Harvest for Massard and Geimer, 2008 Created 31 Jan 12:19

Harvesting Log

[INFO] [2023-01-31 12:19:00] Created harvest instance #4290
[STOP] [2023-01-31 12:19:00] create_harvest_instance
[START] [2023-01-31 12:19:00] fetch_files
[STOP] [2023-01-31 12:19:00] fetch_files
[START] [2023-01-31 12:19:00] validate_each_file
[INFO] [2023-01-31 12:19:00] Looping over 3 formats...
[INFO] [2023-01-31 12:19:00] ...nodes (/app/public/data/massard_geimer_m/taxa.tsv)
[INFO] [2023-01-31 12:19:00] Valid: /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_nodes_30173.csv (95 lines)
[INFO] [2023-01-31 12:19:00] ...occurrences (/app/public/data/massard_geimer_m/occurrences.tsv)
[INFO] [2023-01-31 12:19:00] Valid: /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_occurrences_30174.csv (95 lines)
[INFO] [2023-01-31 12:19:00] ...measurements (/app/public/data/massard_geimer_m/measurementOrFact.tsv)
[INFO] [2023-01-31 12:19:00] Valid: /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_measurements_30175.csv (105 lines)
[STOP] [2023-01-31 12:19:00] validate_each_file
[START] [2023-01-31 12:19:00] convert_to_csv
[INFO] [2023-01-31 12:19:00] Looping over 3 formats...
[INFO] [2023-01-31 12:19:00] ...nodes (/app/public/data/massard_geimer_m/taxa.tsv)
[CMD] [2023-01-31 12:19:00] /usr/bin/sort /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_nodes_30173.csv > /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_nodes_30173.csv_sorted
[INFO] [2023-01-31 12:19:00] Converted: /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_nodes_30173.csv (95 lines)
[INFO] [2023-01-31 12:19:00] ...occurrences (/app/public/data/massard_geimer_m/occurrences.tsv)
[CMD] [2023-01-31 12:19:00] /usr/bin/sort /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_occurrences_30174.csv > /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_occurrences_30174.csv_sorted
[INFO] [2023-01-31 12:19:00] Converted: /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_occurrences_30174.csv (95 lines)
[INFO] [2023-01-31 12:19:00] ...measurements (/app/public/data/massard_geimer_m/measurementOrFact.tsv)
[CMD] [2023-01-31 12:19:00] /usr/bin/sort /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_measurements_30175.csv > /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_measurements_30175.csv_sorted
[INFO] [2023-01-31 12:19:00] Converted: /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_measurements_30175.csv (105 lines)
[STOP] [2023-01-31 12:19:00] convert_to_csv
[START] [2023-01-31 12:19:00] calculate_delta
[INFO] [2023-01-31 12:19:00] Looping over 3 formats...
[INFO] [2023-01-31 12:19:00] ...nodes (/app/public/data/massard_geimer_m/taxa.tsv)
[CMD] [2023-01-31 12:19:00] echo "0a" > /app/public/data/massard_geimer_m/diff/massard_geimer_m_nodes_30173.diff
[CMD] [2023-01-31 12:19:00] tail -n +1 /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_nodes_30173.csv >> /app/public/data/massard_geimer_m/diff/massard_geimer_m_nodes_30173.diff
[CMD] [2023-01-31 12:19:00] echo "." >> /app/public/data/massard_geimer_m/diff/massard_geimer_m_nodes_30173.diff
[INFO] [2023-01-31 12:19:00] Created diff: /app/public/data/massard_geimer_m/diff/massard_geimer_m_nodes_30173.diff (97 lines)
[INFO] [2023-01-31 12:19:00] ...occurrences (/app/public/data/massard_geimer_m/occurrences.tsv)
[CMD] [2023-01-31 12:19:00] echo "0a" > /app/public/data/massard_geimer_m/diff/massard_geimer_m_occurrences_30174.diff
[CMD] [2023-01-31 12:19:00] tail -n +1 /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_occurrences_30174.csv >> /app/public/data/massard_geimer_m/diff/massard_geimer_m_occurrences_30174.diff
[CMD] [2023-01-31 12:19:00] echo "." >> /app/public/data/massard_geimer_m/diff/massard_geimer_m_occurrences_30174.diff
[INFO] [2023-01-31 12:19:00] Created diff: /app/public/data/massard_geimer_m/diff/massard_geimer_m_occurrences_30174.diff (97 lines)
[INFO] [2023-01-31 12:19:00] ...measurements (/app/public/data/massard_geimer_m/measurementOrFact.tsv)
[CMD] [2023-01-31 12:19:00] echo "0a" > /app/public/data/massard_geimer_m/diff/massard_geimer_m_measurements_30175.diff
[CMD] [2023-01-31 12:19:00] tail -n +1 /app/public/data/massard_geimer_m/converted_csv/massard_geimer_m_measurements_30175.csv >> /app/public/data/massard_geimer_m/diff/massard_geimer_m_measurements_30175.diff
[CMD] [2023-01-31 12:19:00] echo "." >> /app/public/data/massard_geimer_m/diff/massard_geimer_m_measurements_30175.diff
[INFO] [2023-01-31 12:19:00] Created diff: /app/public/data/massard_geimer_m/diff/massard_geimer_m_measurements_30175.diff (107 lines)
[STOP] [2023-01-31 12:19:00] calculate_delta
[START] [2023-01-31 12:19:00] parse_diff_and_store
[INFO] [2023-01-31 12:19:00] Handling diff: /app/public/data/massard_geimer_m/diff/massard_geimer_m_nodes_30173.diff (97 lines)
[INFO] [2023-01-31 12:19:00] Loading nodes diff file into memory (97 lines)...
