Harvest for Jori et al 1998 Created 09 Jul 14:38

Stage: completed
Fetched: 09 Jul 14:38
Validated: 09 Jul 14:38
Deltas Created 09 Jul 14:38
Units Normalized: 09 Jul 14:38
Ancestry Built: 09 Jul 14:38
Nodes Matched: 09 Jul 14:38
Names Parsed: 09 Jul 14:38
New Models Stored: 09 Jul 14:38
Indexed: 09 Jul 14:38
Completed: 09 Jul 14:40
Time to Harvest: less than a minute
Harvesting Log

(126 lines)
# Logfile created on 2020-07-09 14:38:34 -0400 by logger.rb/v1.4.2
[INFO] [2020-07-09 14:38:34] ## HARVEST: type = -harvest
[START] [2020-07-09 14:38:35] logged process
[START] [2020-07-09 14:38:35] create_harvest_instance
[STOP] [2020-07-09 14:38:36] create_harvest_instance
[START] [2020-07-09 14:38:36] fetch_files
[STOP] [2020-07-09 14:38:36] fetch_files
[START] [2020-07-09 14:38:36] validate_each_file
[STOP] [2020-07-09 14:38:36] validate_each_file
[START] [2020-07-09 14:38:36] convert_to_csv
[CMD] [2020-07-09 14:38:36] /usr/bin/sort /app/public/converted_csv/jori_et_al_jori__nodes_21530.csv > /app/public/converted_csv/jori_et_al_jori__nodes_21530.csv_sorted
[CMD] [2020-07-09 14:38:36] /usr/bin/sort /app/public/converted_csv/jori_et_al_jori__occurrences_21531.csv > /app/public/converted_csv/jori_et_al_jori__occurrences_21531.csv_sorted
[CMD] [2020-07-09 14:38:36] /usr/bin/sort /app/public/converted_csv/jori_et_al_jori__measurements_21532.csv > /app/public/converted_csv/jori_et_al_jori__measurements_21532.csv_sorted
[STOP] [2020-07-09 14:38:36] convert_to_csv
[START] [2020-07-09 14:38:36] calculate_delta
[CMD] [2020-07-09 14:38:36] echo "0a" > /app/public/diff/jori_et_al_jori__nodes_21530.diff
[CMD] [2020-07-09 14:38:36] tail -n +1 /app/public/converted_csv/jori_et_al_jori__nodes_21530.csv >> /app/public/diff/jori_et_al_jori__nodes_21530.diff
[CMD] [2020-07-09 14:38:36] echo "." >> /app/public/diff/jori_et_al_jori__nodes_21530.diff
[CMD] [2020-07-09 14:38:36] echo "0a" > /app/public/diff/jori_et_al_jori__occurrences_21531.diff
[CMD] [2020-07-09 14:38:36] tail -n +1 /app/public/converted_csv/jori_et_al_jori__occurrences_21531.csv >> /app/public/diff/jori_et_al_jori__occurrences_21531.diff
[CMD] [2020-07-09 14:38:36] echo "." >> /app/public/diff/jori_et_al_jori__occurrences_21531.diff
[CMD] [2020-07-09 14:38:36] echo "0a" > /app/public/diff/jori_et_al_jori__measurements_21532.diff
[CMD] [2020-07-09 14:38:36] tail -n +1 /app/public/converted_csv/jori_et_al_jori__measurements_21532.csv >> /app/public/diff/jori_et_al_jori__measurements_21532.diff
[CMD] [2020-07-09 14:38:36] echo "." >> /app/public/diff/jori_et_al_jori__measurements_21532.diff
[STOP] [2020-07-09 14:38:36] calculate_delta
[START] [2020-07-09 14:38:36] parse_diff_and_store
[INFO] [2020-07-09 14:38:36] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-09 14:38:37] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-09 14:38:37] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-09 14:38:37] Storing 1 ScientificNames
[INFO] [2020-07-09 14:38:37] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-09 14:38:37] Average Time: 0.0
[INFO] [2020-07-09 14:38:37] Total Time: 1s
[INFO] [2020-07-09 14:38:37] Storing 1 Nodes
[INFO] [2020-07-09 14:38:37] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-09 14:38:37] Average Time: 0.01
[INFO] [2020-07-09 14:38:37] Total Time: 1s
[INFO] [2020-07-09 14:38:37] Storing 1 Occurrences
[INFO] [2020-07-09 14:38:37] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-09 14:38:37] Average Time: 0.0
[INFO] [2020-07-09 14:38:37] Total Time: 1s
[INFO] [2020-07-09 14:38:37] Storing 5 Traits
[INFO] [2020-07-09 14:38:37] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-09 14:38:37] Average Time: 0.0
[INFO] [2020-07-09 14:38:37] Total Time: 1s
[INFO] [2020-07-09 14:38:37] Storing 10 MetaTraits
[INFO] [2020-07-09 14:38:37] Processing group of 10 in 1 groups of 1000
[INFO] [2020-07-09 14:38:37] Average Time: 0.0
[INFO] [2020-07-09 14:38:37] Total Time: 1s
[STOP] [2020-07-09 14:38:37] parse_diff_and_store
[START] [2020-07-09 14:38:37] resolve_keys
