Harvest for Dooling et al 2000 Created 31 May 19:52

Stage: completed
Fetched: 31 May 19:52
Validated: 31 May 19:52
Deltas Created 31 May 19:52
Units Normalized: 31 May 19:52
Ancestry Built: 31 May 19:52
Nodes Matched: 31 May 19:52
Names Parsed: 31 May 19:52
New Models Stored: 31 May 19:52
Indexed: 31 May 19:52
Completed: 31 May 19:53
Time to Harvest: less than a minute

Harvesting Log

(168 lines)
[INFO] [2021-05-31 19:52:08] Created harvest instance #3961
[STOP] [2021-05-31 19:52:08] create_harvest_instance
[START] [2021-05-31 19:52:08] fetch_files
[STOP] [2021-05-31 19:52:08] fetch_files
[START] [2021-05-31 19:52:08] validate_each_file
[INFO] [2021-05-31 19:52:08] Looping over 4 formats...
[INFO] [2021-05-31 19:52:08] ...refs (/app/public/data/dooling_et_al_do/references.txt)
[INFO] [2021-05-31 19:52:08] Valid: /app/public/converted_csv/dooling_et_al_do_refs_3961.csv (19 lines)
[INFO] [2021-05-31 19:52:08] ...nodes (/app/public/data/dooling_et_al_do/taxa.txt)
[INFO] [2021-05-31 19:52:08] Valid: /app/public/converted_csv/dooling_et_al_do_nodes_3961.csv (19 lines)
[INFO] [2021-05-31 19:52:08] ...occurrences (/app/public/data/dooling_et_al_do/occurrences.txt)
[INFO] [2021-05-31 19:52:08] Valid: /app/public/converted_csv/dooling_et_al_do_occurrences_3961.csv (19 lines)
[INFO] [2021-05-31 19:52:08] ...measurements (/app/public/data/dooling_et_al_do/measurementsorfacts.txt)
[INFO] [2021-05-31 19:52:08] Valid: /app/public/converted_csv/dooling_et_al_do_measurements_3961.csv (206 lines)
[STOP] [2021-05-31 19:52:08] validate_each_file
[START] [2021-05-31 19:52:08] convert_to_csv
[INFO] [2021-05-31 19:52:08] Looping over 4 formats...
[INFO] [2021-05-31 19:52:08] ...refs (/app/public/data/dooling_et_al_do/references.txt)
[CMD] [2021-05-31 19:52:08] /usr/bin/sort /app/public/converted_csv/dooling_et_al_do_refs_3961.csv > /app/public/converted_csv/dooling_et_al_do_refs_3961.csv_sorted
[INFO] [2021-05-31 19:52:08] Converted: /app/public/converted_csv/dooling_et_al_do_refs_3961.csv (19 lines)
[INFO] [2021-05-31 19:52:08] ...nodes (/app/public/data/dooling_et_al_do/taxa.txt)
[CMD] [2021-05-31 19:52:08] /usr/bin/sort /app/public/converted_csv/dooling_et_al_do_nodes_3961.csv > /app/public/converted_csv/dooling_et_al_do_nodes_3961.csv_sorted
[INFO] [2021-05-31 19:52:09] Converted: /app/public/converted_csv/dooling_et_al_do_nodes_3961.csv (19 lines)
[INFO] [2021-05-31 19:52:09] ...occurrences (/app/public/data/dooling_et_al_do/occurrences.txt)
[CMD] [2021-05-31 19:52:09] /usr/bin/sort /app/public/converted_csv/dooling_et_al_do_occurrences_3961.csv > /app/public/converted_csv/dooling_et_al_do_occurrences_3961.csv_sorted
[INFO] [2021-05-31 19:52:09] Converted: /app/public/converted_csv/dooling_et_al_do_occurrences_3961.csv (19 lines)
[INFO] [2021-05-31 19:52:09] ...measurements (/app/public/data/dooling_et_al_do/measurementsorfacts.txt)
[CMD] [2021-05-31 19:52:09] /usr/bin/sort /app/public/converted_csv/dooling_et_al_do_measurements_3961.csv > /app/public/converted_csv/dooling_et_al_do_measurements_3961.csv_sorted
[INFO] [2021-05-31 19:52:09] Converted: /app/public/converted_csv/dooling_et_al_do_measurements_3961.csv (206 lines)
[STOP] [2021-05-31 19:52:09] convert_to_csv
[START] [2021-05-31 19:52:09] calculate_delta
[INFO] [2021-05-31 19:52:09] Looping over 4 formats...
