Harvest for Sao Tome and Principe Species List Created 15 Oct 16:41

Stage: completed
Fetched: 15 Oct 16:41
Validated: 15 Oct 16:41
Deltas Created 15 Oct 16:41
Units Normalized: 15 Oct 16:44
Ancestry Built: 15 Oct 16:42
Nodes Matched: 15 Oct 16:43
Names Parsed: 15 Oct 16:42
New Models Stored: 15 Oct 16:41
Indexed: 15 Oct 16:44
Completed: 15 Oct 16:45
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:41:35 -0400 by logger.rb/56815
[START] [2019-10-15 16:41:35] logged process
[START] [2019-10-15 16:41:35] create_harvest_instance
[STOP] [2019-10-15 16:41:36] create_harvest_instance
[START] [2019-10-15 16:41:36] fetch_files
[STOP] [2019-10-15 16:41:36] fetch_files
[START] [2019-10-15 16:41:36] validate_each_file
[STOP] [2019-10-15 16:41:36] validate_each_file
[START] [2019-10-15 16:41:36] convert_to_csv
[CMD] [2019-10-15 16:41:36] /usr/bin/sort /app/public/converted_csv/sotpnsl_refs_17093.csv > /app/public/converted_csv/sotpnsl_refs_17093.csv_sorted
[CMD] [2019-10-15 16:41:36] /usr/bin/sort /app/public/converted_csv/sotpnsl_nodes_17094.csv > /app/public/converted_csv/sotpnsl_nodes_17094.csv_sorted
[CMD] [2019-10-15 16:41:37] /usr/bin/sort /app/public/converted_csv/sotpnsl_occurrences_17095.csv > /app/public/converted_csv/sotpnsl_occurrences_17095.csv_sorted
[CMD] [2019-10-15 16:41:37] /usr/bin/sort /app/public/converted_csv/sotpnsl_measurements_17096.csv > /app/public/converted_csv/sotpnsl_measurements_17096.csv_sorted
[STOP] [2019-10-15 16:41:37] convert_to_csv
[START] [2019-10-15 16:41:37] calculate_delta
[CMD] [2019-10-15 16:41:37] echo "0a" > /app/public/diff/sotpnsl_refs_17093.diff
[CMD] [2019-10-15 16:41:37] tail -n +1 /app/public/converted_csv/sotpnsl_refs_17093.csv >> /app/public/diff/sotpnsl_refs_17093.diff
[CMD] [2019-10-15 16:41:38] echo "." >> /app/public/diff/sotpnsl_refs_17093.diff
[CMD] [2019-10-15 16:41:38] echo "0a" > /app/public/diff/sotpnsl_nodes_17094.diff
[CMD] [2019-10-15 16:41:38] tail -n +1 /app/public/converted_csv/sotpnsl_nodes_17094.csv >> /app/public/diff/sotpnsl_nodes_17094.diff
[CMD] [2019-10-15 16:41:39] echo "." >> /app/public/diff/sotpnsl_nodes_17094.diff
[CMD] [2019-10-15 16:41:39] echo "0a" > /app/public/diff/sotpnsl_occurrences_17095.diff
[CMD] [2019-10-15 16:41:39] tail -n +1 /app/public/converted_csv/sotpnsl_occurrences_17095.csv >> /app/public/diff/sotpnsl_occurrences_17095.diff
[CMD] [2019-10-15 16:41:39] echo "." >> /app/public/diff/sotpnsl_occurrences_17095.diff
[CMD] [2019-10-15 16:41:40] echo "0a" > /app/public/diff/sotpnsl_measurements_17096.diff
[CMD] [2019-10-15 16:41:40] tail -n +1 /app/public/converted_csv/sotpnsl_measurements_17096.csv >> /app/public/diff/sotpnsl_measurements_17096.diff
[CMD] [2019-10-15 16:41:40] echo "." >> /app/public/diff/sotpnsl_measurements_17096.diff
[STOP] [2019-10-15 16:41:40] calculate_delta
[START] [2019-10-15 16:41:40] parse_diff_and_store
[INFO] [2019-10-15 16:41:41] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:41:41] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:41:42] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:41:42] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:41:48] Storing 2 References
