Harvest for Lindquist et al 1998 Created 31 May 19:37

Stage: completed
Fetched: 31 May 19:37
Validated: 31 May 19:37
Deltas Created 31 May 19:37
Units Normalized: 31 May 19:37
Ancestry Built: 31 May 19:37
Nodes Matched: 31 May 19:37
Names Parsed: 31 May 19:37
New Models Stored: 31 May 19:37
Indexed: 31 May 19:37
Completed: 31 May 19:38
Time to Harvest: less than a minute
Harvesting Log

(164 lines)
[INFO] [2021-05-31 19:37:19] Created harvest instance #3955
[STOP] [2021-05-31 19:37:19] create_harvest_instance
[START] [2021-05-31 19:37:19] fetch_files
[STOP] [2021-05-31 19:37:19] fetch_files
[START] [2021-05-31 19:37:19] validate_each_file
[INFO] [2021-05-31 19:37:19] Looping over 4 formats...
[INFO] [2021-05-31 19:37:19] ...refs (/app/public/data/lindquist_et_al_/references.txt)
[INFO] [2021-05-31 19:37:19] Valid: /app/public/converted_csv/lindquist_et_al__refs_3955.csv (0 lines)
[INFO] [2021-05-31 19:37:19] ...nodes (/app/public/data/lindquist_et_al_/taxa.txt)
[INFO] [2021-05-31 19:37:19] Valid: /app/public/converted_csv/lindquist_et_al__nodes_3955.csv (1 lines)
[INFO] [2021-05-31 19:37:19] ...occurrences (/app/public/data/lindquist_et_al_/occurrences.txt)
[INFO] [2021-05-31 19:37:19] Valid: /app/public/converted_csv/lindquist_et_al__occurrences_3955.csv (1 lines)
[INFO] [2021-05-31 19:37:19] ...measurements (/app/public/data/lindquist_et_al_/measurementsorfacts.txt)
[INFO] [2021-05-31 19:37:19] Valid: /app/public/converted_csv/lindquist_et_al__measurements_3955.csv (6 lines)
[STOP] [2021-05-31 19:37:19] validate_each_file
[START] [2021-05-31 19:37:19] convert_to_csv
[INFO] [2021-05-31 19:37:19] Looping over 4 formats...
[INFO] [2021-05-31 19:37:19] ...refs (/app/public/data/lindquist_et_al_/references.txt)
[CMD] [2021-05-31 19:37:19] /usr/bin/sort /app/public/converted_csv/lindquist_et_al__refs_3955.csv > /app/public/converted_csv/lindquist_et_al__refs_3955.csv_sorted
[INFO] [2021-05-31 19:37:20] Converted: /app/public/converted_csv/lindquist_et_al__refs_3955.csv (0 lines)
[INFO] [2021-05-31 19:37:20] ...nodes (/app/public/data/lindquist_et_al_/taxa.txt)
[CMD] [2021-05-31 19:37:20] /usr/bin/sort /app/public/converted_csv/lindquist_et_al__nodes_3955.csv > /app/public/converted_csv/lindquist_et_al__nodes_3955.csv_sorted
[INFO] [2021-05-31 19:37:20] Converted: /app/public/converted_csv/lindquist_et_al__nodes_3955.csv (1 lines)
[INFO] [2021-05-31 19:37:20] ...occurrences (/app/public/data/lindquist_et_al_/occurrences.txt)
[CMD] [2021-05-31 19:37:20] /usr/bin/sort /app/public/converted_csv/lindquist_et_al__occurrences_3955.csv > /app/public/converted_csv/lindquist_et_al__occurrences_3955.csv_sorted
[INFO] [2021-05-31 19:37:20] Converted: /app/public/converted_csv/lindquist_et_al__occurrences_3955.csv (1 lines)
[INFO] [2021-05-31 19:37:20] ...measurements (/app/public/data/lindquist_et_al_/measurementsorfacts.txt)
[CMD] [2021-05-31 19:37:20] /usr/bin/sort /app/public/converted_csv/lindquist_et_al__measurements_3955.csv > /app/public/converted_csv/lindquist_et_al__measurements_3955.csv_sorted
[INFO] [2021-05-31 19:37:21] Converted: /app/public/converted_csv/lindquist_et_al__measurements_3955.csv (6 lines)
[STOP] [2021-05-31 19:37:21] convert_to_csv
[START] [2021-05-31 19:37:21] calculate_delta
[INFO] [2021-05-31 19:37:21] Looping over 4 formats...
