Harvest for Microbial Eukaryotes Trophic Guilds Created 05 Oct 14:46

Stage: completed
Fetched: 05 Oct 14:46
Validated: 05 Oct 14:46
Deltas Created 05 Oct 14:46
Units Normalized: 05 Oct 14:46
Ancestry Built: 05 Oct 14:46
Nodes Matched: 05 Oct 14:46
Names Parsed: 05 Oct 14:46
New Models Stored: 05 Oct 14:46
Indexed: 05 Oct 14:46
Completed: 05 Oct 14:47
Time to Harvest: less than a minute
Harvesting Log

(143 lines)
[INFO] [2023-10-05 14:46:10] Created harvest instance #4397
[STOP] [2023-10-05 14:46:10] create_harvest_instance
[START] [2023-10-05 14:46:10] fetch_files
[STOP] [2023-10-05 14:46:10] fetch_files
[START] [2023-10-05 14:46:10] validate_each_file
[INFO] [2023-10-05 14:46:10] Looping over 3 formats...
[INFO] [2023-10-05 14:46:10] ...nodes (/app/public/data/microbial_eukar2/taxon.tab)
[INFO] [2023-10-05 14:46:10] Valid: /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_nodes_30535.csv (496 lines)
[INFO] [2023-10-05 14:46:10] ...occurrences (/app/public/data/microbial_eukar2/occurrence_specific.tab)
[INFO] [2023-10-05 14:46:10] Valid: /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_occurrences_30536.csv (524 lines)
[INFO] [2023-10-05 14:46:10] ...measurements (/app/public/data/microbial_eukar2/measurement_or_fact_specific.tab)
[INFO] [2023-10-05 14:46:10] Valid: /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_measurements_30537.csv (951 lines)
[STOP] [2023-10-05 14:46:10] validate_each_file
[START] [2023-10-05 14:46:10] convert_to_csv
[INFO] [2023-10-05 14:46:10] Looping over 3 formats...
[INFO] [2023-10-05 14:46:10] ...nodes (/app/public/data/microbial_eukar2/taxon.tab)
[CMD] [2023-10-05 14:46:10] /usr/bin/sort /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_nodes_30535.csv > /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_nodes_30535.csv_sorted
[INFO] [2023-10-05 14:46:10] Converted: /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_nodes_30535.csv (496 lines)
[INFO] [2023-10-05 14:46:10] ...occurrences (/app/public/data/microbial_eukar2/occurrence_specific.tab)
[CMD] [2023-10-05 14:46:10] /usr/bin/sort /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_occurrences_30536.csv > /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_occurrences_30536.csv_sorted
[INFO] [2023-10-05 14:46:10] Converted: /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_occurrences_30536.csv (524 lines)
[INFO] [2023-10-05 14:46:10] ...measurements (/app/public/data/microbial_eukar2/measurement_or_fact_specific.tab)
[CMD] [2023-10-05 14:46:10] /usr/bin/sort /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_measurements_30537.csv > /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_measurements_30537.csv_sorted
[INFO] [2023-10-05 14:46:10] Converted: /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_measurements_30537.csv (951 lines)
[STOP] [2023-10-05 14:46:10] convert_to_csv
[START] [2023-10-05 14:46:10] calculate_delta
[INFO] [2023-10-05 14:46:10] Looping over 3 formats...
