Harvest for Guadeloupe Species List Created 13 Oct 05:58

Stage: completed
Fetched: 13 Oct 05:58
Validated: 13 Oct 05:58
Deltas Created 13 Oct 05:58
Units Normalized: 13 Oct 06:01
Ancestry Built: 13 Oct 05:58
Nodes Matched: 13 Oct 06:01
Names Parsed: 13 Oct 05:58
New Models Stored: 13 Oct 05:58
Indexed: 13 Oct 06:01
Completed: 13 Oct 06:03
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-13 05:58:08 -0400 by logger.rb/56815
[START] [2019-10-13 05:58:08] logged process
[START] [2019-10-13 05:58:08] create_harvest_instance
[STOP] [2019-10-13 05:58:09] create_harvest_instance
[START] [2019-10-13 05:58:09] fetch_files
[STOP] [2019-10-13 05:58:09] fetch_files
[START] [2019-10-13 05:58:09] validate_each_file
[STOP] [2019-10-13 05:58:10] validate_each_file
[START] [2019-10-13 05:58:10] convert_to_csv
[CMD] [2019-10-13 05:58:10] /usr/bin/sort /app/public/converted_csv/guadeloupe_sp_li_refs_15899.csv > /app/public/converted_csv/guadeloupe_sp_li_refs_15899.csv_sorted
[CMD] [2019-10-13 05:58:10] /usr/bin/sort /app/public/converted_csv/guadeloupe_sp_li_nodes_15900.csv > /app/public/converted_csv/guadeloupe_sp_li_nodes_15900.csv_sorted
[CMD] [2019-10-13 05:58:10] /usr/bin/sort /app/public/converted_csv/guadeloupe_sp_li_occurrences_15901.csv > /app/public/converted_csv/guadeloupe_sp_li_occurrences_15901.csv_sorted
[CMD] [2019-10-13 05:58:10] /usr/bin/sort /app/public/converted_csv/guadeloupe_sp_li_measurements_15902.csv > /app/public/converted_csv/guadeloupe_sp_li_measurements_15902.csv_sorted
[STOP] [2019-10-13 05:58:11] convert_to_csv
[START] [2019-10-13 05:58:11] calculate_delta
[CMD] [2019-10-13 05:58:11] echo "0a" > /app/public/diff/guadeloupe_sp_li_refs_15899.diff
[CMD] [2019-10-13 05:58:11] tail -n +1 /app/public/converted_csv/guadeloupe_sp_li_refs_15899.csv >> /app/public/diff/guadeloupe_sp_li_refs_15899.diff
[CMD] [2019-10-13 05:58:11] echo "." >> /app/public/diff/guadeloupe_sp_li_refs_15899.diff
[CMD] [2019-10-13 05:58:11] echo "0a" > /app/public/diff/guadeloupe_sp_li_nodes_15900.diff
[CMD] [2019-10-13 05:58:11] tail -n +1 /app/public/converted_csv/guadeloupe_sp_li_nodes_15900.csv >> /app/public/diff/guadeloupe_sp_li_nodes_15900.diff
[CMD] [2019-10-13 05:58:11] echo "." >> /app/public/diff/guadeloupe_sp_li_nodes_15900.diff
[CMD] [2019-10-13 05:58:11] echo "0a" > /app/public/diff/guadeloupe_sp_li_occurrences_15901.diff
[CMD] [2019-10-13 05:58:11] tail -n +1 /app/public/converted_csv/guadeloupe_sp_li_occurrences_15901.csv >> /app/public/diff/guadeloupe_sp_li_occurrences_15901.diff
[CMD] [2019-10-13 05:58:11] echo "." >> /app/public/diff/guadeloupe_sp_li_occurrences_15901.diff
[CMD] [2019-10-13 05:58:11] echo "0a" > /app/public/diff/guadeloupe_sp_li_measurements_15902.diff
[CMD] [2019-10-13 05:58:11] tail -n +1 /app/public/converted_csv/guadeloupe_sp_li_measurements_15902.csv >> /app/public/diff/guadeloupe_sp_li_measurements_15902.diff
[CMD] [2019-10-13 05:58:12] echo "." >> /app/public/diff/guadeloupe_sp_li_measurements_15902.diff
[STOP] [2019-10-13 05:58:12] calculate_delta
[START] [2019-10-13 05:58:12] parse_diff_and_store
