Harvest for Tajikistan Species List Created 16 Oct 11:15

Stage: completed
Fetched: 16 Oct 11:15
Validated: 16 Oct 11:15
Deltas Created 16 Oct 11:15
Units Normalized: 16 Oct 11:19
Ancestry Built: 16 Oct 11:15
Nodes Matched: 16 Oct 11:19
Names Parsed: 16 Oct 11:16
New Models Stored: 16 Oct 11:15
Indexed: 16 Oct 11:19
Completed: 16 Oct 11:21
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-16 11:15:11 -0400 by logger.rb/56815
[START] [2019-10-16 11:15:11] logged process
[START] [2019-10-16 11:15:11] create_harvest_instance
[STOP] [2019-10-16 11:15:12] create_harvest_instance
[START] [2019-10-16 11:15:12] fetch_files
[STOP] [2019-10-16 11:15:12] fetch_files
[START] [2019-10-16 11:15:12] validate_each_file
[STOP] [2019-10-16 11:15:12] validate_each_file
[START] [2019-10-16 11:15:12] convert_to_csv
[CMD] [2019-10-16 11:15:12] /usr/bin/sort /app/public/converted_csv/tajikistan_sp_li_refs_17393.csv > /app/public/converted_csv/tajikistan_sp_li_refs_17393.csv_sorted
[CMD] [2019-10-16 11:15:13] /usr/bin/sort /app/public/converted_csv/tajikistan_sp_li_nodes_17394.csv > /app/public/converted_csv/tajikistan_sp_li_nodes_17394.csv_sorted
[CMD] [2019-10-16 11:15:13] /usr/bin/sort /app/public/converted_csv/tajikistan_sp_li_occurrences_17395.csv > /app/public/converted_csv/tajikistan_sp_li_occurrences_17395.csv_sorted
[CMD] [2019-10-16 11:15:13] /usr/bin/sort /app/public/converted_csv/tajikistan_sp_li_measurements_17396.csv > /app/public/converted_csv/tajikistan_sp_li_measurements_17396.csv_sorted
[STOP] [2019-10-16 11:15:13] convert_to_csv
[START] [2019-10-16 11:15:13] calculate_delta
[CMD] [2019-10-16 11:15:13] echo "0a" > /app/public/diff/tajikistan_sp_li_refs_17393.diff
[CMD] [2019-10-16 11:15:14] tail -n +1 /app/public/converted_csv/tajikistan_sp_li_refs_17393.csv >> /app/public/diff/tajikistan_sp_li_refs_17393.diff
[CMD] [2019-10-16 11:15:14] echo "." >> /app/public/diff/tajikistan_sp_li_refs_17393.diff
[CMD] [2019-10-16 11:15:14] echo "0a" > /app/public/diff/tajikistan_sp_li_nodes_17394.diff
[CMD] [2019-10-16 11:15:15] tail -n +1 /app/public/converted_csv/tajikistan_sp_li_nodes_17394.csv >> /app/public/diff/tajikistan_sp_li_nodes_17394.diff
[CMD] [2019-10-16 11:15:15] echo "." >> /app/public/diff/tajikistan_sp_li_nodes_17394.diff
[CMD] [2019-10-16 11:15:15] echo "0a" > /app/public/diff/tajikistan_sp_li_occurrences_17395.diff
[CMD] [2019-10-16 11:15:15] tail -n +1 /app/public/converted_csv/tajikistan_sp_li_occurrences_17395.csv >> /app/public/diff/tajikistan_sp_li_occurrences_17395.diff
[CMD] [2019-10-16 11:15:16] echo "." >> /app/public/diff/tajikistan_sp_li_occurrences_17395.diff
[CMD] [2019-10-16 11:15:16] echo "0a" > /app/public/diff/tajikistan_sp_li_measurements_17396.diff
[CMD] [2019-10-16 11:15:16] tail -n +1 /app/public/converted_csv/tajikistan_sp_li_measurements_17396.csv >> /app/public/diff/tajikistan_sp_li_measurements_17396.diff
[CMD] [2019-10-16 11:15:17] echo "." >> /app/public/diff/tajikistan_sp_li_measurements_17396.diff
[STOP] [2019-10-16 11:15:17] calculate_delta
[START] [2019-10-16 11:15:17] parse_diff_and_store
