Harvest for Mineralogy Created 11 Oct 09:46

Harvesting Log

[INFO] [2023-10-11 09:46:37] Created harvest instance #4402
[STOP] [2023-10-11 09:46:37] create_harvest_instance
[START] [2023-10-11 09:46:37] fetch_files
[STOP] [2023-10-11 09:46:37] fetch_files
[START] [2023-10-11 09:46:37] validate_each_file
[INFO] [2023-10-11 09:46:37] Looping over 4 formats...
[INFO] [2023-10-11 09:46:37] ...refs (/app/public/data/Mineralogy/references.tsv)
[INFO] [2023-10-11 09:46:38] Valid: /app/public/data/Mineralogy/converted_csv/Mineralogy_refs_30555.csv (85 lines)
[INFO] [2023-10-11 09:46:38] ...nodes (/app/public/data/Mineralogy/taxa.tsv)
[INFO] [2023-10-11 09:46:38] Valid: /app/public/data/Mineralogy/converted_csv/Mineralogy_nodes_30554.csv (277 lines)
[INFO] [2023-10-11 09:46:38] ...occurrences (/app/public/data/Mineralogy/occurrences.txt)
[INFO] [2023-10-11 09:46:38] Valid: /app/public/data/Mineralogy/converted_csv/Mineralogy_occurrences_30556.csv (267 lines)
[INFO] [2023-10-11 09:46:38] ...measurements (/app/public/data/Mineralogy/measurementsorfacts.tsv)
[INFO] [2023-10-11 09:46:38] Valid: /app/public/data/Mineralogy/converted_csv/Mineralogy_measurements_30557.csv (965 lines)
[STOP] [2023-10-11 09:46:38] validate_each_file
[START] [2023-10-11 09:46:38] convert_to_csv
[INFO] [2023-10-11 09:46:38] Looping over 4 formats...
[INFO] [2023-10-11 09:46:38] ...refs (/app/public/data/Mineralogy/references.tsv)
[CMD] [2023-10-11 09:46:38] /usr/bin/sort /app/public/data/Mineralogy/converted_csv/Mineralogy_refs_30555.csv > /app/public/data/Mineralogy/converted_csv/Mineralogy_refs_30555.csv_sorted
[INFO] [2023-10-11 09:46:38] Converted: /app/public/data/Mineralogy/converted_csv/Mineralogy_refs_30555.csv (85 lines)
[INFO] [2023-10-11 09:46:38] ...nodes (/app/public/data/Mineralogy/taxa.tsv)
[CMD] [2023-10-11 09:46:38] /usr/bin/sort /app/public/data/Mineralogy/converted_csv/Mineralogy_nodes_30554.csv > /app/public/data/Mineralogy/converted_csv/Mineralogy_nodes_30554.csv_sorted
[INFO] [2023-10-11 09:46:38] Converted: /app/public/data/Mineralogy/converted_csv/Mineralogy_nodes_30554.csv (277 lines)
[INFO] [2023-10-11 09:46:38] ...occurrences (/app/public/data/Mineralogy/occurrences.txt)
[CMD] [2023-10-11 09:46:38] /usr/bin/sort /app/public/data/Mineralogy/converted_csv/Mineralogy_occurrences_30556.csv > /app/public/data/Mineralogy/converted_csv/Mineralogy_occurrences_30556.csv_sorted
[INFO] [2023-10-11 09:46:38] Converted: /app/public/data/Mineralogy/converted_csv/Mineralogy_occurrences_30556.csv (267 lines)
[INFO] [2023-10-11 09:46:38] ...measurements (/app/public/data/Mineralogy/measurementsorfacts.tsv)
[CMD] [2023-10-11 09:46:38] /usr/bin/sort /app/public/data/Mineralogy/converted_csv/Mineralogy_measurements_30557.csv > /app/public/data/Mineralogy/converted_csv/Mineralogy_measurements_30557.csv_sorted
[INFO] [2023-10-11 09:46:38] Converted: /app/public/data/Mineralogy/converted_csv/Mineralogy_measurements_30557.csv (965 lines)
[STOP] [2023-10-11 09:46:38] convert_to_csv
[START] [2023-10-11 09:46:38] calculate_delta
[INFO] [2023-10-11 09:46:38] Looping over 4 formats...