[INFO] [2019-10-13 05:58:12] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 05:58:12] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 05:58:13] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 05:58:13] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 05:58:20] Storing 2 References
[INFO] [2019-10-13 05:58:20] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 05:58:20] Average Time: 0.0
[INFO] [2019-10-13 05:58:20] Total Time: 1s
[INFO] [2019-10-13 05:58:20] Storing 2384 ScientificNames
[INFO] [2019-10-13 05:58:20] Processing group of 2384 in 3 groups of 1000
[INFO] [2019-10-13 05:58:21] Average Time: 0.307
[INFO] [2019-10-13 05:58:21] Total Time: 1s
[INFO] [2019-10-13 05:58:21] Storing 2384 Nodes
[INFO] [2019-10-13 05:58:21] Processing group of 2384 in 3 groups of 1000
[INFO] [2019-10-13 05:58:22] Average Time: 0.22
[INFO] [2019-10-13 05:58:22] Total Time: 1s
[INFO] [2019-10-13 05:58:22] Storing 964 Occurrences
[INFO] [2019-10-13 05:58:22] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-13 05:58:22] Average Time: 0.11
[INFO] [2019-10-13 05:58:22] Total Time: 1s
[INFO] [2019-10-13 05:58:22] Storing 2410 TraitsReferences
[INFO] [2019-10-13 05:58:22] Processing group of 2410 in 3 groups of 1000
[INFO] [2019-10-13 05:58:22] Average Time: 0.08
[INFO] [2019-10-13 05:58:22] Total Time: 1s
[INFO] [2019-10-13 05:58:22] Storing 2409 Traits
[INFO] [2019-10-13 05:58:22] Processing group of 2409 in 3 groups of 1000
[INFO] [2019-10-13 05:58:23] Average Time: 0.28
[INFO] [2019-10-13 05:58:23] Total Time: 1s
[INFO] [2019-10-13 05:58:23] Storing 2406 MetaTraits
[INFO] [2019-10-13 05:58:23] Processing group of 2406 in 3 groups of 1000
[INFO] [2019-10-13 05:58:23] Average Time: 0.12
[INFO] [2019-10-13 05:58:23] Total Time: 1s
[STOP] [2019-10-13 05:58:23] parse_diff_and_store
[START] [2019-10-13 05:58:23] resolve_keys
[INFO] [2019-10-13 05:58:35] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 05:58:36] traits to occurrences...
[INFO] [2019-10-13 05:58:36] traits to nodes (through occurrences)...
[INFO] [2019-10-13 05:58:36] Traits to sex term...
[INFO] [2019-10-13 05:58:37] Traits to lifestage term...
[INFO] [2019-10-13 05:58:37] MetaTraits to traits...
[INFO] [2019-10-13 05:58:37] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 05:58:38] Assocs to occurrences...
[INFO] [2019-10-13 05:58:38] Assocs to nodes...
[INFO] [2019-10-13 05:58:38] Assoc to sex term...
[INFO] [2019-10-13 05:58:38] Assoc to lifestage term...
[STOP] [2019-10-13 05:58:38] resolve_keys
[START] [2019-10-13 05:58:38] hold_for_later_1
[STOP] [2019-10-13 05:58:38] hold_for_later_1
[START] [2019-10-13 05:58:38] hold_for_later_2
[STOP] [2019-10-13 05:58:38] hold_for_later_2
[START] [2019-10-13 05:58:38] resolve_missing_parents
[STOP] [2019-10-13 05:58:41] resolve_missing_parents
[START] [2019-10-13 05:58:41] rebuild_nodes
[START] [2019-10-13 05:58:41] Flattener#flatten
[START] [2019-10-13 05:58:41] Flattener#study_resource
[START] [2019-10-13 05:58:41] Flattener#build_ancestry
[STOP] [2019-10-13 05:58:41] Flattener#build_ancestry
[INFO] [2019-10-13 05:58:41] 2384 ancestry keys
[START] [2019-10-13 05:58:41] build_node_ancestors
[INFO] [2019-10-13 05:58:41] old ancestors deleted.
