Harvest for Central African Republic Species List Created 12 Oct 02:21

Stage: completed
Fetched: 12 Oct 02:21
Validated: 12 Oct 02:21
Deltas Created 12 Oct 02:21
Units Normalized: 12 Oct 02:26
Ancestry Built: 12 Oct 02:22
Nodes Matched: 12 Oct 02:26
Names Parsed: 12 Oct 02:22
New Models Stored: 12 Oct 02:22
Indexed: 12 Oct 02:26
Completed: 12 Oct 02:28
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2019-10-12 02:21:34 -0400 by logger.rb/56815
[START] [2019-10-12 02:21:34] logged process
[START] [2019-10-12 02:21:34] create_harvest_instance
[STOP] [2019-10-12 02:21:34] create_harvest_instance
[START] [2019-10-12 02:21:34] fetch_files
[STOP] [2019-10-12 02:21:34] fetch_files
[START] [2019-10-12 02:21:34] validate_each_file
[STOP] [2019-10-12 02:21:35] validate_each_file
[START] [2019-10-12 02:21:35] convert_to_csv
[CMD] [2019-10-12 02:21:35] /usr/bin/sort /app/public/converted_csv/carsl_refs_15395.csv > /app/public/converted_csv/carsl_refs_15395.csv_sorted
[CMD] [2019-10-12 02:21:35] /usr/bin/sort /app/public/converted_csv/carsl_nodes_15396.csv > /app/public/converted_csv/carsl_nodes_15396.csv_sorted
[CMD] [2019-10-12 02:21:35] /usr/bin/sort /app/public/converted_csv/carsl_occurrences_15397.csv > /app/public/converted_csv/carsl_occurrences_15397.csv_sorted
[CMD] [2019-10-12 02:21:35] /usr/bin/sort /app/public/converted_csv/carsl_measurements_15398.csv > /app/public/converted_csv/carsl_measurements_15398.csv_sorted
[STOP] [2019-10-12 02:21:35] convert_to_csv
[START] [2019-10-12 02:21:35] calculate_delta
[CMD] [2019-10-12 02:21:35] echo "0a" > /app/public/diff/carsl_refs_15395.diff
[CMD] [2019-10-12 02:21:35] tail -n +1 /app/public/converted_csv/carsl_refs_15395.csv >> /app/public/diff/carsl_refs_15395.diff
[CMD] [2019-10-12 02:21:35] echo "." >> /app/public/diff/carsl_refs_15395.diff
[CMD] [2019-10-12 02:21:36] echo "0a" > /app/public/diff/carsl_nodes_15396.diff
[CMD] [2019-10-12 02:21:36] tail -n +1 /app/public/converted_csv/carsl_nodes_15396.csv >> /app/public/diff/carsl_nodes_15396.diff
[CMD] [2019-10-12 02:21:36] echo "." >> /app/public/diff/carsl_nodes_15396.diff
[CMD] [2019-10-12 02:21:36] echo "0a" > /app/public/diff/carsl_occurrences_15397.diff
[CMD] [2019-10-12 02:21:36] tail -n +1 /app/public/converted_csv/carsl_occurrences_15397.csv >> /app/public/diff/carsl_occurrences_15397.diff
[CMD] [2019-10-12 02:21:36] echo "." >> /app/public/diff/carsl_occurrences_15397.diff
[CMD] [2019-10-12 02:21:36] echo "0a" > /app/public/diff/carsl_measurements_15398.diff
[CMD] [2019-10-12 02:21:36] tail -n +1 /app/public/converted_csv/carsl_measurements_15398.csv >> /app/public/diff/carsl_measurements_15398.diff
[CMD] [2019-10-12 02:21:36] echo "." >> /app/public/diff/carsl_measurements_15398.diff
[STOP] [2019-10-12 02:21:36] calculate_delta
[START] [2019-10-12 02:21:36] parse_diff_and_store
[INFO] [2019-10-12 02:21:37] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 02:21:37] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 02:21:39] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 02:21:39] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 02:21:59] Storing 2 References
[INFO] [2019-10-12 02:21:59] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 02:21:59] Average Time: 0.0
