Harvest for BROT plant trait database for Mediterranean Created 13 Oct 11:18

Harvesting Log

[INFO] [2023-10-13 11:18:02] Created harvest instance #4428
[STOP] [2023-10-13 11:18:02] create_harvest_instance
[START] [2023-10-13 11:18:02] fetch_files
[STOP] [2023-10-13 11:18:02] fetch_files
[START] [2023-10-13 11:18:02] validate_each_file
[INFO] [2023-10-13 11:18:02] Looping over 4 formats...
[INFO] [2023-10-13 11:18:02] ...refs (/app/public/data/BROT/references.txt)
[INFO] [2023-10-13 11:18:02] Valid: /app/public/data/BROT/converted_csv/BROT_refs_30674.csv (295 lines)
[INFO] [2023-10-13 11:18:02] ...nodes (/app/public/data/BROT/taxa.txt)
[INFO] [2023-10-13 11:18:02] Valid: /app/public/data/BROT/converted_csv/BROT_nodes_30673.csv (950 lines)
[INFO] [2023-10-13 11:18:02] ...occurrences (/app/public/data/BROT/occurrences.txt)
[INFO] [2023-10-13 11:18:03] Valid: /app/public/data/BROT/converted_csv/BROT_occurrences_30675.csv (11482 lines)
[INFO] [2023-10-13 11:18:03] ...measurements (/app/public/data/BROT/measurements or facts.txt)
[INFO] [2023-10-13 11:18:04] Valid: /app/public/data/BROT/converted_csv/BROT_measurements_30676.csv (11449 lines)
[STOP] [2023-10-13 11:18:04] validate_each_file
[START] [2023-10-13 11:18:05] convert_to_csv
[INFO] [2023-10-13 11:18:05] Looping over 4 formats...
[INFO] [2023-10-13 11:18:05] ...refs (/app/public/data/BROT/references.txt)
[CMD] [2023-10-13 11:18:05] /usr/bin/sort /app/public/data/BROT/converted_csv/BROT_refs_30674.csv > /app/public/data/BROT/converted_csv/BROT_refs_30674.csv_sorted
[INFO] [2023-10-13 11:18:05] Converted: /app/public/data/BROT/converted_csv/BROT_refs_30674.csv (295 lines)
[INFO] [2023-10-13 11:18:05] ...nodes (/app/public/data/BROT/taxa.txt)
[CMD] [2023-10-13 11:18:05] /usr/bin/sort /app/public/data/BROT/converted_csv/BROT_nodes_30673.csv > /app/public/data/BROT/converted_csv/BROT_nodes_30673.csv_sorted
[INFO] [2023-10-13 11:18:05] Converted: /app/public/data/BROT/converted_csv/BROT_nodes_30673.csv (950 lines)
[INFO] [2023-10-13 11:18:05] ...occurrences (/app/public/data/BROT/occurrences.txt)
[CMD] [2023-10-13 11:18:05] /usr/bin/sort /app/public/data/BROT/converted_csv/BROT_occurrences_30675.csv > /app/public/data/BROT/converted_csv/BROT_occurrences_30675.csv_sorted
[INFO] [2023-10-13 11:18:05] Converted: /app/public/data/BROT/converted_csv/BROT_occurrences_30675.csv (11482 lines)
[INFO] [2023-10-13 11:18:05] ...measurements (/app/public/data/BROT/measurements or facts.txt)
[CMD] [2023-10-13 11:18:05] /usr/bin/sort /app/public/data/BROT/converted_csv/BROT_measurements_30676.csv > /app/public/data/BROT/converted_csv/BROT_measurements_30676.csv_sorted
[INFO] [2023-10-13 11:18:05] Converted: /app/public/data/BROT/converted_csv/BROT_measurements_30676.csv (11449 lines)
[STOP] [2023-10-13 11:18:05] convert_to_csv
[START] [2023-10-13 11:18:05] calculate_delta
[INFO] [2023-10-13 11:18:05] Looping over 4 formats...
