Harvest for Vidan et al 2017 Created 13 Oct 08:53

Harvesting Log

[INFO] [2023-10-13 08:53:07] Created harvest instance #4411
[STOP] [2023-10-13 08:53:07] create_harvest_instance
[START] [2023-10-13 08:53:07] fetch_files
[STOP] [2023-10-13 08:53:07] fetch_files
[START] [2023-10-13 08:53:07] validate_each_file
[INFO] [2023-10-13 08:53:07] Looping over 4 formats...
[INFO] [2023-10-13 08:53:07] ...refs (/app/public/data/vidan_et_al_vida/references.txt)
[INFO] [2023-10-13 08:53:07] Valid: /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_refs_30595.csv (286 lines)
[INFO] [2023-10-13 08:53:07] ...nodes (/app/public/data/vidan_et_al_vida/taxa.txt)
[INFO] [2023-10-13 08:53:07] Valid: /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_nodes_30592.csv (1112 lines)
[INFO] [2023-10-13 08:53:07] ...occurrences (/app/public/data/vidan_et_al_vida/occurrences.txt)
[INFO] [2023-10-13 08:53:07] Valid: /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_occurrences_30593.csv (1112 lines)
[INFO] [2023-10-13 08:53:07] ...measurements (/app/public/data/vidan_et_al_vida/measurementsorfacts.txt)
[INFO] [2023-10-13 08:53:07] Valid: /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_measurements_30594.csv (1113 lines)
[STOP] [2023-10-13 08:53:07] validate_each_file
[START] [2023-10-13 08:53:07] convert_to_csv
[INFO] [2023-10-13 08:53:07] Looping over 4 formats...
[INFO] [2023-10-13 08:53:07] ...refs (/app/public/data/vidan_et_al_vida/references.txt)
[CMD] [2023-10-13 08:53:07] /usr/bin/sort /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_refs_30595.csv > /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_refs_30595.csv_sorted
[INFO] [2023-10-13 08:53:07] Converted: /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_refs_30595.csv (286 lines)
[INFO] [2023-10-13 08:53:07] ...nodes (/app/public/data/vidan_et_al_vida/taxa.txt)
[CMD] [2023-10-13 08:53:07] /usr/bin/sort /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_nodes_30592.csv > /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_nodes_30592.csv_sorted
[INFO] [2023-10-13 08:53:07] Converted: /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_nodes_30592.csv (1112 lines)
[INFO] [2023-10-13 08:53:07] ...occurrences (/app/public/data/vidan_et_al_vida/occurrences.txt)
[CMD] [2023-10-13 08:53:07] /usr/bin/sort /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_occurrences_30593.csv > /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_occurrences_30593.csv_sorted
[INFO] [2023-10-13 08:53:07] Converted: /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_occurrences_30593.csv (1112 lines)
[INFO] [2023-10-13 08:53:07] ...measurements (/app/public/data/vidan_et_al_vida/measurementsorfacts.txt)
[CMD] [2023-10-13 08:53:07] /usr/bin/sort /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_measurements_30594.csv > /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_measurements_30594.csv_sorted
[INFO] [2023-10-13 08:53:07] Converted: /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_measurements_30594.csv (1113 lines)
[STOP] [2023-10-13 08:53:07] convert_to_csv
[START] [2023-10-13 08:53:07] calculate_delta
[INFO] [2023-10-13 08:53:07] Looping over 4 formats...
[INFO] [2023-10-13 08:53:07] ...refs (/app/public/data/vidan_et_al_vida/references.txt)
[CMD] [2023-10-13 08:53:07] echo "0a" > /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_refs_30595.diff
[CMD] [2023-10-13 08:53:07] tail -n +1 /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_refs_30595.csv >> /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_refs_30595.diff
[CMD] [2023-10-13 08:53:07] echo "." >> /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_refs_30595.diff
[INFO] [2023-10-13 08:53:07] Created diff: /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_refs_30595.diff (288 lines)
[INFO] [2023-10-13 08:53:07] ...nodes (/app/public/data/vidan_et_al_vida/taxa.txt)
[CMD] [2023-10-13 08:53:07] echo "0a" > /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_nodes_30592.diff
[CMD] [2023-10-13 08:53:08] tail -n +1 /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_nodes_30592.csv >> /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_nodes_30592.diff
[CMD] [2023-10-13 08:53:08] echo "." >> /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_nodes_30592.diff
[INFO] [2023-10-13 08:53:08] Created diff: /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_nodes_30592.diff (1114 lines)
[INFO] [2023-10-13 08:53:08] ...occurrences (/app/public/data/vidan_et_al_vida/occurrences.txt)
[CMD] [2023-10-13 08:53:08] echo "0a" > /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_occurrences_30593.diff
[CMD] [2023-10-13 08:53:08] tail -n +1 /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_occurrences_30593.csv >> /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_occurrences_30593.diff
[CMD] [2023-10-13 08:53:08] echo "." >> /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_occurrences_30593.diff
[INFO] [2023-10-13 08:53:08] Created diff: /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_occurrences_30593.diff (1114 lines)
[INFO] [2023-10-13 08:53:08] ...measurements (/app/public/data/vidan_et_al_vida/measurementsorfacts.txt)
[CMD] [2023-10-13 08:53:08] echo "0a" > /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_measurements_30594.diff
[CMD] [2023-10-13 08:53:08] tail -n +1 /app/public/data/vidan_et_al_vida/converted_csv/vidan_et_al_vida_measurements_30594.csv >> /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_measurements_30594.diff
[CMD] [2023-10-13 08:53:08] echo "." >> /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_measurements_30594.diff
[INFO] [2023-10-13 08:53:08] Created diff: /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_measurements_30594.diff (1115 lines)
[STOP] [2023-10-13 08:53:08] calculate_delta
[START] [2023-10-13 08:53:08] parse_diff_and_store
[INFO] [2023-10-13 08:53:08] Handling diff: /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_refs_30595.diff (288 lines)
[INFO] [2023-10-13 08:53:08] Loading refs diff file into memory (288 lines)...
