Harvest for Emig 1985 Created 03 Aug 15:43

Stage: completed
Fetched: 03 Aug 15:43
Validated: 03 Aug 15:43
Deltas Created 03 Aug 15:43
Units Normalized: 03 Aug 15:43
Ancestry Built: 03 Aug 15:43
Nodes Matched: 03 Aug 15:43
Names Parsed: 03 Aug 15:43
New Models Stored: 03 Aug 15:43
Indexed: 03 Aug 15:43
Completed: 03 Aug 15:45
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 15:43:16] Created harvest instance #4155
[STOP] [2022-08-03 15:43:16] create_harvest_instance
[START] [2022-08-03 15:43:16] fetch_files
[STOP] [2022-08-03 15:43:16] fetch_files
[START] [2022-08-03 15:43:16] validate_each_file
[INFO] [2022-08-03 15:43:16] Looping over 3 formats...
[INFO] [2022-08-03 15:43:16] ...nodes (/app/public/data/emig_emig_1985/taxa.txt)
[INFO] [2022-08-03 15:43:16] Valid: /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_nodes_29528.csv (1 lines)
[INFO] [2022-08-03 15:43:16] ...occurrences (/app/public/data/emig_emig_1985/occurrences.txt)
[INFO] [2022-08-03 15:43:16] Valid: /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_occurrences_29529.csv (1 lines)
[INFO] [2022-08-03 15:43:16] ...measurements (/app/public/data/emig_emig_1985/measurementOrFact.txt)
[INFO] [2022-08-03 15:43:16] Valid: /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_measurements_29530.csv (4 lines)
[STOP] [2022-08-03 15:43:16] validate_each_file
[START] [2022-08-03 15:43:16] convert_to_csv
[INFO] [2022-08-03 15:43:16] Looping over 3 formats...
[INFO] [2022-08-03 15:43:16] ...nodes (/app/public/data/emig_emig_1985/taxa.txt)
[CMD] [2022-08-03 15:43:16] /usr/bin/sort /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_nodes_29528.csv > /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_nodes_29528.csv_sorted
[INFO] [2022-08-03 15:43:16] Converted: /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_nodes_29528.csv (1 lines)
[INFO] [2022-08-03 15:43:16] ...occurrences (/app/public/data/emig_emig_1985/occurrences.txt)
[CMD] [2022-08-03 15:43:16] /usr/bin/sort /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_occurrences_29529.csv > /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_occurrences_29529.csv_sorted
[INFO] [2022-08-03 15:43:16] Converted: /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_occurrences_29529.csv (1 lines)
[INFO] [2022-08-03 15:43:16] ...measurements (/app/public/data/emig_emig_1985/measurementOrFact.txt)
[CMD] [2022-08-03 15:43:16] /usr/bin/sort /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_measurements_29530.csv > /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_measurements_29530.csv_sorted
[INFO] [2022-08-03 15:43:16] Converted: /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_measurements_29530.csv (4 lines)
[STOP] [2022-08-03 15:43:16] convert_to_csv
[START] [2022-08-03 15:43:16] calculate_delta
[INFO] [2022-08-03 15:43:16] Looping over 3 formats...
