Harvest for French Guiana Species List Created 13 Oct 00:16

Stage: completed
Fetched: 13 Oct 00:16
Validated: 13 Oct 00:16
Deltas Created 13 Oct 00:16
Units Normalized: 13 Oct 00:30
Ancestry Built: 13 Oct 00:19
Nodes Matched: 13 Oct 00:29
Names Parsed: 13 Oct 00:19
New Models Stored: 13 Oct 00:17
Indexed: 13 Oct 00:30
Completed: 13 Oct 00:34
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-13 00:16:12 -0400 by logger.rb/56815
[START] [2019-10-13 00:16:12] logged process
[START] [2019-10-13 00:16:12] create_harvest_instance
[STOP] [2019-10-13 00:16:13] create_harvest_instance
[START] [2019-10-13 00:16:13] fetch_files
[STOP] [2019-10-13 00:16:13] fetch_files
[START] [2019-10-13 00:16:13] validate_each_file
[STOP] [2019-10-13 00:16:17] validate_each_file
[START] [2019-10-13 00:16:17] convert_to_csv
[CMD] [2019-10-13 00:16:17] /usr/bin/sort /app/public/converted_csv/french_guiana_sp_refs_15787.csv > /app/public/converted_csv/french_guiana_sp_refs_15787.csv_sorted
[CMD] [2019-10-13 00:16:17] /usr/bin/sort /app/public/converted_csv/french_guiana_sp_nodes_15788.csv > /app/public/converted_csv/french_guiana_sp_nodes_15788.csv_sorted
[CMD] [2019-10-13 00:16:17] /usr/bin/sort /app/public/converted_csv/french_guiana_sp_occurrences_15789.csv > /app/public/converted_csv/french_guiana_sp_occurrences_15789.csv_sorted
[CMD] [2019-10-13 00:16:17] /usr/bin/sort /app/public/converted_csv/french_guiana_sp_measurements_15790.csv > /app/public/converted_csv/french_guiana_sp_measurements_15790.csv_sorted
[STOP] [2019-10-13 00:16:17] convert_to_csv
[START] [2019-10-13 00:16:17] calculate_delta
[CMD] [2019-10-13 00:16:17] echo "0a" > /app/public/diff/french_guiana_sp_refs_15787.diff
[CMD] [2019-10-13 00:16:17] tail -n +1 /app/public/converted_csv/french_guiana_sp_refs_15787.csv >> /app/public/diff/french_guiana_sp_refs_15787.diff
[CMD] [2019-10-13 00:16:17] echo "." >> /app/public/diff/french_guiana_sp_refs_15787.diff
[CMD] [2019-10-13 00:16:17] echo "0a" > /app/public/diff/french_guiana_sp_nodes_15788.diff
[CMD] [2019-10-13 00:16:17] tail -n +1 /app/public/converted_csv/french_guiana_sp_nodes_15788.csv >> /app/public/diff/french_guiana_sp_nodes_15788.diff
[CMD] [2019-10-13 00:16:17] echo "." >> /app/public/diff/french_guiana_sp_nodes_15788.diff
[CMD] [2019-10-13 00:16:18] echo "0a" > /app/public/diff/french_guiana_sp_occurrences_15789.diff
[CMD] [2019-10-13 00:16:18] tail -n +1 /app/public/converted_csv/french_guiana_sp_occurrences_15789.csv >> /app/public/diff/french_guiana_sp_occurrences_15789.diff
[CMD] [2019-10-13 00:16:18] echo "." >> /app/public/diff/french_guiana_sp_occurrences_15789.diff
[CMD] [2019-10-13 00:16:18] echo "0a" > /app/public/diff/french_guiana_sp_measurements_15790.diff
[CMD] [2019-10-13 00:16:18] tail -n +1 /app/public/converted_csv/french_guiana_sp_measurements_15790.csv >> /app/public/diff/french_guiana_sp_measurements_15790.diff
[CMD] [2019-10-13 00:16:18] echo "." >> /app/public/diff/french_guiana_sp_measurements_15790.diff
[STOP] [2019-10-13 00:16:18] calculate_delta
[START] [2019-10-13 00:16:18] parse_diff_and_store
[INFO] [2019-10-13 00:16:18] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 00:16:18] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 00:16:23] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 00:16:25] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 00:17:22] Storing 2 References
[INFO] [2019-10-13 00:17:22] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 00:17:22] Average Time: 0.0