[INFO] [2019-10-12 02:21:59] Total Time: 1s
[INFO] [2019-10-12 02:21:59] Storing 5133 ScientificNames
[INFO] [2019-10-12 02:21:59] Processing group of 5133 in 6 groups of 1000
[INFO] [2019-10-12 02:22:01] Average Time: 0.378
[INFO] [2019-10-12 02:22:01] Total Time: 3s
[INFO] [2019-10-12 02:22:01] Storing 5133 Nodes
[INFO] [2019-10-12 02:22:01] Processing group of 5133 in 6 groups of 1000
[INFO] [2019-10-12 02:22:03] Average Time: 0.305
[INFO] [2019-10-12 02:22:03] Total Time: 2s
[INFO] [2019-10-12 02:22:03] Storing 2892 Occurrences
[INFO] [2019-10-12 02:22:03] Processing group of 2892 in 3 groups of 1000
[INFO] [2019-10-12 02:22:03] Average Time: 0.107
[INFO] [2019-10-12 02:22:03] Total Time: 1s
[INFO] [2019-10-12 02:22:03] Storing 6696 TraitsReferences
[INFO] [2019-10-12 02:22:03] Processing group of 6696 in 7 groups of 1000
[INFO] [2019-10-12 02:22:04] Average Time: 0.086
[INFO] [2019-10-12 02:22:04] Total Time: 1s
[INFO] [2019-10-12 02:22:04] last 3 / first 3: 0.56
[INFO] [2019-10-12 02:22:04] Std.Dev: 0.044721359549995794; Max: 0.19
[INFO] [2019-10-12 02:22:04] Storing 6695 Traits
[INFO] [2019-10-12 02:22:04] Processing group of 6695 in 7 groups of 1000
[INFO] [2019-10-12 02:22:06] Average Time: 0.334
[INFO] [2019-10-12 02:22:06] Total Time: 3s
[INFO] [2019-10-12 02:22:06] last 3 / first 3: 0.73
[INFO] [2019-10-12 02:22:06] Std.Dev: 0.07071067811865475; Max: 0.45
[INFO] [2019-10-12 02:22:06] Storing 6690 MetaTraits
[INFO] [2019-10-12 02:22:06] Processing group of 6690 in 7 groups of 1000
[INFO] [2019-10-12 02:22:07] Average Time: 0.139
[INFO] [2019-10-12 02:22:07] Total Time: 2s
[INFO] [2019-10-12 02:22:07] last 3 / first 3: 0.75
[INFO] [2019-10-12 02:22:07] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-10-12 02:22:07] parse_diff_and_store
[START] [2019-10-12 02:22:07] resolve_keys
[INFO] [2019-10-12 02:22:29] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 02:22:31] traits to occurrences...
[INFO] [2019-10-12 02:22:33] traits to nodes (through occurrences)...
[INFO] [2019-10-12 02:22:33] Traits to sex term...
[INFO] [2019-10-12 02:22:34] Traits to lifestage term...
[INFO] [2019-10-12 02:22:35] MetaTraits to traits...
[INFO] [2019-10-12 02:22:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 02:22:37] Assocs to occurrences...
[INFO] [2019-10-12 02:22:37] Assocs to nodes...
[INFO] [2019-10-12 02:22:37] Assoc to sex term...
[INFO] [2019-10-12 02:22:37] Assoc to lifestage term...
[STOP] [2019-10-12 02:22:37] resolve_keys
[START] [2019-10-12 02:22:37] hold_for_later_1
[STOP] [2019-10-12 02:22:37] hold_for_later_1
[START] [2019-10-12 02:22:37] hold_for_later_2
[STOP] [2019-10-12 02:22:37] hold_for_later_2
[START] [2019-10-12 02:22:37] resolve_missing_parents
[STOP] [2019-10-12 02:22:47] resolve_missing_parents
[START] [2019-10-12 02:22:47] rebuild_nodes
[START] [2019-10-12 02:22:47] Flattener#flatten
[START] [2019-10-12 02:22:47] Flattener#study_resource
[START] [2019-10-12 02:22:47] Flattener#build_ancestry
[STOP] [2019-10-12 02:22:47] Flattener#build_ancestry
[INFO] [2019-10-12 02:22:47] 5133 ancestry keys
[START] [2019-10-12 02:22:47] build_node_ancestors
[INFO] [2019-10-12 02:22:47] old ancestors deleted.
