Harvest for Von Konrat et al 2008 Created 03 Aug 17:33

Stage: completed
Fetched: 03 Aug 17:33
Validated: 03 Aug 17:33
Deltas Created 03 Aug 17:33
Units Normalized: 03 Aug 17:34
Ancestry Built: 03 Aug 17:34
Nodes Matched: 03 Aug 17:34
Names Parsed: 03 Aug 17:34
New Models Stored: 03 Aug 17:33
Indexed: 03 Aug 17:34
Completed: 03 Aug 17:36
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 17:33:56] Created harvest instance #4202
[STOP] [2022-08-03 17:33:56] create_harvest_instance
[START] [2022-08-03 17:33:56] fetch_files
[STOP] [2022-08-03 17:33:56] fetch_files
[START] [2022-08-03 17:33:56] validate_each_file
[INFO] [2022-08-03 17:33:56] Looping over 3 formats...
[INFO] [2022-08-03 17:33:56] ...nodes (/app/public/data/vkeav/taxa.txt)
[INFO] [2022-08-03 17:33:56] Valid: /app/public/data/vkeav/converted_csv/vkeav_nodes_29668.csv (25 lines)
[INFO] [2022-08-03 17:33:56] ...occurrences (/app/public/data/vkeav/occurrences.txt)
[INFO] [2022-08-03 17:33:56] Valid: /app/public/data/vkeav/converted_csv/vkeav_occurrences_29669.csv (25 lines)
[INFO] [2022-08-03 17:33:56] ...measurements (/app/public/data/vkeav/measurementOrFact.txt)
[INFO] [2022-08-03 17:33:56] Valid: /app/public/data/vkeav/converted_csv/vkeav_measurements_29670.csv (50 lines)
[STOP] [2022-08-03 17:33:56] validate_each_file
[START] [2022-08-03 17:33:56] convert_to_csv
[INFO] [2022-08-03 17:33:56] Looping over 3 formats...
[INFO] [2022-08-03 17:33:56] ...nodes (/app/public/data/vkeav/taxa.txt)
[CMD] [2022-08-03 17:33:56] /usr/bin/sort /app/public/data/vkeav/converted_csv/vkeav_nodes_29668.csv > /app/public/data/vkeav/converted_csv/vkeav_nodes_29668.csv_sorted
[INFO] [2022-08-03 17:33:56] Converted: /app/public/data/vkeav/converted_csv/vkeav_nodes_29668.csv (25 lines)
[INFO] [2022-08-03 17:33:56] ...occurrences (/app/public/data/vkeav/occurrences.txt)
[CMD] [2022-08-03 17:33:56] /usr/bin/sort /app/public/data/vkeav/converted_csv/vkeav_occurrences_29669.csv > /app/public/data/vkeav/converted_csv/vkeav_occurrences_29669.csv_sorted
[INFO] [2022-08-03 17:33:56] Converted: /app/public/data/vkeav/converted_csv/vkeav_occurrences_29669.csv (25 lines)
[INFO] [2022-08-03 17:33:56] ...measurements (/app/public/data/vkeav/measurementOrFact.txt)
[CMD] [2022-08-03 17:33:56] /usr/bin/sort /app/public/data/vkeav/converted_csv/vkeav_measurements_29670.csv > /app/public/data/vkeav/converted_csv/vkeav_measurements_29670.csv_sorted
[INFO] [2022-08-03 17:33:56] Converted: /app/public/data/vkeav/converted_csv/vkeav_measurements_29670.csv (50 lines)
[STOP] [2022-08-03 17:33:56] convert_to_csv
[START] [2022-08-03 17:33:56] calculate_delta
[INFO] [2022-08-03 17:33:56] Looping over 3 formats...
