Harvest for Sudan Species List Created 16 Oct 07:26

Stage: completed
Fetched: 16 Oct 07:26
Validated: 16 Oct 07:26
Deltas Created 16 Oct 07:26
Units Normalized: 16 Oct 07:32
Ancestry Built: 16 Oct 07:27
Nodes Matched: 16 Oct 07:32
Names Parsed: 16 Oct 07:28
New Models Stored: 16 Oct 07:27
Indexed: 16 Oct 07:32
Completed: 16 Oct 07:34
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-16 07:26:50 -0400 by logger.rb/56815
[START] [2019-10-16 07:26:50] logged process
[START] [2019-10-16 07:26:50] create_harvest_instance
[STOP] [2019-10-16 07:26:50] create_harvest_instance
[START] [2019-10-16 07:26:50] fetch_files
[STOP] [2019-10-16 07:26:50] fetch_files
[START] [2019-10-16 07:26:50] validate_each_file
[STOP] [2019-10-16 07:26:51] validate_each_file
[START] [2019-10-16 07:26:51] convert_to_csv
[CMD] [2019-10-16 07:26:51] /usr/bin/sort /app/public/converted_csv/sudan_sp_list_refs_17341.csv > /app/public/converted_csv/sudan_sp_list_refs_17341.csv_sorted
[CMD] [2019-10-16 07:26:51] /usr/bin/sort /app/public/converted_csv/sudan_sp_list_nodes_17342.csv > /app/public/converted_csv/sudan_sp_list_nodes_17342.csv_sorted
[CMD] [2019-10-16 07:26:51] /usr/bin/sort /app/public/converted_csv/sudan_sp_list_occurrences_17343.csv > /app/public/converted_csv/sudan_sp_list_occurrences_17343.csv_sorted
[CMD] [2019-10-16 07:26:52] /usr/bin/sort /app/public/converted_csv/sudan_sp_list_measurements_17344.csv > /app/public/converted_csv/sudan_sp_list_measurements_17344.csv_sorted
[STOP] [2019-10-16 07:26:52] convert_to_csv
[START] [2019-10-16 07:26:52] calculate_delta
[CMD] [2019-10-16 07:26:52] echo "0a" > /app/public/diff/sudan_sp_list_refs_17341.diff
[CMD] [2019-10-16 07:26:52] tail -n +1 /app/public/converted_csv/sudan_sp_list_refs_17341.csv >> /app/public/diff/sudan_sp_list_refs_17341.diff
[CMD] [2019-10-16 07:26:53] echo "." >> /app/public/diff/sudan_sp_list_refs_17341.diff
[CMD] [2019-10-16 07:26:53] echo "0a" > /app/public/diff/sudan_sp_list_nodes_17342.diff
[CMD] [2019-10-16 07:26:53] tail -n +1 /app/public/converted_csv/sudan_sp_list_nodes_17342.csv >> /app/public/diff/sudan_sp_list_nodes_17342.diff
[CMD] [2019-10-16 07:26:54] echo "." >> /app/public/diff/sudan_sp_list_nodes_17342.diff
[CMD] [2019-10-16 07:26:54] echo "0a" > /app/public/diff/sudan_sp_list_occurrences_17343.diff
[CMD] [2019-10-16 07:26:54] tail -n +1 /app/public/converted_csv/sudan_sp_list_occurrences_17343.csv >> /app/public/diff/sudan_sp_list_occurrences_17343.diff
[CMD] [2019-10-16 07:26:54] echo "." >> /app/public/diff/sudan_sp_list_occurrences_17343.diff
[CMD] [2019-10-16 07:26:55] echo "0a" > /app/public/diff/sudan_sp_list_measurements_17344.diff
[CMD] [2019-10-16 07:26:55] tail -n +1 /app/public/converted_csv/sudan_sp_list_measurements_17344.csv >> /app/public/diff/sudan_sp_list_measurements_17344.diff
[CMD] [2019-10-16 07:26:55] echo "." >> /app/public/diff/sudan_sp_list_measurements_17344.diff
[STOP] [2019-10-16 07:26:56] calculate_delta
[START] [2019-10-16 07:26:56] parse_diff_and_store
