Harvest for Triblehorn and Yager 2001 Created 14 Oct 08:31

Stage: completed
Fetched: 14 Oct 08:31
Validated: 14 Oct 08:31
Deltas Created 14 Oct 08:31
Units Normalized: 14 Oct 08:31
Ancestry Built: 14 Oct 08:31
Nodes Matched: 14 Oct 08:31
Names Parsed: 14 Oct 08:31
New Models Stored: 14 Oct 08:31
Indexed: 14 Oct 08:31
Completed: 14 Oct 08:32
Time to Harvest: less than a minute
Harvesting Log

(159 lines)
[INFO] [2023-10-14 08:31:34] Created harvest instance #4472
[STOP] [2023-10-14 08:31:34] create_harvest_instance
[START] [2023-10-14 08:31:34] fetch_files
[STOP] [2023-10-14 08:31:34] fetch_files
[START] [2023-10-14 08:31:34] validate_each_file
[INFO] [2023-10-14 08:31:34] Looping over 4 formats...
[INFO] [2023-10-14 08:31:34] ...refs (/app/public/data/triblehorn_yager/references.txt)
[INFO] [2023-10-14 08:31:34] Valid: /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_refs_30896.csv (1 lines)
[INFO] [2023-10-14 08:31:34] ...nodes (/app/public/data/triblehorn_yager/taxa.txt)
[INFO] [2023-10-14 08:31:34] Valid: /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_nodes_30893.csv (8 lines)
[INFO] [2023-10-14 08:31:34] ...occurrences (/app/public/data/triblehorn_yager/occurrences.txt)
[INFO] [2023-10-14 08:31:34] Valid: /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_occurrences_30894.csv (8 lines)
[INFO] [2023-10-14 08:31:34] ...measurements (/app/public/data/triblehorn_yager/measurementsorfacts.txt)
[INFO] [2023-10-14 08:31:34] Valid: /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_measurements_30895.csv (125 lines)
[STOP] [2023-10-14 08:31:34] validate_each_file
[START] [2023-10-14 08:31:34] convert_to_csv
[INFO] [2023-10-14 08:31:34] Looping over 4 formats...
[INFO] [2023-10-14 08:31:34] ...refs (/app/public/data/triblehorn_yager/references.txt)
[CMD] [2023-10-14 08:31:34] /usr/bin/sort /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_refs_30896.csv > /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_refs_30896.csv_sorted
[INFO] [2023-10-14 08:31:34] Converted: /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_refs_30896.csv (1 lines)
[INFO] [2023-10-14 08:31:34] ...nodes (/app/public/data/triblehorn_yager/taxa.txt)
[CMD] [2023-10-14 08:31:34] /usr/bin/sort /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_nodes_30893.csv > /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_nodes_30893.csv_sorted
[INFO] [2023-10-14 08:31:34] Converted: /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_nodes_30893.csv (8 lines)
[INFO] [2023-10-14 08:31:34] ...occurrences (/app/public/data/triblehorn_yager/occurrences.txt)
[CMD] [2023-10-14 08:31:34] /usr/bin/sort /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_occurrences_30894.csv > /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_occurrences_30894.csv_sorted
[INFO] [2023-10-14 08:31:34] Converted: /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_occurrences_30894.csv (8 lines)
[INFO] [2023-10-14 08:31:34] ...measurements (/app/public/data/triblehorn_yager/measurementsorfacts.txt)
[CMD] [2023-10-14 08:31:34] /usr/bin/sort /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_measurements_30895.csv > /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_measurements_30895.csv_sorted
[INFO] [2023-10-14 08:31:34] Converted: /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_measurements_30895.csv (125 lines)
[STOP] [2023-10-14 08:31:34] convert_to_csv
[START] [2023-10-14 08:31:34] calculate_delta
[INFO] [2023-10-14 08:31:34] Looping over 4 formats...
