_sorted
[INFO] [2023-10-13 09:02:36] Converted: /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_occurrences_30598.csv (9 lines)
[INFO] [2023-10-13 09:02:36] ...measurements (/app/public/data/borges_et_al_bor/measurementsorfacts.txt)
[CMD] [2023-10-13 09:02:36] /usr/bin/sort /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_measurements_30599.csv > /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_measurements_30599.csv_sorted
[INFO] [2023-10-13 09:02:36] Converted: /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_measurements_30599.csv (10 lines)
[STOP] [2023-10-13 09:02:36] convert_to_csv
[START] [2023-10-13 09:02:36] calculate_delta
[INFO] [2023-10-13 09:02:36] Looping over 4 formats...
[INFO] [2023-10-13 09:02:36] ...refs (/app/public/data/borges_et_al_bor/references.txt)
[CMD] [2023-10-13 09:02:36] echo "0a" > /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_refs_30597.diff
[CMD] [2023-10-13 09:02:37] tail -n +1 /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_refs_30597.csv >> /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_refs_30597.diff
[CMD] [2023-10-13 09:02:37] echo "." >> /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_refs_30597.diff
[INFO] [2023-10-13 09:02:37] Created diff: /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_refs_30597.diff (4 lines)
[INFO] [2023-10-13 09:02:37] ...nodes (/app/public/data/borges_et_al_bor/taxa.txt)
[CMD] [2023-10-13 09:02:37] echo "0a" > /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_nodes_30596.diff
[CMD] [2023-10-13 09:02:37] tail -n +1 /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_nodes_30596.csv >> /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_nodes_30596.diff
[CMD] [2023-10-13 09:02:37] echo "." >> /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_nodes_30596.diff
[INFO] [2023-10-13 09:02:37] Created diff: /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_nodes_30596.diff (11 lines)
[INFO] [2023-10-13 09:02:37] ...occurrences (/app/public/data/borges_et_al_bor/occurrences.txt)
[CMD] [2023-10-13 09:02:37] echo "0a" > /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_occurrences_30598.diff
[CMD] [2023-10-13 09:02:37] tail -n +1 /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_occurrences_30598.csv >> /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_occurrences_30598.diff
[CMD] [2023-10-13 09:02:37] echo "." >> /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_occurrences_30598.diff
[INFO] [2023-10-13 09:02:37] Created diff: /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_occurrences_30598.diff (11 lines)
[INFO] [2023-10-13 09:02:37] ...measurements (/app/public/data/borges_et_al_bor/measurementsorfacts.txt)
[CMD] [2023-10-13 09:02:37] echo "0a" > /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_measurements_30599.diff
[CMD] [2023-10-13 09:02:37] tail -n +1 /app/public/data/borges_et_al_bor/converted_csv/borges_et_al_bor_measurements_30599.csv >> /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_measurements_30599.diff
[CMD] [2023-10-13 09:02:37] echo "." >> /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_measurements_30599.diff
[INFO] [2023-10-13 09:02:37] Created diff: /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_measurements_30599.diff (12 lines)
[STOP] [2023-10-13 09:02:37] calculate_delta
[START] [2023-10-13 09:02:37] parse_diff_and_store
[INFO] [2023-10-13 09:02:37] Handling diff: /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_refs_30597.diff (4 lines)
[INFO] [2023-10-13 09:02:37] Loading refs diff file into memory (4 lines)...
[INFO] [2023-10-13 09:02:37] Storing 2 References (2/2/4)
[INFO] [2023-10-13 09:02:37] Handling diff: /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_nodes_30596.diff (11 lines)
[INFO] [2023-10-13 09:02:38] Loading nodes diff file into memory (11 lines)...
[INFO] [2023-10-13 09:02:38] Storing 9 ScientificNames (18/9/11)
[INFO] [2023-10-13 09:02:38] Storing 9 Nodes (18/9/11)
[INFO] [2023-10-13 09:02:38] Handling diff: /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_occurrences_30598.diff (11 lines)
[INFO] [2023-10-13 09:02:38] Loading occurrences diff file into memory (11 lines)...
[INFO] [2023-10-13 09:02:38] Storing 9 Occurrences (18/9/11)
[INFO] [2023-10-13 09:02:38] Storing 9 OccurrenceMetadata (18/9/11)
[INFO] [2023-10-13 09:02:38] Handling diff: /app/public/data/borges_et_al_bor/diff/borges_et_al_bor_measurements_30599.diff (12 lines)
[INFO] [2023-10-13 09:02:38] Loading measurements diff file into memory (12 lines)...
[INFO] [2023-10-13 09:02:38] Storing 9 TraitsReferences (28/10/12)
[INFO] [2023-10-13 09:02:38] Storing 10 Traits (28/10/12)
[INFO] [2023-10-13 09:02:38] Storing 9 MetaTraits (28/10/12)
[STOP] [2023-10-13 09:02:38] parse_diff_and_store
[START] [2023-10-13 09:02:38] resolve_keys
[2023-10-13 09:02:38] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 09:02:46] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 09:02:46] traits to occurrences...
[INFO] [2023-10-13 09:02:46] traits to nodes (through occurrences)...
[INFO] [2023-10-13 09:02:46] Traits to sex term...
[INFO] [2023-10-13 09:02:46] Traits to lifestage term...
[INFO] [2023-10-13 09:02:46] MetaTraits to traits...
[INFO] [2023-10-13 09:02:46] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 09:02:46] Assocs to occurrences...