[INFO] [2022-08-03 17:33:56] ...nodes (/app/public/data/vkeav/taxa.txt)
[CMD] [2022-08-03 17:33:56] echo "0a" > /app/public/data/vkeav/diff/vkeav_nodes_29668.diff
[CMD] [2022-08-03 17:33:56] tail -n +1 /app/public/data/vkeav/converted_csv/vkeav_nodes_29668.csv >> /app/public/data/vkeav/diff/vkeav_nodes_29668.diff
[CMD] [2022-08-03 17:33:56] echo "." >> /app/public/data/vkeav/diff/vkeav_nodes_29668.diff
[INFO] [2022-08-03 17:33:56] Created diff: /app/public/data/vkeav/diff/vkeav_nodes_29668.diff (27 lines)
[INFO] [2022-08-03 17:33:56] ...occurrences (/app/public/data/vkeav/occurrences.txt)
[CMD] [2022-08-03 17:33:56] echo "0a" > /app/public/data/vkeav/diff/vkeav_occurrences_29669.diff
[CMD] [2022-08-03 17:33:56] tail -n +1 /app/public/data/vkeav/converted_csv/vkeav_occurrences_29669.csv >> /app/public/data/vkeav/diff/vkeav_occurrences_29669.diff
[CMD] [2022-08-03 17:33:56] echo "." >> /app/public/data/vkeav/diff/vkeav_occurrences_29669.diff
[INFO] [2022-08-03 17:33:56] Created diff: /app/public/data/vkeav/diff/vkeav_occurrences_29669.diff (27 lines)
[INFO] [2022-08-03 17:33:56] ...measurements (/app/public/data/vkeav/measurementOrFact.txt)
[CMD] [2022-08-03 17:33:56] echo "0a" > /app/public/data/vkeav/diff/vkeav_measurements_29670.diff
[CMD] [2022-08-03 17:33:56] tail -n +1 /app/public/data/vkeav/converted_csv/vkeav_measurements_29670.csv >> /app/public/data/vkeav/diff/vkeav_measurements_29670.diff
[CMD] [2022-08-03 17:33:56] echo "." >> /app/public/data/vkeav/diff/vkeav_measurements_29670.diff
[INFO] [2022-08-03 17:33:56] Created diff: /app/public/data/vkeav/diff/vkeav_measurements_29670.diff (52 lines)
[STOP] [2022-08-03 17:33:56] calculate_delta
[START] [2022-08-03 17:33:56] parse_diff_and_store
[INFO] [2022-08-03 17:33:56] Handling diff: /app/public/data/vkeav/diff/vkeav_nodes_29668.diff (27 lines)
[INFO] [2022-08-03 17:33:57] Loading nodes diff file into memory (27 lines)...
[INFO] [2022-08-03 17:33:57] Storing 25 ScientificNames (50/25/27)
[INFO] [2022-08-03 17:33:57] Storing 25 Nodes (50/25/27)
[INFO] [2022-08-03 17:33:57] Handling diff: /app/public/data/vkeav/diff/vkeav_occurrences_29669.diff (27 lines)
[INFO] [2022-08-03 17:33:57] Loading occurrences diff file into memory (27 lines)...
[INFO] [2022-08-03 17:33:57] Storing 25 Occurrences (25/25/27)
[INFO] [2022-08-03 17:33:57] Handling diff: /app/public/data/vkeav/diff/vkeav_measurements_29670.diff (52 lines)
[INFO] [2022-08-03 17:33:57] Loading measurements diff file into memory (52 lines)...
[INFO] [2022-08-03 17:33:57] Storing 50 Traits (76/50/52)
[INFO] [2022-08-03 17:33:57] Storing 26 MetaTraits (76/50/52)
[STOP] [2022-08-03 17:33:57] parse_diff_and_store
[START] [2022-08-03 17:33:57] resolve_keys
[2022-08-03 17:33:57] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:34:04] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:34:04] traits to occurrences...
[INFO] [2022-08-03 17:34:04] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:34:04] Traits to sex term...
[INFO] [2022-08-03 17:34:04] Traits to lifestage term...
[INFO] [2022-08-03 17:34:04] MetaTraits to traits...
[INFO] [2022-08-03 17:34:04] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:34:04] Assocs to occurrences...
[INFO] [2022-08-03 17:34:04] Assocs to nodes...
[INFO] [2022-08-03 17:34:04] Assoc to sex term...
[INFO] [2022-08-03 17:34:04] Assoc to lifestage term...
[INFO] [2022-08-03 17:34:04] MetaAssoc to assocs...
[STOP] [2022-08-03 17:34:04] resolve_keys
[START] [2022-08-03 17:34:04] hold_for_later_1
[STOP] [2022-08-03 17:34:04] hold_for_later_1
[START] [2022-08-03 17:34:04] hold_for_later_2
[STOP] [2022-08-03 17:34:04] hold_for_later_2
[START] [2022-08-03 17:34:04] resolve_missing_parents
[STOP] [2022-08-03 17:34:04] resolve_missing_parents
[START] [2022-08-03 17:34:04] rebuild_nodes
[START] [2022-08-03 17:34:04] Flattener#flatten
[START] [2022-08-03 17:34:04] Flattener#study_resource
[START] [2022-08-03 17:34:04] Flattener#build_ancestry
[STOP] [2022-08-03 17:34:04] Flattener#build_ancestry
[INFO] [2022-08-03 17:34:04] 25 ancestry keys
[START] [2022-08-03 17:34:04] build_node_ancestors
[INFO] [2022-08-03 17:34:04] old ancestors deleted.