[INFO] [2023-10-13 11:18:05] ...refs (/app/public/data/BROT/references.txt)
[CMD] [2023-10-13 11:18:05] echo "0a" > /app/public/data/BROT/diff/BROT_refs_30674.diff
[CMD] [2023-10-13 11:18:05] tail -n +1 /app/public/data/BROT/converted_csv/BROT_refs_30674.csv >> /app/public/data/BROT/diff/BROT_refs_30674.diff
[CMD] [2023-10-13 11:18:05] echo "." >> /app/public/data/BROT/diff/BROT_refs_30674.diff
[INFO] [2023-10-13 11:18:05] Created diff: /app/public/data/BROT/diff/BROT_refs_30674.diff (297 lines)
[INFO] [2023-10-13 11:18:05] ...nodes (/app/public/data/BROT/taxa.txt)
[CMD] [2023-10-13 11:18:05] echo "0a" > /app/public/data/BROT/diff/BROT_nodes_30673.diff
[CMD] [2023-10-13 11:18:05] tail -n +1 /app/public/data/BROT/converted_csv/BROT_nodes_30673.csv >> /app/public/data/BROT/diff/BROT_nodes_30673.diff
[CMD] [2023-10-13 11:18:06] echo "." >> /app/public/data/BROT/diff/BROT_nodes_30673.diff
[INFO] [2023-10-13 11:18:06] Created diff: /app/public/data/BROT/diff/BROT_nodes_30673.diff (952 lines)
[INFO] [2023-10-13 11:18:06] ...occurrences (/app/public/data/BROT/occurrences.txt)
[CMD] [2023-10-13 11:18:06] echo "0a" > /app/public/data/BROT/diff/BROT_occurrences_30675.diff
[CMD] [2023-10-13 11:18:06] tail -n +1 /app/public/data/BROT/converted_csv/BROT_occurrences_30675.csv >> /app/public/data/BROT/diff/BROT_occurrences_30675.diff
[CMD] [2023-10-13 11:18:06] echo "." >> /app/public/data/BROT/diff/BROT_occurrences_30675.diff
[INFO] [2023-10-13 11:18:06] Created diff: /app/public/data/BROT/diff/BROT_occurrences_30675.diff (11484 lines)
[INFO] [2023-10-13 11:18:06] ...measurements (/app/public/data/BROT/measurements or facts.txt)
[CMD] [2023-10-13 11:18:06] echo "0a" > /app/public/data/BROT/diff/BROT_measurements_30676.diff
[CMD] [2023-10-13 11:18:06] tail -n +1 /app/public/data/BROT/converted_csv/BROT_measurements_30676.csv >> /app/public/data/BROT/diff/BROT_measurements_30676.diff
[CMD] [2023-10-13 11:18:06] echo "." >> /app/public/data/BROT/diff/BROT_measurements_30676.diff
[INFO] [2023-10-13 11:18:06] Created diff: /app/public/data/BROT/diff/BROT_measurements_30676.diff (11451 lines)
[STOP] [2023-10-13 11:18:06] calculate_delta
[START] [2023-10-13 11:18:06] parse_diff_and_store
[INFO] [2023-10-13 11:18:06] Handling diff: /app/public/data/BROT/diff/BROT_refs_30674.diff (297 lines)
[INFO] [2023-10-13 11:18:06] Loading refs diff file into memory (297 lines)...
[INFO] [2023-10-13 11:18:06] Storing 295 References (295/295/297)
[INFO] [2023-10-13 11:18:06] Handling diff: /app/public/data/BROT/diff/BROT_nodes_30673.diff (952 lines)
[INFO] [2023-10-13 11:18:06] Loading nodes diff file into memory (952 lines)...
[INFO] [2023-10-13 11:18:07] Storing 1030 ScientificNames (2060/950/952)
[INFO] [2023-10-13 11:18:07] Storing 1030 Nodes (2060/950/952)
[INFO] [2023-10-13 11:18:07] Handling diff: /app/public/data/BROT/diff/BROT_occurrences_30675.diff (11484 lines)
[INFO] [2023-10-13 11:18:07] Loading occurrences diff file into memory (11484 lines)...
[INFO] [2023-10-13 11:18:10] Storing 9999 Occurrences (18322/10000/11484)
[INFO] [2023-10-13 11:18:11] Storing 8323 OccurrenceMetadata (18322/10000/11484)
[WARN] [2023-10-13 11:18:12] SKIPPED 1401 Occurrence metadata (21206/11482/11484) with resource_pks already be in the database!
