Harvest for SINA audio Created 10 Jul 15:42

Stage: completed
Fetched: 10 Jul 15:42
Validated: 10 Jul 15:42
Deltas Created 10 Jul 15:42
Units Normalized: 10 Jul 15:42
Ancestry Built: 10 Jul 15:42
Nodes Matched: 10 Jul 15:42
Names Parsed: 10 Jul 15:42
New Models Stored: 10 Jul 15:42
Indexed: 10 Jul 15:42
Completed: 10 Jul 15:42
Time to Harvest: less than a minute
Harvesting Log

(126 lines)
[START] [2019-07-10 15:42:03] logged process
[START] [2019-07-10 15:42:03] create_harvest_instance
[STOP] [2019-07-10 15:42:05] create_harvest_instance
[START] [2019-07-10 15:42:05] fetch_files
[STOP] [2019-07-10 15:42:05] fetch_files
[START] [2019-07-10 15:42:05] validate_each_file
[STOP] [2019-07-10 15:42:05] validate_each_file
[START] [2019-07-10 15:42:05] convert_to_csv
[CMD] [2019-07-10 15:42:05] /usr/bin/sort /app/public/converted_csv/sina_audio_audio_agents_14134.csv > /app/public/converted_csv/sina_audio_audio_agents_14134.csv_sorted
[CMD] [2019-07-10 15:42:05] /usr/bin/sort /app/public/converted_csv/sina_audio_audio_refs_14135.csv > /app/public/converted_csv/sina_audio_audio_refs_14135.csv_sorted
[CMD] [2019-07-10 15:42:05] /usr/bin/sort /app/public/converted_csv/sina_audio_audio_nodes_14136.csv > /app/public/converted_csv/sina_audio_audio_nodes_14136.csv_sorted
[CMD] [2019-07-10 15:42:05] /usr/bin/sort /app/public/converted_csv/sina_audio_audio_media_14137.csv > /app/public/converted_csv/sina_audio_audio_media_14137.csv_sorted
[CMD] [2019-07-10 15:42:05] /usr/bin/sort /app/public/converted_csv/sina_audio_audio_vernaculars_14138.csv > /app/public/converted_csv/sina_audio_audio_vernaculars_14138.csv_sorted
[STOP] [2019-07-10 15:42:05] convert_to_csv
[START] [2019-07-10 15:42:05] calculate_delta
[CMD] [2019-07-10 15:42:05] echo "0a" > /app/public/diff/sina_audio_audio_agents_14134.diff
[CMD] [2019-07-10 15:42:05] tail -n +1 /app/public/converted_csv/sina_audio_audio_agents_14134.csv >> /app/public/diff/sina_audio_audio_agents_14134.diff
[CMD] [2019-07-10 15:42:05] echo "." >> /app/public/diff/sina_audio_audio_agents_14134.diff
[CMD] [2019-07-10 15:42:05] echo "0a" > /app/public/diff/sina_audio_audio_refs_14135.diff
[CMD] [2019-07-10 15:42:05] tail -n +1 /app/public/converted_csv/sina_audio_audio_refs_14135.csv >> /app/public/diff/sina_audio_audio_refs_14135.diff
[CMD] [2019-07-10 15:42:05] echo "." >> /app/public/diff/sina_audio_audio_refs_14135.diff
[CMD] [2019-07-10 15:42:05] echo "0a" > /app/public/diff/sina_audio_audio_nodes_14136.diff
[CMD] [2019-07-10 15:42:05] tail -n +1 /app/public/converted_csv/sina_audio_audio_nodes_14136.csv >> /app/public/diff/sina_audio_audio_nodes_14136.diff
[CMD] [2019-07-10 15:42:05] echo "." >> /app/public/diff/sina_audio_audio_nodes_14136.diff
[CMD] [2019-07-10 15:42:05] echo "0a" > /app/public/diff/sina_audio_audio_media_14137.diff
[CMD] [2019-07-10 15:42:05] tail -n +1 /app/public/converted_csv/sina_audio_audio_media_14137.csv >> /app/public/diff/sina_audio_audio_media_14137.diff
[CMD] [2019-07-10 15:42:05] echo "." >> /app/public/diff/sina_audio_audio_media_14137.diff
[CMD] [2019-07-10 15:42:05] echo "0a" > /app/public/diff/sina_audio_audio_vernaculars_14138.diff
[CMD] [2019-07-10 15:42:05] tail -n +1 /app/public/converted_csv/sina_audio_audio_vernaculars_14138.csv >> /app/public/diff/sina_audio_audio_vernaculars_14138.diff
[CMD] [2019-07-10 15:42:05] echo "." >> /app/public/diff/sina_audio_audio_vernaculars_14138.diff
[STOP] [2019-07-10 15:42:05] calculate_delta
[START] [2019-07-10 15:42:05] parse_diff_and_store
[INFO] [2019-07-10 15:42:05] Loading agents diff file into memory (true lines)...
