Harvest for Geng and Mu 2005 Created 16 Jun 09:42

Stage: completed
Fetched: 16 Jun 09:42
Validated: 16 Jun 09:42
Deltas Created 16 Jun 09:42
Units Normalized: 16 Jun 09:42
Ancestry Built: 16 Jun 09:42
Nodes Matched: 16 Jun 09:42
Names Parsed: 16 Jun 09:42
New Models Stored: 16 Jun 09:42
Indexed: 16 Jun 09:42
Completed: 16 Jun 09:44
Time to Harvest: less than a minute
Harvesting Log

(127 lines)
# Logfile created on 2020-06-16 09:42:08 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-16 09:42:08] ## HARVEST: type = -harvest
[START] [2020-06-16 09:42:12] logged process
[START] [2020-06-16 09:42:12] create_harvest_instance
[STOP] [2020-06-16 09:42:13] create_harvest_instance
[START] [2020-06-16 09:42:13] fetch_files
[STOP] [2020-06-16 09:42:13] fetch_files
[START] [2020-06-16 09:42:13] validate_each_file
[STOP] [2020-06-16 09:42:13] validate_each_file
[START] [2020-06-16 09:42:13] convert_to_csv
[CMD] [2020-06-16 09:42:13] /usr/bin/sort /app/public/converted_csv/geng_mu_geng_and_nodes_21300.csv > /app/public/converted_csv/geng_mu_geng_and_nodes_21300.csv_sorted
[CMD] [2020-06-16 09:42:13] /usr/bin/sort /app/public/converted_csv/geng_mu_geng_and_occurrences_21301.csv > /app/public/converted_csv/geng_mu_geng_and_occurrences_21301.csv_sorted
[CMD] [2020-06-16 09:42:13] /usr/bin/sort /app/public/converted_csv/geng_mu_geng_and_measurements_21302.csv > /app/public/converted_csv/geng_mu_geng_and_measurements_21302.csv_sorted
[STOP] [2020-06-16 09:42:13] convert_to_csv
[START] [2020-06-16 09:42:13] calculate_delta
[CMD] [2020-06-16 09:42:13] echo "0a" > /app/public/diff/geng_mu_geng_and_nodes_21300.diff
[CMD] [2020-06-16 09:42:13] tail -n +1 /app/public/converted_csv/geng_mu_geng_and_nodes_21300.csv >> /app/public/diff/geng_mu_geng_and_nodes_21300.diff
[CMD] [2020-06-16 09:42:13] echo "." >> /app/public/diff/geng_mu_geng_and_nodes_21300.diff
[CMD] [2020-06-16 09:42:13] echo "0a" > /app/public/diff/geng_mu_geng_and_occurrences_21301.diff
[CMD] [2020-06-16 09:42:13] tail -n +1 /app/public/converted_csv/geng_mu_geng_and_occurrences_21301.csv >> /app/public/diff/geng_mu_geng_and_occurrences_21301.diff
[CMD] [2020-06-16 09:42:13] echo "." >> /app/public/diff/geng_mu_geng_and_occurrences_21301.diff
[CMD] [2020-06-16 09:42:13] echo "0a" > /app/public/diff/geng_mu_geng_and_measurements_21302.diff
[CMD] [2020-06-16 09:42:13] tail -n +1 /app/public/converted_csv/geng_mu_geng_and_measurements_21302.csv >> /app/public/diff/geng_mu_geng_and_measurements_21302.diff
[CMD] [2020-06-16 09:42:14] echo "." >> /app/public/diff/geng_mu_geng_and_measurements_21302.diff
[STOP] [2020-06-16 09:42:14] calculate_delta
[START] [2020-06-16 09:42:14] parse_diff_and_store
[INFO] [2020-06-16 09:42:14] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-16 09:42:14] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-16 09:42:14] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-16 09:42:14] Storing 4 ScientificNames
[INFO] [2020-06-16 09:42:14] Processing group of 4 in 1 groups of 1000
[INFO] [2020-06-16 09:42:14] Average Time: 0.0
[INFO] [2020-06-16 09:42:14] Total Time: 1s
[INFO] [2020-06-16 09:42:14] Storing 4 Nodes
[INFO] [2020-06-16 09:42:14] Processing group of 4 in 1 groups of 1000
[INFO] [2020-06-16 09:42:14] Average Time: 0.0
[INFO] [2020-06-16 09:42:14] Total Time: 1s
[INFO] [2020-06-16 09:42:14] Storing 1 Occurrences
[INFO] [2020-06-16 09:42:14] Processing group of 1 in 1 groups of 1000
[INFO] [2020-06-16 09:42:14] Average Time: 0.0
[INFO] [2020-06-16 09:42:14] Total Time: 1s
[INFO] [2020-06-16 09:42:14] Storing 2 Traits
[INFO] [2020-06-16 09:42:14] Processing group of 2 in 1 groups of 1000
[INFO] [2020-06-16 09:42:14] Average Time: 0.0
[INFO] [2020-06-16 09:42:14] Total Time: 1s
[INFO] [2020-06-16 09:42:14] Storing 4 MetaTraits
[INFO] [2020-06-16 09:42:14] Processing group of 4 in 1 groups of 1000
[INFO] [2020-06-16 09:42:14] Average Time: 0.0
[INFO] [2020-06-16 09:42:14] Total Time: 1s
[STOP] [2020-06-16 09:42:14] parse_diff_and_store
[START] [2020-06-16 09:42:14] resolve_keys
[INFO] [2020-06-16 09:42:21] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-16 09:42:21] traits to occurrences...