[INFO] [2019-10-16 07:26:56] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 07:26:56] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 07:26:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 07:26:59] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 07:27:11] Storing 2 References
[INFO] [2019-10-16 07:27:11] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 07:27:11] Average Time: 0.0
[INFO] [2019-10-16 07:27:11] Total Time: 1s
[INFO] [2019-10-16 07:27:11] Storing 4346 ScientificNames
[INFO] [2019-10-16 07:27:11] Processing group of 4346 in 5 groups of 1000
[INFO] [2019-10-16 07:27:13] Average Time: 0.324
[INFO] [2019-10-16 07:27:13] Total Time: 2s
[INFO] [2019-10-16 07:27:13] Storing 4346 Nodes
[INFO] [2019-10-16 07:27:13] Processing group of 4346 in 5 groups of 1000
[INFO] [2019-10-16 07:27:14] Average Time: 0.246
[INFO] [2019-10-16 07:27:14] Total Time: 2s
[INFO] [2019-10-16 07:27:14] Storing 1928 Occurrences
[INFO] [2019-10-16 07:27:14] Processing group of 1928 in 2 groups of 1000
[INFO] [2019-10-16 07:27:15] Average Time: 0.105
[INFO] [2019-10-16 07:27:15] Total Time: 1s
[INFO] [2019-10-16 07:27:15] Storing 4550 TraitsReferences
[INFO] [2019-10-16 07:27:15] Processing group of 4550 in 5 groups of 1000
[INFO] [2019-10-16 07:27:15] Average Time: 0.114
[INFO] [2019-10-16 07:27:15] Total Time: 1s
[INFO] [2019-10-16 07:27:15] Storing 4549 Traits
[INFO] [2019-10-16 07:27:15] Processing group of 4549 in 5 groups of 1000
[INFO] [2019-10-16 07:27:17] Average Time: 0.306
[INFO] [2019-10-16 07:27:17] Total Time: 2s
[INFO] [2019-10-16 07:27:17] Storing 4547 MetaTraits
[INFO] [2019-10-16 07:27:17] Processing group of 4547 in 5 groups of 1000
[INFO] [2019-10-16 07:27:17] Average Time: 0.124
[INFO] [2019-10-16 07:27:17] Total Time: 1s
[STOP] [2019-10-16 07:27:17] parse_diff_and_store
[START] [2019-10-16 07:27:17] resolve_keys
[INFO] [2019-10-16 07:27:37] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 07:27:39] traits to occurrences...
[INFO] [2019-10-16 07:27:41] traits to nodes (through occurrences)...
[INFO] [2019-10-16 07:27:41] Traits to sex term...
[INFO] [2019-10-16 07:27:42] Traits to lifestage term...
[INFO] [2019-10-16 07:27:44] MetaTraits to traits...
[INFO] [2019-10-16 07:27:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 07:27:45] Assocs to occurrences...
[INFO] [2019-10-16 07:27:45] Assocs to nodes...
[INFO] [2019-10-16 07:27:45] Assoc to sex term...
[INFO] [2019-10-16 07:27:45] Assoc to lifestage term...
[STOP] [2019-10-16 07:27:45] resolve_keys
[START] [2019-10-16 07:27:45] hold_for_later_1
[STOP] [2019-10-16 07:27:45] hold_for_later_1
[START] [2019-10-16 07:27:45] hold_for_later_2
[STOP] [2019-10-16 07:27:45] hold_for_later_2
[START] [2019-10-16 07:27:45] resolve_missing_parents
[STOP] [2019-10-16 07:27:54] resolve_missing_parents
[START] [2019-10-16 07:27:54] rebuild_nodes
[START] [2019-10-16 07:27:54] Flattener#flatten
[START] [2019-10-16 07:27:54] Flattener#study_resource
[START] [2019-10-16 07:27:54] Flattener#build_ancestry
[STOP] [2019-10-16 07:27:55] Flattener#build_ancestry
[INFO] [2019-10-16 07:27:55] 4346 ancestry keys
[START] [2019-10-16 07:27:55] build_node_ancestors
[INFO] [2019-10-16 07:27:55] old ancestors deleted.