[INFO] [2019-10-15 16:41:48] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:41:48] Average Time: 0.0
[INFO] [2019-10-15 16:41:48] Total Time: 1s
[INFO] [2019-10-15 16:41:48] Storing 1985 ScientificNames
[INFO] [2019-10-15 16:41:48] Processing group of 1985 in 2 groups of 1000
[INFO] [2019-10-15 16:41:49] Average Time: 0.375
[INFO] [2019-10-15 16:41:49] Total Time: 1s
[INFO] [2019-10-15 16:41:49] Storing 1985 Nodes
[INFO] [2019-10-15 16:41:49] Processing group of 1985 in 2 groups of 1000
[INFO] [2019-10-15 16:41:49] Average Time: 0.34
[INFO] [2019-10-15 16:41:49] Total Time: 1s
[INFO] [2019-10-15 16:41:49] Storing 964 Occurrences
[INFO] [2019-10-15 16:41:49] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-15 16:41:50] Average Time: 0.11
[INFO] [2019-10-15 16:41:50] Total Time: 1s
[INFO] [2019-10-15 16:41:50] Storing 1920 TraitsReferences
[INFO] [2019-10-15 16:41:50] Processing group of 1920 in 2 groups of 1000
[INFO] [2019-10-15 16:41:50] Average Time: 0.105
[INFO] [2019-10-15 16:41:50] Total Time: 1s
[INFO] [2019-10-15 16:41:50] Storing 1919 Traits
[INFO] [2019-10-15 16:41:50] Processing group of 1919 in 2 groups of 1000
[INFO] [2019-10-15 16:41:51] Average Time: 0.35
[INFO] [2019-10-15 16:41:51] Total Time: 1s
[INFO] [2019-10-15 16:41:51] Storing 1920 MetaTraits
[INFO] [2019-10-15 16:41:51] Processing group of 1920 in 2 groups of 1000
[INFO] [2019-10-15 16:41:51] Average Time: 0.12
[INFO] [2019-10-15 16:41:51] Total Time: 1s
[STOP] [2019-10-15 16:41:51] parse_diff_and_store
[START] [2019-10-15 16:41:51] resolve_keys
[INFO] [2019-10-15 16:42:01] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:42:02] traits to occurrences...
[INFO] [2019-10-15 16:42:02] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:42:02] Traits to sex term...
[INFO] [2019-10-15 16:42:02] Traits to lifestage term...
[INFO] [2019-10-15 16:42:02] MetaTraits to traits...
[INFO] [2019-10-15 16:42:03] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:42:03] Assocs to occurrences...
[INFO] [2019-10-15 16:42:03] Assocs to nodes...
[INFO] [2019-10-15 16:42:03] Assoc to sex term...
[INFO] [2019-10-15 16:42:03] Assoc to lifestage term...
[STOP] [2019-10-15 16:42:03] resolve_keys
[START] [2019-10-15 16:42:03] hold_for_later_1
[STOP] [2019-10-15 16:42:03] hold_for_later_1
[START] [2019-10-15 16:42:03] hold_for_later_2
[STOP] [2019-10-15 16:42:03] hold_for_later_2
[START] [2019-10-15 16:42:03] resolve_missing_parents
[STOP] [2019-10-15 16:42:05] resolve_missing_parents
[START] [2019-10-15 16:42:05] rebuild_nodes
[START] [2019-10-15 16:42:05] Flattener#flatten
[START] [2019-10-15 16:42:05] Flattener#study_resource
[START] [2019-10-15 16:42:05] Flattener#build_ancestry
[STOP] [2019-10-15 16:42:05] Flattener#build_ancestry
[INFO] [2019-10-15 16:42:05] 1985 ancestry keys
[START] [2019-10-15 16:42:05] build_node_ancestors
[INFO] [2019-10-15 16:42:05] old ancestors deleted.
