Harvest for Mexican Amphibians Created 14 Oct 09:52

Harvesting Log

[INFO] [2023-10-14 09:52:44] Created harvest instance #4481
[STOP] [2023-10-14 09:52:44] create_harvest_instance
[START] [2023-10-14 09:52:44] fetch_files
[STOP] [2023-10-14 09:52:44] fetch_files
[START] [2023-10-14 09:52:44] validate_each_file
[INFO] [2023-10-14 09:52:44] Looping over 4 formats...
[INFO] [2023-10-14 09:52:44] ...refs (/app/public/data/mexican_amphibia/reference.txt)
[INFO] [2023-10-14 09:52:44] Valid: /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_refs_30935.csv (113 lines)
[INFO] [2023-10-14 09:52:44] ...nodes (/app/public/data/mexican_amphibia/taxon.tab)
[INFO] [2023-10-14 09:52:44] Valid: /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_nodes_30932.csv (369 lines)
[INFO] [2023-10-14 09:52:44] ...occurrences (/app/public/data/mexican_amphibia/occurrence.tab)
[INFO] [2023-10-14 09:52:44] Valid: /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_occurrences_30934.csv (1116 lines)
[INFO] [2023-10-14 09:52:44] ...measurements (/app/public/data/mexican_amphibia/measurement_or_fact.txt)
[INFO] [2023-10-14 09:52:44] Valid: /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_measurements_30933.csv (1851 lines)
[STOP] [2023-10-14 09:52:44] validate_each_file
[START] [2023-10-14 09:52:44] convert_to_csv
[INFO] [2023-10-14 09:52:44] Looping over 4 formats...
[INFO] [2023-10-14 09:52:44] ...refs (/app/public/data/mexican_amphibia/reference.txt)
[CMD] [2023-10-14 09:52:44] /usr/bin/sort /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_refs_30935.csv > /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_refs_30935.csv_sorted
[INFO] [2023-10-14 09:52:44] Converted: /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_refs_30935.csv (113 lines)
[INFO] [2023-10-14 09:52:44] ...nodes (/app/public/data/mexican_amphibia/taxon.tab)
[CMD] [2023-10-14 09:52:44] /usr/bin/sort /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_nodes_30932.csv > /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_nodes_30932.csv_sorted
[INFO] [2023-10-14 09:52:44] Converted: /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_nodes_30932.csv (369 lines)
[INFO] [2023-10-14 09:52:44] ...occurrences (/app/public/data/mexican_amphibia/occurrence.tab)
[CMD] [2023-10-14 09:52:44] /usr/bin/sort /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_occurrences_30934.csv > /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_occurrences_30934.csv_sorted
[INFO] [2023-10-14 09:52:45] Converted: /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_occurrences_30934.csv (1116 lines)
[INFO] [2023-10-14 09:52:45] ...measurements (/app/public/data/mexican_amphibia/measurement_or_fact.txt)
[CMD] [2023-10-14 09:52:45] /usr/bin/sort /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_measurements_30933.csv > /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_measurements_30933.csv_sorted
[INFO] [2023-10-14 09:52:45] Converted: /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_measurements_30933.csv (1851 lines)
[STOP] [2023-10-14 09:52:45] convert_to_csv
[START] [2023-10-14 09:52:45] calculate_delta
[INFO] [2023-10-14 09:52:45] Looping over 4 formats...
