Harvest for Montserrat Species List Created 14 Oct 09:24

Stage: completed
Fetched: 14 Oct 09:24
Validated: 14 Oct 09:24
Deltas Created 14 Oct 09:24
Units Normalized: 14 Oct 09:26
Ancestry Built: 14 Oct 09:24
Nodes Matched: 14 Oct 09:26
Names Parsed: 14 Oct 09:25
New Models Stored: 14 Oct 09:24
Indexed: 14 Oct 09:26
Completed: 14 Oct 09:27
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 09:24:46 -0400 by logger.rb/56815
[START] [2019-10-14 09:24:46] logged process
[START] [2019-10-14 09:24:46] create_harvest_instance
[STOP] [2019-10-14 09:24:46] create_harvest_instance
[START] [2019-10-14 09:24:46] fetch_files
[STOP] [2019-10-14 09:24:46] fetch_files
[START] [2019-10-14 09:24:46] validate_each_file
[STOP] [2019-10-14 09:24:46] validate_each_file
[START] [2019-10-14 09:24:46] convert_to_csv
[CMD] [2019-10-14 09:24:46] /usr/bin/sort /app/public/converted_csv/montserrat_sp_li_refs_16627.csv > /app/public/converted_csv/montserrat_sp_li_refs_16627.csv_sorted
[CMD] [2019-10-14 09:24:47] /usr/bin/sort /app/public/converted_csv/montserrat_sp_li_nodes_16628.csv > /app/public/converted_csv/montserrat_sp_li_nodes_16628.csv_sorted
[CMD] [2019-10-14 09:24:47] /usr/bin/sort /app/public/converted_csv/montserrat_sp_li_occurrences_16629.csv > /app/public/converted_csv/montserrat_sp_li_occurrences_16629.csv_sorted
[CMD] [2019-10-14 09:24:47] /usr/bin/sort /app/public/converted_csv/montserrat_sp_li_measurements_16630.csv > /app/public/converted_csv/montserrat_sp_li_measurements_16630.csv_sorted
[STOP] [2019-10-14 09:24:47] convert_to_csv
[START] [2019-10-14 09:24:47] calculate_delta
[CMD] [2019-10-14 09:24:47] echo "0a" > /app/public/diff/montserrat_sp_li_refs_16627.diff
[CMD] [2019-10-14 09:24:47] tail -n +1 /app/public/converted_csv/montserrat_sp_li_refs_16627.csv >> /app/public/diff/montserrat_sp_li_refs_16627.diff
[CMD] [2019-10-14 09:24:47] echo "." >> /app/public/diff/montserrat_sp_li_refs_16627.diff
[CMD] [2019-10-14 09:24:47] echo "0a" > /app/public/diff/montserrat_sp_li_nodes_16628.diff
[CMD] [2019-10-14 09:24:47] tail -n +1 /app/public/converted_csv/montserrat_sp_li_nodes_16628.csv >> /app/public/diff/montserrat_sp_li_nodes_16628.diff
[CMD] [2019-10-14 09:24:47] echo "." >> /app/public/diff/montserrat_sp_li_nodes_16628.diff
[CMD] [2019-10-14 09:24:47] echo "0a" > /app/public/diff/montserrat_sp_li_occurrences_16629.diff
[CMD] [2019-10-14 09:24:47] tail -n +1 /app/public/converted_csv/montserrat_sp_li_occurrences_16629.csv >> /app/public/diff/montserrat_sp_li_occurrences_16629.diff
[CMD] [2019-10-14 09:24:48] echo "." >> /app/public/diff/montserrat_sp_li_occurrences_16629.diff
[CMD] [2019-10-14 09:24:48] echo "0a" > /app/public/diff/montserrat_sp_li_measurements_16630.diff
[CMD] [2019-10-14 09:24:48] tail -n +1 /app/public/converted_csv/montserrat_sp_li_measurements_16630.csv >> /app/public/diff/montserrat_sp_li_measurements_16630.diff
[CMD] [2019-10-14 09:24:48] echo "." >> /app/public/diff/montserrat_sp_li_measurements_16630.diff
[STOP] [2019-10-14 09:24:48] calculate_delta
[START] [2019-10-14 09:24:48] parse_diff_and_store