[INFO] [2019-07-10 15:42:05] Loading refs diff file into memory (true lines)...
[INFO] [2019-07-10 15:42:05] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-10 15:42:05] Loading media diff file into memory (true lines)...
[INFO] [2019-07-10 15:42:05] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-07-10 15:42:06] Storing 207 ScientificNames
[INFO] [2019-07-10 15:42:06] Processing group of 207 in 1 groups of 1000
[INFO] [2019-07-10 15:42:06] Average Time: 0.13
[INFO] [2019-07-10 15:42:06] Total Time: 1s
[INFO] [2019-07-10 15:42:06] Storing 207 Nodes
[INFO] [2019-07-10 15:42:06] Processing group of 207 in 1 groups of 1000
[INFO] [2019-07-10 15:42:06] Average Time: 0.1
[INFO] [2019-07-10 15:42:06] Total Time: 1s
[INFO] [2019-07-10 15:42:06] Storing 265 Media
[INFO] [2019-07-10 15:42:06] Processing group of 265 in 1 groups of 1000
[INFO] [2019-07-10 15:42:06] Average Time: 0.14
[INFO] [2019-07-10 15:42:06] Total Time: 1s
[INFO] [2019-07-10 15:42:06] Storing 203 Vernaculars
[INFO] [2019-07-10 15:42:06] Processing group of 203 in 1 groups of 1000
[INFO] [2019-07-10 15:42:06] Average Time: 0.04
[INFO] [2019-07-10 15:42:06] Total Time: 1s
[STOP] [2019-07-10 15:42:06] parse_diff_and_store
[START] [2019-07-10 15:42:06] resolve_keys
[INFO] [2019-07-10 15:42:10] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-10 15:42:10] traits to occurrences...
[INFO] [2019-07-10 15:42:10] traits to nodes (through occurrences)...
[INFO] [2019-07-10 15:42:10] Traits to sex term...
[INFO] [2019-07-10 15:42:10] Traits to lifestage term...
[INFO] [2019-07-10 15:42:10] MetaTraits to traits...
[INFO] [2019-07-10 15:42:10] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-10 15:42:10] Assocs to occurrences...
[INFO] [2019-07-10 15:42:10] Assocs to nodes...
[INFO] [2019-07-10 15:42:10] Assoc to sex term...
[INFO] [2019-07-10 15:42:10] Assoc to lifestage term...
[STOP] [2019-07-10 15:42:10] resolve_keys
[START] [2019-07-10 15:42:10] hold_for_later_1
[STOP] [2019-07-10 15:42:10] hold_for_later_1
[START] [2019-07-10 15:42:10] hold_for_later_2
[STOP] [2019-07-10 15:42:10] hold_for_later_2
[START] [2019-07-10 15:42:10] resolve_missing_parents
[STOP] [2019-07-10 15:42:10] resolve_missing_parents
[START] [2019-07-10 15:42:10] rebuild_nodes
[START] [2019-07-10 15:42:10] Flattener#flatten
[START] [2019-07-10 15:42:10] Flattener#study_resource
[START] [2019-07-10 15:42:10] Flattener#build_ancestry
[STOP] [2019-07-10 15:42:10] Flattener#build_ancestry
[INFO] [2019-07-10 15:42:10] 207 ancestry keys
[START] [2019-07-10 15:42:10] build_node_ancestors
[INFO] [2019-07-10 15:42:10] old ancestors deleted.
