Stage:
completed
Fetched:
24 Oct 11:27
Validated:
24 Oct 11:27
Deltas Created
24 Oct 11:27
Units Normalized:
24 Oct 11:28
Ancestry Built:
24 Oct 11:27
Nodes Matched:
24 Oct 11:28
Names Parsed:
24 Oct 11:28
New Models Stored:
24 Oct 11:27
Indexed:
24 Oct 11:28
Completed:
24 Oct 11:28
Time to Harvest:
less than a minute
Harvesting Log
(168 lines)
[INFO] [2023-10-24 11:27:24] Created harvest instance #4489
[STOP] [2023-10-24 11:27:24] create_harvest_instance
[START] [2023-10-24 11:27:24] fetch_files
[STOP] [2023-10-24 11:27:24] fetch_files
[START] [2023-10-24 11:27:24] validate_each_file
[INFO] [2023-10-24 11:27:24] Looping over 5 formats...
[INFO] [2023-10-24 11:27:24] ...agents (/app/public/data/fao_sp_tar_gz/agent.tab)
[INFO] [2023-10-24 11:27:24] Valid: /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_agents_30954.csv (1 lines)
[INFO] [2023-10-24 11:27:24] ...refs (/app/public/data/fao_sp_tar_gz/reference.tab)
[INFO] [2023-10-24 11:27:24] Valid: /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_refs_30953.csv (1949 lines)
[INFO] [2023-10-24 11:27:24] ...nodes (/app/public/data/fao_sp_tar_gz/taxon.tab)
[INFO] [2023-10-24 11:27:24] Valid: /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_nodes_30951.csv (539 lines)
[INFO] [2023-10-24 11:27:24] ...media (/app/public/data/fao_sp_tar_gz/media_resource.tab)
[INFO] [2023-10-24 11:27:24] Valid: /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_media_30955.csv (2479 lines)
[INFO] [2023-10-24 11:27:24] ...vernaculars (/app/public/data/fao_sp_tar_gz/vernacular_name.tab)
[INFO] [2023-10-24 11:27:24] Valid: /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_vernaculars_30952.csv (1971 lines)
[STOP] [2023-10-24 11:27:24] validate_each_file
[START] [2023-10-24 11:27:24] convert_to_csv
[INFO] [2023-10-24 11:27:24] Looping over 5 formats...
[INFO] [2023-10-24 11:27:24] ...agents (/app/public/data/fao_sp_tar_gz/agent.tab)
[CMD] [2023-10-24 11:27:24] /usr/bin/sort /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_agents_30954.csv > /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_agents_30954.csv_sorted
[INFO] [2023-10-24 11:27:24] Converted: /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_agents_30954.csv (1 lines)
[INFO] [2023-10-24 11:27:24] ...refs (/app/public/data/fao_sp_tar_gz/reference.tab)
[CMD] [2023-10-24 11:27:24] /usr/bin/sort /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_refs_30953.csv > /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_refs_30953.csv_sorted
[INFO] [2023-10-24 11:27:24] Converted: /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_refs_30953.csv (1949 lines)
[INFO] [2023-10-24 11:27:24] ...nodes (/app/public/data/fao_sp_tar_gz/taxon.tab)
[CMD] [2023-10-24 11:27:24] /usr/bin/sort /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_nodes_30951.csv > /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_nodes_30951.csv_sorted
[INFO] [2023-10-24 11:27:24] Converted: /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_nodes_30951.csv (539 lines)
[INFO] [2023-10-24 11:27:24] ...media (/app/public/data/fao_sp_tar_gz/media_resource.tab)
[CMD] [2023-10-24 11:27:24] /usr/bin/sort /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_media_30955.csv > /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_media_30955.csv_sorted
[INFO] [2023-10-24 11:27:25] Converted: /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_media_30955.csv (2479 lines)
[INFO] [2023-10-24 11:27:25] ...vernaculars (/app/public/data/fao_sp_tar_gz/vernacular_name.tab)
[CMD] [2023-10-24 11:27:25] /usr/bin/sort /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_vernaculars_30952.csv > /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_vernaculars_30952.csv_sorted
[INFO] [2023-10-24 11:27:25] Converted: /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_vernaculars_30952.csv (1971 lines)
[STOP] [2023-10-24 11:27:25] convert_to_csv
[START] [2023-10-24 11:27:25] calculate_delta
[INFO] [2023-10-24 11:27:25] Looping over 5 formats...