[INFO] [2019-10-14 09:24:48] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 09:24:48] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 09:24:49] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 09:24:49] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 09:24:50] Storing 2 References
[INFO] [2019-10-14 09:24:50] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 09:24:50] Average Time: 0.0
[INFO] [2019-10-14 09:24:50] Total Time: 1s
[INFO] [2019-10-14 09:24:50] Storing 724 ScientificNames
[INFO] [2019-10-14 09:24:50] Processing group of 724 in 1 groups of 1000
[INFO] [2019-10-14 09:24:51] Average Time: 0.31
[INFO] [2019-10-14 09:24:51] Total Time: 1s
[INFO] [2019-10-14 09:24:51] Storing 724 Nodes
[INFO] [2019-10-14 09:24:51] Processing group of 724 in 1 groups of 1000
[INFO] [2019-10-14 09:24:51] Average Time: 0.24
[INFO] [2019-10-14 09:24:51] Total Time: 1s
[INFO] [2019-10-14 09:24:51] Storing 267 Occurrences
[INFO] [2019-10-14 09:24:51] Processing group of 267 in 1 groups of 1000
[INFO] [2019-10-14 09:24:51] Average Time: 0.05
[INFO] [2019-10-14 09:24:51] Total Time: 1s
[INFO] [2019-10-14 09:24:51] Storing 534 TraitsReferences
[INFO] [2019-10-14 09:24:51] Processing group of 534 in 1 groups of 1000
[INFO] [2019-10-14 09:24:51] Average Time: 0.12
[INFO] [2019-10-14 09:24:51] Total Time: 1s
[INFO] [2019-10-14 09:24:51] Storing 534 Traits
[INFO] [2019-10-14 09:24:51] Processing group of 534 in 1 groups of 1000
[INFO] [2019-10-14 09:24:51] Average Time: 0.22
[INFO] [2019-10-14 09:24:51] Total Time: 1s
[INFO] [2019-10-14 09:24:51] Storing 534 MetaTraits
[INFO] [2019-10-14 09:24:51] Processing group of 534 in 1 groups of 1000
[INFO] [2019-10-14 09:24:52] Average Time: 0.1
[INFO] [2019-10-14 09:24:52] Total Time: 1s
[STOP] [2019-10-14 09:24:52] parse_diff_and_store
[START] [2019-10-14 09:24:52] resolve_keys
[INFO] [2019-10-14 09:24:56] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 09:24:57] traits to occurrences...
[INFO] [2019-10-14 09:24:57] traits to nodes (through occurrences)...
[INFO] [2019-10-14 09:24:57] Traits to sex term...
[INFO] [2019-10-14 09:24:57] Traits to lifestage term...
[INFO] [2019-10-14 09:24:57] MetaTraits to traits...
[INFO] [2019-10-14 09:24:57] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 09:24:57] Assocs to occurrences...
[INFO] [2019-10-14 09:24:57] Assocs to nodes...
[INFO] [2019-10-14 09:24:57] Assoc to sex term...
[INFO] [2019-10-14 09:24:57] Assoc to lifestage term...
[STOP] [2019-10-14 09:24:57] resolve_keys
[START] [2019-10-14 09:24:57] hold_for_later_1
[STOP] [2019-10-14 09:24:57] hold_for_later_1
[START] [2019-10-14 09:24:57] hold_for_later_2
[STOP] [2019-10-14 09:24:57] hold_for_later_2
[START] [2019-10-14 09:24:57] resolve_missing_parents
[STOP] [2019-10-14 09:24:57] resolve_missing_parents
[START] [2019-10-14 09:24:57] rebuild_nodes
[START] [2019-10-14 09:24:57] Flattener#flatten
[START] [2019-10-14 09:24:57] Flattener#study_resource
[START] [2019-10-14 09:24:57] Flattener#build_ancestry
[STOP] [2019-10-14 09:24:58] Flattener#build_ancestry
[INFO] [2019-10-14 09:24:58] 724 ancestry keys
[START] [2019-10-14 09:24:58] build_node_ancestors
[INFO] [2019-10-14 09:24:58] old ancestors deleted.