[INFO] [2023-10-05 14:46:10] ...nodes (/app/public/data/microbial_eukar2/taxon.tab)
[CMD] [2023-10-05 14:46:10] echo "0a" > /app/public/data/microbial_eukar2/diff/microbial_eukar2_nodes_30535.diff
[CMD] [2023-10-05 14:46:10] tail -n +1 /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_nodes_30535.csv >> /app/public/data/microbial_eukar2/diff/microbial_eukar2_nodes_30535.diff
[CMD] [2023-10-05 14:46:10] echo "." >> /app/public/data/microbial_eukar2/diff/microbial_eukar2_nodes_30535.diff
[INFO] [2023-10-05 14:46:10] Created diff: /app/public/data/microbial_eukar2/diff/microbial_eukar2_nodes_30535.diff (498 lines)
[INFO] [2023-10-05 14:46:10] ...occurrences (/app/public/data/microbial_eukar2/occurrence_specific.tab)
[CMD] [2023-10-05 14:46:10] echo "0a" > /app/public/data/microbial_eukar2/diff/microbial_eukar2_occurrences_30536.diff
[CMD] [2023-10-05 14:46:10] tail -n +1 /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_occurrences_30536.csv >> /app/public/data/microbial_eukar2/diff/microbial_eukar2_occurrences_30536.diff
[CMD] [2023-10-05 14:46:10] echo "." >> /app/public/data/microbial_eukar2/diff/microbial_eukar2_occurrences_30536.diff
[INFO] [2023-10-05 14:46:10] Created diff: /app/public/data/microbial_eukar2/diff/microbial_eukar2_occurrences_30536.diff (526 lines)
[INFO] [2023-10-05 14:46:10] ...measurements (/app/public/data/microbial_eukar2/measurement_or_fact_specific.tab)
[CMD] [2023-10-05 14:46:10] echo "0a" > /app/public/data/microbial_eukar2/diff/microbial_eukar2_measurements_30537.diff
[CMD] [2023-10-05 14:46:10] tail -n +1 /app/public/data/microbial_eukar2/converted_csv/microbial_eukar2_measurements_30537.csv >> /app/public/data/microbial_eukar2/diff/microbial_eukar2_measurements_30537.diff
[CMD] [2023-10-05 14:46:10] echo "." >> /app/public/data/microbial_eukar2/diff/microbial_eukar2_measurements_30537.diff
[INFO] [2023-10-05 14:46:10] Created diff: /app/public/data/microbial_eukar2/diff/microbial_eukar2_measurements_30537.diff (953 lines)
[STOP] [2023-10-05 14:46:10] calculate_delta
[START] [2023-10-05 14:46:10] parse_diff_and_store
[INFO] [2023-10-05 14:46:10] Handling diff: /app/public/data/microbial_eukar2/diff/microbial_eukar2_nodes_30535.diff (498 lines)
[INFO] [2023-10-05 14:46:10] Loading nodes diff file into memory (498 lines)...
[INFO] [2023-10-05 14:46:10] Storing 496 ScientificNames (992/496/498)
[INFO] [2023-10-05 14:46:11] Storing 496 Nodes (992/496/498)
[INFO] [2023-10-05 14:46:11] Handling diff: /app/public/data/microbial_eukar2/diff/microbial_eukar2_occurrences_30536.diff (526 lines)
[INFO] [2023-10-05 14:46:11] Loading occurrences diff file into memory (526 lines)...
[INFO] [2023-10-05 14:46:11] Storing 524 Occurrences (524/524/526)
[INFO] [2023-10-05 14:46:11] Handling diff: /app/public/data/microbial_eukar2/diff/microbial_eukar2_measurements_30537.diff (953 lines)
[INFO] [2023-10-05 14:46:11] Loading measurements diff file into memory (953 lines)...
[INFO] [2023-10-05 14:46:11] Storing 951 Traits (1475/951/953)
[INFO] [2023-10-05 14:46:13] Storing 524 MetaTraits (1475/951/953)
[STOP] [2023-10-05 14:46:13] parse_diff_and_store
[START] [2023-10-05 14:46:13] resolve_keys
[2023-10-05 14:46:14] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-05 14:46:22] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-05 14:46:22] traits to occurrences...
[INFO] [2023-10-05 14:46:22] traits to nodes (through occurrences)...
[INFO] [2023-10-05 14:46:22] Traits to sex term...
[INFO] [2023-10-05 14:46:22] Traits to lifestage term...
[INFO] [2023-10-05 14:46:22] MetaTraits to traits...
[INFO] [2023-10-05 14:46:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-05 14:46:22] Assocs to occurrences...
[INFO] [2023-10-05 14:46:22] Assocs to nodes...
[INFO] [2023-10-05 14:46:22] Assoc to sex term...
[INFO] [2023-10-05 14:46:22] Assoc to lifestage term...
[INFO] [2023-10-05 14:46:22] MetaAssoc to assocs...
[STOP] [2023-10-05 14:46:22] resolve_keys
[START] [2023-10-05 14:46:22] hold_for_later_1
[STOP] [2023-10-05 14:46:22] hold_for_later_1
[START] [2023-10-05 14:46:22] hold_for_later_2
[STOP] [2023-10-05 14:46:22] hold_for_later_2
[START] [2023-10-05 14:46:22] resolve_missing_parents
[STOP] [2023-10-05 14:46:22] resolve_missing_parents
[START] [2023-10-05 14:46:22] rebuild_nodes
[START] [2023-10-05 14:46:22] Flattener#flatten
[START] [2023-10-05 14:46:22] Flattener#study_resource
[START] [2023-10-05 14:46:22] Flattener#build_ancestry
[STOP] [2023-10-05 14:46:22] Flattener#build_ancestry
[INFO] [2023-10-05 14:46:22] 496 ancestry keys
[START] [2023-10-05 14:46:22] build_node_ancestors
[INFO] [2023-10-05 14:46:22] old ancestors deleted.
