Harvest for Appeltans et al Created 13 Oct 11:24

Harvesting Log

[INFO] [2023-10-13 11:24:33] Created harvest instance #4432
[STOP] [2023-10-13 11:24:33] create_harvest_instance
[START] [2023-10-13 11:24:33] fetch_files
[STOP] [2023-10-13 11:24:33] fetch_files
[START] [2023-10-13 11:24:33] validate_each_file
[INFO] [2023-10-13 11:24:33] Looping over 4 formats...
[INFO] [2023-10-13 11:24:33] ...refs (/app/public/data/appeltans_et_al/reference.tab)
[INFO] [2023-10-13 11:24:33] Valid: /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_refs_30698.csv (114 lines)
[INFO] [2023-10-13 11:24:33] ...nodes (/app/public/data/appeltans_et_al/taxon.tab)
[INFO] [2023-10-13 11:24:33] Valid: /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_nodes_30697.csv (158 lines)
[INFO] [2023-10-13 11:24:33] ...occurrences (/app/public/data/appeltans_et_al/occurrence.tab)
[INFO] [2023-10-13 11:24:34] Valid: /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_occurrences_30699.csv (237 lines)
[INFO] [2023-10-13 11:24:34] ...measurements (/app/public/data/appeltans_et_al/measurement_or_fact_specific.tab)
[INFO] [2023-10-13 11:24:34] Valid: /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_measurements_30700.csv (1447 lines)
[STOP] [2023-10-13 11:24:34] validate_each_file
[START] [2023-10-13 11:24:34] convert_to_csv
[INFO] [2023-10-13 11:24:34] Looping over 4 formats...
[INFO] [2023-10-13 11:24:34] ...refs (/app/public/data/appeltans_et_al/reference.tab)
[CMD] [2023-10-13 11:24:34] /usr/bin/sort /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_refs_30698.csv > /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_refs_30698.csv_sorted
[INFO] [2023-10-13 11:24:34] Converted: /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_refs_30698.csv (114 lines)
[INFO] [2023-10-13 11:24:34] ...nodes (/app/public/data/appeltans_et_al/taxon.tab)
[CMD] [2023-10-13 11:24:34] /usr/bin/sort /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_nodes_30697.csv > /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_nodes_30697.csv_sorted
[INFO] [2023-10-13 11:24:34] Converted: /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_nodes_30697.csv (158 lines)
[INFO] [2023-10-13 11:24:34] ...occurrences (/app/public/data/appeltans_et_al/occurrence.tab)
[CMD] [2023-10-13 11:24:34] /usr/bin/sort /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_occurrences_30699.csv > /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_occurrences_30699.csv_sorted
[INFO] [2023-10-13 11:24:34] Converted: /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_occurrences_30699.csv (237 lines)
[INFO] [2023-10-13 11:24:34] ...measurements (/app/public/data/appeltans_et_al/measurement_or_fact_specific.tab)
[CMD] [2023-10-13 11:24:34] /usr/bin/sort /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_measurements_30700.csv > /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_measurements_30700.csv_sorted
[INFO] [2023-10-13 11:24:34] Converted: /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_measurements_30700.csv (1447 lines)
[STOP] [2023-10-13 11:24:34] convert_to_csv
[START] [2023-10-13 11:24:34] calculate_delta
[INFO] [2023-10-13 11:24:34] Looping over 4 formats...