[INFO] [2019-10-16 11:15:17] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 11:15:17] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 11:15:19] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 11:15:19] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 11:15:29] Storing 2 References
[INFO] [2019-10-16 11:15:29] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 11:15:29] Average Time: 0.0
[INFO] [2019-10-16 11:15:29] Total Time: 1s
[INFO] [2019-10-16 11:15:29] Storing 2775 ScientificNames
[INFO] [2019-10-16 11:15:29] Processing group of 2775 in 3 groups of 1000
[INFO] [2019-10-16 11:15:30] Average Time: 0.36
[INFO] [2019-10-16 11:15:30] Total Time: 2s
[INFO] [2019-10-16 11:15:30] Storing 2775 Nodes
[INFO] [2019-10-16 11:15:30] Processing group of 2775 in 3 groups of 1000
[INFO] [2019-10-16 11:15:31] Average Time: 0.273
[INFO] [2019-10-16 11:15:31] Total Time: 1s
[INFO] [2019-10-16 11:15:31] Storing 1446 Occurrences
[INFO] [2019-10-16 11:15:31] Processing group of 1446 in 2 groups of 1000
[INFO] [2019-10-16 11:15:31] Average Time: 0.09
[INFO] [2019-10-16 11:15:31] Total Time: 1s
[INFO] [2019-10-16 11:15:31] Storing 3200 TraitsReferences
[INFO] [2019-10-16 11:15:31] Processing group of 3200 in 4 groups of 1000
[INFO] [2019-10-16 11:15:31] Average Time: 0.068
[INFO] [2019-10-16 11:15:31] Total Time: 1s
[INFO] [2019-10-16 11:15:31] Storing 3199 Traits
[INFO] [2019-10-16 11:15:31] Processing group of 3199 in 4 groups of 1000
[INFO] [2019-10-16 11:15:32] Average Time: 0.245
[INFO] [2019-10-16 11:15:32] Total Time: 2s
[INFO] [2019-10-16 11:15:32] Storing 3200 MetaTraits
[INFO] [2019-10-16 11:15:32] Processing group of 3200 in 4 groups of 1000
[INFO] [2019-10-16 11:15:33] Average Time: 0.14
[INFO] [2019-10-16 11:15:33] Total Time: 1s
[STOP] [2019-10-16 11:15:33] parse_diff_and_store
[START] [2019-10-16 11:15:33] resolve_keys
[INFO] [2019-10-16 11:15:45] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 11:15:46] traits to occurrences...
[INFO] [2019-10-16 11:15:48] traits to nodes (through occurrences)...
[INFO] [2019-10-16 11:15:48] Traits to sex term...
[INFO] [2019-10-16 11:15:49] Traits to lifestage term...
[INFO] [2019-10-16 11:15:50] MetaTraits to traits...
[INFO] [2019-10-16 11:15:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 11:15:51] Assocs to occurrences...
[INFO] [2019-10-16 11:15:51] Assocs to nodes...
[INFO] [2019-10-16 11:15:51] Assoc to sex term...
[INFO] [2019-10-16 11:15:51] Assoc to lifestage term...
[STOP] [2019-10-16 11:15:51] resolve_keys
[START] [2019-10-16 11:15:51] hold_for_later_1
[STOP] [2019-10-16 11:15:51] hold_for_later_1
[START] [2019-10-16 11:15:51] hold_for_later_2
[STOP] [2019-10-16 11:15:51] hold_for_later_2
[START] [2019-10-16 11:15:51] resolve_missing_parents
[STOP] [2019-10-16 11:15:56] resolve_missing_parents
[START] [2019-10-16 11:15:56] rebuild_nodes
[START] [2019-10-16 11:15:56] Flattener#flatten
[START] [2019-10-16 11:15:56] Flattener#study_resource
[START] [2019-10-16 11:15:56] Flattener#build_ancestry
[STOP] [2019-10-16 11:15:56] Flattener#build_ancestry
[INFO] [2019-10-16 11:15:56] 2775 ancestry keys
[START] [2019-10-16 11:15:56] build_node_ancestors
[INFO] [2019-10-16 11:15:56] old ancestors deleted.
