Harvest for Mikmaq names Created 28 Apr 11:49

Stage: completed
Fetched: 28 Apr 11:49
Validated: 28 Apr 11:49
Deltas Created 28 Apr 11:49
Units Normalized: 28 Apr 11:50
Ancestry Built: 28 Apr 11:49
Nodes Matched: 28 Apr 11:50
Names Parsed: 28 Apr 11:49
New Models Stored: 28 Apr 11:49
Indexed: 28 Apr 11:50
Completed: 28 Apr 11:52
Time to Harvest: less than a minute
Harvesting Log

(135 lines)
# Logfile created on 2021-04-26 13:30:58 -0400 by logger.rb/66358
[START] [2021-04-26 13:31:00] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-26 13:31:00] Creating resource from OpenData
[START] [2021-04-26 13:31:00] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-26 13:31:00] Parse meta.xml file and create formats with fields
[STOP] [2021-04-26 13:31:00] Parse meta.xml file and create formats with fields
[STOP] [2021-04-26 13:31:00] Creating resource from OpenData
[INFO] [2021-04-28 11:49:04] ## HARVEST: type = -harvest
[START] [2021-04-28 11:49:09] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-28 11:49:09] create_harvest_instance
[INFO] [2021-04-28 11:49:09] Created harvest instance #3835
[STOP] [2021-04-28 11:49:09] create_harvest_instance
[START] [2021-04-28 11:49:09] fetch_files
[STOP] [2021-04-28 11:49:09] fetch_files
[START] [2021-04-28 11:49:09] validate_each_file
[INFO] [2021-04-28 11:49:09] Looping over 2 formats...
[INFO] [2021-04-28 11:49:09] ...nodes (/app/public/data/mikmaq_names/taxa.txt)
[INFO] [2021-04-28 11:49:09] Valid: /app/public/converted_csv/mikmaq_names_nodes_3835.csv (87 lines)
[INFO] [2021-04-28 11:49:09] ...vernaculars (/app/public/data/mikmaq_names/vernacular_names.txt)
[INFO] [2021-04-28 11:49:09] Valid: /app/public/converted_csv/mikmaq_names_vernaculars_3835.csv (88 lines)
[STOP] [2021-04-28 11:49:09] validate_each_file
[START] [2021-04-28 11:49:09] convert_to_csv
[INFO] [2021-04-28 11:49:09] Looping over 2 formats...
[INFO] [2021-04-28 11:49:09] ...nodes (/app/public/data/mikmaq_names/taxa.txt)
[CMD] [2021-04-28 11:49:09] /usr/bin/sort /app/public/converted_csv/mikmaq_names_nodes_3835.csv > /app/public/converted_csv/mikmaq_names_nodes_3835.csv_sorted
[INFO] [2021-04-28 11:49:10] Converted: /app/public/converted_csv/mikmaq_names_nodes_3835.csv (87 lines)
[INFO] [2021-04-28 11:49:10] ...vernaculars (/app/public/data/mikmaq_names/vernacular_names.txt)
[CMD] [2021-04-28 11:49:10] /usr/bin/sort /app/public/converted_csv/mikmaq_names_vernaculars_3835.csv > /app/public/converted_csv/mikmaq_names_vernaculars_3835.csv_sorted
[INFO] [2021-04-28 11:49:12] Converted: /app/public/converted_csv/mikmaq_names_vernaculars_3835.csv (88 lines)
[STOP] [2021-04-28 11:49:12] convert_to_csv
[START] [2021-04-28 11:49:12] calculate_delta
[INFO] [2021-04-28 11:49:12] Looping over 2 formats...