[STOP] [2023-10-05 14:46:22] build_node_ancestors
[WARN] [2023-10-05 14:46:22] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-05 14:46:22] Flattener#flatten
[STOP] [2023-10-05 14:46:22] rebuild_nodes
[START] [2023-10-05 14:46:22] resolve_missing_media_owners
[STOP] [2023-10-05 14:46:22] resolve_missing_media_owners
[START] [2023-10-05 14:46:22] sanitize_media_verbatims
[STOP] [2023-10-05 14:46:22] sanitize_media_verbatims
[START] [2023-10-05 14:46:22] queue_downloads
[STOP] [2023-10-05 14:46:22] queue_downloads
[START] [2023-10-05 14:46:22] parse_names
[WARN] [2023-10-05 14:46:22] I see 496 names which still need to be parsed.
[WARN] [2023-10-05 14:46:23] Names to parse: 496 formatted: 496 learned: 496 parsed: 496
[STOP] [2023-10-05 14:46:24] parse_names
[START] [2023-10-05 14:46:24] denormalize_canonical_names_to_nodes
[STOP] [2023-10-05 14:46:24] denormalize_canonical_names_to_nodes
[START] [2023-10-05 14:46:24] match_nodes
[START] [2023-10-05 14:46:24] map_all_nodes_to_pages
[STOP] [2023-10-05 14:46:24] map_all_nodes_to_pages
[INFO] [2023-10-05 14:46:24] ZERO unmatched nodes (of 496)! Nicely done.
[START] [2023-10-05 14:46:24] update_nodes
[STOP] [2023-10-05 14:46:24] update_nodes
[STOP] [2023-10-05 14:46:24] match_nodes
[START] [2023-10-05 14:46:24] reindex_search
[STOP] [2023-10-05 14:46:24] reindex_search
[START] [2023-10-05 14:46:24] normalize_units
[STOP] [2023-10-05 14:46:24] normalize_units
[START] [2023-10-05 14:46:25] calculate_statistics
[2023-10-05 14:46:25] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-05 14:46:33] Duplicate page_id count: 0
[STOP] [2023-10-05 14:46:33] calculate_statistics
[START] [2023-10-05 14:46:33] complete_harvest_instance
[START] [2023-10-05 14:46:33] overall_tsv_creation
[INFO] [2023-10-05 14:46:33] Exporting 496 nodes as TSV in batches of 10000...
[INFO] [2023-10-05 14:46:33] Processing group of 496 in 1 batches of 10000
[INFO] [2023-10-05 14:46:34] 524 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-05 14:46:34] Building Traits map for 496 nodes (this can take a while)...
[INFO] [2023-10-05 14:46:34] Mapped 524 traits (524 meta) for 496 nodes.
[INFO] [2023-10-05 14:46:34] Building Associations map (this can take a while)...
[INFO] [2023-10-05 14:46:34] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-05 14:46:34] Adding 524 traits...
[INFO] [2023-10-05 14:46:34] Trait #289642674 in key 289642674 has 123 metadata... that seems high?
[INFO] [2023-10-05 14:46:34] 427 metadata added.
[INFO] [2023-10-05 14:46:34] Adding 0 assocs...
[INFO] [2023-10-05 14:46:34] 0 metadata added.
[INFO] [2023-10-05 14:47:19] Processed 496/496 nodes
[INFO] [2023-10-05 14:47:19] Average Time: 45.58
[INFO] [2023-10-05 14:47:19] Total Time: 46s
[STOP] [2023-10-05 14:47:19] overall_tsv_creation
[INFO] [2023-10-05 14:47:19] Done. Check your files:
[INFO] [2023-10-05 14:47:19] (496 lines) /app/public/data/microbial_eukar2/publish_nodes.tsv
[INFO] [2023-10-05 14:47:19] (496 lines) /app/public/data/microbial_eukar2/publish_scientific_names.tsv
[INFO] [2023-10-05 14:47:19] (525 lines) /app/public/data/microbial_eukar2/publish_traits.tsv
[INFO] [2023-10-05 14:47:19] (428 lines) /app/public/data/microbial_eukar2/publish_metadata.tsv
[STOP] [2023-10-05 14:47:19] complete_harvest_instance
[START] [2023-10-05 14:47:19] completed
[STOP] [2023-10-05 14:47:19] completed
[STOP] [2023-10-05 14:47:19] logged process, took 68.58
Latest Process

05 Oct 14:46 EXITED currently processing 0