Harvest for Salvini Plawen and Mayr 1977 Created 11 Oct 21:03

Harvesting Log

[INFO] [2023-10-11 21:03:43] Created harvest instance #4406
[STOP] [2023-10-11 21:03:43] create_harvest_instance
[START] [2023-10-11 21:03:43] fetch_files
[STOP] [2023-10-11 21:03:43] fetch_files
[START] [2023-10-11 21:03:43] validate_each_file
[INFO] [2023-10-11 21:03:43] Looping over 4 formats...
[INFO] [2023-10-11 21:03:43] ...refs (/app/public/data/salvini_plawen_m/references.tsv)
[INFO] [2023-10-11 21:03:44] Valid: /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_refs_30572.csv (0 lines)
[INFO] [2023-10-11 21:03:44] ...nodes (/app/public/data/salvini_plawen_m/taxa.txt)
[INFO] [2023-10-11 21:03:44] Valid: /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_nodes_30569.csv (34 lines)
[INFO] [2023-10-11 21:03:44] ...occurrences (/app/public/data/salvini_plawen_m/occurrences.txt)
[INFO] [2023-10-11 21:03:44] Valid: /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_occurrences_30570.csv (34 lines)
[INFO] [2023-10-11 21:03:44] ...measurements (/app/public/data/salvini_plawen_m/measurementsorfacts.txt)
[INFO] [2023-10-11 21:03:44] Valid: /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_measurements_30571.csv (117 lines)
[STOP] [2023-10-11 21:03:44] validate_each_file
[START] [2023-10-11 21:03:44] convert_to_csv
[INFO] [2023-10-11 21:03:44] Looping over 4 formats...
[INFO] [2023-10-11 21:03:44] ...refs (/app/public/data/salvini_plawen_m/references.tsv)
[CMD] [2023-10-11 21:03:44] /usr/bin/sort /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_refs_30572.csv > /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_refs_30572.csv_sorted
[INFO] [2023-10-11 21:03:44] Converted: /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_refs_30572.csv (0 lines)
[INFO] [2023-10-11 21:03:44] ...nodes (/app/public/data/salvini_plawen_m/taxa.txt)
[CMD] [2023-10-11 21:03:44] /usr/bin/sort /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_nodes_30569.csv > /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_nodes_30569.csv_sorted
[INFO] [2023-10-11 21:03:44] Converted: /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_nodes_30569.csv (34 lines)
[INFO] [2023-10-11 21:03:44] ...occurrences (/app/public/data/salvini_plawen_m/occurrences.txt)
[CMD] [2023-10-11 21:03:44] /usr/bin/sort /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_occurrences_30570.csv > /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_occurrences_30570.csv_sorted
[INFO] [2023-10-11 21:03:45] Converted: /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_occurrences_30570.csv (34 lines)
[INFO] [2023-10-11 21:03:45] ...measurements (/app/public/data/salvini_plawen_m/measurementsorfacts.txt)
[CMD] [2023-10-11 21:03:45] /usr/bin/sort /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_measurements_30571.csv > /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_measurements_30571.csv_sorted
[INFO] [2023-10-11 21:03:45] Converted: /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_measurements_30571.csv (117 lines)
[STOP] [2023-10-11 21:03:45] convert_to_csv
[START] [2023-10-11 21:03:45] calculate_delta
[INFO] [2023-10-11 21:03:45] Looping over 4 formats...
[INFO] [2023-10-11 21:03:45] ...refs (/app/public/data/salvini_plawen_m/references.tsv)
[CMD] [2023-10-11 21:03:45] echo "0a" > /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_refs_30572.diff
[CMD] [2023-10-11 21:03:45] tail -n +1 /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_refs_30572.csv >> /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_refs_30572.diff
[CMD] [2023-10-11 21:03:45] echo "." >> /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_refs_30572.diff
[INFO] [2023-10-11 21:03:45] Created diff: /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_refs_30572.diff (2 lines)
[INFO] [2023-10-11 21:03:45] ...nodes (/app/public/data/salvini_plawen_m/taxa.txt)
[CMD] [2023-10-11 21:03:45] echo "0a" > /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_nodes_30569.diff
[CMD] [2023-10-11 21:03:45] tail -n +1 /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_nodes_30569.csv >> /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_nodes_30569.diff
[CMD] [2023-10-11 21:03:45] echo "." >> /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_nodes_30569.diff
[INFO] [2023-10-11 21:03:45] Created diff: /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_nodes_30569.diff (36 lines)
[INFO] [2023-10-11 21:03:45] ...occurrences (/app/public/data/salvini_plawen_m/occurrences.txt)
[CMD] [2023-10-11 21:03:45] echo "0a" > /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_occurrences_30570.diff
[CMD] [2023-10-11 21:03:45] tail -n +1 /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_occurrences_30570.csv >> /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_occurrences_30570.diff
[CMD] [2023-10-11 21:03:45] echo "." >> /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_occurrences_30570.diff
[INFO] [2023-10-11 21:03:45] Created diff: /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_occurrences_30570.diff (36 lines)
[INFO] [2023-10-11 21:03:45] ...measurements (/app/public/data/salvini_plawen_m/measurementsorfacts.txt)
[CMD] [2023-10-11 21:03:45] echo "0a" > /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_measurements_30571.diff
[CMD] [2023-10-11 21:03:45] tail -n +1 /app/public/data/salvini_plawen_m/converted_csv/salvini_plawen_m_measurements_30571.csv >> /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_measurements_30571.diff
[CMD] [2023-10-11 21:03:45] echo "." >> /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_measurements_30571.diff
[INFO] [2023-10-11 21:03:45] Created diff: /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_measurements_30571.diff (119 lines)
[STOP] [2023-10-11 21:03:45] calculate_delta
[START] [2023-10-11 21:03:45] parse_diff_and_store
[INFO] [2023-10-11 21:03:45] Handling diff: /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_refs_30572.diff (2 lines)
[INFO] [2023-10-11 21:03:46] Loading refs diff file into memory (2 lines)...