[INFO] [2021-05-31 19:52:09] ...refs (/app/public/data/dooling_et_al_do/references.txt)
[CMD] [2021-05-31 19:52:09] echo "0a" > /app/public/diff/dooling_et_al_do_refs_3961.diff
[CMD] [2021-05-31 19:52:10] tail -n +1 /app/public/converted_csv/dooling_et_al_do_refs_3961.csv >> /app/public/diff/dooling_et_al_do_refs_3961.diff
[CMD] [2021-05-31 19:52:10] echo "." >> /app/public/diff/dooling_et_al_do_refs_3961.diff
[INFO] [2021-05-31 19:52:11] Created diff: /app/public/diff/dooling_et_al_do_refs_3961.diff (21 lines)
[INFO] [2021-05-31 19:52:11] ...nodes (/app/public/data/dooling_et_al_do/taxa.txt)
[CMD] [2021-05-31 19:52:11] echo "0a" > /app/public/diff/dooling_et_al_do_nodes_3961.diff
[CMD] [2021-05-31 19:52:11] tail -n +1 /app/public/converted_csv/dooling_et_al_do_nodes_3961.csv >> /app/public/diff/dooling_et_al_do_nodes_3961.diff
[CMD] [2021-05-31 19:52:11] echo "." >> /app/public/diff/dooling_et_al_do_nodes_3961.diff
[INFO] [2021-05-31 19:52:12] Created diff: /app/public/diff/dooling_et_al_do_nodes_3961.diff (21 lines)
[INFO] [2021-05-31 19:52:12] ...occurrences (/app/public/data/dooling_et_al_do/occurrences.txt)
[CMD] [2021-05-31 19:52:12] echo "0a" > /app/public/diff/dooling_et_al_do_occurrences_3961.diff
[CMD] [2021-05-31 19:52:12] tail -n +1 /app/public/converted_csv/dooling_et_al_do_occurrences_3961.csv >> /app/public/diff/dooling_et_al_do_occurrences_3961.diff
[CMD] [2021-05-31 19:52:12] echo "." >> /app/public/diff/dooling_et_al_do_occurrences_3961.diff
[INFO] [2021-05-31 19:52:13] Created diff: /app/public/diff/dooling_et_al_do_occurrences_3961.diff (21 lines)
[INFO] [2021-05-31 19:52:13] ...measurements (/app/public/data/dooling_et_al_do/measurementsorfacts.txt)
[CMD] [2021-05-31 19:52:13] echo "0a" > /app/public/diff/dooling_et_al_do_measurements_3961.diff
[CMD] [2021-05-31 19:52:13] tail -n +1 /app/public/converted_csv/dooling_et_al_do_measurements_3961.csv >> /app/public/diff/dooling_et_al_do_measurements_3961.diff
[CMD] [2021-05-31 19:52:14] echo "." >> /app/public/diff/dooling_et_al_do_measurements_3961.diff
[INFO] [2021-05-31 19:52:14] Created diff: /app/public/diff/dooling_et_al_do_measurements_3961.diff (208 lines)
[STOP] [2021-05-31 19:52:14] calculate_delta
[START] [2021-05-31 19:52:14] parse_diff_and_store
[INFO] [2021-05-31 19:52:14] Handling diff: /app/public/diff/dooling_et_al_do_refs_3961.diff (21 lines)
[INFO] [2021-05-31 19:52:14] Loading refs diff file into memory (21 /app/public/diff/dooling_et_al_do_refs_3961.diff lines)...
[INFO] [2021-05-31 19:52:15] Handling diff: /app/public/diff/dooling_et_al_do_nodes_3961.diff (21 lines)
[INFO] [2021-05-31 19:52:15] Loading nodes diff file into memory (21 /app/public/diff/dooling_et_al_do_nodes_3961.diff lines)...
