Harvest for Halanych 1996 Created 03 Aug 16:03

Stage: completed
Fetched: 03 Aug 16:03
Validated: 03 Aug 16:03
Deltas Created 03 Aug 16:03
Units Normalized: 03 Aug 16:03
Ancestry Built: 03 Aug 16:03
Nodes Matched: 03 Aug 16:03
Names Parsed: 03 Aug 16:03
New Models Stored: 03 Aug 16:03
Indexed: 03 Aug 16:03
Completed: 03 Aug 16:06
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:03:46] Created harvest instance #4161
[STOP] [2022-08-03 16:03:46] create_harvest_instance
[START] [2022-08-03 16:03:46] fetch_files
[STOP] [2022-08-03 16:03:46] fetch_files
[START] [2022-08-03 16:03:46] validate_each_file
[INFO] [2022-08-03 16:03:46] Looping over 3 formats...
[INFO] [2022-08-03 16:03:46] ...nodes (/app/public/data/halanych_halanyc/taxa.txt)
[INFO] [2022-08-03 16:03:46] Valid: /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_nodes_29546.csv (1 lines)
[INFO] [2022-08-03 16:03:46] ...occurrences (/app/public/data/halanych_halanyc/occurrences.txt)
[INFO] [2022-08-03 16:03:46] Valid: /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_occurrences_29547.csv (1 lines)
[INFO] [2022-08-03 16:03:46] ...measurements (/app/public/data/halanych_halanyc/measurementOrFact.txt)
[INFO] [2022-08-03 16:03:46] Valid: /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_measurements_29548.csv (2 lines)
[STOP] [2022-08-03 16:03:46] validate_each_file
[START] [2022-08-03 16:03:46] convert_to_csv
[INFO] [2022-08-03 16:03:46] Looping over 3 formats...
[INFO] [2022-08-03 16:03:46] ...nodes (/app/public/data/halanych_halanyc/taxa.txt)
[CMD] [2022-08-03 16:03:46] /usr/bin/sort /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_nodes_29546.csv > /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_nodes_29546.csv_sorted
[INFO] [2022-08-03 16:03:46] Converted: /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_nodes_29546.csv (1 lines)
[INFO] [2022-08-03 16:03:46] ...occurrences (/app/public/data/halanych_halanyc/occurrences.txt)
[CMD] [2022-08-03 16:03:46] /usr/bin/sort /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_occurrences_29547.csv > /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_occurrences_29547.csv_sorted
[INFO] [2022-08-03 16:03:46] Converted: /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_occurrences_29547.csv (1 lines)
[INFO] [2022-08-03 16:03:46] ...measurements (/app/public/data/halanych_halanyc/measurementOrFact.txt)
[CMD] [2022-08-03 16:03:46] /usr/bin/sort /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_measurements_29548.csv > /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_measurements_29548.csv_sorted
[INFO] [2022-08-03 16:03:46] Converted: /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_measurements_29548.csv (2 lines)
[STOP] [2022-08-03 16:03:46] convert_to_csv
[START] [2022-08-03 16:03:46] calculate_delta
[INFO] [2022-08-03 16:03:46] Looping over 3 formats...