[INFO] [2023-10-11 09:46:38] ...refs (/app/public/data/Mineralogy/references.tsv)
[CMD] [2023-10-11 09:46:38] echo "0a" > /app/public/data/Mineralogy/diff/Mineralogy_refs_30555.diff
[CMD] [2023-10-11 09:46:38] tail -n +1 /app/public/data/Mineralogy/converted_csv/Mineralogy_refs_30555.csv >> /app/public/data/Mineralogy/diff/Mineralogy_refs_30555.diff
[CMD] [2023-10-11 09:46:38] echo "." >> /app/public/data/Mineralogy/diff/Mineralogy_refs_30555.diff
[INFO] [2023-10-11 09:46:38] Created diff: /app/public/data/Mineralogy/diff/Mineralogy_refs_30555.diff (87 lines)
[INFO] [2023-10-11 09:46:38] ...nodes (/app/public/data/Mineralogy/taxa.tsv)
[CMD] [2023-10-11 09:46:38] echo "0a" > /app/public/data/Mineralogy/diff/Mineralogy_nodes_30554.diff
[CMD] [2023-10-11 09:46:38] tail -n +1 /app/public/data/Mineralogy/converted_csv/Mineralogy_nodes_30554.csv >> /app/public/data/Mineralogy/diff/Mineralogy_nodes_30554.diff
[CMD] [2023-10-11 09:46:38] echo "." >> /app/public/data/Mineralogy/diff/Mineralogy_nodes_30554.diff
[INFO] [2023-10-11 09:46:38] Created diff: /app/public/data/Mineralogy/diff/Mineralogy_nodes_30554.diff (279 lines)
[INFO] [2023-10-11 09:46:38] ...occurrences (/app/public/data/Mineralogy/occurrences.txt)
[CMD] [2023-10-11 09:46:38] echo "0a" > /app/public/data/Mineralogy/diff/Mineralogy_occurrences_30556.diff
[CMD] [2023-10-11 09:46:38] tail -n +1 /app/public/data/Mineralogy/converted_csv/Mineralogy_occurrences_30556.csv >> /app/public/data/Mineralogy/diff/Mineralogy_occurrences_30556.diff
[CMD] [2023-10-11 09:46:38] echo "." >> /app/public/data/Mineralogy/diff/Mineralogy_occurrences_30556.diff
[INFO] [2023-10-11 09:46:38] Created diff: /app/public/data/Mineralogy/diff/Mineralogy_occurrences_30556.diff (269 lines)
[INFO] [2023-10-11 09:46:38] ...measurements (/app/public/data/Mineralogy/measurementsorfacts.tsv)
[CMD] [2023-10-11 09:46:38] echo "0a" > /app/public/data/Mineralogy/diff/Mineralogy_measurements_30557.diff
[CMD] [2023-10-11 09:46:38] tail -n +1 /app/public/data/Mineralogy/converted_csv/Mineralogy_measurements_30557.csv >> /app/public/data/Mineralogy/diff/Mineralogy_measurements_30557.diff
[CMD] [2023-10-11 09:46:38] echo "." >> /app/public/data/Mineralogy/diff/Mineralogy_measurements_30557.diff
[INFO] [2023-10-11 09:46:38] Created diff: /app/public/data/Mineralogy/diff/Mineralogy_measurements_30557.diff (967 lines)
[STOP] [2023-10-11 09:46:38] calculate_delta
[START] [2023-10-11 09:46:38] parse_diff_and_store
[INFO] [2023-10-11 09:46:38] Handling diff: /app/public/data/Mineralogy/diff/Mineralogy_refs_30555.diff (87 lines)
[INFO] [2023-10-11 09:46:38] Loading refs diff file into memory (87 lines)...
[INFO] [2023-10-11 09:46:38] Storing 85 References (85/85/87)
[INFO] [2023-10-11 09:46:38] Handling diff: /app/public/data/Mineralogy/diff/Mineralogy_nodes_30554.diff (279 lines)
[INFO] [2023-10-11 09:46:38] Loading nodes diff file into memory (279 lines)...
