Harvest for Wever 1975 Created 31 May 19:33

Stage: completed
Fetched: 31 May 19:33
Validated: 31 May 19:33
Deltas Created 31 May 19:34
Units Normalized: 31 May 19:34
Ancestry Built: 31 May 19:34
Nodes Matched: 31 May 19:34
Names Parsed: 31 May 19:34
New Models Stored: 31 May 19:34
Indexed: 31 May 19:34
Completed: 31 May 19:35
Time to Harvest: less than a minute
Harvesting Log

(160 lines)
[INFO] [2021-05-31 19:33:58] Created harvest instance #3954
[STOP] [2021-05-31 19:33:58] create_harvest_instance
[START] [2021-05-31 19:33:58] fetch_files
[STOP] [2021-05-31 19:33:58] fetch_files
[START] [2021-05-31 19:33:58] validate_each_file
[INFO] [2021-05-31 19:33:58] Looping over 4 formats...
[INFO] [2021-05-31 19:33:58] ...refs (/app/public/data/wever_wever_1975/references.txt)
[INFO] [2021-05-31 19:33:58] Valid: /app/public/converted_csv/wever_wever_1975_refs_3954.csv (0 lines)
[INFO] [2021-05-31 19:33:58] ...nodes (/app/public/data/wever_wever_1975/taxa.txt)
[INFO] [2021-05-31 19:33:58] Valid: /app/public/converted_csv/wever_wever_1975_nodes_3954.csv (1 lines)
[INFO] [2021-05-31 19:33:58] ...occurrences (/app/public/data/wever_wever_1975/occurrences.txt)
[INFO] [2021-05-31 19:33:58] Valid: /app/public/converted_csv/wever_wever_1975_occurrences_3954.csv (1 lines)
[INFO] [2021-05-31 19:33:58] ...measurements (/app/public/data/wever_wever_1975/measurementsorfacts.txt)
[INFO] [2021-05-31 19:33:58] Valid: /app/public/converted_csv/wever_wever_1975_measurements_3954.csv (12 lines)
[STOP] [2021-05-31 19:33:58] validate_each_file
[START] [2021-05-31 19:33:58] convert_to_csv
[INFO] [2021-05-31 19:33:58] Looping over 4 formats...
[INFO] [2021-05-31 19:33:58] ...refs (/app/public/data/wever_wever_1975/references.txt)
[CMD] [2021-05-31 19:33:58] /usr/bin/sort /app/public/converted_csv/wever_wever_1975_refs_3954.csv > /app/public/converted_csv/wever_wever_1975_refs_3954.csv_sorted
[INFO] [2021-05-31 19:33:58] Converted: /app/public/converted_csv/wever_wever_1975_refs_3954.csv (0 lines)
[INFO] [2021-05-31 19:33:58] ...nodes (/app/public/data/wever_wever_1975/taxa.txt)
[CMD] [2021-05-31 19:33:58] /usr/bin/sort /app/public/converted_csv/wever_wever_1975_nodes_3954.csv > /app/public/converted_csv/wever_wever_1975_nodes_3954.csv_sorted
[INFO] [2021-05-31 19:33:59] Converted: /app/public/converted_csv/wever_wever_1975_nodes_3954.csv (1 lines)
[INFO] [2021-05-31 19:33:59] ...occurrences (/app/public/data/wever_wever_1975/occurrences.txt)
[CMD] [2021-05-31 19:33:59] /usr/bin/sort /app/public/converted_csv/wever_wever_1975_occurrences_3954.csv > /app/public/converted_csv/wever_wever_1975_occurrences_3954.csv_sorted
[INFO] [2021-05-31 19:33:59] Converted: /app/public/converted_csv/wever_wever_1975_occurrences_3954.csv (1 lines)
[INFO] [2021-05-31 19:33:59] ...measurements (/app/public/data/wever_wever_1975/measurementsorfacts.txt)
[CMD] [2021-05-31 19:33:59] /usr/bin/sort /app/public/converted_csv/wever_wever_1975_measurements_3954.csv > /app/public/converted_csv/wever_wever_1975_measurements_3954.csv_sorted
[INFO] [2021-05-31 19:33:59] Converted: /app/public/converted_csv/wever_wever_1975_measurements_3954.csv (12 lines)
[STOP] [2021-05-31 19:33:59] convert_to_csv
[START] [2021-05-31 19:33:59] calculate_delta
[INFO] [2021-05-31 19:33:59] Looping over 4 formats...