[STOP] [2019-10-16 11:15:56] build_node_ancestors
[START] [2019-10-16 11:15:57] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 11:15:57] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 11:15:57] Flattener#flatten
[STOP] [2019-10-16 11:15:57] rebuild_nodes
[START] [2019-10-16 11:15:57] resolve_missing_media_owners
[STOP] [2019-10-16 11:15:57] resolve_missing_media_owners
[START] [2019-10-16 11:15:57] sanitize_media_verbatims
[STOP] [2019-10-16 11:15:57] sanitize_media_verbatims
[START] [2019-10-16 11:15:57] queue_downloads
[STOP] [2019-10-16 11:15:57] queue_downloads
[START] [2019-10-16 11:15:57] parse_names
[WARN] [2019-10-16 11:15:57] I see 2775 names which still need to be parsed.
[STOP] [2019-10-16 11:16:00] parse_names
[START] [2019-10-16 11:16:00] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 11:16:00] denormalize_canonical_names_to_nodes
[START] [2019-10-16 11:16:00] match_nodes
[START] [2019-10-16 11:16:00] map_all_nodes_to_pages
[STOP] [2019-10-16 11:19:01] map_all_nodes_to_pages
[INFO] [2019-10-16 11:19:01] 315 Unmatched nodes (of 2775)! That's too many to output. First 10: Poa zaprjagajevi (#52341071); Leymus thomsonii (#52339473); Oryzopsis vicarium (#52340955); Oryzopsis laterale (#52341395); Polypogon hissarica (#52341211); Carex viridula (#52340912); Pycreus (#52341196); Gnopharmia cocandaria (#52338817); Gnopharmia subrubraria (#52339382); Artemidora symmetrica (#52339458)
[START] [2019-10-16 11:19:01] update_nodes
[STOP] [2019-10-16 11:19:02] update_nodes
[STOP] [2019-10-16 11:19:02] match_nodes
[START] [2019-10-16 11:19:02] reindex_search
[STOP] [2019-10-16 11:19:09] reindex_search
[START] [2019-10-16 11:19:09] normalize_units
[STOP] [2019-10-16 11:19:09] normalize_units
[START] [2019-10-16 11:19:09] calculate_statistics
[STOP] [2019-10-16 11:19:09] calculate_statistics
[START] [2019-10-16 11:19:09] complete_harvest_instance
[START] [2019-10-16 11:19:09] overall_tsv_creation
[INFO] [2019-10-16 11:19:09] Processing group of 2775 in 1 batches of 10000
[INFO] [2019-10-16 11:20:06] 1446 Traits (unfiltered)...
[INFO] [2019-10-16 11:20:19] 1446 Traits (filtered)...
[INFO] [2019-10-16 11:20:19] 0 Associations (filtered)...
[INFO] [2019-10-16 11:20:59] 7230 metadata added.
[INFO] [2019-10-16 11:20:59] 0 metadata added.
[INFO] [2019-10-16 11:20:59] Average Time: 86.59
[INFO] [2019-10-16 11:20:59] Total Time: 1m50s
[STOP] [2019-10-16 11:20:59] overall_tsv_creation
[INFO] [2019-10-16 11:20:59] Done. Check your files:
[INFO] [2019-10-16 11:20:59] (2775 lines) /app/public/data/tajikistan_sp_li/publish_nodes.tsv
[INFO] [2019-10-16 11:20:59] (6396 lines) /app/public/data/tajikistan_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-16 11:20:59] (2775 lines) /app/public/data/tajikistan_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-16 11:21:00] (1447 lines) /app/public/data/tajikistan_sp_li/publish_traits.tsv
[INFO] [2019-10-16 11:21:00] (7231 lines) /app/public/data/tajikistan_sp_li/publish_metadata.tsv
[STOP] [2019-10-16 11:21:00] complete_harvest_instance
[START] [2019-10-16 11:21:00] completed
[STOP] [2019-10-16 11:21:00] completed
[STOP] [2019-10-16 11:21:00] logged process, took 348.97
Latest Process

16 Oct 11:15 EXITED currently processing 0