[STOP] [2019-10-13 05:58:42] build_node_ancestors
[START] [2019-10-13 05:58:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 05:58:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 05:58:42] Flattener#flatten
[STOP] [2019-10-13 05:58:42] rebuild_nodes
[START] [2019-10-13 05:58:42] resolve_missing_media_owners
[STOP] [2019-10-13 05:58:42] resolve_missing_media_owners
[START] [2019-10-13 05:58:42] sanitize_media_verbatims
[STOP] [2019-10-13 05:58:42] sanitize_media_verbatims
[START] [2019-10-13 05:58:42] queue_downloads
[STOP] [2019-10-13 05:58:42] queue_downloads
[START] [2019-10-13 05:58:42] parse_names
[WARN] [2019-10-13 05:58:42] I see 2384 names which still need to be parsed.
[STOP] [2019-10-13 05:58:45] parse_names
[START] [2019-10-13 05:58:45] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 05:58:45] denormalize_canonical_names_to_nodes
[START] [2019-10-13 05:58:45] match_nodes
[START] [2019-10-13 05:58:45] map_all_nodes_to_pages
[STOP] [2019-10-13 06:01:08] map_all_nodes_to_pages
[INFO] [2019-10-13 06:01:08] 168 Unmatched nodes (of 2384)! That's too many to output. First 10: Coerebidae (#49939159); Pheidole laudatana (#49939261); Octostruma lutzi (#49939248); Strumigenys eggersi (#49939405); Strumigenys emmae (#49939808); Rogeria scobinata (#49939296); Limnodromus (#49939956); Tryngites subruficollis (#49941250); Thalaseus (#49939366); Thalaseus maximus (#49939365)
[START] [2019-10-13 06:01:08] update_nodes
[STOP] [2019-10-13 06:01:09] update_nodes
[STOP] [2019-10-13 06:01:09] match_nodes
[START] [2019-10-13 06:01:09] reindex_search
[STOP] [2019-10-13 06:01:13] reindex_search
[START] [2019-10-13 06:01:13] normalize_units
[STOP] [2019-10-13 06:01:13] normalize_units
[START] [2019-10-13 06:01:13] calculate_statistics
[STOP] [2019-10-13 06:01:13] calculate_statistics
[START] [2019-10-13 06:01:13] complete_harvest_instance
[START] [2019-10-13 06:01:13] overall_tsv_creation
[INFO] [2019-10-13 06:01:13] Processing group of 2384 in 1 batches of 10000
[INFO] [2019-10-13 06:02:09] 964 Traits (unfiltered)...
[INFO] [2019-10-13 06:02:23] 964 Traits (filtered)...
[INFO] [2019-10-13 06:02:23] 0 Associations (filtered)...
[INFO] [2019-10-13 06:03:02] 4817 metadata added.
[INFO] [2019-10-13 06:03:02] 0 metadata added.
[INFO] [2019-10-13 06:03:02] Average Time: 85.92
[INFO] [2019-10-13 06:03:02] Total Time: 1m49s
[STOP] [2019-10-13 06:03:02] overall_tsv_creation
[INFO] [2019-10-13 06:03:02] Done. Check your files:
[INFO] [2019-10-13 06:03:02] (2384 lines) /app/public/data/guadeloupe_sp_li/publish_nodes.tsv
[INFO] [2019-10-13 06:03:02] (4493 lines) /app/public/data/guadeloupe_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-13 06:03:02] (2384 lines) /app/public/data/guadeloupe_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-13 06:03:02] (965 lines) /app/public/data/guadeloupe_sp_li/publish_traits.tsv
[INFO] [2019-10-13 06:03:02] (4818 lines) /app/public/data/guadeloupe_sp_li/publish_metadata.tsv
[STOP] [2019-10-13 06:03:02] complete_harvest_instance
[START] [2019-10-13 06:03:02] completed
[STOP] [2019-10-13 06:03:02] completed
[STOP] [2019-10-13 06:03:02] logged process, took 293.9
Latest Process

13 Oct 05:58 EXITED currently processing 0