Harvest for Strand and Sundberg 2015 Created 03 Aug 16:16

Stage: completed
Fetched: 03 Aug 16:16
Validated: 03 Aug 16:16
Deltas Created 03 Aug 16:16
Units Normalized: 03 Aug 16:16
Ancestry Built: 03 Aug 16:16
Nodes Matched: 03 Aug 16:16
Names Parsed: 03 Aug 16:16
New Models Stored: 03 Aug 16:16
Indexed: 03 Aug 16:16
Completed: 03 Aug 16:18
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:16:08] Created harvest instance #4166
[STOP] [2022-08-03 16:16:08] create_harvest_instance
[START] [2022-08-03 16:16:08] fetch_files
[STOP] [2022-08-03 16:16:08] fetch_files
[START] [2022-08-03 16:16:08] validate_each_file
[INFO] [2022-08-03 16:16:08] Looping over 3 formats...
[INFO] [2022-08-03 16:16:08] ...nodes (/app/public/data/strand_sundberg_/taxa.txt)
[INFO] [2022-08-03 16:16:08] Valid: /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__nodes_29561.csv (1 lines)
[INFO] [2022-08-03 16:16:08] ...occurrences (/app/public/data/strand_sundberg_/occurrences.txt)
[INFO] [2022-08-03 16:16:08] Valid: /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__occurrences_29562.csv (1 lines)
[INFO] [2022-08-03 16:16:08] ...measurements (/app/public/data/strand_sundberg_/measurementOrFact.txt)
[INFO] [2022-08-03 16:16:08] Valid: /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__measurements_29563.csv (4 lines)
[STOP] [2022-08-03 16:16:08] validate_each_file
[START] [2022-08-03 16:16:08] convert_to_csv
[INFO] [2022-08-03 16:16:08] Looping over 3 formats...
[INFO] [2022-08-03 16:16:08] ...nodes (/app/public/data/strand_sundberg_/taxa.txt)
[CMD] [2022-08-03 16:16:08] /usr/bin/sort /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__nodes_29561.csv > /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__nodes_29561.csv_sorted
[INFO] [2022-08-03 16:16:08] Converted: /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__nodes_29561.csv (1 lines)
[INFO] [2022-08-03 16:16:08] ...occurrences (/app/public/data/strand_sundberg_/occurrences.txt)
[CMD] [2022-08-03 16:16:08] /usr/bin/sort /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__occurrences_29562.csv > /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__occurrences_29562.csv_sorted
[INFO] [2022-08-03 16:16:08] Converted: /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__occurrences_29562.csv (1 lines)
[INFO] [2022-08-03 16:16:08] ...measurements (/app/public/data/strand_sundberg_/measurementOrFact.txt)
[CMD] [2022-08-03 16:16:08] /usr/bin/sort /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__measurements_29563.csv > /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__measurements_29563.csv_sorted
[INFO] [2022-08-03 16:16:08] Converted: /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__measurements_29563.csv (4 lines)
[STOP] [2022-08-03 16:16:08] convert_to_csv
[START] [2022-08-03 16:16:08] calculate_delta
[INFO] [2022-08-03 16:16:08] Looping over 3 formats...
