Harvest for Stewart 1970 Created 15 Apr 10:08

Stage: completed
Fetched: 15 Apr 10:08
Validated: 15 Apr 10:08
Deltas Created 15 Apr 10:09
Units Normalized: 15 Apr 10:09
Ancestry Built: 15 Apr 10:09
Nodes Matched: 15 Apr 10:09
Names Parsed: 15 Apr 10:09
New Models Stored: 15 Apr 10:09
Indexed: 15 Apr 10:09
Completed: 15 Apr 10:11
Time to Harvest: less than a minute
Harvesting Log

(140 lines)
# Logfile created on 2020-04-15 10:08:41 -0400 by logger.rb/v1.4.2
[INFO] [2020-04-15 10:08:41] ## HARVEST: type = -harvest
[START] [2020-04-15 10:08:43] logged process
[START] [2020-04-15 10:08:43] create_harvest_instance
[STOP] [2020-04-15 10:08:44] create_harvest_instance
[START] [2020-04-15 10:08:44] fetch_files
[STOP] [2020-04-15 10:08:44] fetch_files
[START] [2020-04-15 10:08:44] validate_each_file
[STOP] [2020-04-15 10:08:45] validate_each_file
[START] [2020-04-15 10:08:45] convert_to_csv
[CMD] [2020-04-15 10:08:45] /usr/bin/sort /app/public/converted_csv/stewart_stewart__refs_20767.csv > /app/public/converted_csv/stewart_stewart__refs_20767.csv_sorted
[CMD] [2020-04-15 10:08:46] /usr/bin/sort /app/public/converted_csv/stewart_stewart__nodes_20768.csv > /app/public/converted_csv/stewart_stewart__nodes_20768.csv_sorted
[CMD] [2020-04-15 10:08:47] /usr/bin/sort /app/public/converted_csv/stewart_stewart__occurrences_20769.csv > /app/public/converted_csv/stewart_stewart__occurrences_20769.csv_sorted
[CMD] [2020-04-15 10:08:48] /usr/bin/sort /app/public/converted_csv/stewart_stewart__measurements_20770.csv > /app/public/converted_csv/stewart_stewart__measurements_20770.csv_sorted
[STOP] [2020-04-15 10:08:50] convert_to_csv
[START] [2020-04-15 10:08:50] calculate_delta
[CMD] [2020-04-15 10:08:50] echo "0a" > /app/public/diff/stewart_stewart__refs_20767.diff
[CMD] [2020-04-15 10:08:51] tail -n +1 /app/public/converted_csv/stewart_stewart__refs_20767.csv >> /app/public/diff/stewart_stewart__refs_20767.diff
[CMD] [2020-04-15 10:08:52] echo "." >> /app/public/diff/stewart_stewart__refs_20767.diff
[CMD] [2020-04-15 10:08:54] echo "0a" > /app/public/diff/stewart_stewart__nodes_20768.diff
[CMD] [2020-04-15 10:08:55] tail -n +1 /app/public/converted_csv/stewart_stewart__nodes_20768.csv >> /app/public/diff/stewart_stewart__nodes_20768.diff
[CMD] [2020-04-15 10:08:56] echo "." >> /app/public/diff/stewart_stewart__nodes_20768.diff
[CMD] [2020-04-15 10:08:57] echo "0a" > /app/public/diff/stewart_stewart__occurrences_20769.diff
[CMD] [2020-04-15 10:08:59] tail -n +1 /app/public/converted_csv/stewart_stewart__occurrences_20769.csv >> /app/public/diff/stewart_stewart__occurrences_20769.diff
[CMD] [2020-04-15 10:09:00] echo "." >> /app/public/diff/stewart_stewart__occurrences_20769.diff
[CMD] [2020-04-15 10:09:01] echo "0a" > /app/public/diff/stewart_stewart__measurements_20770.diff
[CMD] [2020-04-15 10:09:02] tail -n +1 /app/public/converted_csv/stewart_stewart__measurements_20770.csv >> /app/public/diff/stewart_stewart__measurements_20770.diff
[CMD] [2020-04-15 10:09:04] echo "." >> /app/public/diff/stewart_stewart__measurements_20770.diff
[STOP] [2020-04-15 10:09:05] calculate_delta
[START] [2020-04-15 10:09:05] parse_diff_and_store
[INFO] [2020-04-15 10:09:06] Loading refs diff file into memory (true lines)...