[STOP] [2019-10-14 09:24:58] build_node_ancestors
[START] [2019-10-14 09:24:58] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 09:24:58] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 09:24:58] Flattener#flatten
[STOP] [2019-10-14 09:24:58] rebuild_nodes
[START] [2019-10-14 09:24:58] resolve_missing_media_owners
[STOP] [2019-10-14 09:24:58] resolve_missing_media_owners
[START] [2019-10-14 09:24:58] sanitize_media_verbatims
[STOP] [2019-10-14 09:24:58] sanitize_media_verbatims
[START] [2019-10-14 09:24:58] queue_downloads
[STOP] [2019-10-14 09:24:58] queue_downloads
[START] [2019-10-14 09:24:58] parse_names
[WARN] [2019-10-14 09:24:58] I see 724 names which still need to be parsed.
[STOP] [2019-10-14 09:25:00] parse_names
[START] [2019-10-14 09:25:00] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 09:25:00] denormalize_canonical_names_to_nodes
[START] [2019-10-14 09:25:00] match_nodes
[START] [2019-10-14 09:25:00] map_all_nodes_to_pages
[STOP] [2019-10-14 09:26:04] map_all_nodes_to_pages
[INFO] [2019-10-14 09:26:04] 32 Unmatched nodes (of 724)! That's too many to output. First 10: Coerebidae (#50790897); Tiaris olivacea (#50791567); Seiurus noveboracensis (#50791021); Seiurus aurocapillus (#50791303); Dendroica (#50791087); Dendroica petechia (#50791086); Dendroica magnolia (#50791244); Thalaseus (#50791284); Thalaseus maximus (#50791283); Strumigenys emmae (#50791275)
[START] [2019-10-14 09:26:04] update_nodes
[STOP] [2019-10-14 09:26:04] update_nodes
[STOP] [2019-10-14 09:26:04] match_nodes
[START] [2019-10-14 09:26:04] reindex_search
[STOP] [2019-10-14 09:26:05] reindex_search
[START] [2019-10-14 09:26:06] normalize_units
[STOP] [2019-10-14 09:26:06] normalize_units
[START] [2019-10-14 09:26:06] calculate_statistics
[STOP] [2019-10-14 09:26:06] calculate_statistics
[START] [2019-10-14 09:26:06] complete_harvest_instance
[START] [2019-10-14 09:26:06] overall_tsv_creation
[INFO] [2019-10-14 09:26:06] Processing group of 724 in 1 batches of 10000
[INFO] [2019-10-14 09:26:53] 267 Traits (unfiltered)...
[INFO] [2019-10-14 09:27:06] 267 Traits (filtered)...
[INFO] [2019-10-14 09:27:06] 0 Associations (filtered)...
[INFO] [2019-10-14 09:27:44] 1335 metadata added.
[INFO] [2019-10-14 09:27:44] 0 metadata added.
[INFO] [2019-10-14 09:27:44] Average Time: 77.46
[INFO] [2019-10-14 09:27:44] Total Time: 1m39s
[STOP] [2019-10-14 09:27:44] overall_tsv_creation
[INFO] [2019-10-14 09:27:44] Done. Check your files:
[INFO] [2019-10-14 09:27:44] (724 lines) /app/public/data/montserrat_sp_li/publish_nodes.tsv
[INFO] [2019-10-14 09:27:44] (3428 lines) /app/public/data/montserrat_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-14 09:27:44] (724 lines) /app/public/data/montserrat_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-14 09:27:44] (268 lines) /app/public/data/montserrat_sp_li/publish_traits.tsv
[INFO] [2019-10-14 09:27:45] (1336 lines) /app/public/data/montserrat_sp_li/publish_metadata.tsv
[STOP] [2019-10-14 09:27:45] complete_harvest_instance
[START] [2019-10-14 09:27:45] completed
[STOP] [2019-10-14 09:27:45] completed
[STOP] [2019-10-14 09:27:45] logged process, took 178.83
Latest Process

14 Oct 09:24 EXITED currently processing 0