[INFO] [2023-10-11 09:46:38] Storing 277 ScientificNames (554/277/279)
[INFO] [2023-10-11 09:46:38] Storing 277 Nodes (554/277/279)
[INFO] [2023-10-11 09:46:38] Handling diff: /app/public/data/Mineralogy/diff/Mineralogy_occurrences_30556.diff (269 lines)
[INFO] [2023-10-11 09:46:38] Loading occurrences diff file into memory (269 lines)...
[INFO] [2023-10-11 09:46:38] Storing 267 Occurrences (271/267/269)
[INFO] [2023-10-11 09:46:38] Storing 4 OccurrenceMetadata (271/267/269)
[INFO] [2023-10-11 09:46:38] Handling diff: /app/public/data/Mineralogy/diff/Mineralogy_measurements_30557.diff (967 lines)
[INFO] [2023-10-11 09:46:38] Loading measurements diff file into memory (967 lines)...
[INFO] [2023-10-11 09:46:39] Storing 965 Traits (2010/965/967)
[INFO] [2023-10-11 09:46:39] Storing 832 MetaTraits (2010/965/967)
[INFO] [2023-10-11 09:46:39] Storing 213 TraitsReferences (2010/965/967)
[STOP] [2023-10-11 09:46:39] parse_diff_and_store
[START] [2023-10-11 09:46:39] resolve_keys
[2023-10-11 09:46:39] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-11 09:46:47] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-11 09:46:47] traits to occurrences...
[INFO] [2023-10-11 09:46:47] traits to nodes (through occurrences)...
[INFO] [2023-10-11 09:46:47] Traits to sex term...
[INFO] [2023-10-11 09:46:47] Traits to lifestage term...
[INFO] [2023-10-11 09:46:47] MetaTraits to traits...
[INFO] [2023-10-11 09:46:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-11 09:46:47] Assocs to occurrences...
[INFO] [2023-10-11 09:46:47] Assocs to nodes...
[INFO] [2023-10-11 09:46:47] Assoc to sex term...
[INFO] [2023-10-11 09:46:47] Assoc to lifestage term...
[INFO] [2023-10-11 09:46:47] MetaAssoc to assocs...
[STOP] [2023-10-11 09:46:47] resolve_keys
[START] [2023-10-11 09:46:47] hold_for_later_1
[STOP] [2023-10-11 09:46:47] hold_for_later_1
[START] [2023-10-11 09:46:47] hold_for_later_2
[STOP] [2023-10-11 09:46:47] hold_for_later_2
[START] [2023-10-11 09:46:47] resolve_missing_parents
[STOP] [2023-10-11 09:46:47] resolve_missing_parents
[START] [2023-10-11 09:46:47] rebuild_nodes
[START] [2023-10-11 09:46:47] Flattener#flatten
[START] [2023-10-11 09:46:47] Flattener#study_resource
[START] [2023-10-11 09:46:47] Flattener#build_ancestry
[STOP] [2023-10-11 09:46:47] Flattener#build_ancestry
[INFO] [2023-10-11 09:46:47] 277 ancestry keys
[START] [2023-10-11 09:46:47] build_node_ancestors
[INFO] [2023-10-11 09:46:47] old ancestors deleted.
[STOP] [2023-10-11 09:46:47] build_node_ancestors
[WARN] [2023-10-11 09:46:47] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-11 09:46:47] Flattener#flatten
[STOP] [2023-10-11 09:46:47] rebuild_nodes
[START] [2023-10-11 09:46:47] resolve_missing_media_owners
[STOP] [2023-10-11 09:46:47] resolve_missing_media_owners
[START] [2023-10-11 09:46:47] sanitize_media_verbatims
[STOP] [2023-10-11 09:46:47] sanitize_media_verbatims
[START] [2023-10-11 09:46:47] queue_downloads
[STOP] [2023-10-11 09:46:47] queue_downloads
[START] [2023-10-11 09:46:47] parse_names
[WARN] [2023-10-11 09:46:47] I see 277 names which still need to be parsed.