[INFO] [2020-04-15 10:09:07] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-15 10:09:09] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-15 10:09:10] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-15 10:09:10] Storing 24 References
[INFO] [2020-04-15 10:09:10] Processing group of 24 in 1 groups of 1000
[INFO] [2020-04-15 10:09:10] Average Time: 0.01
[INFO] [2020-04-15 10:09:10] Total Time: 1s
[INFO] [2020-04-15 10:09:10] Storing 40 ScientificNames
[INFO] [2020-04-15 10:09:10] Processing group of 40 in 1 groups of 1000
[INFO] [2020-04-15 10:09:10] Average Time: 0.02
[INFO] [2020-04-15 10:09:10] Total Time: 1s
[INFO] [2020-04-15 10:09:10] Storing 40 Nodes
[INFO] [2020-04-15 10:09:10] Processing group of 40 in 1 groups of 1000
[INFO] [2020-04-15 10:09:10] Average Time: 0.02
[INFO] [2020-04-15 10:09:10] Total Time: 1s
[INFO] [2020-04-15 10:09:10] Storing 40 Occurrences
[INFO] [2020-04-15 10:09:10] Processing group of 40 in 1 groups of 1000
[INFO] [2020-04-15 10:09:10] Average Time: 0.01
[INFO] [2020-04-15 10:09:10] Total Time: 1s
[INFO] [2020-04-15 10:09:10] Storing 47 TraitsReferences
[INFO] [2020-04-15 10:09:10] Processing group of 47 in 1 groups of 1000
[INFO] [2020-04-15 10:09:10] Average Time: 0.02
[INFO] [2020-04-15 10:09:10] Total Time: 1s
[INFO] [2020-04-15 10:09:10] Storing 40 Traits
[INFO] [2020-04-15 10:09:10] Processing group of 40 in 1 groups of 1000
[INFO] [2020-04-15 10:09:10] Average Time: 0.01
[INFO] [2020-04-15 10:09:10] Total Time: 1s
[INFO] [2020-04-15 10:09:10] Storing 120 MetaTraits
[INFO] [2020-04-15 10:09:10] Processing group of 120 in 1 groups of 1000
[INFO] [2020-04-15 10:09:10] Average Time: 0.02
[INFO] [2020-04-15 10:09:10] Total Time: 1s
[STOP] [2020-04-15 10:09:10] parse_diff_and_store
[START] [2020-04-15 10:09:10] resolve_keys
[INFO] [2020-04-15 10:09:15] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-15 10:09:15] traits to occurrences...
[INFO] [2020-04-15 10:09:15] traits to nodes (through occurrences)...
[INFO] [2020-04-15 10:09:15] Traits to sex term...
[INFO] [2020-04-15 10:09:15] Traits to lifestage term...
[INFO] [2020-04-15 10:09:15] MetaTraits to traits...
[INFO] [2020-04-15 10:09:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-15 10:09:16] Assocs to occurrences...
[INFO] [2020-04-15 10:09:16] Assocs to nodes...
[INFO] [2020-04-15 10:09:16] Assoc to sex term...
[INFO] [2020-04-15 10:09:16] Assoc to lifestage term...
[STOP] [2020-04-15 10:09:16] resolve_keys
[START] [2020-04-15 10:09:16] hold_for_later_1
[STOP] [2020-04-15 10:09:16] hold_for_later_1
[START] [2020-04-15 10:09:16] hold_for_later_2
[STOP] [2020-04-15 10:09:16] hold_for_later_2
[START] [2020-04-15 10:09:16] resolve_missing_parents
[STOP] [2020-04-15 10:09:16] resolve_missing_parents
[START] [2020-04-15 10:09:16] rebuild_nodes
[START] [2020-04-15 10:09:16] Flattener#flatten
[START] [2020-04-15 10:09:16] Flattener#study_resource
[START] [2020-04-15 10:09:16] Flattener#build_ancestry
[STOP] [2020-04-15 10:09:16] Flattener#build_ancestry
[INFO] [2020-04-15 10:09:16] 40 ancestry keys
[START] [2020-04-15 10:09:16] build_node_ancestors
[INFO] [2020-04-15 10:09:16] old ancestors deleted.