[INFO] [2023-10-24 11:27:25] ...agents (/app/public/data/fao_sp_tar_gz/agent.tab)
[CMD] [2023-10-24 11:27:25] echo "0a" > /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_agents_30954.diff
[CMD] [2023-10-24 11:27:25] tail -n +1 /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_agents_30954.csv >> /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_agents_30954.diff
[CMD] [2023-10-24 11:27:25] echo "." >> /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_agents_30954.diff
[INFO] [2023-10-24 11:27:26] Created diff: /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_agents_30954.diff (3 lines)
[INFO] [2023-10-24 11:27:26] ...refs (/app/public/data/fao_sp_tar_gz/reference.tab)
[CMD] [2023-10-24 11:27:26] echo "0a" > /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_refs_30953.diff
[CMD] [2023-10-24 11:27:26] tail -n +1 /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_refs_30953.csv >> /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_refs_30953.diff
[CMD] [2023-10-24 11:27:26] echo "." >> /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_refs_30953.diff
[INFO] [2023-10-24 11:27:26] Created diff: /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_refs_30953.diff (1951 lines)
[INFO] [2023-10-24 11:27:26] ...nodes (/app/public/data/fao_sp_tar_gz/taxon.tab)
[CMD] [2023-10-24 11:27:26] echo "0a" > /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_nodes_30951.diff
[CMD] [2023-10-24 11:27:26] tail -n +1 /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_nodes_30951.csv >> /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_nodes_30951.diff
[CMD] [2023-10-24 11:27:26] echo "." >> /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_nodes_30951.diff
[INFO] [2023-10-24 11:27:26] Created diff: /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_nodes_30951.diff (541 lines)
[INFO] [2023-10-24 11:27:26] ...media (/app/public/data/fao_sp_tar_gz/media_resource.tab)
[CMD] [2023-10-24 11:27:26] echo "0a" > /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_media_30955.diff
[CMD] [2023-10-24 11:27:26] tail -n +1 /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_media_30955.csv >> /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_media_30955.diff
[CMD] [2023-10-24 11:27:26] echo "." >> /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_media_30955.diff
[INFO] [2023-10-24 11:27:27] Created diff: /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_media_30955.diff (2481 lines)
[INFO] [2023-10-24 11:27:27] ...vernaculars (/app/public/data/fao_sp_tar_gz/vernacular_name.tab)
[CMD] [2023-10-24 11:27:27] echo "0a" > /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_vernaculars_30952.diff
[CMD] [2023-10-24 11:27:27] tail -n +1 /app/public/data/fao_sp_tar_gz/converted_csv/fao_sp_tar_gz_vernaculars_30952.csv >> /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_vernaculars_30952.diff
[CMD] [2023-10-24 11:27:27] echo "." >> /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_vernaculars_30952.diff
[INFO] [2023-10-24 11:27:27] Created diff: /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_vernaculars_30952.diff (1973 lines)
[STOP] [2023-10-24 11:27:27] calculate_delta
[START] [2023-10-24 11:27:27] parse_diff_and_store
[INFO] [2023-10-24 11:27:27] Handling diff: /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_agents_30954.diff (3 lines)
[INFO] [2023-10-24 11:27:27] Loading agents diff file into memory (3 lines)...
[INFO] [2023-10-24 11:27:27] Storing 1 Attributions (1/1/3)
[INFO] [2023-10-24 11:27:27] Handling diff: /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_refs_30953.diff (1951 lines)
[INFO] [2023-10-24 11:27:27] Loading refs diff file into memory (1951 lines)...
[INFO] [2023-10-24 11:27:28] Storing 1949 References (1949/1949/1951)
[INFO] [2023-10-24 11:27:28] Handling diff: /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_nodes_30951.diff (541 lines)
[INFO] [2023-10-24 11:27:28] Loading nodes diff file into memory (541 lines)...
[WARN] [2023-10-24 11:27:28] Filtered Scientific Name `Mesoplodon peruvianus ("R, ) ` to `Mesoplodon peruvianus (R, ) `
[INFO] [2023-10-24 11:27:28] Storing 539 ScientificNames (1078/539/541)
[INFO] [2023-10-24 11:27:28] Storing 539 Nodes (1078/539/541)
[INFO] [2023-10-24 11:27:29] Handling diff: /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_media_30955.diff (2481 lines)
[INFO] [2023-10-24 11:27:29] Loading media diff file into memory (2481 lines)...
