Harvest for Johnson et al 2011 Created 10 Jul 14:30

Stage: completed
Fetched: 10 Jul 14:30
Validated: 10 Jul 14:30
Deltas Created 10 Jul 14:30
Units Normalized: 10 Jul 14:30
Ancestry Built: 10 Jul 14:30
Nodes Matched: 10 Jul 14:30
Names Parsed: 10 Jul 14:30
New Models Stored: 10 Jul 14:30
Indexed: 10 Jul 14:30
Completed: 10 Jul 14:31
Time to Harvest: less than a minute
Harvesting Log

(143 lines)
# Logfile created on 2019-07-10 14:30:49 -0400 by logger.rb/56815
[START] [2019-07-10 14:30:49] logged process
[START] [2019-07-10 14:30:49] create_harvest_instance
[STOP] [2019-07-10 14:30:50] create_harvest_instance
[START] [2019-07-10 14:30:50] fetch_files
[STOP] [2019-07-10 14:30:50] fetch_files
[START] [2019-07-10 14:30:50] validate_each_file
[STOP] [2019-07-10 14:30:50] validate_each_file
[START] [2019-07-10 14:30:50] convert_to_csv
[CMD] [2019-07-10 14:30:50] /usr/bin/sort /app/public/converted_csv/protoanguilla_pa_agents_14119.csv > /app/public/converted_csv/protoanguilla_pa_agents_14119.csv_sorted
[CMD] [2019-07-10 14:30:50] /usr/bin/sort /app/public/converted_csv/protoanguilla_pa_refs_14120.csv > /app/public/converted_csv/protoanguilla_pa_refs_14120.csv_sorted
[CMD] [2019-07-10 14:30:50] /usr/bin/sort /app/public/converted_csv/protoanguilla_pa_nodes_14121.csv > /app/public/converted_csv/protoanguilla_pa_nodes_14121.csv_sorted
[CMD] [2019-07-10 14:30:50] /usr/bin/sort /app/public/converted_csv/protoanguilla_pa_media_14122.csv > /app/public/converted_csv/protoanguilla_pa_media_14122.csv_sorted
[STOP] [2019-07-10 14:30:50] convert_to_csv
[START] [2019-07-10 14:30:50] calculate_delta
[CMD] [2019-07-10 14:30:50] echo "0a" > /app/public/diff/protoanguilla_pa_agents_14119.diff
[CMD] [2019-07-10 14:30:50] tail -n +1 /app/public/converted_csv/protoanguilla_pa_agents_14119.csv >> /app/public/diff/protoanguilla_pa_agents_14119.diff
[CMD] [2019-07-10 14:30:50] echo "." >> /app/public/diff/protoanguilla_pa_agents_14119.diff
[CMD] [2019-07-10 14:30:50] echo "0a" > /app/public/diff/protoanguilla_pa_refs_14120.diff
[CMD] [2019-07-10 14:30:50] tail -n +1 /app/public/converted_csv/protoanguilla_pa_refs_14120.csv >> /app/public/diff/protoanguilla_pa_refs_14120.diff
[CMD] [2019-07-10 14:30:50] echo "." >> /app/public/diff/protoanguilla_pa_refs_14120.diff
[CMD] [2019-07-10 14:30:50] echo "0a" > /app/public/diff/protoanguilla_pa_nodes_14121.diff
[CMD] [2019-07-10 14:30:50] tail -n +1 /app/public/converted_csv/protoanguilla_pa_nodes_14121.csv >> /app/public/diff/protoanguilla_pa_nodes_14121.diff
[CMD] [2019-07-10 14:30:50] echo "." >> /app/public/diff/protoanguilla_pa_nodes_14121.diff
[CMD] [2019-07-10 14:30:50] echo "0a" > /app/public/diff/protoanguilla_pa_media_14122.diff
[CMD] [2019-07-10 14:30:50] tail -n +1 /app/public/converted_csv/protoanguilla_pa_media_14122.csv >> /app/public/diff/protoanguilla_pa_media_14122.diff
[CMD] [2019-07-10 14:30:50] echo "." >> /app/public/diff/protoanguilla_pa_media_14122.diff
[STOP] [2019-07-10 14:30:50] calculate_delta
[START] [2019-07-10 14:30:50] parse_diff_and_store
[INFO] [2019-07-10 14:30:50] Loading agents diff file into memory (true lines)...
[INFO] [2019-07-10 14:30:50] Loading refs diff file into memory (true lines)...
[INFO] [2019-07-10 14:30:50] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-10 14:30:50] Loading media diff file into memory (true lines)...
