Harvest for Habitat data for fungi Created 21 Jun 13:32

Harvesting Log

[INFO] [2023-06-21 13:32:51] Created harvest instance #4358
[STOP] [2023-06-21 13:32:51] create_harvest_instance
[START] [2023-06-21 13:32:51] fetch_files
[STOP] [2023-06-21 13:32:51] fetch_files
[START] [2023-06-21 13:32:51] validate_each_file
[INFO] [2023-06-21 13:32:51] Looping over 3 formats...
[INFO] [2023-06-21 13:32:51] ...nodes (/app/public/data/hab_dat_fun/taxon.tab)
[INFO] [2023-06-21 13:32:51] Valid: /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_nodes_30388.csv (6095 lines)
[INFO] [2023-06-21 13:32:51] ...occurrences (/app/public/data/hab_dat_fun/occurrence_specific.tab)
[INFO] [2023-06-21 13:32:51] Valid: /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_occurrences_30389.csv (6271 lines)
[INFO] [2023-06-21 13:32:51] ...measurements (/app/public/data/hab_dat_fun/measurement_or_fact_specific.tab)
[INFO] [2023-06-21 13:32:52] Valid: /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_measurements_30390.csv (11246 lines)
[STOP] [2023-06-21 13:32:52] validate_each_file
[START] [2023-06-21 13:32:52] convert_to_csv
[INFO] [2023-06-21 13:32:52] Looping over 3 formats...
[INFO] [2023-06-21 13:32:52] ...nodes (/app/public/data/hab_dat_fun/taxon.tab)
[CMD] [2023-06-21 13:32:52] /usr/bin/sort /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_nodes_30388.csv > /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_nodes_30388.csv_sorted
[INFO] [2023-06-21 13:32:52] Converted: /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_nodes_30388.csv (6095 lines)
[INFO] [2023-06-21 13:32:52] ...occurrences (/app/public/data/hab_dat_fun/occurrence_specific.tab)
[CMD] [2023-06-21 13:32:52] /usr/bin/sort /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_occurrences_30389.csv > /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_occurrences_30389.csv_sorted
[INFO] [2023-06-21 13:32:52] Converted: /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_occurrences_30389.csv (6271 lines)
[INFO] [2023-06-21 13:32:52] ...measurements (/app/public/data/hab_dat_fun/measurement_or_fact_specific.tab)
[CMD] [2023-06-21 13:32:52] /usr/bin/sort /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_measurements_30390.csv > /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_measurements_30390.csv_sorted
[INFO] [2023-06-21 13:32:52] Converted: /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_measurements_30390.csv (11246 lines)
[STOP] [2023-06-21 13:32:52] convert_to_csv
[START] [2023-06-21 13:32:52] calculate_delta
[INFO] [2023-06-21 13:32:52] Looping over 3 formats...
[INFO] [2023-06-21 13:32:52] ...nodes (/app/public/data/hab_dat_fun/taxon.tab)
[CMD] [2023-06-21 13:32:52] echo "0a" > /app/public/data/hab_dat_fun/diff/hab_dat_fun_nodes_30388.diff
[CMD] [2023-06-21 13:32:52] tail -n +1 /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_nodes_30388.csv >> /app/public/data/hab_dat_fun/diff/hab_dat_fun_nodes_30388.diff
[CMD] [2023-06-21 13:32:52] echo "." >> /app/public/data/hab_dat_fun/diff/hab_dat_fun_nodes_30388.diff
[INFO] [2023-06-21 13:32:52] Created diff: /app/public/data/hab_dat_fun/diff/hab_dat_fun_nodes_30388.diff (6097 lines)
[INFO] [2023-06-21 13:32:52] ...occurrences (/app/public/data/hab_dat_fun/occurrence_specific.tab)
[CMD] [2023-06-21 13:32:52] echo "0a" > /app/public/data/hab_dat_fun/diff/hab_dat_fun_occurrences_30389.diff
[CMD] [2023-06-21 13:32:52] tail -n +1 /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_occurrences_30389.csv >> /app/public/data/hab_dat_fun/diff/hab_dat_fun_occurrences_30389.diff
[CMD] [2023-06-21 13:32:52] echo "." >> /app/public/data/hab_dat_fun/diff/hab_dat_fun_occurrences_30389.diff
[INFO] [2023-06-21 13:32:52] Created diff: /app/public/data/hab_dat_fun/diff/hab_dat_fun_occurrences_30389.diff (6273 lines)
[INFO] [2023-06-21 13:32:52] ...measurements (/app/public/data/hab_dat_fun/measurement_or_fact_specific.tab)
[CMD] [2023-06-21 13:32:52] echo "0a" > /app/public/data/hab_dat_fun/diff/hab_dat_fun_measurements_30390.diff
[CMD] [2023-06-21 13:32:52] tail -n +1 /app/public/data/hab_dat_fun/converted_csv/hab_dat_fun_measurements_30390.csv >> /app/public/data/hab_dat_fun/diff/hab_dat_fun_measurements_30390.diff
[CMD] [2023-06-21 13:32:52] echo "." >> /app/public/data/hab_dat_fun/diff/hab_dat_fun_measurements_30390.diff
[INFO] [2023-06-21 13:32:52] Created diff: /app/public/data/hab_dat_fun/diff/hab_dat_fun_measurements_30390.diff (11248 lines)
[STOP] [2023-06-21 13:32:52] calculate_delta
[START] [2023-06-21 13:32:53] parse_diff_and_store
[INFO] [2023-06-21 13:32:53] Handling diff: /app/public/data/hab_dat_fun/diff/hab_dat_fun_nodes_30388.diff (6097 lines)
[INFO] [2023-06-21 13:32:53] Loading nodes diff file into memory (6097 lines)...