[INFO] [2023-10-13 11:24:34] ...refs (/app/public/data/appeltans_et_al/reference.tab)
[CMD] [2023-10-13 11:24:34] echo "0a" > /app/public/data/appeltans_et_al/diff/appeltans_et_al_refs_30698.diff
[CMD] [2023-10-13 11:24:34] tail -n +1 /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_refs_30698.csv >> /app/public/data/appeltans_et_al/diff/appeltans_et_al_refs_30698.diff
[CMD] [2023-10-13 11:24:34] echo "." >> /app/public/data/appeltans_et_al/diff/appeltans_et_al_refs_30698.diff
[INFO] [2023-10-13 11:24:34] Created diff: /app/public/data/appeltans_et_al/diff/appeltans_et_al_refs_30698.diff (116 lines)
[INFO] [2023-10-13 11:24:34] ...nodes (/app/public/data/appeltans_et_al/taxon.tab)
[CMD] [2023-10-13 11:24:34] echo "0a" > /app/public/data/appeltans_et_al/diff/appeltans_et_al_nodes_30697.diff
[CMD] [2023-10-13 11:24:34] tail -n +1 /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_nodes_30697.csv >> /app/public/data/appeltans_et_al/diff/appeltans_et_al_nodes_30697.diff
[CMD] [2023-10-13 11:24:34] echo "." >> /app/public/data/appeltans_et_al/diff/appeltans_et_al_nodes_30697.diff
[INFO] [2023-10-13 11:24:34] Created diff: /app/public/data/appeltans_et_al/diff/appeltans_et_al_nodes_30697.diff (160 lines)
[INFO] [2023-10-13 11:24:34] ...occurrences (/app/public/data/appeltans_et_al/occurrence.tab)
[CMD] [2023-10-13 11:24:34] echo "0a" > /app/public/data/appeltans_et_al/diff/appeltans_et_al_occurrences_30699.diff
[CMD] [2023-10-13 11:24:34] tail -n +1 /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_occurrences_30699.csv >> /app/public/data/appeltans_et_al/diff/appeltans_et_al_occurrences_30699.diff
[CMD] [2023-10-13 11:24:35] echo "." >> /app/public/data/appeltans_et_al/diff/appeltans_et_al_occurrences_30699.diff
[INFO] [2023-10-13 11:24:35] Created diff: /app/public/data/appeltans_et_al/diff/appeltans_et_al_occurrences_30699.diff (239 lines)
[INFO] [2023-10-13 11:24:35] ...measurements (/app/public/data/appeltans_et_al/measurement_or_fact_specific.tab)
[CMD] [2023-10-13 11:24:35] echo "0a" > /app/public/data/appeltans_et_al/diff/appeltans_et_al_measurements_30700.diff
[CMD] [2023-10-13 11:24:35] tail -n +1 /app/public/data/appeltans_et_al/converted_csv/appeltans_et_al_measurements_30700.csv >> /app/public/data/appeltans_et_al/diff/appeltans_et_al_measurements_30700.diff
[CMD] [2023-10-13 11:24:35] echo "." >> /app/public/data/appeltans_et_al/diff/appeltans_et_al_measurements_30700.diff
[INFO] [2023-10-13 11:24:35] Created diff: /app/public/data/appeltans_et_al/diff/appeltans_et_al_measurements_30700.diff (1449 lines)
[STOP] [2023-10-13 11:24:35] calculate_delta
[START] [2023-10-13 11:24:35] parse_diff_and_store
[INFO] [2023-10-13 11:24:35] Handling diff: /app/public/data/appeltans_et_al/diff/appeltans_et_al_refs_30698.diff (116 lines)
[INFO] [2023-10-13 11:24:35] Loading refs diff file into memory (116 lines)...
[INFO] [2023-10-13 11:24:35] Storing 114 References (114/114/116)
[INFO] [2023-10-13 11:24:35] Handling diff: /app/public/data/appeltans_et_al/diff/appeltans_et_al_nodes_30697.diff (160 lines)
[INFO] [2023-10-13 11:24:35] Loading nodes diff file into memory (160 lines)...
[INFO] [2023-10-13 11:24:35] Storing 163 ScientificNames (326/158/160)
[INFO] [2023-10-13 11:24:35] Storing 163 Nodes (326/158/160)
[INFO] [2023-10-13 11:24:35] Handling diff: /app/public/data/appeltans_et_al/diff/appeltans_et_al_occurrences_30699.diff (239 lines)
[INFO] [2023-10-13 11:24:35] Loading occurrences diff file into memory (239 lines)...