[WARN] [2019-07-10 14:30:50] Could not find a media subtype (format) of "video/x-flv"
[INFO] [2019-07-10 14:30:50] Storing 1 Attributions
[INFO] [2019-07-10 14:30:50] Processing group of 1 in 1 groups of 1000
[INFO] [2019-07-10 14:30:50] Average Time: 0.0
[INFO] [2019-07-10 14:30:50] Total Time: 1s
[INFO] [2019-07-10 14:30:50] Storing 1 References
[INFO] [2019-07-10 14:30:50] Processing group of 1 in 1 groups of 1000
[INFO] [2019-07-10 14:30:50] Average Time: 0.02
[INFO] [2019-07-10 14:30:50] Total Time: 1s
[INFO] [2019-07-10 14:30:50] Storing 7 ScientificNames
[INFO] [2019-07-10 14:30:50] Processing group of 7 in 1 groups of 1000
[INFO] [2019-07-10 14:30:50] Average Time: 0.01
[INFO] [2019-07-10 14:30:50] Total Time: 1s
[INFO] [2019-07-10 14:30:50] Storing 7 Nodes
[INFO] [2019-07-10 14:30:50] Processing group of 7 in 1 groups of 1000
[INFO] [2019-07-10 14:30:50] Average Time: 0.0
[INFO] [2019-07-10 14:30:50] Total Time: 1s
[INFO] [2019-07-10 14:30:50] Storing 1 NodesReferences
[INFO] [2019-07-10 14:30:50] Processing group of 1 in 1 groups of 1000
[INFO] [2019-07-10 14:30:50] Average Time: 0.03
[INFO] [2019-07-10 14:30:50] Total Time: 1s
[INFO] [2019-07-10 14:30:50] Storing 1 MediaReferences
[INFO] [2019-07-10 14:30:50] Processing group of 1 in 1 groups of 1000
[INFO] [2019-07-10 14:30:50] Average Time: 0.0
[INFO] [2019-07-10 14:30:50] Total Time: 1s
[INFO] [2019-07-10 14:30:50] Storing 1 ContentAttributions
[INFO] [2019-07-10 14:30:50] Processing group of 1 in 1 groups of 1000
[INFO] [2019-07-10 14:30:50] Average Time: 0.0
[INFO] [2019-07-10 14:30:50] Total Time: 1s
[INFO] [2019-07-10 14:30:50] Storing 1 Media
[INFO] [2019-07-10 14:30:50] Processing group of 1 in 1 groups of 1000
[INFO] [2019-07-10 14:30:50] Average Time: 0.0
[INFO] [2019-07-10 14:30:50] Total Time: 1s
[STOP] [2019-07-10 14:30:50] parse_diff_and_store
[START] [2019-07-10 14:30:50] resolve_keys
[INFO] [2019-07-10 14:30:54] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-10 14:30:54] traits to occurrences...
[INFO] [2019-07-10 14:30:54] traits to nodes (through occurrences)...
[INFO] [2019-07-10 14:30:54] Traits to sex term...
[INFO] [2019-07-10 14:30:54] Traits to lifestage term...
[INFO] [2019-07-10 14:30:54] MetaTraits to traits...
[INFO] [2019-07-10 14:30:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-10 14:30:54] Assocs to occurrences...
[INFO] [2019-07-10 14:30:54] Assocs to nodes...
[INFO] [2019-07-10 14:30:54] Assoc to sex term...
[INFO] [2019-07-10 14:30:54] Assoc to lifestage term...
[STOP] [2019-07-10 14:30:54] resolve_keys
[START] [2019-07-10 14:30:54] hold_for_later_1
[STOP] [2019-07-10 14:30:54] hold_for_later_1
[START] [2019-07-10 14:30:54] hold_for_later_2
[STOP] [2019-07-10 14:30:54] hold_for_later_2
[START] [2019-07-10 14:30:54] resolve_missing_parents
[STOP] [2019-07-10 14:30:54] resolve_missing_parents
[START] [2019-07-10 14:30:54] rebuild_nodes
[START] [2019-07-10 14:30:54] Flattener#flatten
[START] [2019-07-10 14:30:54] Flattener#study_resource
[START] [2019-07-10 14:30:54] Flattener#build_ancestry
[STOP] [2019-07-10 14:30:54] Flattener#build_ancestry
[INFO] [2019-07-10 14:30:54] 7 ancestry keys
[START] [2019-07-10 14:30:54] build_node_ancestors
[INFO] [2019-07-10 14:30:54] old ancestors deleted.