[STOP] [2019-07-10 15:42:10] build_node_ancestors
[START] [2019-07-10 15:42:10] Flattener#propagate_ancestor_ids
[STOP] [2019-07-10 15:42:10] Flattener#propagate_ancestor_ids
[STOP] [2019-07-10 15:42:10] Flattener#flatten
[STOP] [2019-07-10 15:42:10] rebuild_nodes
[START] [2019-07-10 15:42:10] resolve_missing_media_owners
[STOP] [2019-07-10 15:42:10] resolve_missing_media_owners
[START] [2019-07-10 15:42:10] sanitize_media_verbatims
[STOP] [2019-07-10 15:42:10] sanitize_media_verbatims
[START] [2019-07-10 15:42:10] queue_downloads
[STOP] [2019-07-10 15:42:10] queue_downloads
[START] [2019-07-10 15:42:10] parse_names
[WARN] [2019-07-10 15:42:10] I see 207 names which still need to be parsed.
[STOP] [2019-07-10 15:42:11] parse_names
[START] [2019-07-10 15:42:11] denormalize_canonical_names_to_nodes
[STOP] [2019-07-10 15:42:11] denormalize_canonical_names_to_nodes
[START] [2019-07-10 15:42:11] match_nodes
[START] [2019-07-10 15:42:11] map_all_nodes_to_pages
[STOP] [2019-07-10 15:42:18] map_all_nodes_to_pages
[INFO] [2019-07-10 15:42:18] Unmatched nodes (3 of 207): Antillicharis gryllodes (#44147956); Cycloptilum trogonipalpum (#44148002); Metrioptera roeselii (#44148039)
[START] [2019-07-10 15:42:18] update_nodes
[STOP] [2019-07-10 15:42:18] update_nodes
[STOP] [2019-07-10 15:42:18] match_nodes
[START] [2019-07-10 15:42:18] reindex_search
[STOP] [2019-07-10 15:42:19] reindex_search
[START] [2019-07-10 15:42:19] normalize_units
[STOP] [2019-07-10 15:42:19] normalize_units
[START] [2019-07-10 15:42:19] calculate_statistics
[STOP] [2019-07-10 15:42:19] calculate_statistics
[START] [2019-07-10 15:42:19] complete_harvest_instance
[START] [2019-07-10 15:42:19] overall_tsv_creation
[INFO] [2019-07-10 15:42:19] Processing group of 207 in 1 batches of 10000
[INFO] [2019-07-10 15:42:53] Average Time: 12.54
[INFO] [2019-07-10 15:42:53] Total Time: 34s
[STOP] [2019-07-10 15:42:53] overall_tsv_creation
[INFO] [2019-07-10 15:42:53] Done. Check your files:
[INFO] [2019-07-10 15:42:53] (207 lines) /app/public/data/sina_audio_audio/publish_nodes.tsv
[INFO] [2019-07-10 15:42:53] (818 lines) /app/public/data/sina_audio_audio/publish_node_ancestors.tsv
[INFO] [2019-07-10 15:42:53] (207 lines) /app/public/data/sina_audio_audio/publish_scientific_names.tsv
[INFO] [2019-07-10 15:42:53] (265 lines) /app/public/data/sina_audio_audio/publish_media.tsv
[INFO] [2019-07-10 15:42:53] (203 lines) /app/public/data/sina_audio_audio/publish_vernaculars.tsv
[STOP] [2019-07-10 15:42:53] complete_harvest_instance
[START] [2019-07-10 15:42:53] completed
[STOP] [2019-07-10 15:42:53] completed
[STOP] [2019-07-10 15:42:53] logged process, took 50.65
Latest Process

10 Jul 15:42 EXITED currently processing 0