[INFO] [2019-10-13 00:17:22] Total Time: 1s
[INFO] [2019-10-13 00:17:22] Storing 13915 ScientificNames
[INFO] [2019-10-13 00:17:22] Processing group of 13915 in 14 groups of 1000
[INFO] [2019-10-13 00:17:27] Average Time: 0.398
[INFO] [2019-10-13 00:17:27] Total Time: 6s
[INFO] [2019-10-13 00:17:27] last 3 / first 3: 1.26
[INFO] [2019-10-13 00:17:27] Std.Dev: 0.08944271909999159; Max: 0.63
[INFO] [2019-10-13 00:17:27] Storing 13915 Nodes
[INFO] [2019-10-13 00:17:27] Processing group of 13915 in 14 groups of 1000
[INFO] [2019-10-13 00:17:32] Average Time: 0.295
[INFO] [2019-10-13 00:17:32] Total Time: 5s
[INFO] [2019-10-13 00:17:32] last 3 / first 3: 0.9
[INFO] [2019-10-13 00:17:32] Std.Dev: 0.03162277660168379; Max: 0.36
[INFO] [2019-10-13 00:17:32] Storing 9640 Occurrences
[INFO] [2019-10-13 00:17:32] Processing group of 9640 in 10 groups of 1000
[INFO] [2019-10-13 00:17:33] Average Time: 0.099
[INFO] [2019-10-13 00:17:33] Total Time: 2s
[INFO] [2019-10-13 00:17:33] last 3 / first 3: 0.87
[INFO] [2019-10-13 00:17:33] Std.Dev: 0.0; Max: 0.13
[INFO] [2019-10-13 00:17:33] Storing 20000 TraitsReferences
[INFO] [2019-10-13 00:17:33] Processing group of 20000 in 20 groups of 1000
[INFO] [2019-10-13 00:17:34] Average Time: 0.075
[INFO] [2019-10-13 00:17:34] Total Time: 2s
[INFO] [2019-10-13 00:17:34] last 3 / first 3: 1.0
[INFO] [2019-10-13 00:17:34] Std.Dev: 0.0; Max: 0.14
[INFO] [2019-10-13 00:17:34] Storing 19999 Traits
[INFO] [2019-10-13 00:17:34] Processing group of 19999 in 20 groups of 1000
[INFO] [2019-10-13 00:17:40] Average Time: 0.296
[INFO] [2019-10-13 00:17:40] Total Time: 6s
[INFO] [2019-10-13 00:17:40] last 3 / first 3: 0.91
[INFO] [2019-10-13 00:17:40] Std.Dev: 0.03162277660168379; Max: 0.4
[INFO] [2019-10-13 00:17:40] Storing 19984 MetaTraits
[INFO] [2019-10-13 00:17:40] Processing group of 19984 in 20 groups of 1000
[INFO] [2019-10-13 00:17:43] Average Time: 0.13
[INFO] [2019-10-13 00:17:43] Total Time: 3s
[INFO] [2019-10-13 00:17:43] last 3 / first 3: 1.78
[INFO] [2019-10-13 00:17:43] Std.Dev: 0.044721359549995794; Max: 0.28
[STOP] [2019-10-13 00:17:43] parse_diff_and_store
[START] [2019-10-13 00:17:43] resolve_keys
[INFO] [2019-10-13 00:18:39] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 00:18:44] traits to occurrences...
[INFO] [2019-10-13 00:18:50] traits to nodes (through occurrences)...
[INFO] [2019-10-13 00:18:50] Traits to sex term...
[INFO] [2019-10-13 00:18:56] Traits to lifestage term...
[INFO] [2019-10-13 00:19:01] MetaTraits to traits...
[INFO] [2019-10-13 00:19:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 00:19:05] Assocs to occurrences...
[INFO] [2019-10-13 00:19:05] Assocs to nodes...
[INFO] [2019-10-13 00:19:05] Assoc to sex term...
[INFO] [2019-10-13 00:19:05] Assoc to lifestage term...
[STOP] [2019-10-13 00:19:05] resolve_keys
[START] [2019-10-13 00:19:05] hold_for_later_1
[STOP] [2019-10-13 00:19:05] hold_for_later_1
[START] [2019-10-13 00:19:05] hold_for_later_2
[STOP] [2019-10-13 00:19:05] hold_for_later_2
[START] [2019-10-13 00:19:05] resolve_missing_parents
[STOP] [2019-10-13 00:19:32] resolve_missing_parents
[START] [2019-10-13 00:19:32] rebuild_nodes
[START] [2019-10-13 00:19:32] Flattener#flatten
[START] [2019-10-13 00:19:32] Flattener#study_resource
[START] [2019-10-13 00:19:32] Flattener#build_ancestry
[STOP] [2019-10-13 00:19:33] Flattener#build_ancestry
[INFO] [2019-10-13 00:19:33] 13915 ancestry keys
[START] [2019-10-13 00:19:33] build_node_ancestors
[INFO] [2019-10-13 00:19:33] old ancestors deleted.