[INFO] [2021-05-31 19:37:21] ...refs (/app/public/data/lindquist_et_al_/references.txt)
[CMD] [2021-05-31 19:37:21] echo "0a" > /app/public/diff/lindquist_et_al__refs_3955.diff
[CMD] [2021-05-31 19:37:21] tail -n +1 /app/public/converted_csv/lindquist_et_al__refs_3955.csv >> /app/public/diff/lindquist_et_al__refs_3955.diff
[CMD] [2021-05-31 19:37:22] echo "." >> /app/public/diff/lindquist_et_al__refs_3955.diff
[INFO] [2021-05-31 19:37:22] Created diff: /app/public/diff/lindquist_et_al__refs_3955.diff (2 lines)
[INFO] [2021-05-31 19:37:22] ...nodes (/app/public/data/lindquist_et_al_/taxa.txt)
[CMD] [2021-05-31 19:37:22] echo "0a" > /app/public/diff/lindquist_et_al__nodes_3955.diff
[CMD] [2021-05-31 19:37:22] tail -n +1 /app/public/converted_csv/lindquist_et_al__nodes_3955.csv >> /app/public/diff/lindquist_et_al__nodes_3955.diff
[CMD] [2021-05-31 19:37:23] echo "." >> /app/public/diff/lindquist_et_al__nodes_3955.diff
[INFO] [2021-05-31 19:37:23] Created diff: /app/public/diff/lindquist_et_al__nodes_3955.diff (3 lines)
[INFO] [2021-05-31 19:37:23] ...occurrences (/app/public/data/lindquist_et_al_/occurrences.txt)
[CMD] [2021-05-31 19:37:23] echo "0a" > /app/public/diff/lindquist_et_al__occurrences_3955.diff
[CMD] [2021-05-31 19:37:24] tail -n +1 /app/public/converted_csv/lindquist_et_al__occurrences_3955.csv >> /app/public/diff/lindquist_et_al__occurrences_3955.diff
[CMD] [2021-05-31 19:37:24] echo "." >> /app/public/diff/lindquist_et_al__occurrences_3955.diff
[INFO] [2021-05-31 19:37:24] Created diff: /app/public/diff/lindquist_et_al__occurrences_3955.diff (3 lines)
[INFO] [2021-05-31 19:37:24] ...measurements (/app/public/data/lindquist_et_al_/measurementsorfacts.txt)
[CMD] [2021-05-31 19:37:24] echo "0a" > /app/public/diff/lindquist_et_al__measurements_3955.diff
[CMD] [2021-05-31 19:37:25] tail -n +1 /app/public/converted_csv/lindquist_et_al__measurements_3955.csv >> /app/public/diff/lindquist_et_al__measurements_3955.diff
[CMD] [2021-05-31 19:37:25] echo "." >> /app/public/diff/lindquist_et_al__measurements_3955.diff
[INFO] [2021-05-31 19:37:25] Created diff: /app/public/diff/lindquist_et_al__measurements_3955.diff (8 lines)
[STOP] [2021-05-31 19:37:25] calculate_delta
[START] [2021-05-31 19:37:25] parse_diff_and_store
[INFO] [2021-05-31 19:37:25] Handling diff: /app/public/diff/lindquist_et_al__refs_3955.diff (2 lines)
[INFO] [2021-05-31 19:37:26] Loading refs diff file into memory (2 /app/public/diff/lindquist_et_al__refs_3955.diff lines)...