[STOP] [2019-10-15 16:42:06] build_node_ancestors
[START] [2019-10-15 16:42:06] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:42:06] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:42:06] Flattener#flatten
[STOP] [2019-10-15 16:42:06] rebuild_nodes
[START] [2019-10-15 16:42:06] resolve_missing_media_owners
[STOP] [2019-10-15 16:42:06] resolve_missing_media_owners
[START] [2019-10-15 16:42:06] sanitize_media_verbatims
[STOP] [2019-10-15 16:42:06] sanitize_media_verbatims
[START] [2019-10-15 16:42:06] queue_downloads
[STOP] [2019-10-15 16:42:06] queue_downloads
[START] [2019-10-15 16:42:06] parse_names
[WARN] [2019-10-15 16:42:06] I see 1985 names which still need to be parsed.
[STOP] [2019-10-15 16:42:09] parse_names
[START] [2019-10-15 16:42:09] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:42:09] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:42:09] match_nodes
[START] [2019-10-15 16:42:09] map_all_nodes_to_pages
[STOP] [2019-10-15 16:43:55] map_all_nodes_to_pages
[INFO] [2019-10-15 16:43:55] 94 Unmatched nodes (of 1985)! That's too many to output. First 10: Zosterops leucophoeus (#51759954); Speirops (#51759804); Speirops leucophoeus (#51760224); Nectarinia newtonii (#51760321); Nectarinia hartlaubii (#51760573); Nectarinia thomensis (#51760987); Spermestes cucullatus (#51759940); Crithagra rufobrunneus (#51759800); Crithagra mozambicus (#51759885); Sylvia dohrni (#51759997)
[START] [2019-10-15 16:43:55] update_nodes
[STOP] [2019-10-15 16:43:56] update_nodes
[STOP] [2019-10-15 16:43:56] match_nodes
[START] [2019-10-15 16:43:56] reindex_search
[STOP] [2019-10-15 16:44:00] reindex_search
[START] [2019-10-15 16:44:00] normalize_units
[STOP] [2019-10-15 16:44:00] normalize_units
[START] [2019-10-15 16:44:00] calculate_statistics
[STOP] [2019-10-15 16:44:00] calculate_statistics
[START] [2019-10-15 16:44:00] complete_harvest_instance
[START] [2019-10-15 16:44:00] overall_tsv_creation
[INFO] [2019-10-15 16:44:00] Processing group of 1985 in 1 batches of 10000
[INFO] [2019-10-15 16:44:54] 960 Traits (unfiltered)...
[INFO] [2019-10-15 16:45:08] 960 Traits (filtered)...
[INFO] [2019-10-15 16:45:08] 0 Associations (filtered)...
[INFO] [2019-10-15 16:45:47] 4799 metadata added.
[INFO] [2019-10-15 16:45:47] 0 metadata added.
[INFO] [2019-10-15 16:45:47] Average Time: 84.7
[INFO] [2019-10-15 16:45:47] Total Time: 1m48s
[STOP] [2019-10-15 16:45:47] overall_tsv_creation
[INFO] [2019-10-15 16:45:47] Done. Check your files:
[INFO] [2019-10-15 16:45:47] (1985 lines) /app/public/data/sotpnsl/publish_nodes.tsv
[INFO] [2019-10-15 16:45:48] (4369 lines) /app/public/data/sotpnsl/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:45:48] (1985 lines) /app/public/data/sotpnsl/publish_scientific_names.tsv
[INFO] [2019-10-15 16:45:48] (961 lines) /app/public/data/sotpnsl/publish_traits.tsv
[INFO] [2019-10-15 16:45:49] (4800 lines) /app/public/data/sotpnsl/publish_metadata.tsv
[STOP] [2019-10-15 16:45:49] complete_harvest_instance
[START] [2019-10-15 16:45:49] completed
[STOP] [2019-10-15 16:45:49] completed
[STOP] [2019-10-15 16:45:49] logged process, took 253.31
Latest Process

15 Oct 16:41 EXITED currently processing 0