[STOP] [2019-07-10 14:30:54] build_node_ancestors
[START] [2019-07-10 14:30:54] Flattener#propagate_ancestor_ids
[STOP] [2019-07-10 14:30:54] Flattener#propagate_ancestor_ids
[STOP] [2019-07-10 14:30:54] Flattener#flatten
[STOP] [2019-07-10 14:30:54] rebuild_nodes
[START] [2019-07-10 14:30:54] resolve_missing_media_owners
[STOP] [2019-07-10 14:30:54] resolve_missing_media_owners
[START] [2019-07-10 14:30:54] sanitize_media_verbatims
[STOP] [2019-07-10 14:30:54] sanitize_media_verbatims
[START] [2019-07-10 14:30:54] queue_downloads
[STOP] [2019-07-10 14:30:54] queue_downloads
[START] [2019-07-10 14:30:54] parse_names
[WARN] [2019-07-10 14:30:54] I see 7 names which still need to be parsed.
[STOP] [2019-07-10 14:30:55] parse_names
[START] [2019-07-10 14:30:55] denormalize_canonical_names_to_nodes
[STOP] [2019-07-10 14:30:55] denormalize_canonical_names_to_nodes
[START] [2019-07-10 14:30:55] match_nodes
[START] [2019-07-10 14:30:55] map_all_nodes_to_pages
[STOP] [2019-07-10 14:30:56] map_all_nodes_to_pages
[INFO] [2019-07-10 14:30:56] ZERO unmatched nodes (of 7)! Nicely done.
[START] [2019-07-10 14:30:56] update_nodes
[STOP] [2019-07-10 14:30:56] update_nodes
[STOP] [2019-07-10 14:30:56] match_nodes
[START] [2019-07-10 14:30:56] reindex_search
[STOP] [2019-07-10 14:30:56] reindex_search
[START] [2019-07-10 14:30:56] normalize_units
[STOP] [2019-07-10 14:30:56] normalize_units
[START] [2019-07-10 14:30:56] calculate_statistics
[STOP] [2019-07-10 14:30:56] calculate_statistics
[START] [2019-07-10 14:30:56] complete_harvest_instance
[START] [2019-07-10 14:30:56] overall_tsv_creation
[INFO] [2019-07-10 14:30:56] Processing group of 7 in 1 batches of 10000
[INFO] [2019-07-10 14:31:27] Average Time: 11.2
[INFO] [2019-07-10 14:31:27] Total Time: 32s
[STOP] [2019-07-10 14:31:27] overall_tsv_creation
[INFO] [2019-07-10 14:31:27] Done. Check your files:
[INFO] [2019-07-10 14:31:27] (7 lines) /app/public/data/protoanguilla_pa/publish_nodes.tsv
[INFO] [2019-07-10 14:31:27] (21 lines) /app/public/data/protoanguilla_pa/publish_node_ancestors.tsv
[INFO] [2019-07-10 14:31:27] (7 lines) /app/public/data/protoanguilla_pa/publish_scientific_names.tsv
[INFO] [2019-07-10 14:31:27] (1 lines) /app/public/data/protoanguilla_pa/publish_media.tsv
[INFO] [2019-07-10 14:31:27] (1 lines) /app/public/data/protoanguilla_pa/publish_references.tsv
[INFO] [2019-07-10 14:31:27] (1 lines) /app/public/data/protoanguilla_pa/publish_attributions.tsv
[INFO] [2019-07-10 14:31:27] (1 lines) /app/public/data/protoanguilla_pa/publish_referents.tsv
[STOP] [2019-07-10 14:31:27] complete_harvest_instance
[START] [2019-07-10 14:31:27] completed
[STOP] [2019-07-10 14:31:27] completed
[STOP] [2019-07-10 14:31:27] logged process, took 38.48
[ERR] [2019-07-10 14:33:33][hdls] http://www.youtube.com/v/aOXiDjYOPgA?version=3&f=videos&app=youtube_gdata is application/x-shockwave-flash, which is unsupported. Medium.find(10051625) resource: Johnson et al 2011 (821), PK: f14d1a3a175d8ec27c610bbadd6d562e
[ERR] [2019-07-10 14:33:33][hdls] download_and_prep FAILED for Medium.find(10051625): http://www.youtube.com/v/aOXiDjYOPgA?version=3&f=videos&app=youtube_gdata is application/x-shockwave-flash, which is unsupported. Medium.find(10051625) resource: Johnson et al 2011 (821), PK: f14d1a3a175d8ec27c610bbadd6d562e
Latest Process

10 Jul 14:30 EXITED currently processing 0