Harvest for Cellularity and growth form Created 18 Apr 15:45

Stage: completed
Fetched: 18 Apr 15:45
Validated: 18 Apr 15:45
Deltas Created 18 Apr 15:45
Units Normalized: 18 Apr 15:46
Ancestry Built: 18 Apr 15:46
Nodes Matched: 18 Apr 15:46
Names Parsed: 18 Apr 15:46
New Models Stored: 18 Apr 15:46
Indexed: 18 Apr 15:46
Completed: 18 Apr 15:47
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2023-04-18 15:45:59] Created harvest instance #4337
[STOP] [2023-04-18 15:45:59] create_harvest_instance
[START] [2023-04-18 15:45:59] fetch_files
[STOP] [2023-04-18 15:45:59] fetch_files
[START] [2023-04-18 15:45:59] validate_each_file
[INFO] [2023-04-18 15:45:59] Looping over 3 formats...
[INFO] [2023-04-18 15:45:59] ...nodes (/app/public/data/cellularity_grow/taxon.tab)
[INFO] [2023-04-18 15:45:59] Valid: /app/public/data/cellularity_grow/converted_csv/cellularity_grow_nodes_30302.csv (839 lines)
[INFO] [2023-04-18 15:45:59] ...occurrences (/app/public/data/cellularity_grow/occurrence_specific.tab)
[INFO] [2023-04-18 15:45:59] Valid: /app/public/data/cellularity_grow/converted_csv/cellularity_grow_occurrences_30303.csv (991 lines)
[INFO] [2023-04-18 15:45:59] ...measurements (/app/public/data/cellularity_grow/measurement_or_fact_specific.tab)
[INFO] [2023-04-18 15:45:59] Valid: /app/public/data/cellularity_grow/converted_csv/cellularity_grow_measurements_30304.csv (1748 lines)
[STOP] [2023-04-18 15:45:59] validate_each_file
[START] [2023-04-18 15:45:59] convert_to_csv
[INFO] [2023-04-18 15:45:59] Looping over 3 formats...
[INFO] [2023-04-18 15:45:59] ...nodes (/app/public/data/cellularity_grow/taxon.tab)
[CMD] [2023-04-18 15:45:59] /usr/bin/sort /app/public/data/cellularity_grow/converted_csv/cellularity_grow_nodes_30302.csv > /app/public/data/cellularity_grow/converted_csv/cellularity_grow_nodes_30302.csv_sorted
[INFO] [2023-04-18 15:45:59] Converted: /app/public/data/cellularity_grow/converted_csv/cellularity_grow_nodes_30302.csv (839 lines)
[INFO] [2023-04-18 15:45:59] ...occurrences (/app/public/data/cellularity_grow/occurrence_specific.tab)
[CMD] [2023-04-18 15:45:59] /usr/bin/sort /app/public/data/cellularity_grow/converted_csv/cellularity_grow_occurrences_30303.csv > /app/public/data/cellularity_grow/converted_csv/cellularity_grow_occurrences_30303.csv_sorted
[INFO] [2023-04-18 15:45:59] Converted: /app/public/data/cellularity_grow/converted_csv/cellularity_grow_occurrences_30303.csv (991 lines)
[INFO] [2023-04-18 15:45:59] ...measurements (/app/public/data/cellularity_grow/measurement_or_fact_specific.tab)
[CMD] [2023-04-18 15:45:59] /usr/bin/sort /app/public/data/cellularity_grow/converted_csv/cellularity_grow_measurements_30304.csv > /app/public/data/cellularity_grow/converted_csv/cellularity_grow_measurements_30304.csv_sorted
[INFO] [2023-04-18 15:45:59] Converted: /app/public/data/cellularity_grow/converted_csv/cellularity_grow_measurements_30304.csv (1748 lines)
[STOP] [2023-04-18 15:45:59] convert_to_csv
[START] [2023-04-18 15:45:59] calculate_delta
[INFO] [2023-04-18 15:45:59] Looping over 3 formats...