[STOP] [2019-10-12 02:22:48] build_node_ancestors
[START] [2019-10-12 02:22:49] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 02:22:49] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 02:22:49] Flattener#flatten
[STOP] [2019-10-12 02:22:49] rebuild_nodes
[START] [2019-10-12 02:22:49] resolve_missing_media_owners
[STOP] [2019-10-12 02:22:49] resolve_missing_media_owners
[START] [2019-10-12 02:22:49] sanitize_media_verbatims
[STOP] [2019-10-12 02:22:49] sanitize_media_verbatims
[START] [2019-10-12 02:22:49] queue_downloads
[STOP] [2019-10-12 02:22:49] queue_downloads
[START] [2019-10-12 02:22:49] parse_names
[WARN] [2019-10-12 02:22:49] I see 5133 names which still need to be parsed.
[STOP] [2019-10-12 02:22:53] parse_names
[START] [2019-10-12 02:22:53] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 02:22:54] denormalize_canonical_names_to_nodes
[START] [2019-10-12 02:22:54] match_nodes
[START] [2019-10-12 02:22:54] map_all_nodes_to_pages
[STOP] [2019-10-12 02:26:34] map_all_nodes_to_pages
[INFO] [2019-10-12 02:26:34] 256 Unmatched nodes (of 5133)! That's too many to output. First 10: Albizia altissimum (#49089312); Albizia leptophylla (#49091798); Cassia delagoensis (#49093780); Macrotyloma baumannii (#49091841); Leucomphalos brachycarpus (#49089894); Intsia africana (#49089946); Lonchocarpus laxiflora (#49090208); Baphiastrum brachycarpus (#49091282); Acacia hockii (#49092457); Eriosema pellegrini (#49091814)
[START] [2019-10-12 02:26:34] update_nodes
[STOP] [2019-10-12 02:26:36] update_nodes
[STOP] [2019-10-12 02:26:36] match_nodes
[START] [2019-10-12 02:26:36] reindex_search
[STOP] [2019-10-12 02:26:47] reindex_search
[START] [2019-10-12 02:26:47] normalize_units
[STOP] [2019-10-12 02:26:47] normalize_units
[START] [2019-10-12 02:26:47] calculate_statistics
[STOP] [2019-10-12 02:26:47] calculate_statistics
[START] [2019-10-12 02:26:47] complete_harvest_instance
[START] [2019-10-12 02:26:47] overall_tsv_creation
[INFO] [2019-10-12 02:26:47] Processing group of 5133 in 1 batches of 10000
[INFO] [2019-10-12 02:27:54] 2892 Traits (unfiltered)...
[INFO] [2019-10-12 02:28:08] 2892 Traits (filtered)...
[INFO] [2019-10-12 02:28:08] 0 Associations (filtered)...
[INFO] [2019-10-12 02:28:50] 14454 metadata added.
[INFO] [2019-10-12 02:28:50] 0 metadata added.
[INFO] [2019-10-12 02:28:50] Average Time: 98.92
[INFO] [2019-10-12 02:28:50] Total Time: 2m4s
[STOP] [2019-10-12 02:28:50] overall_tsv_creation
[INFO] [2019-10-12 02:28:50] Done. Check your files:
[INFO] [2019-10-12 02:28:50] (5133 lines) /app/public/data/carsl/publish_nodes.tsv
[INFO] [2019-10-12 02:28:50] (7930 lines) /app/public/data/carsl/publish_node_ancestors.tsv
[INFO] [2019-10-12 02:28:51] (5133 lines) /app/public/data/carsl/publish_scientific_names.tsv
[INFO] [2019-10-12 02:28:51] (2893 lines) /app/public/data/carsl/publish_traits.tsv
[INFO] [2019-10-12 02:28:51] (14455 lines) /app/public/data/carsl/publish_metadata.tsv
[STOP] [2019-10-12 02:28:51] complete_harvest_instance
[START] [2019-10-12 02:28:51] completed
[STOP] [2019-10-12 02:28:51] completed
[STOP] [2019-10-12 02:28:51] logged process, took 437.47
Latest Process

12 Oct 02:21 EXITED currently processing 0