[INFO] [2023-10-24 11:27:32] Storing 1681 BibliographicCitations (22618/2479/2481)
[INFO] [2023-10-24 11:27:32] Storing 13500 ArticlesReferences (22618/2479/2481)
[INFO] [2023-10-24 11:27:33] Storing 2479 ContentAttributions (22618/2479/2481)
[INFO] [2023-10-24 11:27:34] Storing 2479 ArticlesSections (22618/2479/2481)
[INFO] [2023-10-24 11:27:34] Storing 2479 Articles (22618/2479/2481)
[INFO] [2023-10-24 11:27:34] Handling diff: /app/public/data/fao_sp_tar_gz/diff/fao_sp_tar_gz_vernaculars_30952.diff (1973 lines)
[INFO] [2023-10-24 11:27:35] Loading vernaculars diff file into memory (1973 lines)...
[INFO] [2023-10-24 11:27:35] Storing 1971 Vernaculars (1971/1971/1973)
[STOP] [2023-10-24 11:27:35] parse_diff_and_store
[START] [2023-10-24 11:27:35] resolve_keys
[2023-10-24 11:27:35] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-24 11:27:58] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-24 11:27:58] traits to occurrences...
[INFO] [2023-10-24 11:27:58] traits to nodes (through occurrences)...
[INFO] [2023-10-24 11:27:58] Traits to sex term...
[INFO] [2023-10-24 11:27:58] Traits to lifestage term...
[INFO] [2023-10-24 11:27:58] MetaTraits to traits...
[INFO] [2023-10-24 11:27:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-24 11:27:58] Assocs to occurrences...
[INFO] [2023-10-24 11:27:58] Assocs to nodes...
[INFO] [2023-10-24 11:27:58] Assoc to sex term...
[INFO] [2023-10-24 11:27:58] Assoc to lifestage term...
[INFO] [2023-10-24 11:27:58] MetaAssoc to assocs...
[STOP] [2023-10-24 11:27:58] resolve_keys
[START] [2023-10-24 11:27:58] hold_for_later_1
[STOP] [2023-10-24 11:27:58] hold_for_later_1
[START] [2023-10-24 11:27:58] hold_for_later_2
[STOP] [2023-10-24 11:27:58] hold_for_later_2
[START] [2023-10-24 11:27:58] resolve_missing_parents
[STOP] [2023-10-24 11:27:58] resolve_missing_parents
[START] [2023-10-24 11:27:58] rebuild_nodes
[START] [2023-10-24 11:27:58] Flattener#flatten
[START] [2023-10-24 11:27:58] Flattener#study_resource
[START] [2023-10-24 11:27:58] Flattener#build_ancestry
[STOP] [2023-10-24 11:27:58] Flattener#build_ancestry
[INFO] [2023-10-24 11:27:58] 539 ancestry keys
[START] [2023-10-24 11:27:58] build_node_ancestors
[INFO] [2023-10-24 11:27:58] old ancestors deleted.
[STOP] [2023-10-24 11:27:58] build_node_ancestors
[WARN] [2023-10-24 11:27:58] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-24 11:27:58] Flattener#flatten
[STOP] [2023-10-24 11:27:58] rebuild_nodes
[START] [2023-10-24 11:27:58] resolve_missing_media_owners
[STOP] [2023-10-24 11:27:58] resolve_missing_media_owners
[START] [2023-10-24 11:27:58] sanitize_media_verbatims
[STOP] [2023-10-24 11:27:58] sanitize_media_verbatims
[START] [2023-10-24 11:27:58] queue_downloads
[STOP] [2023-10-24 11:27:58] queue_downloads
[START] [2023-10-24 11:27:58] parse_names
[WARN] [2023-10-24 11:27:58] I see 539 names which still need to be parsed.
