Harvest for Rhododendron Images from Curtis Botanical Magazine Created 31 Dec 12:28

Stage: completed
Fetched: 31 Dec 12:28
Validated: 31 Dec 12:28
Deltas Created 31 Dec 12:28
Units Normalized: 31 Dec 12:28
Ancestry Built: 31 Dec 12:28
Nodes Matched: 31 Dec 12:28
Names Parsed: 31 Dec 12:28
New Models Stored: 31 Dec 12:28
Indexed: 31 Dec 12:28
Completed: 31 Dec 12:29
Time to Harvest: less than a minute
Harvesting Log

(123 lines)
# Logfile created on 2019-12-31 12:28:10 -0500 by logger.rb/56815
[START] [2019-12-31 12:28:10] logged process
[START] [2019-12-31 12:28:10] create_harvest_instance
[STOP] [2019-12-31 12:28:11] create_harvest_instance
[START] [2019-12-31 12:28:11] fetch_files
[STOP] [2019-12-31 12:28:11] fetch_files
[START] [2019-12-31 12:28:11] validate_each_file
[STOP] [2019-12-31 12:28:11] validate_each_file
[START] [2019-12-31 12:28:11] convert_to_csv
[CMD] [2019-12-31 12:28:11] /usr/bin/sort /app/public/converted_csv/rifcb_agents_19882.csv > /app/public/converted_csv/rifcb_agents_19882.csv_sorted
[CMD] [2019-12-31 12:28:12] /usr/bin/sort /app/public/converted_csv/rifcb_nodes_19883.csv > /app/public/converted_csv/rifcb_nodes_19883.csv_sorted
[CMD] [2019-12-31 12:28:13] /usr/bin/sort /app/public/converted_csv/rifcb_media_19884.csv > /app/public/converted_csv/rifcb_media_19884.csv_sorted
[STOP] [2019-12-31 12:28:13] convert_to_csv
[START] [2019-12-31 12:28:13] calculate_delta
[CMD] [2019-12-31 12:28:13] echo "0a" > /app/public/diff/rifcb_agents_19882.diff
[CMD] [2019-12-31 12:28:14] tail -n +1 /app/public/converted_csv/rifcb_agents_19882.csv >> /app/public/diff/rifcb_agents_19882.diff
[CMD] [2019-12-31 12:28:15] echo "." >> /app/public/diff/rifcb_agents_19882.diff
[CMD] [2019-12-31 12:28:15] echo "0a" > /app/public/diff/rifcb_nodes_19883.diff
[CMD] [2019-12-31 12:28:16] tail -n +1 /app/public/converted_csv/rifcb_nodes_19883.csv >> /app/public/diff/rifcb_nodes_19883.diff
[CMD] [2019-12-31 12:28:17] echo "." >> /app/public/diff/rifcb_nodes_19883.diff
[CMD] [2019-12-31 12:28:18] echo "0a" > /app/public/diff/rifcb_media_19884.diff
[CMD] [2019-12-31 12:28:18] tail -n +1 /app/public/converted_csv/rifcb_media_19884.csv >> /app/public/diff/rifcb_media_19884.diff
[CMD] [2019-12-31 12:28:19] echo "." >> /app/public/diff/rifcb_media_19884.diff
[STOP] [2019-12-31 12:28:20] calculate_delta
[START] [2019-12-31 12:28:20] parse_diff_and_store
[INFO] [2019-12-31 12:28:20] Loading agents diff file into memory (true lines)...
[INFO] [2019-12-31 12:28:21] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-31 12:28:22] Loading media diff file into memory (true lines)...
[INFO] [2019-12-31 12:28:22] Storing 2 Attributions
[INFO] [2019-12-31 12:28:22] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-31 12:28:22] Average Time: 0.0
[INFO] [2019-12-31 12:28:22] Total Time: 1s
[INFO] [2019-12-31 12:28:22] Storing 60 ScientificNames
[INFO] [2019-12-31 12:28:22] Processing group of 60 in 1 groups of 1000
[INFO] [2019-12-31 12:28:22] Average Time: 0.03
[INFO] [2019-12-31 12:28:22] Total Time: 1s
[INFO] [2019-12-31 12:28:22] Storing 60 Nodes
[INFO] [2019-12-31 12:28:22] Processing group of 60 in 1 groups of 1000
[INFO] [2019-12-31 12:28:22] Average Time: 0.02
[INFO] [2019-12-31 12:28:22] Total Time: 1s
[INFO] [2019-12-31 12:28:22] Storing 59 BibliographicCitations
[INFO] [2019-12-31 12:28:22] Processing group of 59 in 1 groups of 1000
[INFO] [2019-12-31 12:28:22] Average Time: 0.01
[INFO] [2019-12-31 12:28:22] Total Time: 1s
[INFO] [2019-12-31 12:28:22] Storing 118 ContentAttributions
[INFO] [2019-12-31 12:28:22] Processing group of 118 in 1 groups of 1000
[INFO] [2019-12-31 12:28:22] Average Time: 0.05
[INFO] [2019-12-31 12:28:22] Total Time: 1s
[INFO] [2019-12-31 12:28:22] Storing 59 Media
[INFO] [2019-12-31 12:28:22] Processing group of 59 in 1 groups of 1000
[INFO] [2019-12-31 12:28:22] Average Time: 0.04
[INFO] [2019-12-31 12:28:22] Total Time: 1s
[STOP] [2019-12-31 12:28:22] parse_diff_and_store
[START] [2019-12-31 12:28:22] resolve_keys