[INFO] [2022-08-03 15:43:16] ...nodes (/app/public/data/emig_emig_1985/taxa.txt)
[CMD] [2022-08-03 15:43:16] echo "0a" > /app/public/data/emig_emig_1985/diff/emig_emig_1985_nodes_29528.diff
[CMD] [2022-08-03 15:43:16] tail -n +1 /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_nodes_29528.csv >> /app/public/data/emig_emig_1985/diff/emig_emig_1985_nodes_29528.diff
[CMD] [2022-08-03 15:43:16] echo "." >> /app/public/data/emig_emig_1985/diff/emig_emig_1985_nodes_29528.diff
[INFO] [2022-08-03 15:43:16] Created diff: /app/public/data/emig_emig_1985/diff/emig_emig_1985_nodes_29528.diff (3 lines)
[INFO] [2022-08-03 15:43:16] ...occurrences (/app/public/data/emig_emig_1985/occurrences.txt)
[CMD] [2022-08-03 15:43:16] echo "0a" > /app/public/data/emig_emig_1985/diff/emig_emig_1985_occurrences_29529.diff
[CMD] [2022-08-03 15:43:16] tail -n +1 /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_occurrences_29529.csv >> /app/public/data/emig_emig_1985/diff/emig_emig_1985_occurrences_29529.diff
[CMD] [2022-08-03 15:43:16] echo "." >> /app/public/data/emig_emig_1985/diff/emig_emig_1985_occurrences_29529.diff
[INFO] [2022-08-03 15:43:16] Created diff: /app/public/data/emig_emig_1985/diff/emig_emig_1985_occurrences_29529.diff (3 lines)
[INFO] [2022-08-03 15:43:16] ...measurements (/app/public/data/emig_emig_1985/measurementOrFact.txt)
[CMD] [2022-08-03 15:43:16] echo "0a" > /app/public/data/emig_emig_1985/diff/emig_emig_1985_measurements_29530.diff
[CMD] [2022-08-03 15:43:16] tail -n +1 /app/public/data/emig_emig_1985/converted_csv/emig_emig_1985_measurements_29530.csv >> /app/public/data/emig_emig_1985/diff/emig_emig_1985_measurements_29530.diff
[CMD] [2022-08-03 15:43:16] echo "." >> /app/public/data/emig_emig_1985/diff/emig_emig_1985_measurements_29530.diff
[INFO] [2022-08-03 15:43:16] Created diff: /app/public/data/emig_emig_1985/diff/emig_emig_1985_measurements_29530.diff (6 lines)
[STOP] [2022-08-03 15:43:16] calculate_delta
[START] [2022-08-03 15:43:16] parse_diff_and_store
[INFO] [2022-08-03 15:43:16] Handling diff: /app/public/data/emig_emig_1985/diff/emig_emig_1985_nodes_29528.diff (3 lines)
[INFO] [2022-08-03 15:43:16] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 15:43:16] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 15:43:16] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 15:43:16] Handling diff: /app/public/data/emig_emig_1985/diff/emig_emig_1985_occurrences_29529.diff (3 lines)
[INFO] [2022-08-03 15:43:16] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 15:43:16] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 15:43:16] Handling diff: /app/public/data/emig_emig_1985/diff/emig_emig_1985_measurements_29530.diff (6 lines)
[INFO] [2022-08-03 15:43:16] Loading measurements diff file into memory (6 lines)...
[INFO] [2022-08-03 15:43:17] Storing 4 Traits (6/4/6)
[INFO] [2022-08-03 15:43:17] Storing 2 MetaTraits (6/4/6)
[STOP] [2022-08-03 15:43:17] parse_diff_and_store
[START] [2022-08-03 15:43:17] resolve_keys
[2022-08-03 15:43:17] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 15:43:24] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 15:43:24] traits to occurrences...
[INFO] [2022-08-03 15:43:24] traits to nodes (through occurrences)...
[INFO] [2022-08-03 15:43:24] Traits to sex term...
[INFO] [2022-08-03 15:43:24] Traits to lifestage term...
[INFO] [2022-08-03 15:43:24] MetaTraits to traits...
[INFO] [2022-08-03 15:43:24] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 15:43:24] Assocs to occurrences...
[INFO] [2022-08-03 15:43:24] Assocs to nodes...
[INFO] [2022-08-03 15:43:24] Assoc to sex term...
[INFO] [2022-08-03 15:43:24] Assoc to lifestage term...
[INFO] [2022-08-03 15:43:24] MetaAssoc to assocs...
[STOP] [2022-08-03 15:43:24] resolve_keys
[START] [2022-08-03 15:43:24] hold_for_later_1
[STOP] [2022-08-03 15:43:24] hold_for_later_1
[START] [2022-08-03 15:43:24] hold_for_later_2
[STOP] [2022-08-03 15:43:24] hold_for_later_2
[START] [2022-08-03 15:43:24] resolve_missing_parents
[STOP] [2022-08-03 15:43:24] resolve_missing_parents
[START] [2022-08-03 15:43:24] rebuild_nodes
[START] [2022-08-03 15:43:24] Flattener#flatten
[START] [2022-08-03 15:43:24] Flattener#study_resource
[START] [2022-08-03 15:43:24] Flattener#build_ancestry
[STOP] [2022-08-03 15:43:24] Flattener#build_ancestry
[INFO] [2022-08-03 15:43:24] 1 ancestry keys
[START] [2022-08-03 15:43:24] build_node_ancestors
[INFO] [2022-08-03 15:43:24] old ancestors deleted.