[INFO] [2023-06-21 13:32:54] Storing 6096 ScientificNames (12192/6095/6097)
[INFO] [2023-06-21 13:32:56] Storing 6096 Nodes (12192/6095/6097)
[INFO] [2023-06-21 13:32:58] Handling diff: /app/public/data/hab_dat_fun/diff/hab_dat_fun_occurrences_30389.diff (6273 lines)
[INFO] [2023-06-21 13:32:58] Loading occurrences diff file into memory (6273 lines)...
[INFO] [2023-06-21 13:32:59] Storing 6271 Occurrences (6271/6271/6273)
[INFO] [2023-06-21 13:33:00] Handling diff: /app/public/data/hab_dat_fun/diff/hab_dat_fun_measurements_30390.diff (11248 lines)
[INFO] [2023-06-21 13:33:00] Loading measurements diff file into memory (11248 lines)...
[INFO] [2023-06-21 13:33:06] Storing 9999 Traits (15606/10000/11248)
[INFO] [2023-06-21 13:33:14] Storing 5607 MetaTraits (15606/10000/11248)
[INFO] [2023-06-21 13:33:17] Storing 1247 Traits (17517/11246/11248)
[INFO] [2023-06-21 13:33:18] Storing 664 MetaTraits (17517/11246/11248)
[STOP] [2023-06-21 13:33:18] parse_diff_and_store
[START] [2023-06-21 13:33:18] resolve_keys
[2023-06-21 13:33:20] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-06-21 13:33:28] Occurrences to nodes (through scientific_names)...
[INFO] [2023-06-21 13:33:28] traits to occurrences...
[INFO] [2023-06-21 13:33:28] traits to nodes (through occurrences)...
[INFO] [2023-06-21 13:33:30] Traits to sex term...
[INFO] [2023-06-21 13:33:30] Traits to lifestage term...
[INFO] [2023-06-21 13:33:30] MetaTraits to traits...
[INFO] [2023-06-21 13:33:34] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-06-21 13:33:34] Assocs to occurrences...
[INFO] [2023-06-21 13:33:34] Assocs to nodes...
[INFO] [2023-06-21 13:33:34] Assoc to sex term...
[INFO] [2023-06-21 13:33:34] Assoc to lifestage term...
[INFO] [2023-06-21 13:33:34] MetaAssoc to assocs...
[STOP] [2023-06-21 13:33:34] resolve_keys
[START] [2023-06-21 13:33:34] hold_for_later_1
[STOP] [2023-06-21 13:33:35] hold_for_later_1
[START] [2023-06-21 13:33:35] hold_for_later_2
[STOP] [2023-06-21 13:33:35] hold_for_later_2
[START] [2023-06-21 13:33:35] resolve_missing_parents
[STOP] [2023-06-21 13:33:35] resolve_missing_parents
[START] [2023-06-21 13:33:35] rebuild_nodes
[START] [2023-06-21 13:33:35] Flattener#flatten
[START] [2023-06-21 13:33:35] Flattener#study_resource
[START] [2023-06-21 13:33:35] Flattener#build_ancestry
[STOP] [2023-06-21 13:33:35] Flattener#build_ancestry
[INFO] [2023-06-21 13:33:35] 6096 ancestry keys
[START] [2023-06-21 13:33:35] build_node_ancestors
[INFO] [2023-06-21 13:33:35] old ancestors deleted.
[STOP] [2023-06-21 13:33:36] build_node_ancestors
[START] [2023-06-21 13:33:36] Flattener#propagate_ancestor_ids
[STOP] [2023-06-21 13:33:36] Flattener#propagate_ancestor_ids
[STOP] [2023-06-21 13:33:36] Flattener#flatten
[STOP] [2023-06-21 13:33:36] rebuild_nodes
[START] [2023-06-21 13:33:36] resolve_missing_media_owners
[STOP] [2023-06-21 13:33:36] resolve_missing_media_owners
[START] [2023-06-21 13:33:36] sanitize_media_verbatims
[STOP] [2023-06-21 13:33:36] sanitize_media_verbatims
[START] [2023-06-21 13:33:36] queue_downloads
[STOP] [2023-06-21 13:33:36] queue_downloads
[START] [2023-06-21 13:33:36] parse_names
[WARN] [2023-06-21 13:33:36] I see 6096 names which still need to be parsed.