[INFO] [2021-04-28 11:49:12] ...nodes (/app/public/data/mikmaq_names/taxa.txt)
[CMD] [2021-04-28 11:49:12] echo "0a" > /app/public/diff/mikmaq_names_nodes_3835.diff
[CMD] [2021-04-28 11:49:13] tail -n +1 /app/public/converted_csv/mikmaq_names_nodes_3835.csv >> /app/public/diff/mikmaq_names_nodes_3835.diff
[CMD] [2021-04-28 11:49:14] echo "." >> /app/public/diff/mikmaq_names_nodes_3835.diff
[INFO] [2021-04-28 11:49:15] Created diff: /app/public/diff/mikmaq_names_nodes_3835.diff (89 lines)
[INFO] [2021-04-28 11:49:15] ...vernaculars (/app/public/data/mikmaq_names/vernacular_names.txt)
[CMD] [2021-04-28 11:49:15] echo "0a" > /app/public/diff/mikmaq_names_vernaculars_3835.diff
[CMD] [2021-04-28 11:49:17] tail -n +1 /app/public/converted_csv/mikmaq_names_vernaculars_3835.csv >> /app/public/diff/mikmaq_names_vernaculars_3835.diff
[CMD] [2021-04-28 11:49:18] echo "." >> /app/public/diff/mikmaq_names_vernaculars_3835.diff
[INFO] [2021-04-28 11:49:19] Created diff: /app/public/diff/mikmaq_names_vernaculars_3835.diff (90 lines)
[STOP] [2021-04-28 11:49:19] calculate_delta
[START] [2021-04-28 11:49:19] parse_diff_and_store
[INFO] [2021-04-28 11:49:19] Handling diff: /app/public/diff/mikmaq_names_nodes_3835.diff (89 lines)
[INFO] [2021-04-28 11:49:20] Loading nodes diff file into memory (89 /app/public/diff/mikmaq_names_nodes_3835.diff lines)...
[INFO] [2021-04-28 11:49:22] Handling diff: /app/public/diff/mikmaq_names_vernaculars_3835.diff (90 lines)
[INFO] [2021-04-28 11:49:23] Loading vernaculars diff file into memory (90 /app/public/diff/mikmaq_names_vernaculars_3835.diff lines)...
[INFO] [2021-04-28 11:49:25] Storing 95 ScientificNames
[INFO] [2021-04-28 11:49:25] Processing group of 95 in 1 groups of 1000
[INFO] [2021-04-28 11:49:25] Average Time: 0.09
[INFO] [2021-04-28 11:49:25] Total Time: 1s
[INFO] [2021-04-28 11:49:25] Storing 95 Nodes
[INFO] [2021-04-28 11:49:25] Processing group of 95 in 1 groups of 1000
[INFO] [2021-04-28 11:49:25] Average Time: 0.08
[INFO] [2021-04-28 11:49:25] Total Time: 1s
[INFO] [2021-04-28 11:49:25] Storing 88 Vernaculars
[INFO] [2021-04-28 11:49:25] Processing group of 88 in 1 groups of 1000
[INFO] [2021-04-28 11:49:25] Average Time: 0.02
[INFO] [2021-04-28 11:49:25] Total Time: 1s
[STOP] [2021-04-28 11:49:25] parse_diff_and_store
[START] [2021-04-28 11:49:25] resolve_keys
[INFO] [2021-04-28 11:49:32] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-28 11:49:32] traits to occurrences...
[INFO] [2021-04-28 11:49:32] traits to nodes (through occurrences)...
[INFO] [2021-04-28 11:49:32] Traits to sex term...
[INFO] [2021-04-28 11:49:32] Traits to lifestage term...
[INFO] [2021-04-28 11:49:32] MetaTraits to traits...
[INFO] [2021-04-28 11:49:32] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-28 11:49:32] Assocs to occurrences...
[INFO] [2021-04-28 11:49:32] Assocs to nodes...
[INFO] [2021-04-28 11:49:32] Assoc to sex term...
[INFO] [2021-04-28 11:49:32] Assoc to lifestage term...
[INFO] [2021-04-28 11:49:32] MetaAssoc to assocs...
[STOP] [2021-04-28 11:49:32] resolve_keys
[START] [2021-04-28 11:49:32] hold_for_later_1
[STOP] [2021-04-28 11:49:32] hold_for_later_1
[START] [2021-04-28 11:49:32] hold_for_later_2
[STOP] [2021-04-28 11:49:32] hold_for_later_2
[START] [2021-04-28 11:49:32] resolve_missing_parents
[STOP] [2021-04-28 11:49:32] resolve_missing_parents
[START] [2021-04-28 11:49:32] rebuild_nodes
[START] [2021-04-28 11:49:32] Flattener#flatten
[START] [2021-04-28 11:49:32] Flattener#study_resource
[START] [2021-04-28 11:49:32] Flattener#build_ancestry
[STOP] [2021-04-28 11:49:32] Flattener#build_ancestry
[INFO] [2021-04-28 11:49:32] 95 ancestry keys
[START] [2021-04-28 11:49:32] build_node_ancestors
[INFO] [2021-04-28 11:49:32] old ancestors deleted.