[STOP] [2022-08-03 15:43:24] build_node_ancestors
[WARN] [2022-08-03 15:43:24] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 15:43:24] Flattener#flatten
[STOP] [2022-08-03 15:43:24] rebuild_nodes
[START] [2022-08-03 15:43:24] resolve_missing_media_owners
[STOP] [2022-08-03 15:43:24] resolve_missing_media_owners
[START] [2022-08-03 15:43:24] sanitize_media_verbatims
[STOP] [2022-08-03 15:43:24] sanitize_media_verbatims
[START] [2022-08-03 15:43:24] queue_downloads
[STOP] [2022-08-03 15:43:24] queue_downloads
[START] [2022-08-03 15:43:24] parse_names
[WARN] [2022-08-03 15:43:24] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 15:43:24] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 15:43:25] parse_names
[START] [2022-08-03 15:43:25] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 15:43:25] denormalize_canonical_names_to_nodes
[START] [2022-08-03 15:43:25] match_nodes
[START] [2022-08-03 15:43:25] map_all_nodes_to_pages
[STOP] [2022-08-03 15:43:25] map_all_nodes_to_pages
[INFO] [2022-08-03 15:43:25] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 15:43:25] update_nodes
[STOP] [2022-08-03 15:43:25] update_nodes
[STOP] [2022-08-03 15:43:25] match_nodes
[START] [2022-08-03 15:43:25] reindex_search
[STOP] [2022-08-03 15:43:25] reindex_search
[START] [2022-08-03 15:43:25] normalize_units
[STOP] [2022-08-03 15:43:25] normalize_units
[START] [2022-08-03 15:43:25] calculate_statistics
[2022-08-03 15:43:25] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 15:43:25] Duplicate page_id count: 0
[STOP] [2022-08-03 15:43:25] calculate_statistics
[START] [2022-08-03 15:43:25] complete_harvest_instance
[START] [2022-08-03 15:43:25] overall_tsv_creation
[INFO] [2022-08-03 15:43:25] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 15:43:25] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 15:44:07] 2 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 15:44:07] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 15:45:00] Mapped 2 traits (2 meta) for 1 nodes.
[INFO] [2022-08-03 15:45:00] Building Associations map (this can take a while)...
[INFO] [2022-08-03 15:45:00] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 15:45:03] Adding 2 traits...
[INFO] [2022-08-03 15:45:03] 2 metadata added.
[INFO] [2022-08-03 15:45:03] Adding 0 assocs...
[INFO] [2022-08-03 15:45:03] 0 metadata added.
[INFO] [2022-08-03 15:45:45] Processed 1/1 nodes
[INFO] [2022-08-03 15:45:45] Average Time: 114.05
[INFO] [2022-08-03 15:45:45] Total Time: 2m20s
[STOP] [2022-08-03 15:45:45] overall_tsv_creation
[INFO] [2022-08-03 15:45:45] Done. Check your files:
[INFO] [2022-08-03 15:45:45] (1 lines) /app/public/data/emig_emig_1985/publish_nodes.tsv
[INFO] [2022-08-03 15:45:45] (1 lines) /app/public/data/emig_emig_1985/publish_scientific_names.tsv
[INFO] [2022-08-03 15:45:45] (3 lines) /app/public/data/emig_emig_1985/publish_traits.tsv
[INFO] [2022-08-03 15:45:45] (3 lines) /app/public/data/emig_emig_1985/publish_metadata.tsv
[STOP] [2022-08-03 15:45:45] complete_harvest_instance
[START] [2022-08-03 15:45:45] completed
[STOP] [2022-08-03 15:45:45] completed
[STOP] [2022-08-03 15:45:45] logged process, took 149.04
Latest Process

03 Aug 15:42 EXITED currently processing 0