[WARN] [2023-10-11 09:46:47] Names to parse: 277 formatted: 277 learned: 277 parsed: 277
[STOP] [2023-10-11 09:46:48] parse_names
[START] [2023-10-11 09:46:48] denormalize_canonical_names_to_nodes
[STOP] [2023-10-11 09:46:48] denormalize_canonical_names_to_nodes
[START] [2023-10-11 09:46:48] match_nodes
[START] [2023-10-11 09:46:48] map_all_nodes_to_pages
[STOP] [2023-10-11 09:46:49] map_all_nodes_to_pages
[INFO] [2023-10-11 09:46:49] ZERO unmatched nodes (of 277)! Nicely done.
[START] [2023-10-11 09:46:49] update_nodes
[STOP] [2023-10-11 09:46:49] update_nodes
[STOP] [2023-10-11 09:46:49] match_nodes
[START] [2023-10-11 09:46:49] reindex_search
[STOP] [2023-10-11 09:46:49] reindex_search
[START] [2023-10-11 09:46:49] normalize_units
[STOP] [2023-10-11 09:46:49] normalize_units
[START] [2023-10-11 09:46:49] calculate_statistics
[2023-10-11 09:46:49] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-11 09:46:49] Duplicate page_id count: 0
[STOP] [2023-10-11 09:46:49] calculate_statistics
[START] [2023-10-11 09:46:49] complete_harvest_instance
[START] [2023-10-11 09:46:49] overall_tsv_creation
[INFO] [2023-10-11 09:46:49] Exporting 277 nodes as TSV in batches of 10000...
[INFO] [2023-10-11 09:46:49] Processing group of 277 in 1 batches of 10000
[INFO] [2023-10-11 09:46:49] 319 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-11 09:46:49] Building Traits map for 277 nodes (this can take a while)...
[INFO] [2023-10-11 09:46:50] Mapped 319 traits (832 meta) for 277 nodes.
[INFO] [2023-10-11 09:46:50] Building Associations map (this can take a while)...
[INFO] [2023-10-11 09:46:50] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-11 09:46:50] Adding 319 traits...
[INFO] [2023-10-11 09:46:50] Trait #289647023 in key 289647023 has 36 metadata... that seems high?
[INFO] [2023-10-11 09:46:50] Trait #289647196 in key 289647196 has 30 metadata... that seems high?
[INFO] [2023-10-11 09:46:50] Trait #289647244 in key 289647244 has 42 metadata... that seems high?
[INFO] [2023-10-11 09:46:50] Trait #289647479 in key 289647479 has 25 metadata... that seems high?
[INFO] [2023-10-11 09:46:50] 1075 metadata added.
[INFO] [2023-10-11 09:46:50] Adding 0 assocs...
[INFO] [2023-10-11 09:46:50] 0 metadata added.
[INFO] [2023-10-11 09:47:35] Processed 277/277 nodes
[INFO] [2023-10-11 09:47:35] Average Time: 45.69
[INFO] [2023-10-11 09:47:35] Total Time: 46s
[STOP] [2023-10-11 09:47:35] overall_tsv_creation
[INFO] [2023-10-11 09:47:35] Done. Check your files:
[INFO] [2023-10-11 09:47:35] (277 lines) /app/public/data/Mineralogy/publish_nodes.tsv
[INFO] [2023-10-11 09:47:35] (277 lines) /app/public/data/Mineralogy/publish_scientific_names.tsv
[INFO] [2023-10-11 09:47:35] (320 lines) /app/public/data/Mineralogy/publish_traits.tsv
[INFO] [2023-10-11 09:47:35] (1076 lines) /app/public/data/Mineralogy/publish_metadata.tsv
[STOP] [2023-10-11 09:47:35] complete_harvest_instance
[START] [2023-10-11 09:47:35] completed
[STOP] [2023-10-11 09:47:35] completed
[STOP] [2023-10-11 09:47:35] logged process, took 58.12

Latest Process

11 Oct 09:46 EXITED currently processing 0