[INFO] [2023-10-13 08:53:08] Storing 286 References (286/286/288)
[INFO] [2023-10-13 08:53:08] Handling diff: /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_nodes_30592.diff (1114 lines)
[INFO] [2023-10-13 08:53:08] Loading nodes diff file into memory (1114 lines)...
[INFO] [2023-10-13 08:53:09] Storing 1116 ScientificNames (2232/1112/1114)
[INFO] [2023-10-13 08:53:09] Storing 1116 Nodes (2232/1112/1114)
[INFO] [2023-10-13 08:53:09] Handling diff: /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_occurrences_30593.diff (1114 lines)
[INFO] [2023-10-13 08:53:09] Loading occurrences diff file into memory (1114 lines)...
[INFO] [2023-10-13 08:53:10] Storing 1112 Occurrences (1112/1112/1114)
[INFO] [2023-10-13 08:53:10] Handling diff: /app/public/data/vidan_et_al_vida/diff/vidan_et_al_vida_measurements_30594.diff (1115 lines)
[INFO] [2023-10-13 08:53:10] Loading measurements diff file into memory (1115 lines)...
[INFO] [2023-10-13 08:53:10] Storing 1113 TraitsReferences (3339/1113/1115)
[INFO] [2023-10-13 08:53:10] Storing 1113 Traits (3339/1113/1115)
[INFO] [2023-10-13 08:53:11] Storing 1113 MetaTraits (3339/1113/1115)
[STOP] [2023-10-13 08:53:11] parse_diff_and_store
[START] [2023-10-13 08:53:11] resolve_keys
[2023-10-13 08:53:11] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 08:53:19] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 08:53:19] traits to occurrences...
[INFO] [2023-10-13 08:53:19] traits to nodes (through occurrences)...
[INFO] [2023-10-13 08:53:19] Traits to sex term...
[INFO] [2023-10-13 08:53:19] Traits to lifestage term...
[INFO] [2023-10-13 08:53:19] MetaTraits to traits...
[INFO] [2023-10-13 08:53:19] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 08:53:19] Assocs to occurrences...
[INFO] [2023-10-13 08:53:19] Assocs to nodes...
[INFO] [2023-10-13 08:53:19] Assoc to sex term...
[INFO] [2023-10-13 08:53:19] Assoc to lifestage term...
[INFO] [2023-10-13 08:53:19] MetaAssoc to assocs...
[STOP] [2023-10-13 08:53:19] resolve_keys
[START] [2023-10-13 08:53:19] hold_for_later_1
[STOP] [2023-10-13 08:53:19] hold_for_later_1
[START] [2023-10-13 08:53:19] hold_for_later_2
[STOP] [2023-10-13 08:53:19] hold_for_later_2
[START] [2023-10-13 08:53:19] resolve_missing_parents
[STOP] [2023-10-13 08:53:19] resolve_missing_parents
[START] [2023-10-13 08:53:19] rebuild_nodes
[START] [2023-10-13 08:53:19] Flattener#flatten
[START] [2023-10-13 08:53:19] Flattener#study_resource
[START] [2023-10-13 08:53:19] Flattener#build_ancestry
[STOP] [2023-10-13 08:53:19] Flattener#build_ancestry
[INFO] [2023-10-13 08:53:19] 1116 ancestry keys
[START] [2023-10-13 08:53:19] build_node_ancestors
[INFO] [2023-10-13 08:53:19] old ancestors deleted.