[INFO] [2023-10-11 21:03:46] Handling diff: /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_nodes_30569.diff (36 lines)
[INFO] [2023-10-11 21:03:46] Loading nodes diff file into memory (36 lines)...
[WARN] [2023-10-11 21:03:46] Filtered Scientific Name `Mya  arenaria` to `Mya arenaria`
[INFO] [2023-10-11 21:03:46] Storing 34 ScientificNames (68/34/36)
[INFO] [2023-10-11 21:03:46] Storing 34 Nodes (68/34/36)
[INFO] [2023-10-11 21:03:46] Handling diff: /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_occurrences_30570.diff (36 lines)
[INFO] [2023-10-11 21:03:46] Loading occurrences diff file into memory (36 lines)...
[INFO] [2023-10-11 21:03:46] Storing 34 Occurrences (42/34/36)
[INFO] [2023-10-11 21:03:46] Storing 8 OccurrenceMetadata (42/34/36)
[INFO] [2023-10-11 21:03:46] Handling diff: /app/public/data/salvini_plawen_m/diff/salvini_plawen_m_measurements_30571.diff (119 lines)
[INFO] [2023-10-11 21:03:46] Loading measurements diff file into memory (119 lines)...
[WARN] [2023-10-11 21:03:46] IGNORING a measurement NOT of a taxon (3a) with NO parent and NO occurrence ID.
[WARN] [2023-10-11 21:03:46] IGNORING a measurement NOT of a taxon (3b) with NO parent and NO occurrence ID.
[WARN] [2023-10-11 21:03:46] IGNORING a measurement NOT of a taxon (3c) with NO parent and NO occurrence ID.
[WARN] [2023-10-11 21:03:46] IGNORING a measurement NOT of a taxon (3d) with NO parent and NO occurrence ID.
[WARN] [2023-10-11 21:03:46] IGNORING a measurement NOT of a taxon (3e) with NO parent and NO occurrence ID.
[WARN] [2023-10-11 21:03:46] IGNORING a measurement NOT of a taxon (3f) with NO parent and NO occurrence ID.
[INFO] [2023-10-11 21:03:46] Storing 111 Traits (156/117/119)
[INFO] [2023-10-11 21:03:46] Storing 45 MetaTraits (156/117/119)
[STOP] [2023-10-11 21:03:46] parse_diff_and_store
[START] [2023-10-11 21:03:46] resolve_keys
[2023-10-11 21:03:46] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-11 21:03:54] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-11 21:03:54] traits to occurrences...
[INFO] [2023-10-11 21:03:54] traits to nodes (through occurrences)...
[INFO] [2023-10-11 21:03:54] Traits to sex term...
[INFO] [2023-10-11 21:03:54] Traits to lifestage term...
[INFO] [2023-10-11 21:03:54] MetaTraits to traits...
[INFO] [2023-10-11 21:03:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-11 21:03:54] Assocs to occurrences...
[INFO] [2023-10-11 21:03:54] Assocs to nodes...
[INFO] [2023-10-11 21:03:54] Assoc to sex term...
[INFO] [2023-10-11 21:03:54] Assoc to lifestage term...
[INFO] [2023-10-11 21:03:54] MetaAssoc to assocs...
