Harvest for video formats Created 21 Oct 10:56

Stage: completed
Fetched: 21 Oct 10:56
Validated: 21 Oct 10:56
Deltas Created 21 Oct 10:56
Units Normalized: 21 Oct 10:57
Ancestry Built: 21 Oct 10:56
Nodes Matched: 21 Oct 10:57
Names Parsed: 21 Oct 10:57
New Models Stored: 21 Oct 10:56
Indexed: 21 Oct 10:57
Completed: 21 Oct 10:59
Time to Harvest: less than a minute
Harvesting Log

(123 lines)
# Logfile created on 2020-10-21 10:56:17 -0400 by logger.rb/v1.4.2
[START] [2020-10-21 10:56:17] logged process
[START] [2020-10-21 10:56:17] Creating resource from OpenData
[START] [2020-10-21 10:56:18] logged process
[START] [2020-10-21 10:56:18] Parse meta.xml file and create formats with fields
[STOP] [2020-10-21 10:56:18] Parse meta.xml file and create formats with fields
[STOP] [2020-10-21 10:56:18] Creating resource from OpenData
[INFO] [2020-10-21 10:56:43] ## HARVEST: type = -harvest
[START] [2020-10-21 10:56:45] logged process
[START] [2020-10-21 10:56:45] create_harvest_instance
[STOP] [2020-10-21 10:56:46] create_harvest_instance
[START] [2020-10-21 10:56:46] fetch_files
[STOP] [2020-10-21 10:56:47] fetch_files
[START] [2020-10-21 10:56:47] validate_each_file
[STOP] [2020-10-21 10:56:47] validate_each_file
[START] [2020-10-21 10:56:47] convert_to_csv
[CMD] [2020-10-21 10:56:47] /usr/bin/sort /app/public/converted_csv/vid_formats_nodes_22839.csv > /app/public/converted_csv/vid_formats_nodes_22839.csv_sorted
[CMD] [2020-10-21 10:56:47] /usr/bin/sort /app/public/converted_csv/vid_formats_media_22840.csv > /app/public/converted_csv/vid_formats_media_22840.csv_sorted
[STOP] [2020-10-21 10:56:47] convert_to_csv
[START] [2020-10-21 10:56:47] calculate_delta
[CMD] [2020-10-21 10:56:47] echo "0a" > /app/public/diff/vid_formats_nodes_22839.diff
[CMD] [2020-10-21 10:56:47] tail -n +1 /app/public/converted_csv/vid_formats_nodes_22839.csv >> /app/public/diff/vid_formats_nodes_22839.diff
[CMD] [2020-10-21 10:56:47] echo "." >> /app/public/diff/vid_formats_nodes_22839.diff
[CMD] [2020-10-21 10:56:47] echo "0a" > /app/public/diff/vid_formats_media_22840.diff
[CMD] [2020-10-21 10:56:47] tail -n +1 /app/public/converted_csv/vid_formats_media_22840.csv >> /app/public/diff/vid_formats_media_22840.diff
[CMD] [2020-10-21 10:56:47] echo "." >> /app/public/diff/vid_formats_media_22840.diff
[STOP] [2020-10-21 10:56:47] calculate_delta
[START] [2020-10-21 10:56:47] parse_diff_and_store
[INFO] [2020-10-21 10:56:47] Loading nodes diff file into memory (true lines)...
[INFO] [2020-10-21 10:56:47] Loading media diff file into memory (true lines)...
[WARN] [2020-10-21 10:56:47] Could not find a media subtype (format) of "video/x-flv"
[WARN] [2020-10-21 10:56:47] skipping invalid medium with resource_pk 40552871210_video, subclass video (from http://purl.org/dc/dcmitype/movingimage), format  (from video/x-flv)
[INFO] [2020-10-21 10:56:47] Storing 11 ScientificNames
[INFO] [2020-10-21 10:56:47] Processing group of 11 in 1 groups of 1000
[INFO] [2020-10-21 10:56:47] Average Time: 0.1
[INFO] [2020-10-21 10:56:47] Total Time: 1s
[INFO] [2020-10-21 10:56:47] Storing 11 Nodes
[INFO] [2020-10-21 10:56:47] Processing group of 11 in 1 groups of 1000
[INFO] [2020-10-21 10:56:47] Average Time: 0.11
[INFO] [2020-10-21 10:56:47] Total Time: 1s
[INFO] [2020-10-21 10:56:47] Storing 1 Articles
[INFO] [2020-10-21 10:56:47] Processing group of 1 in 1 groups of 1000
[INFO] [2020-10-21 10:56:47] Average Time: 0.08
[INFO] [2020-10-21 10:56:47] Total Time: 1s
[INFO] [2020-10-21 10:56:47] Storing 2 Media
[INFO] [2020-10-21 10:56:47] Processing group of 2 in 1 groups of 1000
[INFO] [2020-10-21 10:56:47] Average Time: 0.03
[INFO] [2020-10-21 10:56:47] Total Time: 1s
[STOP] [2020-10-21 10:56:47] parse_diff_and_store
[START] [2020-10-21 10:56:47] resolve_keys
[INFO] [2020-10-21 10:56:57] Occurrences to nodes (through scientific_names)...
[INFO] [2020-10-21 10:56:57] traits to occurrences...