[INFO] [2022-08-03 16:03:46] ...nodes (/app/public/data/halanych_halanyc/taxa.txt)
[CMD] [2022-08-03 16:03:46] echo "0a" > /app/public/data/halanych_halanyc/diff/halanych_halanyc_nodes_29546.diff
[CMD] [2022-08-03 16:03:46] tail -n +1 /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_nodes_29546.csv >> /app/public/data/halanych_halanyc/diff/halanych_halanyc_nodes_29546.diff
[CMD] [2022-08-03 16:03:46] echo "." >> /app/public/data/halanych_halanyc/diff/halanych_halanyc_nodes_29546.diff
[INFO] [2022-08-03 16:03:46] Created diff: /app/public/data/halanych_halanyc/diff/halanych_halanyc_nodes_29546.diff (3 lines)
[INFO] [2022-08-03 16:03:46] ...occurrences (/app/public/data/halanych_halanyc/occurrences.txt)
[CMD] [2022-08-03 16:03:46] echo "0a" > /app/public/data/halanych_halanyc/diff/halanych_halanyc_occurrences_29547.diff
[CMD] [2022-08-03 16:03:46] tail -n +1 /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_occurrences_29547.csv >> /app/public/data/halanych_halanyc/diff/halanych_halanyc_occurrences_29547.diff
[CMD] [2022-08-03 16:03:46] echo "." >> /app/public/data/halanych_halanyc/diff/halanych_halanyc_occurrences_29547.diff
[INFO] [2022-08-03 16:03:46] Created diff: /app/public/data/halanych_halanyc/diff/halanych_halanyc_occurrences_29547.diff (3 lines)
[INFO] [2022-08-03 16:03:46] ...measurements (/app/public/data/halanych_halanyc/measurementOrFact.txt)
[CMD] [2022-08-03 16:03:46] echo "0a" > /app/public/data/halanych_halanyc/diff/halanych_halanyc_measurements_29548.diff
[CMD] [2022-08-03 16:03:46] tail -n +1 /app/public/data/halanych_halanyc/converted_csv/halanych_halanyc_measurements_29548.csv >> /app/public/data/halanych_halanyc/diff/halanych_halanyc_measurements_29548.diff
[CMD] [2022-08-03 16:03:47] echo "." >> /app/public/data/halanych_halanyc/diff/halanych_halanyc_measurements_29548.diff
[INFO] [2022-08-03 16:03:47] Created diff: /app/public/data/halanych_halanyc/diff/halanych_halanyc_measurements_29548.diff (4 lines)
[STOP] [2022-08-03 16:03:47] calculate_delta
[START] [2022-08-03 16:03:47] parse_diff_and_store
[INFO] [2022-08-03 16:03:47] Handling diff: /app/public/data/halanych_halanyc/diff/halanych_halanyc_nodes_29546.diff (3 lines)
[INFO] [2022-08-03 16:03:47] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:03:47] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:03:47] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:03:47] Handling diff: /app/public/data/halanych_halanyc/diff/halanych_halanyc_occurrences_29547.diff (3 lines)
[INFO] [2022-08-03 16:03:47] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:03:47] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:03:47] Handling diff: /app/public/data/halanych_halanyc/diff/halanych_halanyc_measurements_29548.diff (4 lines)
[INFO] [2022-08-03 16:03:47] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 16:03:47] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 16:03:47] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 16:03:47] parse_diff_and_store
[START] [2022-08-03 16:03:47] resolve_keys
[2022-08-03 16:03:47] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:03:54] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:03:54] traits to occurrences...
[INFO] [2022-08-03 16:03:54] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:03:54] Traits to sex term...
[INFO] [2022-08-03 16:03:54] Traits to lifestage term...
[INFO] [2022-08-03 16:03:54] MetaTraits to traits...
[INFO] [2022-08-03 16:03:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:03:54] Assocs to occurrences...
[INFO] [2022-08-03 16:03:54] Assocs to nodes...
[INFO] [2022-08-03 16:03:54] Assoc to sex term...
[INFO] [2022-08-03 16:03:54] Assoc to lifestage term...
[INFO] [2022-08-03 16:03:54] MetaAssoc to assocs...
[STOP] [2022-08-03 16:03:54] resolve_keys
[START] [2022-08-03 16:03:54] hold_for_later_1
[STOP] [2022-08-03 16:03:54] hold_for_later_1
[START] [2022-08-03 16:03:54] hold_for_later_2
[STOP] [2022-08-03 16:03:54] hold_for_later_2
[START] [2022-08-03 16:03:54] resolve_missing_parents
[STOP] [2022-08-03 16:03:54] resolve_missing_parents
[START] [2022-08-03 16:03:54] rebuild_nodes
[START] [2022-08-03 16:03:54] Flattener#flatten
[START] [2022-08-03 16:03:54] Flattener#study_resource
[START] [2022-08-03 16:03:54] Flattener#build_ancestry
[STOP] [2022-08-03 16:03:54] Flattener#build_ancestry
[INFO] [2022-08-03 16:03:54] 1 ancestry keys
[START] [2022-08-03 16:03:54] build_node_ancestors
[INFO] [2022-08-03 16:03:54] old ancestors deleted.