[INFO] [2021-05-31 19:37:26] Handling diff: /app/public/diff/lindquist_et_al__nodes_3955.diff (3 lines)
[INFO] [2021-05-31 19:37:26] Loading nodes diff file into memory (3 /app/public/diff/lindquist_et_al__nodes_3955.diff lines)...
[INFO] [2021-05-31 19:37:27] Handling diff: /app/public/diff/lindquist_et_al__occurrences_3955.diff (3 lines)
[INFO] [2021-05-31 19:37:27] Loading occurrences diff file into memory (3 /app/public/diff/lindquist_et_al__occurrences_3955.diff lines)...
[INFO] [2021-05-31 19:37:28] Handling diff: /app/public/diff/lindquist_et_al__measurements_3955.diff (8 lines)
[INFO] [2021-05-31 19:37:28] Loading measurements diff file into memory (8 /app/public/diff/lindquist_et_al__measurements_3955.diff lines)...
[INFO] [2021-05-31 19:37:28] Storing 1 ScientificNames
[INFO] [2021-05-31 19:37:28] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:37:28] Average Time: 0.0
[INFO] [2021-05-31 19:37:28] Total Time: 1s
[INFO] [2021-05-31 19:37:28] Storing 1 Nodes
[INFO] [2021-05-31 19:37:28] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:37:28] Average Time: 0.0
[INFO] [2021-05-31 19:37:28] Total Time: 1s
[INFO] [2021-05-31 19:37:28] Storing 1 Occurrences
[INFO] [2021-05-31 19:37:28] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:37:28] Average Time: 0.0
[INFO] [2021-05-31 19:37:28] Total Time: 1s
[INFO] [2021-05-31 19:37:28] Storing 1 OccurrenceMetadata
[INFO] [2021-05-31 19:37:28] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:37:28] Average Time: 0.0
[INFO] [2021-05-31 19:37:28] Total Time: 1s
[INFO] [2021-05-31 19:37:28] Storing 6 Traits
[INFO] [2021-05-31 19:37:28] Processing group of 6 in 1 groups of 1000
[INFO] [2021-05-31 19:37:28] Average Time: 0.0
[INFO] [2021-05-31 19:37:28] Total Time: 1s
[INFO] [2021-05-31 19:37:28] Storing 5 MetaTraits
[INFO] [2021-05-31 19:37:28] Processing group of 5 in 1 groups of 1000
[INFO] [2021-05-31 19:37:28] Average Time: 0.0
[INFO] [2021-05-31 19:37:28] Total Time: 1s
[STOP] [2021-05-31 19:37:28] parse_diff_and_store
[START] [2021-05-31 19:37:28] resolve_keys
[INFO] [2021-05-31 19:37:34] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-31 19:37:34] traits to occurrences...
[INFO] [2021-05-31 19:37:34] traits to nodes (through occurrences)...
[INFO] [2021-05-31 19:37:34] Traits to sex term...
[INFO] [2021-05-31 19:37:34] Traits to lifestage term...
[INFO] [2021-05-31 19:37:34] MetaTraits to traits...
[INFO] [2021-05-31 19:37:34] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-31 19:37:34] Assocs to occurrences...
[INFO] [2021-05-31 19:37:34] Assocs to nodes...
[INFO] [2021-05-31 19:37:34] Assoc to sex term...
[INFO] [2021-05-31 19:37:34] Assoc to lifestage term...
[INFO] [2021-05-31 19:37:34] MetaAssoc to assocs...
[STOP] [2021-05-31 19:37:34] resolve_keys
[START] [2021-05-31 19:37:34] hold_for_later_1
[STOP] [2021-05-31 19:37:34] hold_for_later_1
[START] [2021-05-31 19:37:34] hold_for_later_2
[STOP] [2021-05-31 19:37:34] hold_for_later_2
[START] [2021-05-31 19:37:34] resolve_missing_parents
[STOP] [2021-05-31 19:37:34] resolve_missing_parents
[START] [2021-05-31 19:37:34] rebuild_nodes
[START] [2021-05-31 19:37:34] Flattener#flatten
[START] [2021-05-31 19:37:34] Flattener#study_resource
[START] [2021-05-31 19:37:34] Flattener#build_ancestry
[STOP] [2021-05-31 19:37:34] Flattener#build_ancestry
[INFO] [2021-05-31 19:37:34] 1 ancestry keys
[START] [2021-05-31 19:37:34] build_node_ancestors
[INFO] [2021-05-31 19:37:34] old ancestors deleted.