[INFO] [2020-10-21 10:56:57] traits to nodes (through occurrences)...
[INFO] [2020-10-21 10:56:57] Traits to sex term...
[INFO] [2020-10-21 10:56:57] Traits to lifestage term...
[INFO] [2020-10-21 10:56:57] MetaTraits to traits...
[INFO] [2020-10-21 10:56:57] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-10-21 10:56:57] Assocs to occurrences...
[INFO] [2020-10-21 10:56:57] Assocs to nodes...
[INFO] [2020-10-21 10:56:57] Assoc to sex term...
[INFO] [2020-10-21 10:56:57] Assoc to lifestage term...
[INFO] [2020-10-21 10:56:57] MetaAssoc to assocs...
[STOP] [2020-10-21 10:56:57] resolve_keys
[START] [2020-10-21 10:56:57] hold_for_later_1
[STOP] [2020-10-21 10:56:57] hold_for_later_1
[START] [2020-10-21 10:56:57] hold_for_later_2
[STOP] [2020-10-21 10:56:57] hold_for_later_2
[START] [2020-10-21 10:56:57] resolve_missing_parents
[STOP] [2020-10-21 10:56:57] resolve_missing_parents
[START] [2020-10-21 10:56:57] rebuild_nodes
[START] [2020-10-21 10:56:57] Flattener#flatten
[START] [2020-10-21 10:56:57] Flattener#study_resource
[START] [2020-10-21 10:56:57] Flattener#build_ancestry
[STOP] [2020-10-21 10:56:57] Flattener#build_ancestry
[INFO] [2020-10-21 10:56:57] 11 ancestry keys
[START] [2020-10-21 10:56:57] build_node_ancestors
[INFO] [2020-10-21 10:56:57] old ancestors deleted.
[STOP] [2020-10-21 10:56:57] build_node_ancestors
[START] [2020-10-21 10:56:57] Flattener#propagate_ancestor_ids
[STOP] [2020-10-21 10:56:57] Flattener#propagate_ancestor_ids
[STOP] [2020-10-21 10:56:57] Flattener#flatten
[STOP] [2020-10-21 10:56:57] rebuild_nodes
[START] [2020-10-21 10:56:57] resolve_missing_media_owners
[STOP] [2020-10-21 10:56:57] resolve_missing_media_owners
[START] [2020-10-21 10:56:57] sanitize_media_verbatims
[STOP] [2020-10-21 10:56:57] sanitize_media_verbatims
[START] [2020-10-21 10:56:57] queue_downloads
[STOP] [2020-10-21 10:56:57] queue_downloads
[START] [2020-10-21 10:56:57] parse_names
[WARN] [2020-10-21 10:56:57] I see 11 names which still need to be parsed.
[WARN] [2020-10-21 10:56:59] I see 1 names which still need to be parsed.
[STOP] [2020-10-21 10:57:00] parse_names
[START] [2020-10-21 10:57:00] denormalize_canonical_names_to_nodes
[STOP] [2020-10-21 10:57:00] denormalize_canonical_names_to_nodes
[START] [2020-10-21 10:57:00] match_nodes
[START] [2020-10-21 10:57:00] map_all_nodes_to_pages
[STOP] [2020-10-21 10:57:05] map_all_nodes_to_pages
[INFO] [2020-10-21 10:57:05] ZERO unmatched nodes (of 11)! Nicely done.
[START] [2020-10-21 10:57:05] update_nodes
[STOP] [2020-10-21 10:57:05] update_nodes
[STOP] [2020-10-21 10:57:05] match_nodes
[START] [2020-10-21 10:57:05] reindex_search
[STOP] [2020-10-21 10:57:06] reindex_search
[START] [2020-10-21 10:57:06] normalize_units
[STOP] [2020-10-21 10:57:06] normalize_units
[START] [2020-10-21 10:57:06] calculate_statistics
[STOP] [2020-10-21 10:57:06] calculate_statistics
[START] [2020-10-21 10:57:06] complete_harvest_instance
[START] [2020-10-21 10:57:06] overall_tsv_creation
[INFO] [2020-10-21 10:57:06] Processing group of 11 in 1 batches of 10000
[INFO] [2020-10-21 10:59:10] Average Time: 9.5
[INFO] [2020-10-21 10:59:10] Total Time: 2m5s
[STOP] [2020-10-21 10:59:10] overall_tsv_creation
[INFO] [2020-10-21 10:59:10] Done. Check your files:
[INFO] [2020-10-21 10:59:10] (11 lines) /app/public/data/vid_formats/publish_nodes.tsv
[INFO] [2020-10-21 10:59:10] (27 lines) /app/public/data/vid_formats/publish_node_ancestors.tsv
[INFO] [2020-10-21 10:59:10] (11 lines) /app/public/data/vid_formats/publish_scientific_names.tsv
[INFO] [2020-10-21 10:59:10] (2 lines) /app/public/data/vid_formats/publish_media.tsv
[INFO] [2020-10-21 10:59:10] (1 lines) /app/public/data/vid_formats/publish_articles.tsv
[STOP] [2020-10-21 10:59:11] complete_harvest_instance
[START] [2020-10-21 10:59:11] completed
[STOP] [2020-10-21 10:59:11] completed
[STOP] [2020-10-21 10:59:11] logged process, took 145.4
Latest Process

21 Oct 10:56 EXITED currently processing 0