[INFO] [2023-10-14 08:31:34] ...refs (/app/public/data/triblehorn_yager/references.txt)
[CMD] [2023-10-14 08:31:34] echo "0a" > /app/public/data/triblehorn_yager/diff/triblehorn_yager_refs_30896.diff
[CMD] [2023-10-14 08:31:34] tail -n +1 /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_refs_30896.csv >> /app/public/data/triblehorn_yager/diff/triblehorn_yager_refs_30896.diff
[CMD] [2023-10-14 08:31:34] echo "." >> /app/public/data/triblehorn_yager/diff/triblehorn_yager_refs_30896.diff
[INFO] [2023-10-14 08:31:34] Created diff: /app/public/data/triblehorn_yager/diff/triblehorn_yager_refs_30896.diff (3 lines)
[INFO] [2023-10-14 08:31:34] ...nodes (/app/public/data/triblehorn_yager/taxa.txt)
[CMD] [2023-10-14 08:31:34] echo "0a" > /app/public/data/triblehorn_yager/diff/triblehorn_yager_nodes_30893.diff
[CMD] [2023-10-14 08:31:34] tail -n +1 /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_nodes_30893.csv >> /app/public/data/triblehorn_yager/diff/triblehorn_yager_nodes_30893.diff
[CMD] [2023-10-14 08:31:34] echo "." >> /app/public/data/triblehorn_yager/diff/triblehorn_yager_nodes_30893.diff
[INFO] [2023-10-14 08:31:35] Created diff: /app/public/data/triblehorn_yager/diff/triblehorn_yager_nodes_30893.diff (10 lines)
[INFO] [2023-10-14 08:31:35] ...occurrences (/app/public/data/triblehorn_yager/occurrences.txt)
[CMD] [2023-10-14 08:31:35] echo "0a" > /app/public/data/triblehorn_yager/diff/triblehorn_yager_occurrences_30894.diff
[CMD] [2023-10-14 08:31:35] tail -n +1 /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_occurrences_30894.csv >> /app/public/data/triblehorn_yager/diff/triblehorn_yager_occurrences_30894.diff
[CMD] [2023-10-14 08:31:35] echo "." >> /app/public/data/triblehorn_yager/diff/triblehorn_yager_occurrences_30894.diff
[INFO] [2023-10-14 08:31:35] Created diff: /app/public/data/triblehorn_yager/diff/triblehorn_yager_occurrences_30894.diff (10 lines)
[INFO] [2023-10-14 08:31:35] ...measurements (/app/public/data/triblehorn_yager/measurementsorfacts.txt)
[CMD] [2023-10-14 08:31:35] echo "0a" > /app/public/data/triblehorn_yager/diff/triblehorn_yager_measurements_30895.diff
[CMD] [2023-10-14 08:31:35] tail -n +1 /app/public/data/triblehorn_yager/converted_csv/triblehorn_yager_measurements_30895.csv >> /app/public/data/triblehorn_yager/diff/triblehorn_yager_measurements_30895.diff
[CMD] [2023-10-14 08:31:35] echo "." >> /app/public/data/triblehorn_yager/diff/triblehorn_yager_measurements_30895.diff
[INFO] [2023-10-14 08:31:35] Created diff: /app/public/data/triblehorn_yager/diff/triblehorn_yager_measurements_30895.diff (127 lines)
[STOP] [2023-10-14 08:31:35] calculate_delta
[START] [2023-10-14 08:31:35] parse_diff_and_store
[INFO] [2023-10-14 08:31:35] Handling diff: /app/public/data/triblehorn_yager/diff/triblehorn_yager_refs_30896.diff (3 lines)
[INFO] [2023-10-14 08:31:35] Loading refs diff file into memory (3 lines)...
[INFO] [2023-10-14 08:31:35] Storing 1 References (1/1/3)
[INFO] [2023-10-14 08:31:35] Handling diff: /app/public/data/triblehorn_yager/diff/triblehorn_yager_nodes_30893.diff (10 lines)
[INFO] [2023-10-14 08:31:35] Loading nodes diff file into memory (10 lines)...