[STOP] [2023-10-13 08:53:19] build_node_ancestors
[START] [2023-10-13 08:53:20] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 08:53:20] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 08:53:20] Flattener#flatten
[STOP] [2023-10-13 08:53:20] rebuild_nodes
[START] [2023-10-13 08:53:20] resolve_missing_media_owners
[STOP] [2023-10-13 08:53:20] resolve_missing_media_owners
[START] [2023-10-13 08:53:20] sanitize_media_verbatims
[STOP] [2023-10-13 08:53:20] sanitize_media_verbatims
[START] [2023-10-13 08:53:20] queue_downloads
[STOP] [2023-10-13 08:53:20] queue_downloads
[START] [2023-10-13 08:53:20] parse_names
[WARN] [2023-10-13 08:53:20] I see 1116 names which still need to be parsed.
[WARN] [2023-10-13 08:53:20] Names to parse: 1116 formatted: 1116 learned: 1116 parsed: 1116
[STOP] [2023-10-13 08:53:21] parse_names
[START] [2023-10-13 08:53:21] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 08:53:21] denormalize_canonical_names_to_nodes
[START] [2023-10-13 08:53:21] match_nodes
[START] [2023-10-13 08:53:22] map_all_nodes_to_pages
[STOP] [2023-10-13 08:53:53] map_all_nodes_to_pages
[INFO] [2023-10-13 08:53:53] Unmatched nodes (6 of 1116): Canonical: Altiphylax yarkandensis; Node#136981473; ResourceID: Altiphylax yarkandensis; Canonical: Eutopis ashwamedhi; Node#136981902; ResourceID: Eutopis ashwamedhi; Canonical: Gehyra mutilata; Node#136981925; ResourceID: Gehyra mutilata; Canonical: Gekko taylori; Node#136981958; ResourceID: Gekko taylori; Canonical: Japalura vela; Node#136982092; ResourceID: Japalura vela; Canonical: Sitana ponticeriana; Node#136982383; ResourceID: Sitana ponticeriana
[START] [2023-10-13 08:53:53] update_nodes
[STOP] [2023-10-13 08:53:54] update_nodes
[STOP] [2023-10-13 08:53:54] match_nodes
[START] [2023-10-13 08:53:54] reindex_search
[STOP] [2023-10-13 08:53:54] reindex_search
[START] [2023-10-13 08:53:54] normalize_units
[STOP] [2023-10-13 08:53:54] normalize_units
[START] [2023-10-13 08:53:54] calculate_statistics
[INFO] [2023-10-13 08:53:58] Duplicate page_id count: 0
[STOP] [2023-10-13 08:53:58] calculate_statistics
[START] [2023-10-13 08:53:58] complete_harvest_instance
[START] [2023-10-13 08:53:58] overall_tsv_creation
[INFO] [2023-10-13 08:53:58] Exporting 1116 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 08:53:58] Processing group of 1116 in 1 batches of 10000
[INFO] [2023-10-13 08:54:00] 1113 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 08:54:00] Building Traits map for 1116 nodes (this can take a while)...
[INFO] [2023-10-13 08:54:00] Mapped 1113 traits (1113 meta) for 1116 nodes.
[INFO] [2023-10-13 08:54:00] Building Associations map (this can take a while)...
[INFO] [2023-10-13 08:54:00] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 08:54:00] Adding 1113 traits...
[INFO] [2023-10-13 08:54:00] 1109 metadata added.
[INFO] [2023-10-13 08:54:00] Adding 0 assocs...
[INFO] [2023-10-13 08:54:00] 0 metadata added.
[INFO] [2023-10-13 08:54:45] Processed 1116/1116 nodes
[INFO] [2023-10-13 08:54:45] Average Time: 46.62
[INFO] [2023-10-13 08:54:45] Total Time: 48s
[STOP] [2023-10-13 08:54:45] overall_tsv_creation
[INFO] [2023-10-13 08:54:45] Done. Check your files:
[INFO] [2023-10-13 08:54:45] (1116 lines) /app/public/data/vidan_et_al_vida/publish_nodes.tsv
[INFO] [2023-10-13 08:54:45] (4454 lines) /app/public/data/vidan_et_al_vida/publish_node_ancestors.tsv
[INFO] [2023-10-13 08:54:45] (1116 lines) /app/public/data/vidan_et_al_vida/publish_scientific_names.tsv
[INFO] [2023-10-13 08:54:45] (1114 lines) /app/public/data/vidan_et_al_vida/publish_traits.tsv
[INFO] [2023-10-13 08:54:45] (1110 lines) /app/public/data/vidan_et_al_vida/publish_metadata.tsv
[STOP] [2023-10-13 08:54:45] complete_harvest_instance
[START] [2023-10-13 08:54:45] completed
[STOP] [2023-10-13 08:54:45] completed
[STOP] [2023-10-13 08:54:45] logged process, took 98.86

Latest Process

13 Oct 08:53 EXITED currently processing 0