[STOP] [2019-10-13 00:19:35] build_node_ancestors
[START] [2019-10-13 00:19:38] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 00:19:38] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 00:19:38] Flattener#flatten
[STOP] [2019-10-13 00:19:38] rebuild_nodes
[START] [2019-10-13 00:19:38] resolve_missing_media_owners
[STOP] [2019-10-13 00:19:38] resolve_missing_media_owners
[START] [2019-10-13 00:19:38] sanitize_media_verbatims
[STOP] [2019-10-13 00:19:38] sanitize_media_verbatims
[START] [2019-10-13 00:19:38] queue_downloads
[STOP] [2019-10-13 00:19:38] queue_downloads
[START] [2019-10-13 00:19:38] parse_names
[WARN] [2019-10-13 00:19:38] I see 13915 names which still need to be parsed.
[STOP] [2019-10-13 00:19:50] parse_names
[START] [2019-10-13 00:19:50] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 00:19:50] denormalize_canonical_names_to_nodes
[START] [2019-10-13 00:19:50] match_nodes
[START] [2019-10-13 00:19:50] map_all_nodes_to_pages
[STOP] [2019-10-13 00:29:30] map_all_nodes_to_pages
[INFO] [2019-10-13 00:29:30] 829 Unmatched nodes (of 13915)! That's too many to output. First 10: Neogovea (#49757029); Neogovea virginie (#49757028); Discocyrtus (#49759236); Discocyrtus carvalhoi (#49759235); Inga nouragensis (#49753759); Inga albicoria (#49754228); Inga sarmentosa (#49754616); Inga comewynensis (#49760106); Inga cordato-alata (#49761119); Inga loubryana (#49762825)
[START] [2019-10-13 00:29:30] update_nodes
[STOP] [2019-10-13 00:29:35] update_nodes
[STOP] [2019-10-13 00:29:35] match_nodes
[START] [2019-10-13 00:29:35] reindex_search
[STOP] [2019-10-13 00:30:03] reindex_search
[START] [2019-10-13 00:30:03] normalize_units
[STOP] [2019-10-13 00:30:03] normalize_units
[START] [2019-10-13 00:30:03] calculate_statistics
[STOP] [2019-10-13 00:30:03] calculate_statistics
[START] [2019-10-13 00:30:03] complete_harvest_instance
[START] [2019-10-13 00:30:03] overall_tsv_creation
[INFO] [2019-10-13 00:30:03] Processing group of 13915 in 2 batches of 10000
[INFO] [2019-10-13 00:31:31] 6864 Traits (unfiltered)...
[INFO] [2019-10-13 00:31:45] 6864 Traits (filtered)...
[INFO] [2019-10-13 00:31:45] 0 Associations (filtered)...
[INFO] [2019-10-13 00:32:35] 34315 metadata added.
[INFO] [2019-10-13 00:32:35] 0 metadata added.
[INFO] [2019-10-13 00:33:38] 2776 Traits (unfiltered)...
[INFO] [2019-10-13 00:33:52] 2776 Traits (filtered)...
[INFO] [2019-10-13 00:33:52] 0 Associations (filtered)...
[INFO] [2019-10-13 00:34:35] 13870 metadata added.
[INFO] [2019-10-13 00:34:35] 0 metadata added.
[INFO] [2019-10-13 00:34:35] Average Time: 111.16
[INFO] [2019-10-13 00:34:35] Total Time: 4m33s
[STOP] [2019-10-13 00:34:35] overall_tsv_creation
[INFO] [2019-10-13 00:34:35] Done. Check your files:
[INFO] [2019-10-13 00:34:35] (13915 lines) /app/public/data/french_guiana_sp/publish_nodes.tsv
[INFO] [2019-10-13 00:34:35] (33859 lines) /app/public/data/french_guiana_sp/publish_node_ancestors.tsv
[INFO] [2019-10-13 00:34:35] (13915 lines) /app/public/data/french_guiana_sp/publish_scientific_names.tsv
[INFO] [2019-10-13 00:34:35] (9641 lines) /app/public/data/french_guiana_sp/publish_traits.tsv
[INFO] [2019-10-13 00:34:35] (48186 lines) /app/public/data/french_guiana_sp/publish_metadata.tsv
[STOP] [2019-10-13 00:34:36] complete_harvest_instance
[START] [2019-10-13 00:34:36] completed
[STOP] [2019-10-13 00:34:36] completed
[STOP] [2019-10-13 00:34:36] logged process, took 1103.42
Latest Process

13 Oct 00:16 EXITED currently processing 0