[INFO] [2019-12-31 12:28:27] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-31 12:28:27] traits to occurrences...
[INFO] [2019-12-31 12:28:27] traits to nodes (through occurrences)...
[INFO] [2019-12-31 12:28:27] Traits to sex term...
[INFO] [2019-12-31 12:28:27] Traits to lifestage term...
[INFO] [2019-12-31 12:28:27] MetaTraits to traits...
[INFO] [2019-12-31 12:28:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-31 12:28:27] Assocs to occurrences...
[INFO] [2019-12-31 12:28:27] Assocs to nodes...
[INFO] [2019-12-31 12:28:27] Assoc to sex term...
[INFO] [2019-12-31 12:28:27] Assoc to lifestage term...
[STOP] [2019-12-31 12:28:27] resolve_keys
[START] [2019-12-31 12:28:27] hold_for_later_1
[STOP] [2019-12-31 12:28:27] hold_for_later_1
[START] [2019-12-31 12:28:27] hold_for_later_2
[STOP] [2019-12-31 12:28:27] hold_for_later_2
[START] [2019-12-31 12:28:27] resolve_missing_parents
[STOP] [2019-12-31 12:28:27] resolve_missing_parents
[START] [2019-12-31 12:28:27] rebuild_nodes
[START] [2019-12-31 12:28:27] Flattener#flatten
[START] [2019-12-31 12:28:27] Flattener#study_resource
[START] [2019-12-31 12:28:27] Flattener#build_ancestry
[STOP] [2019-12-31 12:28:27] Flattener#build_ancestry
[INFO] [2019-12-31 12:28:27] 60 ancestry keys
[START] [2019-12-31 12:28:27] build_node_ancestors
[INFO] [2019-12-31 12:28:27] old ancestors deleted.
[STOP] [2019-12-31 12:28:27] build_node_ancestors
[START] [2019-12-31 12:28:27] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 12:28:27] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 12:28:27] Flattener#flatten
[STOP] [2019-12-31 12:28:27] rebuild_nodes
[START] [2019-12-31 12:28:27] resolve_missing_media_owners
[STOP] [2019-12-31 12:28:27] resolve_missing_media_owners
[START] [2019-12-31 12:28:27] sanitize_media_verbatims
[STOP] [2019-12-31 12:28:27] sanitize_media_verbatims
[START] [2019-12-31 12:28:27] queue_downloads
[STOP] [2019-12-31 12:28:27] queue_downloads
[START] [2019-12-31 12:28:27] parse_names
[WARN] [2019-12-31 12:28:27] I see 60 names which still need to be parsed.
[STOP] [2019-12-31 12:28:28] parse_names
[START] [2019-12-31 12:28:28] denormalize_canonical_names_to_nodes
[STOP] [2019-12-31 12:28:28] denormalize_canonical_names_to_nodes
[START] [2019-12-31 12:28:28] match_nodes
[START] [2019-12-31 12:28:28] map_all_nodes_to_pages
[STOP] [2019-12-31 12:28:34] map_all_nodes_to_pages
[INFO] [2019-12-31 12:28:34] Unmatched nodes (6 of 60): Rhododendron falconeri exinuum (#62791586); Rhododendron fortune fortunei (#62791588); Rhododendron iiroratum irroratum (#62791595); Rhododendron neriiflonim neriiflorum (#62791605); Rhododendron virgatum oleifoiium (#62791620); Rhododendron virgatum virgatum (#62791621)
[START] [2019-12-31 12:28:34] update_nodes
[STOP] [2019-12-31 12:28:34] update_nodes
[STOP] [2019-12-31 12:28:34] match_nodes
[START] [2019-12-31 12:28:34] reindex_search
[STOP] [2019-12-31 12:28:35] reindex_search
[START] [2019-12-31 12:28:35] normalize_units
[STOP] [2019-12-31 12:28:35] normalize_units
[START] [2019-12-31 12:28:35] calculate_statistics
[STOP] [2019-12-31 12:28:35] calculate_statistics
[START] [2019-12-31 12:28:35] complete_harvest_instance
[START] [2019-12-31 12:28:35] overall_tsv_creation
[INFO] [2019-12-31 12:28:35] Processing group of 60 in 1 batches of 10000
[INFO] [2019-12-31 12:29:09] Average Time: 12.32
[INFO] [2019-12-31 12:29:09] Total Time: 35s
[STOP] [2019-12-31 12:29:09] overall_tsv_creation
[INFO] [2019-12-31 12:29:09] Done. Check your files:
[INFO] [2019-12-31 12:29:10] (60 lines) /app/public/data/rifcb/publish_nodes.tsv
[INFO] [2019-12-31 12:29:11] (174 lines) /app/public/data/rifcb/publish_node_ancestors.tsv
[INFO] [2019-12-31 12:29:12] (60 lines) /app/public/data/rifcb/publish_scientific_names.tsv
[STOP] [2019-12-31 12:29:12] complete_harvest_instance
[START] [2019-12-31 12:29:12] completed
[STOP] [2019-12-31 12:29:12] completed
[STOP] [2019-12-31 12:29:12] logged process, took 61.21
Latest Process

31 Dec 12:28 EXITED currently processing 0