[INFO] [2021-05-31 19:33:59] ...refs (/app/public/data/wever_wever_1975/references.txt)
[CMD] [2021-05-31 19:33:59] echo "0a" > /app/public/diff/wever_wever_1975_refs_3954.diff
[CMD] [2021-05-31 19:34:00] tail -n +1 /app/public/converted_csv/wever_wever_1975_refs_3954.csv >> /app/public/diff/wever_wever_1975_refs_3954.diff
[CMD] [2021-05-31 19:34:00] echo "." >> /app/public/diff/wever_wever_1975_refs_3954.diff
[INFO] [2021-05-31 19:34:01] Created diff: /app/public/diff/wever_wever_1975_refs_3954.diff (2 lines)
[INFO] [2021-05-31 19:34:01] ...nodes (/app/public/data/wever_wever_1975/taxa.txt)
[CMD] [2021-05-31 19:34:01] echo "0a" > /app/public/diff/wever_wever_1975_nodes_3954.diff
[CMD] [2021-05-31 19:34:01] tail -n +1 /app/public/converted_csv/wever_wever_1975_nodes_3954.csv >> /app/public/diff/wever_wever_1975_nodes_3954.diff
[CMD] [2021-05-31 19:34:01] echo "." >> /app/public/diff/wever_wever_1975_nodes_3954.diff
[INFO] [2021-05-31 19:34:02] Created diff: /app/public/diff/wever_wever_1975_nodes_3954.diff (3 lines)
[INFO] [2021-05-31 19:34:02] ...occurrences (/app/public/data/wever_wever_1975/occurrences.txt)
[CMD] [2021-05-31 19:34:02] echo "0a" > /app/public/diff/wever_wever_1975_occurrences_3954.diff
[CMD] [2021-05-31 19:34:02] tail -n +1 /app/public/converted_csv/wever_wever_1975_occurrences_3954.csv >> /app/public/diff/wever_wever_1975_occurrences_3954.diff
[CMD] [2021-05-31 19:34:03] echo "." >> /app/public/diff/wever_wever_1975_occurrences_3954.diff
[INFO] [2021-05-31 19:34:03] Created diff: /app/public/diff/wever_wever_1975_occurrences_3954.diff (3 lines)
[INFO] [2021-05-31 19:34:03] ...measurements (/app/public/data/wever_wever_1975/measurementsorfacts.txt)
[CMD] [2021-05-31 19:34:03] echo "0a" > /app/public/diff/wever_wever_1975_measurements_3954.diff
[CMD] [2021-05-31 19:34:03] tail -n +1 /app/public/converted_csv/wever_wever_1975_measurements_3954.csv >> /app/public/diff/wever_wever_1975_measurements_3954.diff
[CMD] [2021-05-31 19:34:04] echo "." >> /app/public/diff/wever_wever_1975_measurements_3954.diff
[INFO] [2021-05-31 19:34:04] Created diff: /app/public/diff/wever_wever_1975_measurements_3954.diff (14 lines)
[STOP] [2021-05-31 19:34:04] calculate_delta
[START] [2021-05-31 19:34:04] parse_diff_and_store
[INFO] [2021-05-31 19:34:04] Handling diff: /app/public/diff/wever_wever_1975_refs_3954.diff (2 lines)
[INFO] [2021-05-31 19:34:04] Loading refs diff file into memory (2 /app/public/diff/wever_wever_1975_refs_3954.diff lines)...