[INFO] [2023-04-18 15:45:59] ...nodes (/app/public/data/cellularity_grow/taxon.tab)
[CMD] [2023-04-18 15:45:59] echo "0a" > /app/public/data/cellularity_grow/diff/cellularity_grow_nodes_30302.diff
[CMD] [2023-04-18 15:45:59] tail -n +1 /app/public/data/cellularity_grow/converted_csv/cellularity_grow_nodes_30302.csv >> /app/public/data/cellularity_grow/diff/cellularity_grow_nodes_30302.diff
[CMD] [2023-04-18 15:45:59] echo "." >> /app/public/data/cellularity_grow/diff/cellularity_grow_nodes_30302.diff
[INFO] [2023-04-18 15:45:59] Created diff: /app/public/data/cellularity_grow/diff/cellularity_grow_nodes_30302.diff (841 lines)
[INFO] [2023-04-18 15:45:59] ...occurrences (/app/public/data/cellularity_grow/occurrence_specific.tab)
[CMD] [2023-04-18 15:45:59] echo "0a" > /app/public/data/cellularity_grow/diff/cellularity_grow_occurrences_30303.diff
[CMD] [2023-04-18 15:45:59] tail -n +1 /app/public/data/cellularity_grow/converted_csv/cellularity_grow_occurrences_30303.csv >> /app/public/data/cellularity_grow/diff/cellularity_grow_occurrences_30303.diff
[CMD] [2023-04-18 15:45:59] echo "." >> /app/public/data/cellularity_grow/diff/cellularity_grow_occurrences_30303.diff
[INFO] [2023-04-18 15:45:59] Created diff: /app/public/data/cellularity_grow/diff/cellularity_grow_occurrences_30303.diff (993 lines)
[INFO] [2023-04-18 15:45:59] ...measurements (/app/public/data/cellularity_grow/measurement_or_fact_specific.tab)
[CMD] [2023-04-18 15:45:59] echo "0a" > /app/public/data/cellularity_grow/diff/cellularity_grow_measurements_30304.diff
[CMD] [2023-04-18 15:45:59] tail -n +1 /app/public/data/cellularity_grow/converted_csv/cellularity_grow_measurements_30304.csv >> /app/public/data/cellularity_grow/diff/cellularity_grow_measurements_30304.diff
[CMD] [2023-04-18 15:45:59] echo "." >> /app/public/data/cellularity_grow/diff/cellularity_grow_measurements_30304.diff
[INFO] [2023-04-18 15:45:59] Created diff: /app/public/data/cellularity_grow/diff/cellularity_grow_measurements_30304.diff (1750 lines)
[STOP] [2023-04-18 15:45:59] calculate_delta
[START] [2023-04-18 15:45:59] parse_diff_and_store
[INFO] [2023-04-18 15:45:59] Handling diff: /app/public/data/cellularity_grow/diff/cellularity_grow_nodes_30302.diff (841 lines)
[INFO] [2023-04-18 15:45:59] Loading nodes diff file into memory (841 lines)...
[INFO] [2023-04-18 15:45:59] Storing 839 ScientificNames (1678/839/841)
[INFO] [2023-04-18 15:46:00] Storing 839 Nodes (1678/839/841)
[INFO] [2023-04-18 15:46:00] Handling diff: /app/public/data/cellularity_grow/diff/cellularity_grow_occurrences_30303.diff (993 lines)
[INFO] [2023-04-18 15:46:00] Loading occurrences diff file into memory (993 lines)...
[INFO] [2023-04-18 15:46:00] Storing 991 Occurrences (991/991/993)
[INFO] [2023-04-18 15:46:00] Handling diff: /app/public/data/cellularity_grow/diff/cellularity_grow_measurements_30304.diff (1750 lines)
[INFO] [2023-04-18 15:46:00] Loading measurements diff file into memory (1750 lines)...
[INFO] [2023-04-18 15:46:01] Storing 1748 Traits (2742/1748/1750)
[INFO] [2023-04-18 15:46:02] Storing 994 MetaTraits (2742/1748/1750)
[STOP] [2023-04-18 15:46:02] parse_diff_and_store
[START] [2023-04-18 15:46:02] resolve_keys
[2023-04-18 15:46:02] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-04-18 15:46:10] Occurrences to nodes (through scientific_names)...
[INFO] [2023-04-18 15:46:10] traits to occurrences...
[INFO] [2023-04-18 15:46:11] traits to nodes (through occurrences)...
[INFO] [2023-04-18 15:46:11] Traits to sex term...
[INFO] [2023-04-18 15:46:11] Traits to lifestage term...
[INFO] [2023-04-18 15:46:11] MetaTraits to traits...
[INFO] [2023-04-18 15:46:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-04-18 15:46:11] Assocs to occurrences...
[INFO] [2023-04-18 15:46:11] Assocs to nodes...
[INFO] [2023-04-18 15:46:11] Assoc to sex term...
[INFO] [2023-04-18 15:46:11] Assoc to lifestage term...
[INFO] [2023-04-18 15:46:11] MetaAssoc to assocs...
[STOP] [2023-04-18 15:46:11] resolve_keys
[START] [2023-04-18 15:46:11] hold_for_later_1
[STOP] [2023-04-18 15:46:11] hold_for_later_1
[START] [2023-04-18 15:46:11] hold_for_later_2
[STOP] [2023-04-18 15:46:11] hold_for_later_2
[START] [2023-04-18 15:46:11] resolve_missing_parents
[STOP] [2023-04-18 15:46:11] resolve_missing_parents
[START] [2023-04-18 15:46:11] rebuild_nodes
[START] [2023-04-18 15:46:11] Flattener#flatten
[START] [2023-04-18 15:46:11] Flattener#study_resource
[START] [2023-04-18 15:46:11] Flattener#build_ancestry
[STOP] [2023-04-18 15:46:11] Flattener#build_ancestry
[INFO] [2023-04-18 15:46:11] 839 ancestry keys
[START] [2023-04-18 15:46:11] build_node_ancestors
[INFO] [2023-04-18 15:46:11] old ancestors deleted.
