Harvest for Da Silva et al 2020 Created 31 May 19:50

Stage: completed
Fetched: 31 May 19:50
Validated: 31 May 19:50
Deltas Created 31 May 19:50
Units Normalized: 31 May 19:50
Ancestry Built: 31 May 19:50
Nodes Matched: 31 May 19:50
Names Parsed: 31 May 19:50
New Models Stored: 31 May 19:50
Indexed: 31 May 19:50
Completed: 31 May 19:52
Time to Harvest: less than a minute
Harvesting Log

(148 lines)
[INFO] [2021-05-31 19:50:28] Created harvest instance #3960
[STOP] [2021-05-31 19:50:28] create_harvest_instance
[START] [2021-05-31 19:50:28] fetch_files
[STOP] [2021-05-31 19:50:28] fetch_files
[START] [2021-05-31 19:50:29] validate_each_file
[INFO] [2021-05-31 19:50:29] Looping over 3 formats...
[INFO] [2021-05-31 19:50:29] ...nodes (/app/public/data/dsead/taxa.txt)
[INFO] [2021-05-31 19:50:29] Valid: /app/public/converted_csv/dsead_nodes_3960.csv (44 lines)
[INFO] [2021-05-31 19:50:29] ...occurrences (/app/public/data/dsead/occurrences.txt)
[INFO] [2021-05-31 19:50:29] Valid: /app/public/converted_csv/dsead_occurrences_3960.csv (44 lines)
[INFO] [2021-05-31 19:50:29] ...measurements (/app/public/data/dsead/measurementsorfacts.txt)
[INFO] [2021-05-31 19:50:29] Valid: /app/public/converted_csv/dsead_measurements_3960.csv (220 lines)
[STOP] [2021-05-31 19:50:29] validate_each_file
[START] [2021-05-31 19:50:29] convert_to_csv
[INFO] [2021-05-31 19:50:29] Looping over 3 formats...
[INFO] [2021-05-31 19:50:29] ...nodes (/app/public/data/dsead/taxa.txt)
[CMD] [2021-05-31 19:50:29] /usr/bin/sort /app/public/converted_csv/dsead_nodes_3960.csv > /app/public/converted_csv/dsead_nodes_3960.csv_sorted
[INFO] [2021-05-31 19:50:29] Converted: /app/public/converted_csv/dsead_nodes_3960.csv (44 lines)
[INFO] [2021-05-31 19:50:29] ...occurrences (/app/public/data/dsead/occurrences.txt)
[CMD] [2021-05-31 19:50:29] /usr/bin/sort /app/public/converted_csv/dsead_occurrences_3960.csv > /app/public/converted_csv/dsead_occurrences_3960.csv_sorted
[INFO] [2021-05-31 19:50:29] Converted: /app/public/converted_csv/dsead_occurrences_3960.csv (44 lines)
[INFO] [2021-05-31 19:50:29] ...measurements (/app/public/data/dsead/measurementsorfacts.txt)
[CMD] [2021-05-31 19:50:29] /usr/bin/sort /app/public/converted_csv/dsead_measurements_3960.csv > /app/public/converted_csv/dsead_measurements_3960.csv_sorted
[INFO] [2021-05-31 19:50:30] Converted: /app/public/converted_csv/dsead_measurements_3960.csv (220 lines)
[STOP] [2021-05-31 19:50:30] convert_to_csv
[START] [2021-05-31 19:50:30] calculate_delta
[INFO] [2021-05-31 19:50:30] Looping over 3 formats...