[INFO] [2021-05-31 19:34:05] Handling diff: /app/public/diff/wever_wever_1975_nodes_3954.diff (3 lines)
[INFO] [2021-05-31 19:34:05] Loading nodes diff file into memory (3 /app/public/diff/wever_wever_1975_nodes_3954.diff lines)...
[INFO] [2021-05-31 19:34:05] Handling diff: /app/public/diff/wever_wever_1975_occurrences_3954.diff (3 lines)
[INFO] [2021-05-31 19:34:06] Loading occurrences diff file into memory (3 /app/public/diff/wever_wever_1975_occurrences_3954.diff lines)...
[INFO] [2021-05-31 19:34:06] Handling diff: /app/public/diff/wever_wever_1975_measurements_3954.diff (14 lines)
[INFO] [2021-05-31 19:34:07] Loading measurements diff file into memory (14 /app/public/diff/wever_wever_1975_measurements_3954.diff lines)...
[INFO] [2021-05-31 19:34:07] Storing 1 ScientificNames
[INFO] [2021-05-31 19:34:07] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:34:07] Average Time: 0.0
[INFO] [2021-05-31 19:34:07] Total Time: 1s
[INFO] [2021-05-31 19:34:07] Storing 1 Nodes
[INFO] [2021-05-31 19:34:07] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:34:07] Average Time: 0.0
[INFO] [2021-05-31 19:34:07] Total Time: 1s
[INFO] [2021-05-31 19:34:07] Storing 1 Occurrences
[INFO] [2021-05-31 19:34:07] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:34:07] Average Time: 0.0
[INFO] [2021-05-31 19:34:07] Total Time: 1s
[INFO] [2021-05-31 19:34:07] Storing 12 Traits
[INFO] [2021-05-31 19:34:07] Processing group of 12 in 1 groups of 1000
[INFO] [2021-05-31 19:34:07] Average Time: 0.01
[INFO] [2021-05-31 19:34:07] Total Time: 1s
[INFO] [2021-05-31 19:34:07] Storing 8 MetaTraits
[INFO] [2021-05-31 19:34:07] Processing group of 8 in 1 groups of 1000
[INFO] [2021-05-31 19:34:07] Average Time: 0.0
[INFO] [2021-05-31 19:34:07] Total Time: 1s
[STOP] [2021-05-31 19:34:07] parse_diff_and_store
[START] [2021-05-31 19:34:07] resolve_keys
[INFO] [2021-05-31 19:34:13] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-31 19:34:13] traits to occurrences...
[INFO] [2021-05-31 19:34:13] traits to nodes (through occurrences)...
[INFO] [2021-05-31 19:34:13] Traits to sex term...
[INFO] [2021-05-31 19:34:13] Traits to lifestage term...
[INFO] [2021-05-31 19:34:13] MetaTraits to traits...
[INFO] [2021-05-31 19:34:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-31 19:34:13] Assocs to occurrences...
[INFO] [2021-05-31 19:34:13] Assocs to nodes...
[INFO] [2021-05-31 19:34:13] Assoc to sex term...
[INFO] [2021-05-31 19:34:13] Assoc to lifestage term...
[INFO] [2021-05-31 19:34:13] MetaAssoc to assocs...
[STOP] [2021-05-31 19:34:13] resolve_keys
[START] [2021-05-31 19:34:13] hold_for_later_1
[STOP] [2021-05-31 19:34:13] hold_for_later_1
[START] [2021-05-31 19:34:13] hold_for_later_2
[STOP] [2021-05-31 19:34:13] hold_for_later_2
[START] [2021-05-31 19:34:13] resolve_missing_parents
[STOP] [2021-05-31 19:34:13] resolve_missing_parents
[START] [2021-05-31 19:34:13] rebuild_nodes
[START] [2021-05-31 19:34:13] Flattener#flatten
[START] [2021-05-31 19:34:13] Flattener#study_resource
[START] [2021-05-31 19:34:13] Flattener#build_ancestry
[STOP] [2021-05-31 19:34:13] Flattener#build_ancestry
[INFO] [2021-05-31 19:34:13] 1 ancestry keys
[START] [2021-05-31 19:34:13] build_node_ancestors
[INFO] [2021-05-31 19:34:13] old ancestors deleted.