[WARN] [2023-06-21 13:33:37] Names to parse: 6096 formatted: 6096 learned: 6096 parsed: 6096
[STOP] [2023-06-21 13:33:41] parse_names
[START] [2023-06-21 13:33:41] denormalize_canonical_names_to_nodes
[STOP] [2023-06-21 13:33:41] denormalize_canonical_names_to_nodes
[START] [2023-06-21 13:33:41] match_nodes
[START] [2023-06-21 13:33:41] map_all_nodes_to_pages
[STOP] [2023-06-21 13:34:03] map_all_nodes_to_pages
[INFO] [2023-06-21 13:34:03] 46 Unmatched nodes (of 6096)! That's too many to output. Full list in /app/public/data/hab_dat_fun/unmatched_nodes.txt ; First 10: Canonical: Acerviclypeatus; Node#134959892; ResourceID: Acerviclypeatus; Canonical: Apomelasmia; Node#134960185; ResourceID: Apomelasmia; Canonical: Bacusphaeria nypenthi; Node#134960452; ResourceID: Bacusphaeria_nypenthi; Canonical: Bhatia; Node#134960524; ResourceID: Bhatia; Canonical: Candida aaseri; Node#134960756; ResourceID: Candida_aaseri; Canonical: Candida thaimeueangensis; Node#134960814; ResourceID: Candida_thaimeueangensis; Canonical: Cerillum; Node#134960917; ResourceID: Cerillum; Canonical: Ceuthodiplospora; Node#134960933; ResourceID: Ceuthodiplospora; Canonical: Coccostromella; Node#134961142; ResourceID: Coccostromella; Canonical: Cryptophaea; Node#134961316; ResourceID: Cryptophaea
[START] [2023-06-21 13:34:03] update_nodes
[STOP] [2023-06-21 13:34:03] update_nodes
[STOP] [2023-06-21 13:34:03] match_nodes
[START] [2023-06-21 13:34:03] reindex_search
[STOP] [2023-06-21 13:34:07] reindex_search
[START] [2023-06-21 13:34:07] normalize_units
[STOP] [2023-06-21 13:34:07] normalize_units
[START] [2023-06-21 13:34:07] calculate_statistics
[INFO] [2023-06-21 13:34:11] Duplicate page_id count: 52
[STOP] [2023-06-21 13:34:11] calculate_statistics
[START] [2023-06-21 13:34:11] complete_harvest_instance
[START] [2023-06-21 13:34:11] overall_tsv_creation
[INFO] [2023-06-21 13:34:11] Exporting 6096 nodes as TSV in batches of 10000...
[INFO] [2023-06-21 13:34:11] Processing group of 6096 in 1 batches of 10000
[INFO] [2023-06-21 13:34:20] 6271 Traits (unfiltered) and 0 associations...
[INFO] [2023-06-21 13:34:20] Building Traits map for 6096 nodes (this can take a while)...
[INFO] [2023-06-21 13:34:25] Mapped 6271 traits (6271 meta) for 6096 nodes.
[INFO] [2023-06-21 13:34:25] Building Associations map (this can take a while)...
[INFO] [2023-06-21 13:34:31] Done. 0 assocs mapped (0 meta).
[INFO] [2023-06-21 13:34:31] Adding 6271 traits...
[INFO] [2023-06-21 13:34:32] 4975 metadata added.
[INFO] [2023-06-21 13:34:32] Adding 0 assocs...
[INFO] [2023-06-21 13:34:32] 0 metadata added.
[INFO] [2023-06-21 13:35:41] Processed 6096/6096 nodes
[INFO] [2023-06-21 13:35:41] Average Time: 88.05
[INFO] [2023-06-21 13:35:41] Total Time: 1m30s
[STOP] [2023-06-21 13:35:41] overall_tsv_creation
[INFO] [2023-06-21 13:35:41] Done. Check your files:
[INFO] [2023-06-21 13:35:41] (6096 lines) /app/public/data/hab_dat_fun/publish_nodes.tsv
[INFO] [2023-06-21 13:35:41] (6095 lines) /app/public/data/hab_dat_fun/publish_node_ancestors.tsv
[INFO] [2023-06-21 13:35:41] (6096 lines) /app/public/data/hab_dat_fun/publish_scientific_names.tsv
[INFO] [2023-06-21 13:35:41] (6272 lines) /app/public/data/hab_dat_fun/publish_traits.tsv
[INFO] [2023-06-21 13:35:41] (4976 lines) /app/public/data/hab_dat_fun/publish_metadata.tsv
[STOP] [2023-06-21 13:35:41] complete_harvest_instance
[START] [2023-06-21 13:35:41] completed
[STOP] [2023-06-21 13:35:41] completed
[STOP] [2023-06-21 13:35:41] logged process, took 170.55

Latest Process

21 Jun 13:32 EXITED currently processing 0