[INFO] [2023-10-13 11:24:36] Storing 237 Occurrences (325/237/239)
[INFO] [2023-10-13 11:24:36] Storing 88 OccurrenceMetadata (325/237/239)
[INFO] [2023-10-13 11:24:36] Handling diff: /app/public/data/appeltans_et_al/diff/appeltans_et_al_measurements_30700.diff (1449 lines)
[INFO] [2023-10-13 11:24:36] Loading measurements diff file into memory (1449 lines)...
[INFO] [2023-10-13 11:24:36] Storing 1447 Traits (4022/1447/1449)
[INFO] [2023-10-13 11:24:37] Storing 2434 MetaTraits (4022/1447/1449)
[INFO] [2023-10-13 11:24:37] Storing 141 TraitsReferences (4022/1447/1449)
[STOP] [2023-10-13 11:24:37] parse_diff_and_store
[START] [2023-10-13 11:24:37] resolve_keys
[2023-10-13 11:24:38] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 11:24:46] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 11:24:46] traits to occurrences...
[INFO] [2023-10-13 11:24:46] traits to nodes (through occurrences)...
[INFO] [2023-10-13 11:24:46] Traits to sex term...
[INFO] [2023-10-13 11:24:46] Traits to lifestage term...
[INFO] [2023-10-13 11:24:46] MetaTraits to traits...
[INFO] [2023-10-13 11:24:46] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 11:24:46] Assocs to occurrences...
[INFO] [2023-10-13 11:24:46] Assocs to nodes...
[INFO] [2023-10-13 11:24:46] Assoc to sex term...
[INFO] [2023-10-13 11:24:46] Assoc to lifestage term...
[INFO] [2023-10-13 11:24:46] MetaAssoc to assocs...
[STOP] [2023-10-13 11:24:46] resolve_keys
[START] [2023-10-13 11:24:46] hold_for_later_1
[STOP] [2023-10-13 11:24:46] hold_for_later_1
[START] [2023-10-13 11:24:46] hold_for_later_2
[STOP] [2023-10-13 11:24:46] hold_for_later_2
[START] [2023-10-13 11:24:46] resolve_missing_parents
[STOP] [2023-10-13 11:24:46] resolve_missing_parents
[START] [2023-10-13 11:24:46] rebuild_nodes
[START] [2023-10-13 11:24:46] Flattener#flatten
[START] [2023-10-13 11:24:46] Flattener#study_resource
[START] [2023-10-13 11:24:46] Flattener#build_ancestry
[STOP] [2023-10-13 11:24:46] Flattener#build_ancestry
[INFO] [2023-10-13 11:24:46] 163 ancestry keys
[START] [2023-10-13 11:24:46] build_node_ancestors
[INFO] [2023-10-13 11:24:46] old ancestors deleted.
[STOP] [2023-10-13 11:24:46] build_node_ancestors
[START] [2023-10-13 11:24:46] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:24:46] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:24:46] Flattener#flatten
[STOP] [2023-10-13 11:24:46] rebuild_nodes
[START] [2023-10-13 11:24:46] resolve_missing_media_owners
[STOP] [2023-10-13 11:24:46] resolve_missing_media_owners
[START] [2023-10-13 11:24:46] sanitize_media_verbatims
[STOP] [2023-10-13 11:24:46] sanitize_media_verbatims
[START] [2023-10-13 11:24:46] queue_downloads
[STOP] [2023-10-13 11:24:46] queue_downloads
[START] [2023-10-13 11:24:46] parse_names
[WARN] [2023-10-13 11:24:46] I see 163 names which still need to be parsed.