[STOP] [2021-04-28 11:49:32] build_node_ancestors
[START] [2021-04-28 11:49:32] Flattener#propagate_ancestor_ids
[STOP] [2021-04-28 11:49:32] Flattener#propagate_ancestor_ids
[STOP] [2021-04-28 11:49:32] Flattener#flatten
[STOP] [2021-04-28 11:49:32] rebuild_nodes
[START] [2021-04-28 11:49:32] resolve_missing_media_owners
[STOP] [2021-04-28 11:49:32] resolve_missing_media_owners
[START] [2021-04-28 11:49:32] sanitize_media_verbatims
[STOP] [2021-04-28 11:49:32] sanitize_media_verbatims
[START] [2021-04-28 11:49:32] queue_downloads
[STOP] [2021-04-28 11:49:32] queue_downloads
[START] [2021-04-28 11:49:32] parse_names
[WARN] [2021-04-28 11:49:32] I see 95 names which still need to be parsed.
[WARN] [2021-04-28 11:49:33] I see 1 names which still need to be parsed.
[STOP] [2021-04-28 11:49:34] parse_names
[START] [2021-04-28 11:49:34] denormalize_canonical_names_to_nodes
[STOP] [2021-04-28 11:49:34] denormalize_canonical_names_to_nodes
[START] [2021-04-28 11:49:34] match_nodes
[START] [2021-04-28 11:49:34] map_all_nodes_to_pages
[STOP] [2021-04-28 11:50:11] map_all_nodes_to_pages
[INFO] [2021-04-28 11:50:11] Unmatched nodes (5 of 95): Arctostaphylos (#93345372); Matteuccia struthiopteris (#93345408); Rhododenrdon groenlandicum (#93345427); Vaccinum (#93345447); Dendragapus canadensis (#93345392)
[START] [2021-04-28 11:50:11] update_nodes
[STOP] [2021-04-28 11:50:11] update_nodes
[STOP] [2021-04-28 11:50:11] match_nodes
[START] [2021-04-28 11:50:11] reindex_search
[STOP] [2021-04-28 11:50:12] reindex_search
[START] [2021-04-28 11:50:12] normalize_units
[STOP] [2021-04-28 11:50:12] normalize_units
[START] [2021-04-28 11:50:12] calculate_statistics
[STOP] [2021-04-28 11:50:12] calculate_statistics
[START] [2021-04-28 11:50:12] complete_harvest_instance
[START] [2021-04-28 11:50:12] overall_tsv_creation
[INFO] [2021-04-28 11:50:12] Processing group of 95 in 1 batches of 10000
[2021-04-28 11:51:58] Encountered new language, please assign it to a Locale and give it a name: mic
[INFO] [2021-04-28 11:52:05] Average Time: 6.66
[INFO] [2021-04-28 11:52:05] Total Time: 1m53s
[STOP] [2021-04-28 11:52:05] overall_tsv_creation
[INFO] [2021-04-28 11:52:05] Done. Check your files:
[INFO] [2021-04-28 11:52:06] (94 lines) /app/public/data/mikmaq_names/publish_nodes.tsv
[INFO] [2021-04-28 11:52:07] (210 lines) /app/public/data/mikmaq_names/publish_node_ancestors.tsv
[INFO] [2021-04-28 11:52:09] (95 lines) /app/public/data/mikmaq_names/publish_scientific_names.tsv
[INFO] [2021-04-28 11:52:10] (88 lines) /app/public/data/mikmaq_names/publish_vernaculars.tsv
[STOP] [2021-04-28 11:52:10] complete_harvest_instance
[START] [2021-04-28 11:52:10] completed
[STOP] [2021-04-28 11:52:10] completed
[STOP] [2021-04-28 11:52:10] logged process, took 182.44
Latest Process

28 Apr 11:49 EXITED currently processing 0