[INFO] [2022-08-03 16:16:08] ...nodes (/app/public/data/strand_sundberg_/taxa.txt)
[CMD] [2022-08-03 16:16:08] echo "0a" > /app/public/data/strand_sundberg_/diff/strand_sundberg__nodes_29561.diff
[CMD] [2022-08-03 16:16:08] tail -n +1 /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__nodes_29561.csv >> /app/public/data/strand_sundberg_/diff/strand_sundberg__nodes_29561.diff
[CMD] [2022-08-03 16:16:08] echo "." >> /app/public/data/strand_sundberg_/diff/strand_sundberg__nodes_29561.diff
[INFO] [2022-08-03 16:16:08] Created diff: /app/public/data/strand_sundberg_/diff/strand_sundberg__nodes_29561.diff (3 lines)
[INFO] [2022-08-03 16:16:08] ...occurrences (/app/public/data/strand_sundberg_/occurrences.txt)
[CMD] [2022-08-03 16:16:08] echo "0a" > /app/public/data/strand_sundberg_/diff/strand_sundberg__occurrences_29562.diff
[CMD] [2022-08-03 16:16:08] tail -n +1 /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__occurrences_29562.csv >> /app/public/data/strand_sundberg_/diff/strand_sundberg__occurrences_29562.diff
[CMD] [2022-08-03 16:16:08] echo "." >> /app/public/data/strand_sundberg_/diff/strand_sundberg__occurrences_29562.diff
[INFO] [2022-08-03 16:16:08] Created diff: /app/public/data/strand_sundberg_/diff/strand_sundberg__occurrences_29562.diff (3 lines)
[INFO] [2022-08-03 16:16:08] ...measurements (/app/public/data/strand_sundberg_/measurementOrFact.txt)
[CMD] [2022-08-03 16:16:08] echo "0a" > /app/public/data/strand_sundberg_/diff/strand_sundberg__measurements_29563.diff
[CMD] [2022-08-03 16:16:08] tail -n +1 /app/public/data/strand_sundberg_/converted_csv/strand_sundberg__measurements_29563.csv >> /app/public/data/strand_sundberg_/diff/strand_sundberg__measurements_29563.diff
[CMD] [2022-08-03 16:16:08] echo "." >> /app/public/data/strand_sundberg_/diff/strand_sundberg__measurements_29563.diff
[INFO] [2022-08-03 16:16:08] Created diff: /app/public/data/strand_sundberg_/diff/strand_sundberg__measurements_29563.diff (6 lines)
[STOP] [2022-08-03 16:16:08] calculate_delta
[START] [2022-08-03 16:16:08] parse_diff_and_store
[INFO] [2022-08-03 16:16:08] Handling diff: /app/public/data/strand_sundberg_/diff/strand_sundberg__nodes_29561.diff (3 lines)
[INFO] [2022-08-03 16:16:08] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:16:08] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:16:08] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:16:08] Handling diff: /app/public/data/strand_sundberg_/diff/strand_sundberg__occurrences_29562.diff (3 lines)
[INFO] [2022-08-03 16:16:08] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:16:08] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:16:08] Handling diff: /app/public/data/strand_sundberg_/diff/strand_sundberg__measurements_29563.diff (6 lines)
[INFO] [2022-08-03 16:16:08] Loading measurements diff file into memory (6 lines)...
[INFO] [2022-08-03 16:16:08] Storing 4 Traits (6/4/6)
[INFO] [2022-08-03 16:16:08] Storing 2 MetaTraits (6/4/6)
[STOP] [2022-08-03 16:16:08] parse_diff_and_store
[START] [2022-08-03 16:16:08] resolve_keys
[2022-08-03 16:16:08] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:16:15] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:16:15] traits to occurrences...
[INFO] [2022-08-03 16:16:15] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:16:15] Traits to sex term...
[INFO] [2022-08-03 16:16:15] Traits to lifestage term...
[INFO] [2022-08-03 16:16:15] MetaTraits to traits...
[INFO] [2022-08-03 16:16:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:16:15] Assocs to occurrences...
[INFO] [2022-08-03 16:16:16] Assocs to nodes...
[INFO] [2022-08-03 16:16:16] Assoc to sex term...
[INFO] [2022-08-03 16:16:16] Assoc to lifestage term...
[INFO] [2022-08-03 16:16:16] MetaAssoc to assocs...
[STOP] [2022-08-03 16:16:16] resolve_keys
[START] [2022-08-03 16:16:16] hold_for_later_1
[STOP] [2022-08-03 16:16:16] hold_for_later_1
[START] [2022-08-03 16:16:16] hold_for_later_2
[STOP] [2022-08-03 16:16:16] hold_for_later_2
[START] [2022-08-03 16:16:16] resolve_missing_parents
[STOP] [2022-08-03 16:16:16] resolve_missing_parents
[START] [2022-08-03 16:16:16] rebuild_nodes
[START] [2022-08-03 16:16:16] Flattener#flatten
[START] [2022-08-03 16:16:16] Flattener#study_resource
[START] [2022-08-03 16:16:16] Flattener#build_ancestry
[STOP] [2022-08-03 16:16:16] Flattener#build_ancestry
[INFO] [2022-08-03 16:16:16] 1 ancestry keys
[START] [2022-08-03 16:16:16] build_node_ancestors
[INFO] [2022-08-03 16:16:16] old ancestors deleted.