[INFO] [2020-06-16 09:42:21] traits to nodes (through occurrences)...
[INFO] [2020-06-16 09:42:21] Traits to sex term...
[INFO] [2020-06-16 09:42:21] Traits to lifestage term...
[INFO] [2020-06-16 09:42:21] MetaTraits to traits...
[INFO] [2020-06-16 09:42:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-16 09:42:21] Assocs to occurrences...
[INFO] [2020-06-16 09:42:21] Assocs to nodes...
[INFO] [2020-06-16 09:42:21] Assoc to sex term...
[INFO] [2020-06-16 09:42:21] Assoc to lifestage term...
[STOP] [2020-06-16 09:42:21] resolve_keys
[START] [2020-06-16 09:42:21] hold_for_later_1
[STOP] [2020-06-16 09:42:21] hold_for_later_1
[START] [2020-06-16 09:42:21] hold_for_later_2
[STOP] [2020-06-16 09:42:21] hold_for_later_2
[START] [2020-06-16 09:42:21] resolve_missing_parents
[STOP] [2020-06-16 09:42:21] resolve_missing_parents
[START] [2020-06-16 09:42:21] rebuild_nodes
[START] [2020-06-16 09:42:21] Flattener#flatten
[START] [2020-06-16 09:42:21] Flattener#study_resource
[START] [2020-06-16 09:42:21] Flattener#build_ancestry
[STOP] [2020-06-16 09:42:21] Flattener#build_ancestry
[INFO] [2020-06-16 09:42:21] 4 ancestry keys
[START] [2020-06-16 09:42:21] build_node_ancestors
[INFO] [2020-06-16 09:42:21] old ancestors deleted.
[STOP] [2020-06-16 09:42:21] build_node_ancestors
[START] [2020-06-16 09:42:21] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:42:21] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:42:21] Flattener#flatten
[STOP] [2020-06-16 09:42:21] rebuild_nodes
[START] [2020-06-16 09:42:21] resolve_missing_media_owners
[STOP] [2020-06-16 09:42:21] resolve_missing_media_owners
[START] [2020-06-16 09:42:21] sanitize_media_verbatims
[STOP] [2020-06-16 09:42:21] sanitize_media_verbatims
[START] [2020-06-16 09:42:21] queue_downloads
[STOP] [2020-06-16 09:42:21] queue_downloads
[START] [2020-06-16 09:42:21] parse_names
[WARN] [2020-06-16 09:42:21] I see 4 names which still need to be parsed.
[STOP] [2020-06-16 09:42:22] parse_names
[START] [2020-06-16 09:42:22] denormalize_canonical_names_to_nodes
[STOP] [2020-06-16 09:42:22] denormalize_canonical_names_to_nodes
[START] [2020-06-16 09:42:22] match_nodes
[START] [2020-06-16 09:42:22] map_all_nodes_to_pages
[STOP] [2020-06-16 09:42:22] map_all_nodes_to_pages
[INFO] [2020-06-16 09:42:22] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2020-06-16 09:42:22] update_nodes
[STOP] [2020-06-16 09:42:22] update_nodes
[STOP] [2020-06-16 09:42:22] match_nodes
[START] [2020-06-16 09:42:22] reindex_search
[STOP] [2020-06-16 09:42:22] reindex_search
[START] [2020-06-16 09:42:22] normalize_units
[STOP] [2020-06-16 09:42:22] normalize_units
[START] [2020-06-16 09:42:22] calculate_statistics
[STOP] [2020-06-16 09:42:22] calculate_statistics
[START] [2020-06-16 09:42:22] complete_harvest_instance
[START] [2020-06-16 09:42:22] overall_tsv_creation
[INFO] [2020-06-16 09:42:22] Processing group of 4 in 1 batches of 10000
[INFO] [2020-06-16 09:43:13] 1 Traits (unfiltered)...
[INFO] [2020-06-16 09:43:26] 1 Traits (filtered)...
[INFO] [2020-06-16 09:43:26] 0 Associations (filtered)...
[INFO] [2020-06-16 09:44:03] 4 metadata added.
[INFO] [2020-06-16 09:44:03] 0 metadata added.
[INFO] [2020-06-16 09:44:03] Average Time: 73.04
[INFO] [2020-06-16 09:44:03] Total Time: 1m42s
[STOP] [2020-06-16 09:44:03] overall_tsv_creation
[INFO] [2020-06-16 09:44:03] Done. Check your files:
[INFO] [2020-06-16 09:44:03] (4 lines) /app/public/data/geng_mu_geng_and/publish_nodes.tsv
[INFO] [2020-06-16 09:44:03] (6 lines) /app/public/data/geng_mu_geng_and/publish_node_ancestors.tsv
[INFO] [2020-06-16 09:44:03] (4 lines) /app/public/data/geng_mu_geng_and/publish_scientific_names.tsv
[INFO] [2020-06-16 09:44:03] (2 lines) /app/public/data/geng_mu_geng_and/publish_traits.tsv
[INFO] [2020-06-16 09:44:03] (5 lines) /app/public/data/geng_mu_geng_and/publish_metadata.tsv
[STOP] [2020-06-16 09:44:03] complete_harvest_instance
[START] [2020-06-16 09:44:04] completed
[STOP] [2020-06-16 09:44:04] completed
[STOP] [2020-06-16 09:44:04] logged process, took 111.32
Latest Process

16 Jun 09:42 EXITED currently processing 0