[STOP] [2022-08-03 17:34:04] build_node_ancestors
[WARN] [2022-08-03 17:34:04] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:34:04] Flattener#flatten
[STOP] [2022-08-03 17:34:04] rebuild_nodes
[START] [2022-08-03 17:34:04] resolve_missing_media_owners
[STOP] [2022-08-03 17:34:04] resolve_missing_media_owners
[START] [2022-08-03 17:34:04] sanitize_media_verbatims
[STOP] [2022-08-03 17:34:04] sanitize_media_verbatims
[START] [2022-08-03 17:34:04] queue_downloads
[STOP] [2022-08-03 17:34:04] queue_downloads
[START] [2022-08-03 17:34:04] parse_names
[WARN] [2022-08-03 17:34:04] I see 25 names which still need to be parsed.
[WARN] [2022-08-03 17:34:04] Names to parse: 25 formatted: 25 learned: 25 parsed: 25
[STOP] [2022-08-03 17:34:05] parse_names
[START] [2022-08-03 17:34:05] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:34:05] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:34:05] match_nodes
[START] [2022-08-03 17:34:05] map_all_nodes_to_pages
[STOP] [2022-08-03 17:34:05] map_all_nodes_to_pages
[INFO] [2022-08-03 17:34:05] ZERO unmatched nodes (of 25)! Nicely done.
[START] [2022-08-03 17:34:05] update_nodes
[STOP] [2022-08-03 17:34:05] update_nodes
[STOP] [2022-08-03 17:34:05] match_nodes
[START] [2022-08-03 17:34:05] reindex_search
[STOP] [2022-08-03 17:34:06] reindex_search
[START] [2022-08-03 17:34:06] normalize_units
[STOP] [2022-08-03 17:34:06] normalize_units
[START] [2022-08-03 17:34:06] calculate_statistics
[2022-08-03 17:34:06] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:34:08] Duplicate page_id count: 0
[STOP] [2022-08-03 17:34:08] calculate_statistics
[START] [2022-08-03 17:34:08] complete_harvest_instance
[START] [2022-08-03 17:34:08] overall_tsv_creation
[INFO] [2022-08-03 17:34:08] Exporting 25 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:34:08] Processing group of 25 in 1 batches of 10000
[INFO] [2022-08-03 17:34:50] 25 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:34:50] Building Traits map for 25 nodes (this can take a while)...
[INFO] [2022-08-03 17:35:45] Mapped 25 traits (26 meta) for 25 nodes.
[INFO] [2022-08-03 17:35:45] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:35:45] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:35:45] Adding 25 traits...
[INFO] [2022-08-03 17:35:45] 25 metadata added.
[INFO] [2022-08-03 17:35:45] Adding 0 assocs...
[INFO] [2022-08-03 17:35:45] 0 metadata added.
[INFO] [2022-08-03 17:36:27] Processed 25/25 nodes
[INFO] [2022-08-03 17:36:27] Average Time: 114.01
[INFO] [2022-08-03 17:36:27] Total Time: 2m20s
[STOP] [2022-08-03 17:36:27] overall_tsv_creation
[INFO] [2022-08-03 17:36:27] Done. Check your files:
[INFO] [2022-08-03 17:36:27] (25 lines) /app/public/data/vkeav/publish_nodes.tsv
[INFO] [2022-08-03 17:36:27] (25 lines) /app/public/data/vkeav/publish_scientific_names.tsv
[INFO] [2022-08-03 17:36:27] (26 lines) /app/public/data/vkeav/publish_traits.tsv
[INFO] [2022-08-03 17:36:27] (26 lines) /app/public/data/vkeav/publish_metadata.tsv
[STOP] [2022-08-03 17:36:27] complete_harvest_instance
[START] [2022-08-03 17:36:27] completed
[STOP] [2022-08-03 17:36:27] completed
[STOP] [2022-08-03 17:36:27] logged process, took 150.72
Latest Process

03 Aug 17:33 EXITED currently processing 0