[STOP] [2023-10-11 21:03:54] resolve_keys
[START] [2023-10-11 21:03:54] hold_for_later_1
[STOP] [2023-10-11 21:03:54] hold_for_later_1
[START] [2023-10-11 21:03:54] hold_for_later_2
[STOP] [2023-10-11 21:03:54] hold_for_later_2
[START] [2023-10-11 21:03:54] resolve_missing_parents
[STOP] [2023-10-11 21:03:54] resolve_missing_parents
[START] [2023-10-11 21:03:54] rebuild_nodes
[START] [2023-10-11 21:03:54] Flattener#flatten
[START] [2023-10-11 21:03:54] Flattener#study_resource
[START] [2023-10-11 21:03:54] Flattener#build_ancestry
[STOP] [2023-10-11 21:03:54] Flattener#build_ancestry
[INFO] [2023-10-11 21:03:54] 34 ancestry keys
[START] [2023-10-11 21:03:54] build_node_ancestors
[INFO] [2023-10-11 21:03:54] old ancestors deleted.
[STOP] [2023-10-11 21:03:54] build_node_ancestors
[WARN] [2023-10-11 21:03:54] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-11 21:03:54] Flattener#flatten
[STOP] [2023-10-11 21:03:54] rebuild_nodes
[START] [2023-10-11 21:03:54] resolve_missing_media_owners
[STOP] [2023-10-11 21:03:54] resolve_missing_media_owners
[START] [2023-10-11 21:03:54] sanitize_media_verbatims
[STOP] [2023-10-11 21:03:54] sanitize_media_verbatims
[START] [2023-10-11 21:03:54] queue_downloads
[STOP] [2023-10-11 21:03:54] queue_downloads
[START] [2023-10-11 21:03:54] parse_names
[WARN] [2023-10-11 21:03:54] I see 34 names which still need to be parsed.
[WARN] [2023-10-11 21:03:54] Names to parse: 34 formatted: 34 learned: 34 parsed: 34
[STOP] [2023-10-11 21:03:55] parse_names
[START] [2023-10-11 21:03:55] denormalize_canonical_names_to_nodes
[STOP] [2023-10-11 21:03:55] denormalize_canonical_names_to_nodes
[START] [2023-10-11 21:03:55] match_nodes
[START] [2023-10-11 21:03:55] map_all_nodes_to_pages
[STOP] [2023-10-11 21:03:55] map_all_nodes_to_pages
[INFO] [2023-10-11 21:03:55] ZERO unmatched nodes (of 34)! Nicely done.
[START] [2023-10-11 21:03:55] update_nodes
[STOP] [2023-10-11 21:03:55] update_nodes
[STOP] [2023-10-11 21:03:55] match_nodes
[START] [2023-10-11 21:03:55] reindex_search
[STOP] [2023-10-11 21:03:55] reindex_search
[START] [2023-10-11 21:03:55] normalize_units
[STOP] [2023-10-11 21:03:55] normalize_units
[START] [2023-10-11 21:03:55] calculate_statistics
[2023-10-11 21:03:55] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-11 21:03:55] Duplicate page_id count: 0
[STOP] [2023-10-11 21:03:55] calculate_statistics
[START] [2023-10-11 21:03:55] complete_harvest_instance
[START] [2023-10-11 21:03:55] overall_tsv_creation
[INFO] [2023-10-11 21:03:55] Exporting 34 nodes as TSV in batches of 10000...
[INFO] [2023-10-11 21:03:55] Processing group of 34 in 1 batches of 10000
[INFO] [2023-10-11 21:03:55] 35 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-11 21:03:55] Building Traits map for 34 nodes (this can take a while)...
[INFO] [2023-10-11 21:03:55] Mapped 35 traits (44 meta) for 34 nodes.
[INFO] [2023-10-11 21:03:55] Building Associations map (this can take a while)...
[INFO] [2023-10-11 21:03:55] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-11 21:03:55] Adding 35 traits...
[INFO] [2023-10-11 21:03:55] 76 metadata added.
[INFO] [2023-10-11 21:03:55] Adding 0 assocs...
[INFO] [2023-10-11 21:03:55] 0 metadata added.
[INFO] [2023-10-11 21:04:40] Processed 34/34 nodes
[INFO] [2023-10-11 21:04:40] Average Time: 44.39
[INFO] [2023-10-11 21:04:40] Total Time: 45s
[STOP] [2023-10-11 21:04:40] overall_tsv_creation
[INFO] [2023-10-11 21:04:40] Done. Check your files:
[INFO] [2023-10-11 21:04:40] (34 lines) /app/public/data/salvini_plawen_m/publish_nodes.tsv
[INFO] [2023-10-11 21:04:40] (34 lines) /app/public/data/salvini_plawen_m/publish_scientific_names.tsv
[INFO] [2023-10-11 21:04:40] (36 lines) /app/public/data/salvini_plawen_m/publish_traits.tsv
[INFO] [2023-10-11 21:04:40] (77 lines) /app/public/data/salvini_plawen_m/publish_metadata.tsv
[STOP] [2023-10-11 21:04:40] complete_harvest_instance
[START] [2023-10-11 21:04:40] completed
[STOP] [2023-10-11 21:04:40] completed
[STOP] [2023-10-11 21:04:40] logged process, took 57.55

Latest Process

11 Oct 21:03 EXITED currently processing 0