[WARN] [2023-10-24 11:27:59] Names to parse: 539 formatted: 539 learned: 539 parsed: 539
[STOP] [2023-10-24 11:28:00] parse_names
[START] [2023-10-24 11:28:00] denormalize_canonical_names_to_nodes
[STOP] [2023-10-24 11:28:00] denormalize_canonical_names_to_nodes
[START] [2023-10-24 11:28:00] match_nodes
[START] [2023-10-24 11:28:00] map_all_nodes_to_pages
[STOP] [2023-10-24 11:28:06] map_all_nodes_to_pages
[INFO] [2023-10-24 11:28:06] 16 Unmatched nodes (of 539)! That's too many to output. Full list in /app/public/data/fao_sp_tar_gz/unmatched_nodes.txt ; First 10: Canonical: Centrophorus acus; Node#137237569; ResourceID: 1090100805; Canonical: Centrophorus niaukang; Node#137237572; ResourceID: 1090100808; Canonical: Sardinops caeruleus; Node#137237635; ResourceID: 1210501302; Canonical: Sardinops sagax; Node#137237636; ResourceID: 1210501303; Canonical: Sardinops ocellatus; Node#137237637; ResourceID: 1210501305; Canonical: Gadus ogac; Node#137237690; ResourceID: 1480400212; Canonical: Sebastes marinus; Node#137237806; ResourceID: 1780100101; Canonical: Pseudopleuronectes; Node#137237826; ResourceID: 1830205001; Canonical: Trachypenaeus curvirostris; Node#137237853; ResourceID: 2280104302; Canonical: Procambarus clarkii; Node#137237863; ResourceID: 2290400101
[START] [2023-10-24 11:28:06] update_nodes
[STOP] [2023-10-24 11:28:06] update_nodes
[STOP] [2023-10-24 11:28:06] match_nodes
[START] [2023-10-24 11:28:06] reindex_search
[STOP] [2023-10-24 11:28:06] reindex_search
[START] [2023-10-24 11:28:06] normalize_units
[STOP] [2023-10-24 11:28:06] normalize_units
[START] [2023-10-24 11:28:06] calculate_statistics
[2023-10-24 11:28:06] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-24 11:28:07] Duplicate page_id count: 0
[STOP] [2023-10-24 11:28:07] calculate_statistics
[START] [2023-10-24 11:28:07] complete_harvest_instance
[START] [2023-10-24 11:28:07] overall_tsv_creation
[INFO] [2023-10-24 11:28:07] Exporting 539 nodes as TSV in batches of 10000...
[INFO] [2023-10-24 11:28:07] Processing group of 539 in 1 batches of 10000
[INFO] [2023-10-24 11:28:17] Processed 539/539 nodes
[INFO] [2023-10-24 11:28:17] Average Time: 2.64
[INFO] [2023-10-24 11:28:17] Total Time: 11s
[STOP] [2023-10-24 11:28:17] overall_tsv_creation
[INFO] [2023-10-24 11:28:17] Done. Check your files:
[INFO] [2023-10-24 11:28:17] (1681 lines) /app/public/data/fao_sp_tar_gz/publish_bibliographic_citations.tsv
[INFO] [2023-10-24 11:28:17] (539 lines) /app/public/data/fao_sp_tar_gz/publish_nodes.tsv
[INFO] [2023-10-24 11:28:18] (539 lines) /app/public/data/fao_sp_tar_gz/publish_scientific_names.tsv
[INFO] [2023-10-24 11:28:18] (2479 lines) /app/public/data/fao_sp_tar_gz/publish_articles.tsv
[INFO] [2023-10-24 11:28:18] (1971 lines) /app/public/data/fao_sp_tar_gz/publish_vernaculars.tsv
[INFO] [2023-10-24 11:28:18] (1949 lines) /app/public/data/fao_sp_tar_gz/publish_references.tsv
[INFO] [2023-10-24 11:28:18] (2479 lines) /app/public/data/fao_sp_tar_gz/publish_attributions.tsv
[INFO] [2023-10-24 11:28:18] (2479 lines) /app/public/data/fao_sp_tar_gz/publish_content_sections.tsv
[INFO] [2023-10-24 11:28:18] (1949 lines) /app/public/data/fao_sp_tar_gz/publish_referents.tsv
[STOP] [2023-10-24 11:28:18] complete_harvest_instance
[START] [2023-10-24 11:28:18] completed
[STOP] [2023-10-24 11:28:18] completed
[STOP] [2023-10-24 11:28:18] logged process, took 54.81
Latest Process