[STOP] [2021-05-31 19:34:13] build_node_ancestors
[WARN] [2021-05-31 19:34:13] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-05-31 19:34:13] Flattener#flatten
[STOP] [2021-05-31 19:34:13] rebuild_nodes
[START] [2021-05-31 19:34:13] resolve_missing_media_owners
[STOP] [2021-05-31 19:34:13] resolve_missing_media_owners
[START] [2021-05-31 19:34:13] sanitize_media_verbatims
[STOP] [2021-05-31 19:34:13] sanitize_media_verbatims
[START] [2021-05-31 19:34:13] queue_downloads
[STOP] [2021-05-31 19:34:13] queue_downloads
[START] [2021-05-31 19:34:13] parse_names
[WARN] [2021-05-31 19:34:13] I see 1 names which still need to be parsed.
[STOP] [2021-05-31 19:34:14] parse_names
[START] [2021-05-31 19:34:14] denormalize_canonical_names_to_nodes
[STOP] [2021-05-31 19:34:14] denormalize_canonical_names_to_nodes
[START] [2021-05-31 19:34:14] match_nodes
[START] [2021-05-31 19:34:14] map_all_nodes_to_pages
[STOP] [2021-05-31 19:34:14] map_all_nodes_to_pages
[INFO] [2021-05-31 19:34:14] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-05-31 19:34:14] update_nodes
[STOP] [2021-05-31 19:34:14] update_nodes
[STOP] [2021-05-31 19:34:14] match_nodes
[START] [2021-05-31 19:34:14] reindex_search
[STOP] [2021-05-31 19:34:14] reindex_search
[START] [2021-05-31 19:34:14] normalize_units
[STOP] [2021-05-31 19:34:14] normalize_units
[START] [2021-05-31 19:34:14] calculate_statistics
[2021-05-31 19:34:14] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-05-31 19:34:14] calculate_statistics
[START] [2021-05-31 19:34:14] complete_harvest_instance
[START] [2021-05-31 19:34:14] overall_tsv_creation
[INFO] [2021-05-31 19:34:14] Processing group of 1 in 1 batches of 10000
[INFO] [2021-05-31 19:34:46] 4 Traits (unfiltered)...
[INFO] [2021-05-31 19:35:10] 4 Traits (filtered)...
[INFO] [2021-05-31 19:35:10] 0 Associations (filtered)...
[INFO] [2021-05-31 19:35:10] 8 metadata added.
[INFO] [2021-05-31 19:35:10] 0 metadata added.
[INFO] [2021-05-31 19:35:32] Average Time: 56.5
[INFO] [2021-05-31 19:35:32] Total Time: 1m18s
[STOP] [2021-05-31 19:35:32] overall_tsv_creation
[INFO] [2021-05-31 19:35:32] Done. Check your files:
[INFO] [2021-05-31 19:35:33] (1 lines) /app/public/data/wever_wever_1975/publish_nodes.tsv
[INFO] [2021-05-31 19:35:33] (1 lines) /app/public/data/wever_wever_1975/publish_scientific_names.tsv
[INFO] [2021-05-31 19:35:33] (5 lines) /app/public/data/wever_wever_1975/publish_traits.tsv
[INFO] [2021-05-31 19:35:34] (9 lines) /app/public/data/wever_wever_1975/publish_metadata.tsv
[STOP] [2021-05-31 19:35:34] complete_harvest_instance
[START] [2021-05-31 19:35:34] completed
[STOP] [2021-05-31 19:35:34] completed
[STOP] [2021-05-31 19:35:34] logged process, took 96.28
Latest Process

31 May 19:33 EXITED currently processing 0