[STOP] [2022-08-03 16:03:54] build_node_ancestors
[WARN] [2022-08-03 16:03:54] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:03:54] Flattener#flatten
[STOP] [2022-08-03 16:03:54] rebuild_nodes
[START] [2022-08-03 16:03:54] resolve_missing_media_owners
[STOP] [2022-08-03 16:03:54] resolve_missing_media_owners
[START] [2022-08-03 16:03:54] sanitize_media_verbatims
[STOP] [2022-08-03 16:03:54] sanitize_media_verbatims
[START] [2022-08-03 16:03:54] queue_downloads
[STOP] [2022-08-03 16:03:54] queue_downloads
[START] [2022-08-03 16:03:54] parse_names
[WARN] [2022-08-03 16:03:54] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:03:54] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:03:55] parse_names
[START] [2022-08-03 16:03:55] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:03:55] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:03:55] match_nodes
[START] [2022-08-03 16:03:55] map_all_nodes_to_pages
[STOP] [2022-08-03 16:03:55] map_all_nodes_to_pages
[INFO] [2022-08-03 16:03:55] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:03:55] update_nodes
[STOP] [2022-08-03 16:03:55] update_nodes
[STOP] [2022-08-03 16:03:55] match_nodes
[START] [2022-08-03 16:03:55] reindex_search
[STOP] [2022-08-03 16:03:55] reindex_search
[START] [2022-08-03 16:03:55] normalize_units
[STOP] [2022-08-03 16:03:55] normalize_units
[START] [2022-08-03 16:03:55] calculate_statistics
[2022-08-03 16:03:55] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:03:55] Duplicate page_id count: 0
[STOP] [2022-08-03 16:03:55] calculate_statistics
[START] [2022-08-03 16:03:55] complete_harvest_instance
[START] [2022-08-03 16:03:55] overall_tsv_creation
[INFO] [2022-08-03 16:03:55] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:03:55] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:04:37] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:04:37] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:05:30] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 16:05:30] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:05:30] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:05:30] Adding 1 traits...
[INFO] [2022-08-03 16:05:30] 1 metadata added.
[INFO] [2022-08-03 16:05:30] Adding 0 assocs...
[INFO] [2022-08-03 16:05:30] 0 metadata added.
[INFO] [2022-08-03 16:06:13] Processed 1/1 nodes
[INFO] [2022-08-03 16:06:13] Average Time: 111.91
[INFO] [2022-08-03 16:06:13] Total Time: 2m18s
[STOP] [2022-08-03 16:06:13] overall_tsv_creation
[INFO] [2022-08-03 16:06:13] Done. Check your files:
[INFO] [2022-08-03 16:06:13] (1 lines) /app/public/data/halanych_halanyc/publish_nodes.tsv
[INFO] [2022-08-03 16:06:13] (1 lines) /app/public/data/halanych_halanyc/publish_scientific_names.tsv
[INFO] [2022-08-03 16:06:13] (2 lines) /app/public/data/halanych_halanyc/publish_traits.tsv
[INFO] [2022-08-03 16:06:13] (2 lines) /app/public/data/halanych_halanyc/publish_metadata.tsv
[STOP] [2022-08-03 16:06:13] complete_harvest_instance
[START] [2022-08-03 16:06:13] completed
[STOP] [2022-08-03 16:06:13] completed
[STOP] [2022-08-03 16:06:13] logged process, took 146.69
Latest Process

03 Aug 16:01 EXITED currently processing 0