[INFO] [2023-01-31 12:19:00] Storing 111 ScientificNames (222/95/97)
[INFO] [2023-01-31 12:19:00] Storing 111 Nodes (222/95/97)
[INFO] [2023-01-31 12:19:00] Handling diff: /app/public/data/massard_geimer_m/diff/massard_geimer_m_occurrences_30174.diff (97 lines)
[INFO] [2023-01-31 12:19:00] Loading occurrences diff file into memory (97 lines)...
[INFO] [2023-01-31 12:19:00] Storing 95 Occurrences (95/95/97)
[INFO] [2023-01-31 12:19:01] Handling diff: /app/public/data/massard_geimer_m/diff/massard_geimer_m_measurements_30175.diff (107 lines)
[INFO] [2023-01-31 12:19:01] Loading measurements diff file into memory (107 lines)...
[INFO] [2023-01-31 12:19:01] Storing 105 Traits (200/105/107)
[INFO] [2023-01-31 12:19:01] Storing 95 MetaTraits (200/105/107)
[STOP] [2023-01-31 12:19:01] parse_diff_and_store
[START] [2023-01-31 12:19:01] resolve_keys
[2023-01-31 12:19:01] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-31 12:19:08] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-31 12:19:08] traits to occurrences...
[INFO] [2023-01-31 12:19:08] traits to nodes (through occurrences)...
[INFO] [2023-01-31 12:19:08] Traits to sex term...
[INFO] [2023-01-31 12:19:08] Traits to lifestage term...
[INFO] [2023-01-31 12:19:08] MetaTraits to traits...
[INFO] [2023-01-31 12:19:08] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-31 12:19:08] Assocs to occurrences...
[INFO] [2023-01-31 12:19:08] Assocs to nodes...
[INFO] [2023-01-31 12:19:08] Assoc to sex term...
[INFO] [2023-01-31 12:19:08] Assoc to lifestage term...
[INFO] [2023-01-31 12:19:08] MetaAssoc to assocs...
[STOP] [2023-01-31 12:19:08] resolve_keys
[START] [2023-01-31 12:19:08] hold_for_later_1
[STOP] [2023-01-31 12:19:08] hold_for_later_1
[START] [2023-01-31 12:19:08] hold_for_later_2
[STOP] [2023-01-31 12:19:08] hold_for_later_2
[START] [2023-01-31 12:19:08] resolve_missing_parents
[STOP] [2023-01-31 12:19:08] resolve_missing_parents
[START] [2023-01-31 12:19:08] rebuild_nodes
[START] [2023-01-31 12:19:08] Flattener#flatten
[START] [2023-01-31 12:19:08] Flattener#study_resource
[START] [2023-01-31 12:19:08] Flattener#build_ancestry
[STOP] [2023-01-31 12:19:08] Flattener#build_ancestry
[INFO] [2023-01-31 12:19:08] 111 ancestry keys
[START] [2023-01-31 12:19:08] build_node_ancestors
[INFO] [2023-01-31 12:19:08] old ancestors deleted.
[STOP] [2023-01-31 12:19:08] build_node_ancestors
[START] [2023-01-31 12:19:08] Flattener#propagate_ancestor_ids
[STOP] [2023-01-31 12:19:08] Flattener#propagate_ancestor_ids
[STOP] [2023-01-31 12:19:08] Flattener#flatten
[STOP] [2023-01-31 12:19:08] rebuild_nodes
[START] [2023-01-31 12:19:08] resolve_missing_media_owners
[STOP] [2023-01-31 12:19:08] resolve_missing_media_owners
[START] [2023-01-31 12:19:08] sanitize_media_verbatims
[STOP] [2023-01-31 12:19:08] sanitize_media_verbatims
[START] [2023-01-31 12:19:08] queue_downloads
[STOP] [2023-01-31 12:19:08] queue_downloads
[START] [2023-01-31 12:19:08] parse_names
[WARN] [2023-01-31 12:19:08] I see 111 names which still need to be parsed.