[INFO] [2023-10-13 11:18:12] Storing 1483 Occurrences (21206/11482/11484)
[INFO] [2023-10-13 11:18:12] Storing 0 OccurrenceMetadata (21206/11482/11484)
[WARN] [2023-10-13 11:18:12] No models to import, skipping!
[INFO] [2023-10-13 11:18:12] Handling diff: /app/public/data/BROT/diff/BROT_measurements_30676.diff (11451 lines)
[INFO] [2023-10-13 11:18:13] Loading measurements diff file into memory (11451 lines)...
[INFO] [2023-10-13 11:18:20] Storing 8554 TraitsReferences (49541/10000/11451)
[INFO] [2023-10-13 11:18:21] Storing 9999 Traits (49541/10000/11451)
[INFO] [2023-10-13 11:18:24] Storing 30988 MetaTraits (49541/10000/11451)
[INFO] [2023-10-13 11:18:29] Storing 1450 TraitsReferences (56646/11449/11451)
[INFO] [2023-10-13 11:18:29] Storing 1450 Traits (56646/11449/11451)
[INFO] [2023-10-13 11:18:30] Storing 4205 MetaTraits (56646/11449/11451)
[STOP] [2023-10-13 11:18:30] parse_diff_and_store
[START] [2023-10-13 11:18:30] resolve_keys
[2023-10-13 11:18:30] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 11:18:38] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 11:18:38] traits to occurrences...
[INFO] [2023-10-13 11:18:39] traits to nodes (through occurrences)...
[INFO] [2023-10-13 11:18:39] Traits to sex term...
[INFO] [2023-10-13 11:18:39] Traits to lifestage term...
[INFO] [2023-10-13 11:18:39] MetaTraits to traits...
[INFO] [2023-10-13 11:18:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 11:18:41] Assocs to occurrences...
[INFO] [2023-10-13 11:18:41] Assocs to nodes...
[INFO] [2023-10-13 11:18:41] Assoc to sex term...
[INFO] [2023-10-13 11:18:41] Assoc to lifestage term...
[INFO] [2023-10-13 11:18:41] MetaAssoc to assocs...
[STOP] [2023-10-13 11:18:41] resolve_keys
[START] [2023-10-13 11:18:41] hold_for_later_1
[STOP] [2023-10-13 11:18:41] hold_for_later_1
[START] [2023-10-13 11:18:41] hold_for_later_2
[STOP] [2023-10-13 11:18:41] hold_for_later_2
[START] [2023-10-13 11:18:41] resolve_missing_parents
[STOP] [2023-10-13 11:18:41] resolve_missing_parents
[START] [2023-10-13 11:18:41] rebuild_nodes
[START] [2023-10-13 11:18:41] Flattener#flatten
[START] [2023-10-13 11:18:41] Flattener#study_resource
[START] [2023-10-13 11:18:41] Flattener#build_ancestry
[STOP] [2023-10-13 11:18:41] Flattener#build_ancestry
[INFO] [2023-10-13 11:18:41] 1030 ancestry keys
[START] [2023-10-13 11:18:41] build_node_ancestors
[INFO] [2023-10-13 11:18:41] old ancestors deleted.
[STOP] [2023-10-13 11:18:41] build_node_ancestors
[START] [2023-10-13 11:18:41] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:18:41] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:18:41] Flattener#flatten
[STOP] [2023-10-13 11:18:41] rebuild_nodes
[START] [2023-10-13 11:18:41] resolve_missing_media_owners
[STOP] [2023-10-13 11:18:41] resolve_missing_media_owners
[START] [2023-10-13 11:18:41] sanitize_media_verbatims
[STOP] [2023-10-13 11:18:41] sanitize_media_verbatims
[START] [2023-10-13 11:18:41] queue_downloads
[STOP] [2023-10-13 11:18:41] queue_downloads
[START] [2023-10-13 11:18:41] parse_names
[WARN] [2023-10-13 11:18:41] I see 1030 names which still need to be parsed.