[INFO] [2021-05-31 19:50:30] ...nodes (/app/public/data/dsead/taxa.txt)
[CMD] [2021-05-31 19:50:30] echo "0a" > /app/public/diff/dsead_nodes_3960.diff
[CMD] [2021-05-31 19:50:30] tail -n +1 /app/public/converted_csv/dsead_nodes_3960.csv >> /app/public/diff/dsead_nodes_3960.diff
[CMD] [2021-05-31 19:50:30] echo "." >> /app/public/diff/dsead_nodes_3960.diff
[INFO] [2021-05-31 19:50:31] Created diff: /app/public/diff/dsead_nodes_3960.diff (46 lines)
[INFO] [2021-05-31 19:50:31] ...occurrences (/app/public/data/dsead/occurrences.txt)
[CMD] [2021-05-31 19:50:31] echo "0a" > /app/public/diff/dsead_occurrences_3960.diff
[CMD] [2021-05-31 19:50:31] tail -n +1 /app/public/converted_csv/dsead_occurrences_3960.csv >> /app/public/diff/dsead_occurrences_3960.diff
[CMD] [2021-05-31 19:50:32] echo "." >> /app/public/diff/dsead_occurrences_3960.diff
[INFO] [2021-05-31 19:50:32] Created diff: /app/public/diff/dsead_occurrences_3960.diff (46 lines)
[INFO] [2021-05-31 19:50:32] ...measurements (/app/public/data/dsead/measurementsorfacts.txt)
[CMD] [2021-05-31 19:50:32] echo "0a" > /app/public/diff/dsead_measurements_3960.diff
[CMD] [2021-05-31 19:50:32] tail -n +1 /app/public/converted_csv/dsead_measurements_3960.csv >> /app/public/diff/dsead_measurements_3960.diff
[CMD] [2021-05-31 19:50:33] echo "." >> /app/public/diff/dsead_measurements_3960.diff
[INFO] [2021-05-31 19:50:33] Created diff: /app/public/diff/dsead_measurements_3960.diff (222 lines)
[STOP] [2021-05-31 19:50:33] calculate_delta
[START] [2021-05-31 19:50:33] parse_diff_and_store
[INFO] [2021-05-31 19:50:33] Handling diff: /app/public/diff/dsead_nodes_3960.diff (46 lines)
[INFO] [2021-05-31 19:50:33] Loading nodes diff file into memory (46 /app/public/diff/dsead_nodes_3960.diff lines)...
[INFO] [2021-05-31 19:50:34] Handling diff: /app/public/diff/dsead_occurrences_3960.diff (46 lines)
[INFO] [2021-05-31 19:50:34] Loading occurrences diff file into memory (46 /app/public/diff/dsead_occurrences_3960.diff lines)...
[INFO] [2021-05-31 19:50:34] Handling diff: /app/public/diff/dsead_measurements_3960.diff (222 lines)
[INFO] [2021-05-31 19:50:35] Loading measurements diff file into memory (222 /app/public/diff/dsead_measurements_3960.diff lines)...
[INFO] [2021-05-31 19:50:35] Storing 44 ScientificNames
[INFO] [2021-05-31 19:50:35] Processing group of 44 in 1 groups of 1000
[INFO] [2021-05-31 19:50:35] Average Time: 0.01
[INFO] [2021-05-31 19:50:35] Total Time: 1s
[INFO] [2021-05-31 19:50:35] Storing 44 Nodes
[INFO] [2021-05-31 19:50:35] Processing group of 44 in 1 groups of 1000
[INFO] [2021-05-31 19:50:35] Average Time: 0.01
[INFO] [2021-05-31 19:50:35] Total Time: 1s
[INFO] [2021-05-31 19:50:35] Storing 44 Occurrences
[INFO] [2021-05-31 19:50:35] Processing group of 44 in 1 groups of 1000
[INFO] [2021-05-31 19:50:35] Average Time: 0.01
[INFO] [2021-05-31 19:50:35] Total Time: 1s
[INFO] [2021-05-31 19:50:35] Storing 220 Traits
[INFO] [2021-05-31 19:50:35] Processing group of 220 in 1 groups of 1000
[INFO] [2021-05-31 19:50:35] Average Time: 0.07
[INFO] [2021-05-31 19:50:35] Total Time: 1s
[INFO] [2021-05-31 19:50:35] Storing 132 MetaTraits
[INFO] [2021-05-31 19:50:35] Processing group of 132 in 1 groups of 1000
[INFO] [2021-05-31 19:50:35] Average Time: 0.02
[INFO] [2021-05-31 19:50:35] Total Time: 1s
[STOP] [2021-05-31 19:50:35] parse_diff_and_store
[START] [2021-05-31 19:50:36] resolve_keys
[INFO] [2021-05-31 19:50:41] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-31 19:50:41] traits to occurrences...
[INFO] [2021-05-31 19:50:41] traits to nodes (through occurrences)...
[INFO] [2021-05-31 19:50:41] Traits to sex term...
[INFO] [2021-05-31 19:50:41] Traits to lifestage term...
[INFO] [2021-05-31 19:50:41] MetaTraits to traits...
[INFO] [2021-05-31 19:50:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-31 19:50:41] Assocs to occurrences...
[INFO] [2021-05-31 19:50:41] Assocs to nodes...
[INFO] [2021-05-31 19:50:41] Assoc to sex term...
[INFO] [2021-05-31 19:50:41] Assoc to lifestage term...
[INFO] [2021-05-31 19:50:41] MetaAssoc to assocs...