[WARN] [2023-01-31 12:19:09] Names to parse: 111 formatted: 111 learned: 111 parsed: 111
[STOP] [2023-01-31 12:19:10] parse_names
[START] [2023-01-31 12:19:10] denormalize_canonical_names_to_nodes
[STOP] [2023-01-31 12:19:10] denormalize_canonical_names_to_nodes
[START] [2023-01-31 12:19:10] match_nodes
[START] [2023-01-31 12:19:10] map_all_nodes_to_pages
[STOP] [2023-01-31 12:19:20] map_all_nodes_to_pages
[INFO] [2023-01-31 12:19:20] 59 Unmatched nodes (of 111)! That's too many to output. Full list in /app/public/data/massard_geimer_m/unmatched_nodes.txt ; First 10: Canonical: Phylactolaemata; Node#122870096; ResourceID: Metazoa/Bryozoa/Phylactolaemata; Canonical: Plumatellida; Node#122870097; ResourceID: Metazoa/Bryozoa/Phylactolaemata/Plumatellida; Canonical: Plumatellidae; Node#122870098; ResourceID: Metazoa/Bryozoa/Phylactolaemata/Plumatellida/Plumatellidae; Canonical: Afrindella philippinensis; Node#122870100; ResourceID: Afrindella philippinensis (Kraepelin, 1887); Canonical: Afrindella testitudinicola; Node#122870102; ResourceID: Afrindella testitudinicola (Annandale, 1912); Canonical: Plumatella bombayensis; Node#122870147; ResourceID: Plumatella bombayensis Annandale, 1908; Canonical: Plumatella bushnelli; Node#122870148; ResourceID: Plumatella bushnelli Wood, 2001; Canonical: Plumatella casmiana; Node#122870150; ResourceID: Plumatella casmiana Oka, 1907; Canonical: Plumatella emarginata; Node#122870153; ResourceID: Plumatella emarginata Allman, 1844; Canonical: Plumatella fruticosa; Node#122870155; ResourceID: Plumatella fruticosa Allman, 1844
[START] [2023-01-31 12:19:20] update_nodes
[STOP] [2023-01-31 12:19:20] update_nodes
[STOP] [2023-01-31 12:19:20] match_nodes
[START] [2023-01-31 12:19:20] reindex_search
[STOP] [2023-01-31 12:19:20] reindex_search
[START] [2023-01-31 12:19:20] normalize_units
[STOP] [2023-01-31 12:19:20] normalize_units
[START] [2023-01-31 12:19:20] calculate_statistics
[INFO] [2023-01-31 12:19:20] Duplicate page_id count: 0
[2023-01-31 12:19:20] WARNING: 1 trait(s) without source found! Please confirm that this is intentional.
[2023-01-31 12:19:20] traits w/o source (up to 100):
[2023-01-31 12:19:20] (resource_pk: 59, id: 286504288)
[STOP] [2023-01-31 12:19:20] calculate_statistics
[START] [2023-01-31 12:19:20] complete_harvest_instance
[START] [2023-01-31 12:19:20] overall_tsv_creation
[INFO] [2023-01-31 12:19:20] Exporting 111 nodes as TSV in batches of 10000...
[INFO] [2023-01-31 12:19:20] Processing group of 111 in 1 batches of 10000
[INFO] [2023-01-31 12:19:21] 95 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-31 12:19:21] Building Traits map for 111 nodes (this can take a while)...
[INFO] [2023-01-31 12:19:21] Mapped 95 traits (95 meta) for 111 nodes.
[INFO] [2023-01-31 12:19:21] Building Associations map (this can take a while)...
[INFO] [2023-01-31 12:19:21] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-31 12:19:21] Adding 95 traits...
[INFO] [2023-01-31 12:19:21] 8 metadata added.
[INFO] [2023-01-31 12:19:21] Adding 0 assocs...
[INFO] [2023-01-31 12:19:21] 0 metadata added.
[INFO] [2023-01-31 12:20:06] Processed 111/111 nodes
[INFO] [2023-01-31 12:20:06] Average Time: 45.06
[INFO] [2023-01-31 12:20:06] Total Time: 46s
[STOP] [2023-01-31 12:20:06] overall_tsv_creation
[INFO] [2023-01-31 12:20:06] Done. Check your files:
[INFO] [2023-01-31 12:20:06] (111 lines) /app/public/data/massard_geimer_m/publish_nodes.tsv
[INFO] [2023-01-31 12:20:06] (492 lines) /app/public/data/massard_geimer_m/publish_node_ancestors.tsv
[INFO] [2023-01-31 12:20:06] (111 lines) /app/public/data/massard_geimer_m/publish_scientific_names.tsv
[INFO] [2023-01-31 12:20:06] (96 lines) /app/public/data/massard_geimer_m/publish_traits.tsv
[INFO] [2023-01-31 12:20:06] (9 lines) /app/public/data/massard_geimer_m/publish_metadata.tsv
[STOP] [2023-01-31 12:20:06] complete_harvest_instance
[START] [2023-01-31 12:20:06] completed
[STOP] [2023-01-31 12:20:06] completed
[STOP] [2023-01-31 12:20:06] logged process, took 65.89

Latest Process

31 Jan 12:16 EXITED currently processing 0