[STOP] [2021-05-31 19:37:34] build_node_ancestors
[WARN] [2021-05-31 19:37:34] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-05-31 19:37:34] Flattener#flatten
[STOP] [2021-05-31 19:37:34] rebuild_nodes
[START] [2021-05-31 19:37:34] resolve_missing_media_owners
[STOP] [2021-05-31 19:37:34] resolve_missing_media_owners
[START] [2021-05-31 19:37:34] sanitize_media_verbatims
[STOP] [2021-05-31 19:37:34] sanitize_media_verbatims
[START] [2021-05-31 19:37:34] queue_downloads
[STOP] [2021-05-31 19:37:34] queue_downloads
[START] [2021-05-31 19:37:34] parse_names
[WARN] [2021-05-31 19:37:34] I see 1 names which still need to be parsed.
[STOP] [2021-05-31 19:37:35] parse_names
[START] [2021-05-31 19:37:35] denormalize_canonical_names_to_nodes
[STOP] [2021-05-31 19:37:35] denormalize_canonical_names_to_nodes
[START] [2021-05-31 19:37:35] match_nodes
[START] [2021-05-31 19:37:35] map_all_nodes_to_pages
[STOP] [2021-05-31 19:37:35] map_all_nodes_to_pages
[INFO] [2021-05-31 19:37:35] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-05-31 19:37:35] update_nodes
[STOP] [2021-05-31 19:37:35] update_nodes
[STOP] [2021-05-31 19:37:35] match_nodes
[START] [2021-05-31 19:37:35] reindex_search
[STOP] [2021-05-31 19:37:35] reindex_search
[START] [2021-05-31 19:37:35] normalize_units
[STOP] [2021-05-31 19:37:35] normalize_units
[START] [2021-05-31 19:37:35] calculate_statistics
[2021-05-31 19:37:35] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-05-31 19:37:35] calculate_statistics
[START] [2021-05-31 19:37:35] complete_harvest_instance
[START] [2021-05-31 19:37:35] overall_tsv_creation
[INFO] [2021-05-31 19:37:36] Processing group of 1 in 1 batches of 10000
[INFO] [2021-05-31 19:38:07] 3 Traits (unfiltered)...
[INFO] [2021-05-31 19:38:31] 3 Traits (filtered)...
[INFO] [2021-05-31 19:38:31] 0 Associations (filtered)...
[INFO] [2021-05-31 19:38:31] 3 metadata added.
[INFO] [2021-05-31 19:38:31] 0 metadata added.
[INFO] [2021-05-31 19:38:54] Average Time: 56.9
[INFO] [2021-05-31 19:38:54] Total Time: 1m19s
[STOP] [2021-05-31 19:38:54] overall_tsv_creation
[INFO] [2021-05-31 19:38:54] Done. Check your files:
[INFO] [2021-05-31 19:38:54] (1 lines) /app/public/data/lindquist_et_al_/publish_nodes.tsv
[INFO] [2021-05-31 19:38:55] (1 lines) /app/public/data/lindquist_et_al_/publish_scientific_names.tsv
[INFO] [2021-05-31 19:38:55] (4 lines) /app/public/data/lindquist_et_al_/publish_traits.tsv
[INFO] [2021-05-31 19:38:55] (4 lines) /app/public/data/lindquist_et_al_/publish_metadata.tsv
[STOP] [2021-05-31 19:38:55] complete_harvest_instance
[START] [2021-05-31 19:38:55] completed
[STOP] [2021-05-31 19:38:55] completed
[STOP] [2021-05-31 19:38:55] logged process, took 96.46
Latest Process

31 May 19:37 EXITED currently processing 0