[INFO] [2021-05-31 19:52:15] Handling diff: /app/public/diff/dooling_et_al_do_occurrences_3961.diff (21 lines)
[INFO] [2021-05-31 19:52:16] Loading occurrences diff file into memory (21 /app/public/diff/dooling_et_al_do_occurrences_3961.diff lines)...
[INFO] [2021-05-31 19:52:16] Handling diff: /app/public/diff/dooling_et_al_do_measurements_3961.diff (208 lines)
[INFO] [2021-05-31 19:52:17] Loading measurements diff file into memory (208 /app/public/diff/dooling_et_al_do_measurements_3961.diff lines)...
[INFO] [2021-05-31 19:52:17] Storing 19 References
[INFO] [2021-05-31 19:52:17] Processing group of 19 in 1 groups of 1000
[INFO] [2021-05-31 19:52:17] Average Time: 0.01
[INFO] [2021-05-31 19:52:17] Total Time: 1s
[INFO] [2021-05-31 19:52:17] Storing 19 ScientificNames
[INFO] [2021-05-31 19:52:17] Processing group of 19 in 1 groups of 1000
[INFO] [2021-05-31 19:52:17] Average Time: 0.01
[INFO] [2021-05-31 19:52:17] Total Time: 1s
[INFO] [2021-05-31 19:52:17] Storing 19 Nodes
[INFO] [2021-05-31 19:52:17] Processing group of 19 in 1 groups of 1000
[INFO] [2021-05-31 19:52:17] Average Time: 0.01
[INFO] [2021-05-31 19:52:17] Total Time: 1s
[INFO] [2021-05-31 19:52:17] Storing 19 Occurrences
[INFO] [2021-05-31 19:52:17] Processing group of 19 in 1 groups of 1000
[INFO] [2021-05-31 19:52:17] Average Time: 0.0
[INFO] [2021-05-31 19:52:17] Total Time: 1s
[INFO] [2021-05-31 19:52:17] Storing 147 TraitsReferences
[INFO] [2021-05-31 19:52:17] Processing group of 147 in 1 groups of 1000
[INFO] [2021-05-31 19:52:17] Average Time: 0.04
[INFO] [2021-05-31 19:52:17] Total Time: 1s
[INFO] [2021-05-31 19:52:17] Storing 206 Traits
[INFO] [2021-05-31 19:52:17] Processing group of 206 in 1 groups of 1000
[INFO] [2021-05-31 19:52:17] Average Time: 0.08
[INFO] [2021-05-31 19:52:17] Total Time: 1s
[INFO] [2021-05-31 19:52:17] Storing 149 MetaTraits
[INFO] [2021-05-31 19:52:17] Processing group of 149 in 1 groups of 1000
[INFO] [2021-05-31 19:52:17] Average Time: 0.02
[INFO] [2021-05-31 19:52:17] Total Time: 1s
[STOP] [2021-05-31 19:52:17] parse_diff_and_store
[START] [2021-05-31 19:52:17] resolve_keys
[INFO] [2021-05-31 19:52:23] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-31 19:52:23] traits to occurrences...
[INFO] [2021-05-31 19:52:23] traits to nodes (through occurrences)...
[INFO] [2021-05-31 19:52:23] Traits to sex term...
[INFO] [2021-05-31 19:52:23] Traits to lifestage term...
[INFO] [2021-05-31 19:52:23] MetaTraits to traits...
[INFO] [2021-05-31 19:52:23] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-31 19:52:23] Assocs to occurrences...
[INFO] [2021-05-31 19:52:23] Assocs to nodes...
[INFO] [2021-05-31 19:52:23] Assoc to sex term...
[INFO] [2021-05-31 19:52:23] Assoc to lifestage term...
[INFO] [2021-05-31 19:52:23] MetaAssoc to assocs...