[STOP] [2023-04-18 15:46:11] build_node_ancestors
[WARN] [2023-04-18 15:46:11] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-04-18 15:46:11] Flattener#flatten
[STOP] [2023-04-18 15:46:11] rebuild_nodes
[START] [2023-04-18 15:46:11] resolve_missing_media_owners
[STOP] [2023-04-18 15:46:11] resolve_missing_media_owners
[START] [2023-04-18 15:46:11] sanitize_media_verbatims
[STOP] [2023-04-18 15:46:11] sanitize_media_verbatims
[START] [2023-04-18 15:46:11] queue_downloads
[STOP] [2023-04-18 15:46:11] queue_downloads
[START] [2023-04-18 15:46:11] parse_names
[WARN] [2023-04-18 15:46:11] I see 839 names which still need to be parsed.
[WARN] [2023-04-18 15:46:11] Names to parse: 839 formatted: 839 learned: 839 parsed: 839
[STOP] [2023-04-18 15:46:12] parse_names
[START] [2023-04-18 15:46:12] denormalize_canonical_names_to_nodes
[STOP] [2023-04-18 15:46:13] denormalize_canonical_names_to_nodes
[START] [2023-04-18 15:46:13] match_nodes
[START] [2023-04-18 15:46:13] map_all_nodes_to_pages
[STOP] [2023-04-18 15:46:13] map_all_nodes_to_pages
[INFO] [2023-04-18 15:46:13] Unmatched nodes (1 of 839): Canonical: Candida thaimeueangensis; Node#134298809; ResourceID: Candida_thaimeueangensis
[START] [2023-04-18 15:46:13] update_nodes
[STOP] [2023-04-18 15:46:13] update_nodes
[STOP] [2023-04-18 15:46:13] match_nodes
[START] [2023-04-18 15:46:13] reindex_search
[STOP] [2023-04-18 15:46:14] reindex_search
[START] [2023-04-18 15:46:14] normalize_units
[STOP] [2023-04-18 15:46:14] normalize_units
[START] [2023-04-18 15:46:14] calculate_statistics
[2023-04-18 15:46:14] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-04-18 15:46:14] Duplicate page_id count: 2
[STOP] [2023-04-18 15:46:14] calculate_statistics
[START] [2023-04-18 15:46:14] complete_harvest_instance
[START] [2023-04-18 15:46:14] overall_tsv_creation
[INFO] [2023-04-18 15:46:14] Exporting 839 nodes as TSV in batches of 10000...
[INFO] [2023-04-18 15:46:14] Processing group of 839 in 1 batches of 10000
[INFO] [2023-04-18 15:46:16] 994 Traits (unfiltered) and 0 associations...
[INFO] [2023-04-18 15:46:16] Building Traits map for 839 nodes (this can take a while)...
[INFO] [2023-04-18 15:46:17] Mapped 994 traits (994 meta) for 839 nodes.
[INFO] [2023-04-18 15:46:17] Building Associations map (this can take a while)...
[INFO] [2023-04-18 15:46:17] Done. 0 assocs mapped (0 meta).
[INFO] [2023-04-18 15:46:17] Adding 994 traits...
[INFO] [2023-04-18 15:46:17] 754 metadata added.
[INFO] [2023-04-18 15:46:17] Adding 0 assocs...
[INFO] [2023-04-18 15:46:17] 0 metadata added.
[INFO] [2023-04-18 15:47:06] Processed 839/839 nodes
[INFO] [2023-04-18 15:47:06] Average Time: 51.63
[INFO] [2023-04-18 15:47:06] Total Time: 53s
[STOP] [2023-04-18 15:47:06] overall_tsv_creation
[INFO] [2023-04-18 15:47:06] Done. Check your files:
[INFO] [2023-04-18 15:47:06] (839 lines) /app/public/data/cellularity_grow/publish_nodes.tsv
[INFO] [2023-04-18 15:47:06] (839 lines) /app/public/data/cellularity_grow/publish_scientific_names.tsv
[INFO] [2023-04-18 15:47:06] (995 lines) /app/public/data/cellularity_grow/publish_traits.tsv
[INFO] [2023-04-18 15:47:06] (755 lines) /app/public/data/cellularity_grow/publish_metadata.tsv
[STOP] [2023-04-18 15:47:06] complete_harvest_instance
[START] [2023-04-18 15:47:06] completed
[STOP] [2023-04-18 15:47:06] completed
[STOP] [2023-04-18 15:47:06] logged process, took 67.62
Latest Process

18 Apr 15:42 EXITED currently processing 0