[INFO] [2023-10-14 08:31:35] Storing 8 ScientificNames (16/8/10)
[INFO] [2023-10-14 08:31:35] Storing 8 Nodes (16/8/10)
[INFO] [2023-10-14 08:31:35] Handling diff: /app/public/data/triblehorn_yager/diff/triblehorn_yager_occurrences_30894.diff (10 lines)
[INFO] [2023-10-14 08:31:35] Loading occurrences diff file into memory (10 lines)...
[INFO] [2023-10-14 08:31:35] Storing 8 Occurrences (8/8/10)
[INFO] [2023-10-14 08:31:35] Handling diff: /app/public/data/triblehorn_yager/diff/triblehorn_yager_measurements_30895.diff (127 lines)
[INFO] [2023-10-14 08:31:35] Loading measurements diff file into memory (127 lines)...
[INFO] [2023-10-14 08:31:35] Storing 3 TraitsReferences (167/125/127)
[INFO] [2023-10-14 08:31:35] Storing 125 Traits (167/125/127)
[INFO] [2023-10-14 08:31:35] Storing 39 MetaTraits (167/125/127)
[STOP] [2023-10-14 08:31:35] parse_diff_and_store
[START] [2023-10-14 08:31:35] resolve_keys
[2023-10-14 08:31:35] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-14 08:31:43] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-14 08:31:43] traits to occurrences...
[INFO] [2023-10-14 08:31:43] traits to nodes (through occurrences)...
[INFO] [2023-10-14 08:31:43] Traits to sex term...
[INFO] [2023-10-14 08:31:43] Traits to lifestage term...
[INFO] [2023-10-14 08:31:43] MetaTraits to traits...
[INFO] [2023-10-14 08:31:43] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-14 08:31:43] Assocs to occurrences...
[INFO] [2023-10-14 08:31:43] Assocs to nodes...
[INFO] [2023-10-14 08:31:43] Assoc to sex term...
[INFO] [2023-10-14 08:31:43] Assoc to lifestage term...
[INFO] [2023-10-14 08:31:43] MetaAssoc to assocs...
[STOP] [2023-10-14 08:31:43] resolve_keys
[START] [2023-10-14 08:31:43] hold_for_later_1
[STOP] [2023-10-14 08:31:43] hold_for_later_1
[START] [2023-10-14 08:31:43] hold_for_later_2
[STOP] [2023-10-14 08:31:43] hold_for_later_2
[START] [2023-10-14 08:31:43] resolve_missing_parents
[STOP] [2023-10-14 08:31:43] resolve_missing_parents
[START] [2023-10-14 08:31:43] rebuild_nodes
[START] [2023-10-14 08:31:43] Flattener#flatten
[START] [2023-10-14 08:31:43] Flattener#study_resource
[START] [2023-10-14 08:31:43] Flattener#build_ancestry
[STOP] [2023-10-14 08:31:43] Flattener#build_ancestry
[INFO] [2023-10-14 08:31:43] 8 ancestry keys
[START] [2023-10-14 08:31:43] build_node_ancestors
[INFO] [2023-10-14 08:31:43] old ancestors deleted.
[STOP] [2023-10-14 08:31:43] build_node_ancestors
[WARN] [2023-10-14 08:31:43] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-14 08:31:43] Flattener#flatten
[STOP] [2023-10-14 08:31:43] rebuild_nodes
[START] [2023-10-14 08:31:43] resolve_missing_media_owners
[STOP] [2023-10-14 08:31:43] resolve_missing_media_owners
[START] [2023-10-14 08:31:43] sanitize_media_verbatims
[STOP] [2023-10-14 08:31:43] sanitize_media_verbatims
[START] [2023-10-14 08:31:43] queue_downloads
[STOP] [2023-10-14 08:31:43] queue_downloads
[START] [2023-10-14 08:31:43] parse_names
[WARN] [2023-10-14 08:31:43] I see 8 names which still need to be parsed.
