Harvest for Feldman and Meiri 2014 Created 13 Oct 08:49

Harvesting Log

[INFO] [2023-10-13 08:49:34] Created harvest instance #4410
[STOP] [2023-10-13 08:49:34] create_harvest_instance
[START] [2023-10-13 08:49:34] fetch_files
[STOP] [2023-10-13 08:49:34] fetch_files
[START] [2023-10-13 08:49:34] validate_each_file
[INFO] [2023-10-13 08:49:34] Looping over 4 formats...
[INFO] [2023-10-13 08:49:34] ...refs (/app/public/data/feldman_meiri_fe/references.txt)
[INFO] [2023-10-13 08:49:34] Valid: /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_refs_30591.csv (19 lines)
[INFO] [2023-10-13 08:49:34] ...nodes (/app/public/data/feldman_meiri_fe/taxa.txt)
[INFO] [2023-10-13 08:49:34] Valid: /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_nodes_30588.csv (146 lines)
[INFO] [2023-10-13 08:49:34] ...occurrences (/app/public/data/feldman_meiri_fe/occurrences.txt)
[INFO] [2023-10-13 08:49:34] Valid: /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_occurrences_30589.csv (292 lines)
[INFO] [2023-10-13 08:49:34] ...measurements (/app/public/data/feldman_meiri_fe/measurementsorfacts.txt)
[INFO] [2023-10-13 08:49:34] Valid: /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_measurements_30590.csv (743 lines)
[STOP] [2023-10-13 08:49:34] validate_each_file
[START] [2023-10-13 08:49:34] convert_to_csv
[INFO] [2023-10-13 08:49:34] Looping over 4 formats...
[INFO] [2023-10-13 08:49:34] ...refs (/app/public/data/feldman_meiri_fe/references.txt)
[CMD] [2023-10-13 08:49:34] /usr/bin/sort /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_refs_30591.csv > /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_refs_30591.csv_sorted
[INFO] [2023-10-13 08:49:35] Converted: /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_refs_30591.csv (19 lines)
[INFO] [2023-10-13 08:49:35] ...nodes (/app/public/data/feldman_meiri_fe/taxa.txt)
[CMD] [2023-10-13 08:49:35] /usr/bin/sort /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_nodes_30588.csv > /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_nodes_30588.csv_sorted
[INFO] [2023-10-13 08:49:35] Converted: /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_nodes_30588.csv (146 lines)
[INFO] [2023-10-13 08:49:35] ...occurrences (/app/public/data/feldman_meiri_fe/occurrences.txt)
[CMD] [2023-10-13 08:49:35] /usr/bin/sort /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_occurrences_30589.csv > /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_occurrences_30589.csv_sorted
[INFO] [2023-10-13 08:49:35] Converted: /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_occurrences_30589.csv (292 lines)
[INFO] [2023-10-13 08:49:35] ...measurements (/app/public/data/feldman_meiri_fe/measurementsorfacts.txt)
[CMD] [2023-10-13 08:49:35] /usr/bin/sort /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_measurements_30590.csv > /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_measurements_30590.csv_sorted
[INFO] [2023-10-13 08:49:35] Converted: /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_measurements_30590.csv (743 lines)
[STOP] [2023-10-13 08:49:35] convert_to_csv
[START] [2023-10-13 08:49:35] calculate_delta
[INFO] [2023-10-13 08:49:35] Looping over 4 formats...