[INFO] [2023-10-13 09:02:46] Assocs to nodes...
[INFO] [2023-10-13 09:02:46] Assoc to sex term...
[INFO] [2023-10-13 09:02:46] Assoc to lifestage term...
[INFO] [2023-10-13 09:02:46] MetaAssoc to assocs...
[STOP] [2023-10-13 09:02:46] resolve_keys
[START] [2023-10-13 09:02:46] hold_for_later_1
[STOP] [2023-10-13 09:02:46] hold_for_later_1
[START] [2023-10-13 09:02:46] hold_for_later_2
[STOP] [2023-10-13 09:02:46] hold_for_later_2
[START] [2023-10-13 09:02:46] resolve_missing_parents
[STOP] [2023-10-13 09:02:46] resolve_missing_parents
[START] [2023-10-13 09:02:46] rebuild_nodes
[START] [2023-10-13 09:02:46] Flattener#flatten
[START] [2023-10-13 09:02:46] Flattener#study_resource
[START] [2023-10-13 09:02:46] Flattener#build_ancestry
[STOP] [2023-10-13 09:02:46] Flattener#build_ancestry
[INFO] [2023-10-13 09:02:46] 9 ancestry keys
[START] [2023-10-13 09:02:46] build_node_ancestors
[INFO] [2023-10-13 09:02:46] old ancestors deleted.
[STOP] [2023-10-13 09:02:46] build_node_ancestors
[WARN] [2023-10-13 09:02:46] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 09:02:46] Flattener#flatten
[STOP] [2023-10-13 09:02:46] rebuild_nodes
[START] [2023-10-13 09:02:46] resolve_missing_media_owners
[STOP] [2023-10-13 09:02:46] resolve_missing_media_owners
[START] [2023-10-13 09:02:46] sanitize_media_verbatims
[STOP] [2023-10-13 09:02:46] sanitize_media_verbatims
[START] [2023-10-13 09:02:46] queue_downloads
[STOP] [2023-10-13 09:02:46] queue_downloads
[START] [2023-10-13 09:02:46] parse_names
[WARN] [2023-10-13 09:02:46] I see 9 names which still need to be parsed.
[WARN] [2023-10-13 09:02:46] Names to parse: 9 formatted: 9 learned: 9 parsed: 9
[STOP] [2023-10-13 09:02:47] parse_names
[START] [2023-10-13 09:02:47] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 09:02:47] denormalize_canonical_names_to_nodes
[START] [2023-10-13 09:02:47] match_nodes
[START] [2023-10-13 09:02:47] map_all_nodes_to_pages
[STOP] [2023-10-13 09:02:47] map_all_nodes_to_pages
[INFO] [2023-10-13 09:02:47] ZERO unmatched nodes (of 9)! Nicely done.
[START] [2023-10-13 09:02:47] update_nodes
[STOP] [2023-10-13 09:02:47] update_nodes
[STOP] [2023-10-13 09:02:47] match_nodes
[START] [2023-10-13 09:02:47] reindex_search
[STOP] [2023-10-13 09:02:47] reindex_search
[START] [2023-10-13 09:02:47] normalize_units
[STOP] [2023-10-13 09:02:47] normalize_units
[START] [2023-10-13 09:02:47] calculate_statistics
[2023-10-13 09:02:47] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 09:02:47] Duplicate page_id count: 0
[STOP] [2023-10-13 09:02:47] calculate_statistics
[START] [2023-10-13 09:02:47] complete_harvest_instance
[START] [2023-10-13 09:02:47] overall_tsv_creation
[INFO] [2023-10-13 09:02:48] Exporting 9 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 09:02:48] Processing group of 9 in 1 batches of 10000
[INFO] [2023-10-13 09:02:48] 9 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 09:02:48] Building Traits map for 9 nodes (this can take a while)...
[INFO] [2023-10-13 09:02:48] Mapped 9 traits (9 meta) for 9 nodes.
[INFO] [2023-10-13 09:02:48] Building Associations map (this can take a while)...
[INFO] [2023-10-13 09:02:48] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 09:02:48] Adding 9 traits...
[INFO] [2023-10-13 09:02:48] 10 metadata added.
[INFO] [2023-10-13 09:02:48] Adding 0 assocs...
[INFO] [2023-10-13 09:02:48] 0 metadata added.
[INFO] [2023-10-13 09:03:32] Processed 9/9 nodes
[INFO] [2023-10-13 09:03:32] Average Time: 44.36
[INFO] [2023-10-13 09:03:32] Total Time: 45s
[STOP] [2023-10-13 09:03:32] overall_tsv_creation
[INFO] [2023-10-13 09:03:32] Done. Check your files:
[INFO] [2023-10-13 09:03:32] (9 lines) /app/public/data/borges_et_al_bor/publish_nodes.tsv
[INFO] [2023-10-13 09:03:32] (9 lines) /app/public/data/borges_et_al_bor/publish_scientific_names.tsv
[INFO] [2023-10-13 09:03:32] (10 lines) /app/public/data/borges_et_al_bor/publish_traits.tsv
[INFO] [2023-10-13 09:03:32] (11 lines) /app/public/data/borges_et_al_bor/publish_metadata.tsv
[STOP] [2023-10-13 09:03:32] complete_harvest_instance
[START] [2023-10-13 09:03:32] completed
[STOP] [2023-10-13 09:03:32] completed
[STOP] [2023-10-13 09:03:32] logged process, took 56.32
Latest Process

13 Oct 09:02 EXITED currently processing 0