[INFO] [2020-07-09 14:38:43] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-09 14:38:43] traits to occurrences...
[INFO] [2020-07-09 14:38:43] traits to nodes (through occurrences)...
[INFO] [2020-07-09 14:38:43] Traits to sex term...
[INFO] [2020-07-09 14:38:43] Traits to lifestage term...
[INFO] [2020-07-09 14:38:43] MetaTraits to traits...
[INFO] [2020-07-09 14:38:43] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-09 14:38:43] Assocs to occurrences...
[INFO] [2020-07-09 14:38:43] Assocs to nodes...
[INFO] [2020-07-09 14:38:43] Assoc to sex term...
[INFO] [2020-07-09 14:38:43] Assoc to lifestage term...
[STOP] [2020-07-09 14:38:43] resolve_keys
[START] [2020-07-09 14:38:43] hold_for_later_1
[STOP] [2020-07-09 14:38:43] hold_for_later_1
[START] [2020-07-09 14:38:43] hold_for_later_2
[STOP] [2020-07-09 14:38:43] hold_for_later_2
[START] [2020-07-09 14:38:43] resolve_missing_parents
[STOP] [2020-07-09 14:38:43] resolve_missing_parents
[START] [2020-07-09 14:38:43] rebuild_nodes
[START] [2020-07-09 14:38:43] Flattener#flatten
[START] [2020-07-09 14:38:43] Flattener#study_resource
[START] [2020-07-09 14:38:43] Flattener#build_ancestry
[STOP] [2020-07-09 14:38:43] Flattener#build_ancestry
[INFO] [2020-07-09 14:38:43] 1 ancestry keys
[START] [2020-07-09 14:38:43] build_node_ancestors
[INFO] [2020-07-09 14:38:43] old ancestors deleted.
[STOP] [2020-07-09 14:38:43] build_node_ancestors
[WARN] [2020-07-09 14:38:43] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-09 14:38:43] Flattener#flatten
[STOP] [2020-07-09 14:38:43] rebuild_nodes
[START] [2020-07-09 14:38:43] resolve_missing_media_owners
[STOP] [2020-07-09 14:38:43] resolve_missing_media_owners
[START] [2020-07-09 14:38:43] sanitize_media_verbatims
[STOP] [2020-07-09 14:38:43] sanitize_media_verbatims
[START] [2020-07-09 14:38:43] queue_downloads
[STOP] [2020-07-09 14:38:43] queue_downloads
[START] [2020-07-09 14:38:43] parse_names
[WARN] [2020-07-09 14:38:43] I see 1 names which still need to be parsed.
[STOP] [2020-07-09 14:38:44] parse_names
[START] [2020-07-09 14:38:44] denormalize_canonical_names_to_nodes
[STOP] [2020-07-09 14:38:44] denormalize_canonical_names_to_nodes
[START] [2020-07-09 14:38:45] match_nodes
[START] [2020-07-09 14:38:45] map_all_nodes_to_pages
[STOP] [2020-07-09 14:38:45] map_all_nodes_to_pages
[INFO] [2020-07-09 14:38:45] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-09 14:38:45] update_nodes
[STOP] [2020-07-09 14:38:45] update_nodes
[STOP] [2020-07-09 14:38:45] match_nodes
[START] [2020-07-09 14:38:45] reindex_search
[STOP] [2020-07-09 14:38:45] reindex_search
[START] [2020-07-09 14:38:45] normalize_units
[STOP] [2020-07-09 14:38:45] normalize_units
[START] [2020-07-09 14:38:45] calculate_statistics
[2020-07-09 14:38:45] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-09 14:38:45] calculate_statistics
[START] [2020-07-09 14:38:45] complete_harvest_instance
[START] [2020-07-09 14:38:45] overall_tsv_creation
[INFO] [2020-07-09 14:38:45] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-09 14:39:33] 5 Traits (unfiltered)...
[INFO] [2020-07-09 14:39:45] 5 Traits (filtered)...
[INFO] [2020-07-09 14:39:45] 0 Associations (filtered)...
[INFO] [2020-07-09 14:40:19] 10 metadata added.
[INFO] [2020-07-09 14:40:19] 0 metadata added.
[INFO] [2020-07-09 14:40:19] Average Time: 66.71
[INFO] [2020-07-09 14:40:19] Total Time: 1m35s
[STOP] [2020-07-09 14:40:19] overall_tsv_creation
[INFO] [2020-07-09 14:40:19] Done. Check your files:
[INFO] [2020-07-09 14:40:19] (1 lines) /app/public/data/jori_et_al_jori_/publish_nodes.tsv
[INFO] [2020-07-09 14:40:19] (1 lines) /app/public/data/jori_et_al_jori_/publish_scientific_names.tsv
[INFO] [2020-07-09 14:40:19] (6 lines) /app/public/data/jori_et_al_jori_/publish_traits.tsv
[INFO] [2020-07-09 14:40:19] (11 lines) /app/public/data/jori_et_al_jori_/publish_metadata.tsv
[STOP] [2020-07-09 14:40:19] complete_harvest_instance
[START] [2020-07-09 14:40:19] completed
[STOP] [2020-07-09 14:40:19] completed
[STOP] [2020-07-09 14:40:19] logged process, took 104.02
Latest Process

09 Jul 14:38 EXITED currently processing 0