[WARN] [2023-10-14 08:31:43] Names to parse: 8 formatted: 8 learned: 8 parsed: 8
[STOP] [2023-10-14 08:31:44] parse_names
[START] [2023-10-14 08:31:44] denormalize_canonical_names_to_nodes
[STOP] [2023-10-14 08:31:44] denormalize_canonical_names_to_nodes
[START] [2023-10-14 08:31:44] match_nodes
[START] [2023-10-14 08:31:44] map_all_nodes_to_pages
[STOP] [2023-10-14 08:31:44] map_all_nodes_to_pages
[INFO] [2023-10-14 08:31:44] ZERO unmatched nodes (of 8)! Nicely done.
[START] [2023-10-14 08:31:44] update_nodes
[STOP] [2023-10-14 08:31:44] update_nodes
[STOP] [2023-10-14 08:31:44] match_nodes
[START] [2023-10-14 08:31:44] reindex_search
[STOP] [2023-10-14 08:31:44] reindex_search
[START] [2023-10-14 08:31:45] normalize_units
[STOP] [2023-10-14 08:31:45] normalize_units
[START] [2023-10-14 08:31:45] calculate_statistics
[2023-10-14 08:31:45] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-14 08:31:45] Duplicate page_id count: 0
[STOP] [2023-10-14 08:31:45] calculate_statistics
[START] [2023-10-14 08:31:45] complete_harvest_instance
[START] [2023-10-14 08:31:45] overall_tsv_creation
[INFO] [2023-10-14 08:31:45] Exporting 8 nodes as TSV in batches of 10000...
[INFO] [2023-10-14 08:31:45] Processing group of 8 in 1 batches of 10000
[INFO] [2023-10-14 08:31:45] 31 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-14 08:31:45] Building Traits map for 8 nodes (this can take a while)...
[INFO] [2023-10-14 08:31:45] Mapped 31 traits (39 meta) for 8 nodes.
[INFO] [2023-10-14 08:31:45] Building Associations map (this can take a while)...
[INFO] [2023-10-14 08:31:45] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-14 08:31:45] Adding 31 traits...
[INFO] [2023-10-14 08:31:45] Trait #291668723 in key 291668723 has 33 metadata... that seems high?
[INFO] [2023-10-14 08:31:45] Trait #291668774 in key 291668774 has 32 metadata... that seems high?
[INFO] [2023-10-14 08:31:45] Trait #291668808 in key 291668808 has 32 metadata... that seems high?
[INFO] [2023-10-14 08:31:45] 97 metadata added.
[INFO] [2023-10-14 08:31:45] Adding 0 assocs...
[INFO] [2023-10-14 08:31:45] 0 metadata added.
[INFO] [2023-10-14 08:32:29] Processed 8/8 nodes
[INFO] [2023-10-14 08:32:29] Average Time: 43.98
[INFO] [2023-10-14 08:32:29] Total Time: 45s
[STOP] [2023-10-14 08:32:29] overall_tsv_creation
[INFO] [2023-10-14 08:32:29] Done. Check your files:
[INFO] [2023-10-14 08:32:29] (8 lines) /app/public/data/triblehorn_yager/publish_nodes.tsv
[INFO] [2023-10-14 08:32:29] (8 lines) /app/public/data/triblehorn_yager/publish_scientific_names.tsv
[INFO] [2023-10-14 08:32:29] (32 lines) /app/public/data/triblehorn_yager/publish_traits.tsv
[INFO] [2023-10-14 08:32:29] (98 lines) /app/public/data/triblehorn_yager/publish_metadata.tsv
[STOP] [2023-10-14 08:32:29] complete_harvest_instance
[START] [2023-10-14 08:32:29] completed
[STOP] [2023-10-14 08:32:29] completed
[STOP] [2023-10-14 08:32:29] logged process, took 55.52
Latest Process

14 Oct 08:31 EXITED currently processing 0