[STOP] [2019-10-16 07:27:56] build_node_ancestors
[START] [2019-10-16 07:27:57] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 07:27:57] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 07:27:57] Flattener#flatten
[STOP] [2019-10-16 07:27:57] rebuild_nodes
[START] [2019-10-16 07:27:57] resolve_missing_media_owners
[STOP] [2019-10-16 07:27:57] resolve_missing_media_owners
[START] [2019-10-16 07:27:57] sanitize_media_verbatims
[STOP] [2019-10-16 07:27:57] sanitize_media_verbatims
[START] [2019-10-16 07:27:57] queue_downloads
[STOP] [2019-10-16 07:27:57] queue_downloads
[START] [2019-10-16 07:27:57] parse_names
[WARN] [2019-10-16 07:27:57] I see 4346 names which still need to be parsed.
[STOP] [2019-10-16 07:28:02] parse_names
[START] [2019-10-16 07:28:02] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 07:28:02] denormalize_canonical_names_to_nodes
[START] [2019-10-16 07:28:02] match_nodes
[START] [2019-10-16 07:28:02] map_all_nodes_to_pages
[STOP] [2019-10-16 07:32:20] map_all_nodes_to_pages
[INFO] [2019-10-16 07:32:20] 259 Unmatched nodes (of 4346)! That's too many to output. First 10: Pennisetum ramosum (#52206703); Brachiaria kotschyanum (#52207358); Cyperus aristatus (#52207989); Schoenoplectiella articulatus (#52209942); Xanthorrhoeaceae (#52206683); Stuckenia pectinatus (#52207624); Wisneria (#52209152); Commelina forskalaei (#52209991); Sylvia rueppelli (#52208663); Hippolais pallida (#52207122)
[START] [2019-10-16 07:32:20] update_nodes
[STOP] [2019-10-16 07:32:21] update_nodes
[STOP] [2019-10-16 07:32:21] match_nodes
[START] [2019-10-16 07:32:21] reindex_search
[STOP] [2019-10-16 07:32:32] reindex_search
[START] [2019-10-16 07:32:32] normalize_units
[STOP] [2019-10-16 07:32:32] normalize_units
[START] [2019-10-16 07:32:32] calculate_statistics
[STOP] [2019-10-16 07:32:32] calculate_statistics
[START] [2019-10-16 07:32:32] complete_harvest_instance
[START] [2019-10-16 07:32:32] overall_tsv_creation
[INFO] [2019-10-16 07:32:32] Processing group of 4346 in 1 batches of 10000
[INFO] [2019-10-16 07:33:36] 1928 Traits (unfiltered)...
[INFO] [2019-10-16 07:33:49] 1928 Traits (filtered)...
[INFO] [2019-10-16 07:33:49] 0 Associations (filtered)...
[INFO] [2019-10-16 07:34:32] 9639 metadata added.
[INFO] [2019-10-16 07:34:32] 0 metadata added.
[INFO] [2019-10-16 07:34:32] Average Time: 95.71
[INFO] [2019-10-16 07:34:32] Total Time: 1m60s
[STOP] [2019-10-16 07:34:32] overall_tsv_creation
[INFO] [2019-10-16 07:34:32] Done. Check your files:
[INFO] [2019-10-16 07:34:32] (4346 lines) /app/public/data/sudan_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 07:34:32] (13363 lines) /app/public/data/sudan_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 07:34:33] (4346 lines) /app/public/data/sudan_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 07:34:33] (1929 lines) /app/public/data/sudan_sp_list/publish_traits.tsv
[INFO] [2019-10-16 07:34:33] (9640 lines) /app/public/data/sudan_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 07:34:33] complete_harvest_instance
[START] [2019-10-16 07:34:33] completed
[STOP] [2019-10-16 07:34:33] completed
[STOP] [2019-10-16 07:34:34] logged process, took 463.69
Latest Process

16 Oct 07:26 EXITED currently processing 0