[WARN] [2023-10-13 11:18:41] Names to parse: 1030 formatted: 1030 learned: 1030 parsed: 1030
[STOP] [2023-10-13 11:18:43] parse_names
[START] [2023-10-13 11:18:43] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 11:18:43] denormalize_canonical_names_to_nodes
[START] [2023-10-13 11:18:43] match_nodes
[START] [2023-10-13 11:18:43] map_all_nodes_to_pages
[STOP] [2023-10-13 11:18:54] map_all_nodes_to_pages
[INFO] [2023-10-13 11:18:54] 45 Unmatched nodes (of 1030)! That's too many to output. Full list in /app/public/data/BROT/unmatched_nodes.txt ; First 10: Canonical: Aetheorhiza bulbosa bulbosa; Node#137152301; ResourceID: Aetheorhiza bulbosa ssp. bulbosa; Canonical: Centaurea boissieri duffourii; Node#137152485; ResourceID: Centaurea boissieri ssp. duffourii; Canonical: Centaurea linifolia linifolia; Node#137152489; ResourceID: Centaurea linifolia ssp. linifolia; Canonical: Chrysanthemum segetum; Node#137152520; ResourceID: Chrysanthemum segetum; Canonical: Hypochoeris glabra; Node#137152825; ResourceID: Hypochoeris glabra; Canonical: Hypochoeris radicata; Node#137152826; ResourceID: Hypochoeris radicata; Canonical: Inula conyza; Node#137152830; ResourceID: Inula conyza; Canonical: Inula montana; Node#137152831; ResourceID: Inula montana; Canonical: Leuzea conifera; Node#137152874; ResourceID: Leuzea conifera; Canonical: Scorzonera graminifolia; Node#137153146; ResourceID: Scorzonera graminifolia
[START] [2023-10-13 11:18:54] update_nodes
[STOP] [2023-10-13 11:18:54] update_nodes
[STOP] [2023-10-13 11:18:54] match_nodes
[START] [2023-10-13 11:18:54] reindex_search
[STOP] [2023-10-13 11:18:55] reindex_search
[START] [2023-10-13 11:18:55] normalize_units
[STOP] [2023-10-13 11:19:00] normalize_units
[START] [2023-10-13 11:19:00] calculate_statistics
[INFO] [2023-10-13 11:19:01] Duplicate page_id count: 0
[STOP] [2023-10-13 11:19:01] calculate_statistics
[START] [2023-10-13 11:19:01] complete_harvest_instance
[START] [2023-10-13 11:19:01] overall_tsv_creation
[INFO] [2023-10-13 11:19:01] Exporting 1030 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 11:19:01] Processing group of 1030 in 1 batches of 10000
[INFO] [2023-10-13 11:19:03] 11449 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 11:19:03] Building Traits map for 1030 nodes (this can take a while)...
[INFO] [2023-10-13 11:19:08] Mapped 11449 traits (35193 meta) for 1030 nodes.
[INFO] [2023-10-13 11:19:08] Building Associations map (this can take a while)...
[INFO] [2023-10-13 11:19:08] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 11:19:08] Adding 11449 traits...
[INFO] [2023-10-13 11:19:11] 18020 metadata added.
[INFO] [2023-10-13 11:19:11] Adding 0 assocs...
[INFO] [2023-10-13 11:19:11] 0 metadata added.
[INFO] [2023-10-13 11:19:58] Processed 1030/1030 nodes
[INFO] [2023-10-13 11:19:58] Average Time: 56.13
[INFO] [2023-10-13 11:19:58] Total Time: 57s
[STOP] [2023-10-13 11:19:58] overall_tsv_creation
[INFO] [2023-10-13 11:19:58] Done. Check your files:
[INFO] [2023-10-13 11:19:58] (1030 lines) /app/public/data/BROT/publish_nodes.tsv
[INFO] [2023-10-13 11:19:58] (1979 lines) /app/public/data/BROT/publish_node_ancestors.tsv
[INFO] [2023-10-13 11:19:58] (1030 lines) /app/public/data/BROT/publish_scientific_names.tsv
[INFO] [2023-10-13 11:19:58] (11450 lines) /app/public/data/BROT/publish_traits.tsv
[INFO] [2023-10-13 11:19:58] (18021 lines) /app/public/data/BROT/publish_metadata.tsv
[STOP] [2023-10-13 11:19:58] complete_harvest_instance
[START] [2023-10-13 11:19:58] completed
[STOP] [2023-10-13 11:19:58] completed
[STOP] [2023-10-13 11:19:58] logged process, took 116.38

Latest Process

13 Oct 11:17 EXITED currently processing 0