[INFO] [2023-10-14 09:52:45] ...refs (/app/public/data/mexican_amphibia/reference.txt)
[CMD] [2023-10-14 09:52:45] echo "0a" > /app/public/data/mexican_amphibia/diff/mexican_amphibia_refs_30935.diff
[CMD] [2023-10-14 09:52:45] tail -n +1 /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_refs_30935.csv >> /app/public/data/mexican_amphibia/diff/mexican_amphibia_refs_30935.diff
[CMD] [2023-10-14 09:52:45] echo "." >> /app/public/data/mexican_amphibia/diff/mexican_amphibia_refs_30935.diff
[INFO] [2023-10-14 09:52:45] Created diff: /app/public/data/mexican_amphibia/diff/mexican_amphibia_refs_30935.diff (115 lines)
[INFO] [2023-10-14 09:52:45] ...nodes (/app/public/data/mexican_amphibia/taxon.tab)
[CMD] [2023-10-14 09:52:45] echo "0a" > /app/public/data/mexican_amphibia/diff/mexican_amphibia_nodes_30932.diff
[CMD] [2023-10-14 09:52:45] tail -n +1 /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_nodes_30932.csv >> /app/public/data/mexican_amphibia/diff/mexican_amphibia_nodes_30932.diff
[CMD] [2023-10-14 09:52:45] echo "." >> /app/public/data/mexican_amphibia/diff/mexican_amphibia_nodes_30932.diff
[INFO] [2023-10-14 09:52:45] Created diff: /app/public/data/mexican_amphibia/diff/mexican_amphibia_nodes_30932.diff (371 lines)
[INFO] [2023-10-14 09:52:45] ...occurrences (/app/public/data/mexican_amphibia/occurrence.tab)
[CMD] [2023-10-14 09:52:45] echo "0a" > /app/public/data/mexican_amphibia/diff/mexican_amphibia_occurrences_30934.diff
[CMD] [2023-10-14 09:52:45] tail -n +1 /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_occurrences_30934.csv >> /app/public/data/mexican_amphibia/diff/mexican_amphibia_occurrences_30934.diff
[CMD] [2023-10-14 09:52:45] echo "." >> /app/public/data/mexican_amphibia/diff/mexican_amphibia_occurrences_30934.diff
[INFO] [2023-10-14 09:52:45] Created diff: /app/public/data/mexican_amphibia/diff/mexican_amphibia_occurrences_30934.diff (1118 lines)
[INFO] [2023-10-14 09:52:45] ...measurements (/app/public/data/mexican_amphibia/measurement_or_fact.txt)
[CMD] [2023-10-14 09:52:45] echo "0a" > /app/public/data/mexican_amphibia/diff/mexican_amphibia_measurements_30933.diff
[CMD] [2023-10-14 09:52:46] tail -n +1 /app/public/data/mexican_amphibia/converted_csv/mexican_amphibia_measurements_30933.csv >> /app/public/data/mexican_amphibia/diff/mexican_amphibia_measurements_30933.diff
[CMD] [2023-10-14 09:52:46] echo "." >> /app/public/data/mexican_amphibia/diff/mexican_amphibia_measurements_30933.diff
[INFO] [2023-10-14 09:52:46] Created diff: /app/public/data/mexican_amphibia/diff/mexican_amphibia_measurements_30933.diff (1853 lines)
[STOP] [2023-10-14 09:52:46] calculate_delta
[START] [2023-10-14 09:52:46] parse_diff_and_store
[INFO] [2023-10-14 09:52:46] Handling diff: /app/public/data/mexican_amphibia/diff/mexican_amphibia_refs_30935.diff (115 lines)
[INFO] [2023-10-14 09:52:46] Loading refs diff file into memory (115 lines)...
[INFO] [2023-10-14 09:52:46] Storing 113 References (113/113/115)
[INFO] [2023-10-14 09:52:46] Handling diff: /app/public/data/mexican_amphibia/diff/mexican_amphibia_nodes_30932.diff (371 lines)
[INFO] [2023-10-14 09:52:46] Loading nodes diff file into memory (371 lines)...
[INFO] [2023-10-14 09:52:46] Storing 369 ScientificNames (738/369/371)
[INFO] [2023-10-14 09:52:46] Storing 369 Nodes (738/369/371)
[INFO] [2023-10-14 09:52:47] Handling diff: /app/public/data/mexican_amphibia/diff/mexican_amphibia_occurrences_30934.diff (1118 lines)
[INFO] [2023-10-14 09:52:47] Loading occurrences diff file into memory (1118 lines)...