[WARN] [2023-10-13 11:24:46] Names to parse: 163 formatted: 163 learned: 159 parsed: 163
[STOP] [2023-10-13 11:24:47] parse_names
[START] [2023-10-13 11:24:47] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 11:24:47] denormalize_canonical_names_to_nodes
[START] [2023-10-13 11:24:47] match_nodes
[START] [2023-10-13 11:24:47] map_all_nodes_to_pages
[STOP] [2023-10-13 11:24:52] map_all_nodes_to_pages
[INFO] [2023-10-13 11:24:52] 24 Unmatched nodes (of 163)! That's too many to output. Full list in /app/public/data/appeltans_et_al/unmatched_nodes.txt ; First 10: Canonical: Acanthocephala; Node#137154310; ResourceID: Acanthocephala; Canonical: Acarina; Node#137154311; ResourceID: Acarina; Canonical: Biota; Node#137154330; ResourceID: Biota; Canonical: Caridea; Node#137154337; ResourceID: Caridea; Canonical: Catenulida; Node#137154339; ResourceID: Catenulida; Canonical: Ctenophora; Node#137154360; ResourceID: Ctenophora; Canonical: Digenea; Node#137154366; ResourceID: Digenea; Canonical: Mesozoa; Node#137154405; ResourceID: Mesozoa; Canonical: Mictacea; Node#137154406; ResourceID: Mictacea; Canonical: Oligochaeta; Node#137154421; ResourceID: Oligochaeta
[START] [2023-10-13 11:24:52] update_nodes
[STOP] [2023-10-13 11:24:52] update_nodes
[STOP] [2023-10-13 11:24:52] match_nodes
[START] [2023-10-13 11:24:52] reindex_search
[STOP] [2023-10-13 11:24:53] reindex_search
[START] [2023-10-13 11:24:53] normalize_units
[STOP] [2023-10-13 11:24:53] normalize_units
[START] [2023-10-13 11:24:53] calculate_statistics
[INFO] [2023-10-13 11:24:53] Duplicate page_id count: 0
[STOP] [2023-10-13 11:24:53] calculate_statistics
[START] [2023-10-13 11:24:53] complete_harvest_instance
[START] [2023-10-13 11:24:53] overall_tsv_creation
[INFO] [2023-10-13 11:24:54] Exporting 163 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 11:24:54] Processing group of 163 in 1 batches of 10000
[INFO] [2023-10-13 11:24:54] 1309 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 11:24:54] Building Traits map for 163 nodes (this can take a while)...
[INFO] [2023-10-13 11:24:54] Mapped 1309 traits (2383 meta) for 163 nodes.
[INFO] [2023-10-13 11:24:54] Building Associations map (this can take a while)...
[INFO] [2023-10-13 11:24:54] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 11:24:54] Adding 1309 traits...
[INFO] [2023-10-13 11:24:54] 327 metadata added.
[INFO] [2023-10-13 11:24:54] Adding 0 assocs...
[INFO] [2023-10-13 11:24:54] 0 metadata added.
[INFO] [2023-10-13 11:25:39] Processed 163/163 nodes
[INFO] [2023-10-13 11:25:39] Average Time: 45.36
[INFO] [2023-10-13 11:25:39] Total Time: 46s
[STOP] [2023-10-13 11:25:39] overall_tsv_creation
[INFO] [2023-10-13 11:25:39] Done. Check your files:
[INFO] [2023-10-13 11:25:39] (159 lines) /app/public/data/appeltans_et_al/publish_nodes.tsv
[INFO] [2023-10-13 11:25:39] (154 lines) /app/public/data/appeltans_et_al/publish_node_ancestors.tsv
[INFO] [2023-10-13 11:25:39] (163 lines) /app/public/data/appeltans_et_al/publish_scientific_names.tsv
[INFO] [2023-10-13 11:25:39] (1310 lines) /app/public/data/appeltans_et_al/publish_traits.tsv
[INFO] [2023-10-13 11:25:39] (328 lines) /app/public/data/appeltans_et_al/publish_metadata.tsv
[STOP] [2023-10-13 11:25:39] complete_harvest_instance
[START] [2023-10-13 11:25:39] completed
[STOP] [2023-10-13 11:25:39] completed
[STOP] [2023-10-13 11:25:39] logged process, took 66.07

Latest Process

13 Oct 11:24 EXITED currently processing 0