[STOP] [2022-08-03 16:16:16] build_node_ancestors
[WARN] [2022-08-03 16:16:16] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:16:16] Flattener#flatten
[STOP] [2022-08-03 16:16:16] rebuild_nodes
[START] [2022-08-03 16:16:16] resolve_missing_media_owners
[STOP] [2022-08-03 16:16:16] resolve_missing_media_owners
[START] [2022-08-03 16:16:16] sanitize_media_verbatims
[STOP] [2022-08-03 16:16:16] sanitize_media_verbatims
[START] [2022-08-03 16:16:16] queue_downloads
[STOP] [2022-08-03 16:16:16] queue_downloads
[START] [2022-08-03 16:16:16] parse_names
[WARN] [2022-08-03 16:16:16] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:16:16] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:16:17] parse_names
[START] [2022-08-03 16:16:17] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:16:17] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:16:17] match_nodes
[START] [2022-08-03 16:16:17] map_all_nodes_to_pages
[STOP] [2022-08-03 16:16:17] map_all_nodes_to_pages
[INFO] [2022-08-03 16:16:17] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:16:17] update_nodes
[STOP] [2022-08-03 16:16:17] update_nodes
[STOP] [2022-08-03 16:16:17] match_nodes
[START] [2022-08-03 16:16:17] reindex_search
[STOP] [2022-08-03 16:16:18] reindex_search
[START] [2022-08-03 16:16:18] normalize_units
[STOP] [2022-08-03 16:16:18] normalize_units
[START] [2022-08-03 16:16:18] calculate_statistics
[2022-08-03 16:16:18] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:16:18] Duplicate page_id count: 0
[STOP] [2022-08-03 16:16:18] calculate_statistics
[START] [2022-08-03 16:16:18] complete_harvest_instance
[START] [2022-08-03 16:16:18] overall_tsv_creation
[INFO] [2022-08-03 16:16:18] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:16:18] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:16:59] 2 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:16:59] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:17:50] Mapped 2 traits (2 meta) for 1 nodes.
[INFO] [2022-08-03 16:17:50] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:17:50] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:17:50] Adding 2 traits...
[INFO] [2022-08-03 16:17:50] 2 metadata added.
[INFO] [2022-08-03 16:17:50] Adding 0 assocs...
[INFO] [2022-08-03 16:17:50] 0 metadata added.
[INFO] [2022-08-03 16:18:33] Processed 1/1 nodes
[INFO] [2022-08-03 16:18:33] Average Time: 109.7
[INFO] [2022-08-03 16:18:33] Total Time: 2m15s
[STOP] [2022-08-03 16:18:33] overall_tsv_creation
[INFO] [2022-08-03 16:18:33] Done. Check your files:
[INFO] [2022-08-03 16:18:33] (1 lines) /app/public/data/strand_sundberg_/publish_nodes.tsv
[INFO] [2022-08-03 16:18:33] (1 lines) /app/public/data/strand_sundberg_/publish_scientific_names.tsv
[INFO] [2022-08-03 16:18:33] (3 lines) /app/public/data/strand_sundberg_/publish_traits.tsv
[INFO] [2022-08-03 16:18:33] (3 lines) /app/public/data/strand_sundberg_/publish_metadata.tsv
[STOP] [2022-08-03 16:18:33] complete_harvest_instance
[START] [2022-08-03 16:18:33] completed
[STOP] [2022-08-03 16:18:33] completed
[STOP] [2022-08-03 16:18:33] logged process, took 145.03
Latest Process

03 Aug 16:16 EXITED currently processing 0