[INFO] [2023-10-14 09:52:47] Storing 1116 Occurrences (1323/1116/1118)
[INFO] [2023-10-14 09:52:47] Storing 207 OccurrenceMetadata (1323/1116/1118)
[INFO] [2023-10-14 09:52:47] Handling diff: /app/public/data/mexican_amphibia/diff/mexican_amphibia_measurements_30933.diff (1853 lines)
[INFO] [2023-10-14 09:52:47] Loading measurements diff file into memory (1853 lines)...
[INFO] [2023-10-14 09:52:48] Storing 1851 Traits (5208/1851/1853)
[INFO] [2023-10-14 09:52:49] Storing 860 TraitsReferences (5208/1851/1853)
[INFO] [2023-10-14 09:52:49] Storing 2497 MetaTraits (5208/1851/1853)
[STOP] [2023-10-14 09:52:49] parse_diff_and_store
[START] [2023-10-14 09:52:49] resolve_keys
[2023-10-14 09:52:50] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-14 09:52:58] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-14 09:52:58] traits to occurrences...
[INFO] [2023-10-14 09:52:58] traits to nodes (through occurrences)...
[INFO] [2023-10-14 09:52:58] Traits to sex term...
[INFO] [2023-10-14 09:52:58] Traits to lifestage term...
[INFO] [2023-10-14 09:52:58] MetaTraits to traits...
[INFO] [2023-10-14 09:52:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-14 09:52:58] Assocs to occurrences...
[INFO] [2023-10-14 09:52:58] Assocs to nodes...
[INFO] [2023-10-14 09:52:58] Assoc to sex term...
[INFO] [2023-10-14 09:52:58] Assoc to lifestage term...
[INFO] [2023-10-14 09:52:58] MetaAssoc to assocs...
[STOP] [2023-10-14 09:52:58] resolve_keys
[START] [2023-10-14 09:52:58] hold_for_later_1
[STOP] [2023-10-14 09:52:58] hold_for_later_1
[START] [2023-10-14 09:52:58] hold_for_later_2
[STOP] [2023-10-14 09:52:58] hold_for_later_2
[START] [2023-10-14 09:52:58] resolve_missing_parents
[STOP] [2023-10-14 09:52:58] resolve_missing_parents
[START] [2023-10-14 09:52:58] rebuild_nodes
[START] [2023-10-14 09:52:58] Flattener#flatten
[START] [2023-10-14 09:52:58] Flattener#study_resource
[START] [2023-10-14 09:52:58] Flattener#build_ancestry
[STOP] [2023-10-14 09:52:58] Flattener#build_ancestry
[INFO] [2023-10-14 09:52:58] 369 ancestry keys
[START] [2023-10-14 09:52:58] build_node_ancestors
[INFO] [2023-10-14 09:52:58] old ancestors deleted.
[STOP] [2023-10-14 09:52:58] build_node_ancestors
[START] [2023-10-14 09:52:58] Flattener#propagate_ancestor_ids
[STOP] [2023-10-14 09:52:58] Flattener#propagate_ancestor_ids
[STOP] [2023-10-14 09:52:58] Flattener#flatten
[STOP] [2023-10-14 09:52:58] rebuild_nodes
[START] [2023-10-14 09:52:58] resolve_missing_media_owners
[STOP] [2023-10-14 09:52:58] resolve_missing_media_owners
[START] [2023-10-14 09:52:58] sanitize_media_verbatims
[STOP] [2023-10-14 09:52:58] sanitize_media_verbatims
[START] [2023-10-14 09:52:58] queue_downloads
[STOP] [2023-10-14 09:52:58] queue_downloads
[START] [2023-10-14 09:52:58] parse_names
[WARN] [2023-10-14 09:52:58] I see 369 names which still need to be parsed.