[STOP] [2020-04-15 10:09:16] build_node_ancestors
[WARN] [2020-04-15 10:09:16] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-15 10:09:16] Flattener#flatten
[STOP] [2020-04-15 10:09:16] rebuild_nodes
[START] [2020-04-15 10:09:16] resolve_missing_media_owners
[STOP] [2020-04-15 10:09:16] resolve_missing_media_owners
[START] [2020-04-15 10:09:16] sanitize_media_verbatims
[STOP] [2020-04-15 10:09:16] sanitize_media_verbatims
[START] [2020-04-15 10:09:16] queue_downloads
[STOP] [2020-04-15 10:09:16] queue_downloads
[START] [2020-04-15 10:09:16] parse_names
[WARN] [2020-04-15 10:09:16] I see 40 names which still need to be parsed.
[WARN] [2020-04-15 10:09:17] I see 1 names which still need to be parsed.
[STOP] [2020-04-15 10:09:18] parse_names
[START] [2020-04-15 10:09:18] denormalize_canonical_names_to_nodes
[STOP] [2020-04-15 10:09:18] denormalize_canonical_names_to_nodes
[START] [2020-04-15 10:09:18] match_nodes
[START] [2020-04-15 10:09:18] map_all_nodes_to_pages
[STOP] [2020-04-15 10:09:18] map_all_nodes_to_pages
[INFO] [2020-04-15 10:09:18] Unmatched nodes (3 of 40): Aulosira feryilissima (#68875764); Cylindrospermum gorakhporense (#68875771); Cylindrospermum sphaerica (#68875774)
[START] [2020-04-15 10:09:18] update_nodes
[STOP] [2020-04-15 10:09:18] update_nodes
[STOP] [2020-04-15 10:09:18] match_nodes
[START] [2020-04-15 10:09:18] reindex_search
[STOP] [2020-04-15 10:09:18] reindex_search
[START] [2020-04-15 10:09:18] normalize_units
[STOP] [2020-04-15 10:09:18] normalize_units
[START] [2020-04-15 10:09:18] calculate_statistics
[2020-04-15 10:09:18] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-15 10:09:18] calculate_statistics
[START] [2020-04-15 10:09:18] complete_harvest_instance
[START] [2020-04-15 10:09:18] overall_tsv_creation
[INFO] [2020-04-15 10:09:18] Processing group of 40 in 1 batches of 10000
[INFO] [2020-04-15 10:10:10] 40 Traits (unfiltered)...
[INFO] [2020-04-15 10:10:23] 40 Traits (filtered)...
[INFO] [2020-04-15 10:10:23] 0 Associations (filtered)...
[INFO] [2020-04-15 10:10:59] 167 metadata added.
[INFO] [2020-04-15 10:10:59] 0 metadata added.
[INFO] [2020-04-15 10:10:59] Average Time: 71.48
[INFO] [2020-04-15 10:10:59] Total Time: 1m41s
[STOP] [2020-04-15 10:10:59] overall_tsv_creation
[INFO] [2020-04-15 10:10:59] Done. Check your files:
[INFO] [2020-04-15 10:11:00] (39 lines) /app/public/data/stewart_stewart_/publish_nodes.tsv
[INFO] [2020-04-15 10:11:01] (40 lines) /app/public/data/stewart_stewart_/publish_scientific_names.tsv
[INFO] [2020-04-15 10:11:03] (41 lines) /app/public/data/stewart_stewart_/publish_traits.tsv
[INFO] [2020-04-15 10:11:04] (168 lines) /app/public/data/stewart_stewart_/publish_metadata.tsv
[STOP] [2020-04-15 10:11:04] complete_harvest_instance
[START] [2020-04-15 10:11:04] completed
[STOP] [2020-04-15 10:11:04] completed
[STOP] [2020-04-15 10:11:04] logged process, took 140.62
Latest Process

15 Apr 10:08 EXITED currently processing 0