[STOP] [2021-05-31 19:52:23] resolve_keys
[START] [2021-05-31 19:52:23] hold_for_later_1
[STOP] [2021-05-31 19:52:23] hold_for_later_1
[START] [2021-05-31 19:52:23] hold_for_later_2
[STOP] [2021-05-31 19:52:23] hold_for_later_2
[START] [2021-05-31 19:52:23] resolve_missing_parents
[STOP] [2021-05-31 19:52:23] resolve_missing_parents
[START] [2021-05-31 19:52:23] rebuild_nodes
[START] [2021-05-31 19:52:23] Flattener#flatten
[START] [2021-05-31 19:52:23] Flattener#study_resource
[START] [2021-05-31 19:52:23] Flattener#build_ancestry
[STOP] [2021-05-31 19:52:23] Flattener#build_ancestry
[INFO] [2021-05-31 19:52:23] 19 ancestry keys
[START] [2021-05-31 19:52:23] build_node_ancestors
[INFO] [2021-05-31 19:52:23] old ancestors deleted.
[STOP] [2021-05-31 19:52:23] build_node_ancestors
[WARN] [2021-05-31 19:52:23] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-05-31 19:52:23] Flattener#flatten
[STOP] [2021-05-31 19:52:23] rebuild_nodes
[START] [2021-05-31 19:52:23] resolve_missing_media_owners
[STOP] [2021-05-31 19:52:23] resolve_missing_media_owners
[START] [2021-05-31 19:52:23] sanitize_media_verbatims
[STOP] [2021-05-31 19:52:23] sanitize_media_verbatims
[START] [2021-05-31 19:52:23] queue_downloads
[STOP] [2021-05-31 19:52:23] queue_downloads
[START] [2021-05-31 19:52:23] parse_names
[WARN] [2021-05-31 19:52:23] I see 19 names which still need to be parsed.
[STOP] [2021-05-31 19:52:24] parse_names
[START] [2021-05-31 19:52:24] denormalize_canonical_names_to_nodes
[STOP] [2021-05-31 19:52:24] denormalize_canonical_names_to_nodes
[START] [2021-05-31 19:52:24] match_nodes
[START] [2021-05-31 19:52:24] map_all_nodes_to_pages
[STOP] [2021-05-31 19:52:24] map_all_nodes_to_pages
[INFO] [2021-05-31 19:52:24] ZERO unmatched nodes (of 19)! Nicely done.
[START] [2021-05-31 19:52:24] update_nodes
[STOP] [2021-05-31 19:52:24] update_nodes
[STOP] [2021-05-31 19:52:24] match_nodes
[START] [2021-05-31 19:52:24] reindex_search
[STOP] [2021-05-31 19:52:24] reindex_search
[START] [2021-05-31 19:52:24] normalize_units
[STOP] [2021-05-31 19:52:25] normalize_units
[START] [2021-05-31 19:52:25] calculate_statistics
[2021-05-31 19:52:25] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-05-31 19:52:25] calculate_statistics
[START] [2021-05-31 19:52:25] complete_harvest_instance
[START] [2021-05-31 19:52:25] overall_tsv_creation
[INFO] [2021-05-31 19:52:25] Processing group of 19 in 1 batches of 10000
[INFO] [2021-05-31 19:52:57] 75 Traits (unfiltered)...
[INFO] [2021-05-31 19:53:23] 75 Traits (filtered)...
[INFO] [2021-05-31 19:53:23] 0 Associations (filtered)...
[INFO] [2021-05-31 19:53:23] 274 metadata added.
[INFO] [2021-05-31 19:53:23] 0 metadata added.
[INFO] [2021-05-31 19:53:45] Average Time: 58.93
[INFO] [2021-05-31 19:53:45] Total Time: 1m21s
[STOP] [2021-05-31 19:53:45] overall_tsv_creation
[INFO] [2021-05-31 19:53:45] Done. Check your files:
[INFO] [2021-05-31 19:53:46] (19 lines) /app/public/data/dooling_et_al_do/publish_nodes.tsv
[INFO] [2021-05-31 19:53:46] (19 lines) /app/public/data/dooling_et_al_do/publish_scientific_names.tsv
[INFO] [2021-05-31 19:53:46] (76 lines) /app/public/data/dooling_et_al_do/publish_traits.tsv
[INFO] [2021-05-31 19:53:47] (275 lines) /app/public/data/dooling_et_al_do/publish_metadata.tsv
[STOP] [2021-05-31 19:53:47] complete_harvest_instance
[START] [2021-05-31 19:53:47] completed
[STOP] [2021-05-31 19:53:47] completed
[STOP] [2021-05-31 19:53:47] logged process, took 99.56

Latest Process