[STOP] [2021-05-31 19:50:41] resolve_keys
[START] [2021-05-31 19:50:41] hold_for_later_1
[STOP] [2021-05-31 19:50:41] hold_for_later_1
[START] [2021-05-31 19:50:41] hold_for_later_2
[STOP] [2021-05-31 19:50:41] hold_for_later_2
[START] [2021-05-31 19:50:41] resolve_missing_parents
[STOP] [2021-05-31 19:50:41] resolve_missing_parents
[START] [2021-05-31 19:50:41] rebuild_nodes
[START] [2021-05-31 19:50:41] Flattener#flatten
[START] [2021-05-31 19:50:41] Flattener#study_resource
[START] [2021-05-31 19:50:41] Flattener#build_ancestry
[STOP] [2021-05-31 19:50:41] Flattener#build_ancestry
[INFO] [2021-05-31 19:50:41] 44 ancestry keys
[START] [2021-05-31 19:50:41] build_node_ancestors
[INFO] [2021-05-31 19:50:41] old ancestors deleted.
[STOP] [2021-05-31 19:50:41] build_node_ancestors
[WARN] [2021-05-31 19:50:41] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-05-31 19:50:41] Flattener#flatten
[STOP] [2021-05-31 19:50:41] rebuild_nodes
[START] [2021-05-31 19:50:41] resolve_missing_media_owners
[STOP] [2021-05-31 19:50:41] resolve_missing_media_owners
[START] [2021-05-31 19:50:41] sanitize_media_verbatims
[STOP] [2021-05-31 19:50:41] sanitize_media_verbatims
[START] [2021-05-31 19:50:41] queue_downloads
[STOP] [2021-05-31 19:50:41] queue_downloads
[START] [2021-05-31 19:50:41] parse_names
[WARN] [2021-05-31 19:50:41] I see 44 names which still need to be parsed.
[STOP] [2021-05-31 19:50:43] parse_names
[START] [2021-05-31 19:50:43] denormalize_canonical_names_to_nodes
[STOP] [2021-05-31 19:50:43] denormalize_canonical_names_to_nodes
[START] [2021-05-31 19:50:43] match_nodes
[START] [2021-05-31 19:50:43] map_all_nodes_to_pages
[STOP] [2021-05-31 19:50:43] map_all_nodes_to_pages
[INFO] [2021-05-31 19:50:43] ZERO unmatched nodes (of 44)! Nicely done.
[START] [2021-05-31 19:50:43] update_nodes
[STOP] [2021-05-31 19:50:43] update_nodes
[STOP] [2021-05-31 19:50:43] match_nodes
[START] [2021-05-31 19:50:43] reindex_search
[STOP] [2021-05-31 19:50:43] reindex_search
[START] [2021-05-31 19:50:43] normalize_units
[STOP] [2021-05-31 19:50:43] normalize_units
[START] [2021-05-31 19:50:43] calculate_statistics
[2021-05-31 19:50:43] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-05-31 19:50:43] calculate_statistics
[START] [2021-05-31 19:50:43] complete_harvest_instance
[START] [2021-05-31 19:50:43] overall_tsv_creation
[INFO] [2021-05-31 19:50:43] Processing group of 44 in 1 batches of 10000
[INFO] [2021-05-31 19:51:16] 132 Traits (unfiltered)...
[INFO] [2021-05-31 19:51:42] 132 Traits (filtered)...
[INFO] [2021-05-31 19:51:42] 0 Associations (filtered)...
[INFO] [2021-05-31 19:51:42] 44 metadata added.
[INFO] [2021-05-31 19:51:42] 0 metadata added.
[INFO] [2021-05-31 19:52:06] Average Time: 60.8
[INFO] [2021-05-31 19:52:06] Total Time: 1m23s
[STOP] [2021-05-31 19:52:06] overall_tsv_creation
[INFO] [2021-05-31 19:52:06] Done. Check your files:
[INFO] [2021-05-31 19:52:06] (44 lines) /app/public/data/dsead/publish_nodes.tsv
[INFO] [2021-05-31 19:52:06] (44 lines) /app/public/data/dsead/publish_scientific_names.tsv
[INFO] [2021-05-31 19:52:07] (133 lines) /app/public/data/dsead/publish_traits.tsv
[INFO] [2021-05-31 19:52:07] (45 lines) /app/public/data/dsead/publish_metadata.tsv
[STOP] [2021-05-31 19:52:07] complete_harvest_instance
[START] [2021-05-31 19:52:07] completed
[STOP] [2021-05-31 19:52:07] completed
[STOP] [2021-05-31 19:52:07] logged process, took 99.03
Latest Process

31 May 19:50 EXITED currently processing 0