[INFO] [2023-10-13 08:49:35] ...refs (/app/public/data/feldman_meiri_fe/references.txt)
[CMD] [2023-10-13 08:49:35] echo "0a" > /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_refs_30591.diff
[CMD] [2023-10-13 08:49:35] tail -n +1 /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_refs_30591.csv >> /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_refs_30591.diff
[CMD] [2023-10-13 08:49:35] echo "." >> /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_refs_30591.diff
[INFO] [2023-10-13 08:49:35] Created diff: /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_refs_30591.diff (21 lines)
[INFO] [2023-10-13 08:49:35] ...nodes (/app/public/data/feldman_meiri_fe/taxa.txt)
[CMD] [2023-10-13 08:49:35] echo "0a" > /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_nodes_30588.diff
[CMD] [2023-10-13 08:49:35] tail -n +1 /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_nodes_30588.csv >> /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_nodes_30588.diff
[CMD] [2023-10-13 08:49:35] echo "." >> /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_nodes_30588.diff
[INFO] [2023-10-13 08:49:35] Created diff: /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_nodes_30588.diff (148 lines)
[INFO] [2023-10-13 08:49:35] ...occurrences (/app/public/data/feldman_meiri_fe/occurrences.txt)
[CMD] [2023-10-13 08:49:35] echo "0a" > /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_occurrences_30589.diff
[CMD] [2023-10-13 08:49:35] tail -n +1 /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_occurrences_30589.csv >> /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_occurrences_30589.diff
[CMD] [2023-10-13 08:49:35] echo "." >> /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_occurrences_30589.diff
[INFO] [2023-10-13 08:49:36] Created diff: /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_occurrences_30589.diff (294 lines)
[INFO] [2023-10-13 08:49:36] ...measurements (/app/public/data/feldman_meiri_fe/measurementsorfacts.txt)
[CMD] [2023-10-13 08:49:36] echo "0a" > /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_measurements_30590.diff
[CMD] [2023-10-13 08:49:36] tail -n +1 /app/public/data/feldman_meiri_fe/converted_csv/feldman_meiri_fe_measurements_30590.csv >> /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_measurements_30590.diff
[CMD] [2023-10-13 08:49:36] echo "." >> /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_measurements_30590.diff
[INFO] [2023-10-13 08:49:36] Created diff: /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_measurements_30590.diff (745 lines)
[STOP] [2023-10-13 08:49:36] calculate_delta
[START] [2023-10-13 08:49:36] parse_diff_and_store
[INFO] [2023-10-13 08:49:36] Handling diff: /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_refs_30591.diff (21 lines)
[INFO] [2023-10-13 08:49:36] Loading refs diff file into memory (21 lines)...
[INFO] [2023-10-13 08:49:36] Storing 19 References (19/19/21)
[INFO] [2023-10-13 08:49:36] Handling diff: /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_nodes_30588.diff (148 lines)
[INFO] [2023-10-13 08:49:36] Loading nodes diff file into memory (148 lines)...
[INFO] [2023-10-13 08:49:36] Storing 154 ScientificNames (308/146/148)
[INFO] [2023-10-13 08:49:36] Storing 154 Nodes (308/146/148)
[INFO] [2023-10-13 08:49:36] Handling diff: /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_occurrences_30589.diff (294 lines)
[INFO] [2023-10-13 08:49:36] Loading occurrences diff file into memory (294 lines)...
[INFO] [2023-10-13 08:49:36] Storing 292 Occurrences (438/292/294)
[INFO] [2023-10-13 08:49:36] Storing 146 OccurrenceMetadata (438/292/294)
[INFO] [2023-10-13 08:49:36] Handling diff: /app/public/data/feldman_meiri_fe/diff/feldman_meiri_fe_measurements_30590.diff (745 lines)
[INFO] [2023-10-13 08:49:36] Loading measurements diff file into memory (745 lines)...
[INFO] [2023-10-13 08:49:37] Storing 1808 TraitsReferences (3732/743/745)
[INFO] [2023-10-13 08:49:37] Storing 743 Traits (3732/743/745)
[INFO] [2023-10-13 08:49:37] Storing 1181 MetaTraits (3732/743/745)
[STOP] [2023-10-13 08:49:37] parse_diff_and_store
[START] [2023-10-13 08:49:37] resolve_keys
[2023-10-13 08:49:37] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 08:49:45] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 08:49:45] traits to occurrences...
[INFO] [2023-10-13 08:49:45] traits to nodes (through occurrences)...
[INFO] [2023-10-13 08:49:45] Traits to sex term...
[INFO] [2023-10-13 08:49:45] Traits to lifestage term...
[INFO] [2023-10-13 08:49:45] MetaTraits to traits...
[INFO] [2023-10-13 08:49:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 08:49:45] Assocs to occurrences...
[INFO] [2023-10-13 08:49:45] Assocs to nodes...
[INFO] [2023-10-13 08:49:45] Assoc to sex term...
[INFO] [2023-10-13 08:49:45] Assoc to lifestage term...
[INFO] [2023-10-13 08:49:45] MetaAssoc to assocs...
[STOP] [2023-10-13 08:49:45] resolve_keys
[START] [2023-10-13 08:49:45] hold_for_later_1
[STOP] [2023-10-13 08:49:45] hold_for_later_1
[START] [2023-10-13 08:49:45] hold_for_later_2
[STOP] [2023-10-13 08:49:45] hold_for_later_2
[START] [2023-10-13 08:49:45] resolve_missing_parents
[STOP] [2023-10-13 08:49:45] resolve_missing_parents
[START] [2023-10-13 08:49:45] rebuild_nodes
[START] [2023-10-13 08:49:45] Flattener#flatten
[START] [2023-10-13 08:49:45] Flattener#study_resource
[START] [2023-10-13 08:49:45] Flattener#build_ancestry
[STOP] [2023-10-13 08:49:45] Flattener#build_ancestry
[INFO] [2023-10-13 08:49:45] 154 ancestry keys
[START] [2023-10-13 08:49:45] build_node_ancestors
[INFO] [2023-10-13 08:49:45] old ancestors deleted.