[WARN] [2023-10-14 09:52:59] Names to parse: 369 formatted: 369 learned: 369 parsed: 369
[STOP] [2023-10-14 09:53:00] parse_names
[START] [2023-10-14 09:53:00] denormalize_canonical_names_to_nodes
[STOP] [2023-10-14 09:53:00] denormalize_canonical_names_to_nodes
[START] [2023-10-14 09:53:00] match_nodes
[START] [2023-10-14 09:53:00] map_all_nodes_to_pages
[STOP] [2023-10-14 09:53:04] map_all_nodes_to_pages
[INFO] [2023-10-14 09:53:04] Unmatched nodes (5 of 369): Canonical: Pachymedusa; Node#137232256; ResourceID: T452; Canonical: Triprion; Node#137232272; ResourceID: T468; Canonical: Ceciliidae; Node#137232211; ResourceID: T407; Canonical: Eleutherodactylus rufescens; Node#137232031; ResourceID: T227; Canonical: Leiuperidae; Node#137232213; ResourceID: T409
[START] [2023-10-14 09:53:04] update_nodes
[STOP] [2023-10-14 09:53:04] update_nodes
[STOP] [2023-10-14 09:53:04] match_nodes
[START] [2023-10-14 09:53:04] reindex_search
[STOP] [2023-10-14 09:53:04] reindex_search
[START] [2023-10-14 09:53:04] normalize_units
[STOP] [2023-10-14 09:53:07] normalize_units
[START] [2023-10-14 09:53:07] calculate_statistics
[INFO] [2023-10-14 09:53:08] Duplicate page_id count: 0
[2023-10-14 09:53:08] WARNING: 4 trait(s) without source found! Please confirm that this is intentional.
[2023-10-14 09:53:08] traits w/o source (up to 100):
[2023-10-14 09:53:08] (resource_pk: M1562, id: 291921456)
[2023-10-14 09:53:08] (resource_pk: M1972, id: 291921864)
[2023-10-14 09:53:08] (resource_pk: M2149, id: 291922041)
[2023-10-14 09:53:08] (resource_pk: M2308, id: 291922198)
[STOP] [2023-10-14 09:53:08] calculate_statistics
[START] [2023-10-14 09:53:08] complete_harvest_instance
[START] [2023-10-14 09:53:08] overall_tsv_creation
[INFO] [2023-10-14 09:53:08] Exporting 369 nodes as TSV in batches of 10000...
[INFO] [2023-10-14 09:53:08] Processing group of 369 in 1 batches of 10000
[INFO] [2023-10-14 09:53:09] 1704 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-14 09:53:09] Building Traits map for 369 nodes (this can take a while)...
[INFO] [2023-10-14 09:53:09] Mapped 1704 traits (2497 meta) for 369 nodes.
[INFO] [2023-10-14 09:53:09] Building Associations map (this can take a while)...
[INFO] [2023-10-14 09:53:09] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-14 09:53:09] Adding 1704 traits...
[INFO] [2023-10-14 09:53:09] 1223 metadata added.
[INFO] [2023-10-14 09:53:09] Adding 0 assocs...
[INFO] [2023-10-14 09:53:09] 0 metadata added.
[INFO] [2023-10-14 09:53:54] Processed 369/369 nodes
[INFO] [2023-10-14 09:53:54] Average Time: 45.65
[INFO] [2023-10-14 09:53:54] Total Time: 46s
[STOP] [2023-10-14 09:53:54] overall_tsv_creation
[INFO] [2023-10-14 09:53:54] Done. Check your files:
[INFO] [2023-10-14 09:53:54] (369 lines) /app/public/data/mexican_amphibia/publish_nodes.tsv
[INFO] [2023-10-14 09:53:54] (1022 lines) /app/public/data/mexican_amphibia/publish_node_ancestors.tsv
[INFO] [2023-10-14 09:53:54] (369 lines) /app/public/data/mexican_amphibia/publish_scientific_names.tsv
[INFO] [2023-10-14 09:53:54] (1705 lines) /app/public/data/mexican_amphibia/publish_traits.tsv
[INFO] [2023-10-14 09:53:54] (1224 lines) /app/public/data/mexican_amphibia/publish_metadata.tsv
[STOP] [2023-10-14 09:53:54] complete_harvest_instance
[START] [2023-10-14 09:53:54] completed
[STOP] [2023-10-14 09:53:54] completed
[STOP] [2023-10-14 09:53:54] logged process, took 70.29

Latest Process

14 Oct 09:52 EXITED currently processing 0