[STOP] [2023-10-13 08:49:45] build_node_ancestors
[START] [2023-10-13 08:49:46] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 08:49:46] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 08:49:46] Flattener#flatten
[STOP] [2023-10-13 08:49:46] rebuild_nodes
[START] [2023-10-13 08:49:46] resolve_missing_media_owners
[STOP] [2023-10-13 08:49:46] resolve_missing_media_owners
[START] [2023-10-13 08:49:46] sanitize_media_verbatims
[STOP] [2023-10-13 08:49:46] sanitize_media_verbatims
[START] [2023-10-13 08:49:46] queue_downloads
[STOP] [2023-10-13 08:49:46] queue_downloads
[START] [2023-10-13 08:49:46] parse_names
[WARN] [2023-10-13 08:49:46] I see 154 names which still need to be parsed.
[WARN] [2023-10-13 08:49:46] Names to parse: 154 formatted: 154 learned: 154 parsed: 154
[STOP] [2023-10-13 08:49:47] parse_names
[START] [2023-10-13 08:49:47] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 08:49:47] denormalize_canonical_names_to_nodes
[START] [2023-10-13 08:49:47] match_nodes
[START] [2023-10-13 08:49:47] map_all_nodes_to_pages
[STOP] [2023-10-13 08:49:52] map_all_nodes_to_pages
[INFO] [2023-10-13 08:49:52] Unmatched nodes (2 of 154): Canonical: Morelia kinghorni; Node#136981322; ResourceID: Morelia kinghorni; Canonical: Dendrelaphis calligastra; Node#136981298; ResourceID: Dendrelaphis calligastra
[START] [2023-10-13 08:49:52] update_nodes
[STOP] [2023-10-13 08:49:52] update_nodes
[STOP] [2023-10-13 08:49:52] match_nodes
[START] [2023-10-13 08:49:52] reindex_search
[STOP] [2023-10-13 08:49:53] reindex_search
[START] [2023-10-13 08:49:53] normalize_units
[STOP] [2023-10-13 08:49:54] normalize_units
[START] [2023-10-13 08:49:54] calculate_statistics
[INFO] [2023-10-13 08:49:54] Duplicate page_id count: 0
[STOP] [2023-10-13 08:49:54] calculate_statistics
[START] [2023-10-13 08:49:54] complete_harvest_instance
[START] [2023-10-13 08:49:54] overall_tsv_creation
[INFO] [2023-10-13 08:49:54] Exporting 154 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 08:49:54] Processing group of 154 in 1 batches of 10000
[INFO] [2023-10-13 08:49:54] 743 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 08:49:54] Building Traits map for 154 nodes (this can take a while)...
[INFO] [2023-10-13 08:49:55] Mapped 743 traits (1181 meta) for 154 nodes.
[INFO] [2023-10-13 08:49:55] Building Associations map (this can take a while)...
[INFO] [2023-10-13 08:49:55] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 08:49:55] Adding 743 traits...
[INFO] [2023-10-13 08:49:55] 1198 metadata added.
[INFO] [2023-10-13 08:49:55] Adding 0 assocs...
[INFO] [2023-10-13 08:49:55] 0 metadata added.
[INFO] [2023-10-13 08:50:40] Processed 154/154 nodes
[INFO] [2023-10-13 08:50:40] Average Time: 45.61
[INFO] [2023-10-13 08:50:40] Total Time: 46s
[STOP] [2023-10-13 08:50:40] overall_tsv_creation
[INFO] [2023-10-13 08:50:40] Done. Check your files:
[INFO] [2023-10-13 08:50:40] (154 lines) /app/public/data/feldman_meiri_fe/publish_nodes.tsv
[INFO] [2023-10-13 08:50:40] (752 lines) /app/public/data/feldman_meiri_fe/publish_node_ancestors.tsv
[INFO] [2023-10-13 08:50:40] (154 lines) /app/public/data/feldman_meiri_fe/publish_scientific_names.tsv
[INFO] [2023-10-13 08:50:40] (744 lines) /app/public/data/feldman_meiri_fe/publish_traits.tsv
[INFO] [2023-10-13 08:50:40] (1199 lines) /app/public/data/feldman_meiri_fe/publish_metadata.tsv
[STOP] [2023-10-13 08:50:40] complete_harvest_instance
[START] [2023-10-13 08:50:40] completed
[STOP] [2023-10-13 08:50:40] completed
[STOP] [2023-10-13 08:50:40] logged process, took 66.03

Latest Process

13 Oct 08:49 EXITED currently processing 0