Harvest for Strayer et al 2010 Created 30 Jul 12:23

Stage: completed
Fetched: 30 Jul 12:23
Validated: 30 Jul 12:23
Deltas Created 30 Jul 12:23
Units Normalized: 30 Jul 12:23
Ancestry Built: 30 Jul 12:23
Nodes Matched: 30 Jul 12:23
Names Parsed: 30 Jul 12:23
New Models Stored: 30 Jul 12:23
Indexed: 30 Jul 12:23
Completed: 30 Jul 12:25
Time to Harvest: less than a minute
Harvesting Log

(137 lines)
# Logfile created on 2020-07-30 12:23:12 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 12:23:12] logged process
[START] [2020-07-30 12:23:12] Creating resource from OpenData
[START] [2020-07-30 12:23:13] logged process
[START] [2020-07-30 12:23:13] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:23:13] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:23:13] Creating resource from OpenData
[INFO] [2020-07-30 12:23:27] ## HARVEST: type = -harvest
[START] [2020-07-30 12:23:31] logged process
[START] [2020-07-30 12:23:31] create_harvest_instance
[STOP] [2020-07-30 12:23:33] create_harvest_instance
[START] [2020-07-30 12:23:33] fetch_files
[STOP] [2020-07-30 12:23:33] fetch_files
[START] [2020-07-30 12:23:33] validate_each_file
[STOP] [2020-07-30 12:23:33] validate_each_file
[START] [2020-07-30 12:23:33] convert_to_csv
[CMD] [2020-07-30 12:23:33] /usr/bin/sort /app/public/converted_csv/strayer_et_al_st_refs_22200.csv > /app/public/converted_csv/strayer_et_al_st_refs_22200.csv_sorted
[CMD] [2020-07-30 12:23:33] /usr/bin/sort /app/public/converted_csv/strayer_et_al_st_nodes_22201.csv > /app/public/converted_csv/strayer_et_al_st_nodes_22201.csv_sorted
[CMD] [2020-07-30 12:23:33] /usr/bin/sort /app/public/converted_csv/strayer_et_al_st_occurrences_22202.csv > /app/public/converted_csv/strayer_et_al_st_occurrences_22202.csv_sorted
[CMD] [2020-07-30 12:23:33] /usr/bin/sort /app/public/converted_csv/strayer_et_al_st_measurements_22203.csv > /app/public/converted_csv/strayer_et_al_st_measurements_22203.csv_sorted
[STOP] [2020-07-30 12:23:33] convert_to_csv
[START] [2020-07-30 12:23:33] calculate_delta
[CMD] [2020-07-30 12:23:33] echo "0a" > /app/public/diff/strayer_et_al_st_refs_22200.diff
[CMD] [2020-07-30 12:23:33] tail -n +1 /app/public/converted_csv/strayer_et_al_st_refs_22200.csv >> /app/public/diff/strayer_et_al_st_refs_22200.diff
[CMD] [2020-07-30 12:23:33] echo "." >> /app/public/diff/strayer_et_al_st_refs_22200.diff
[CMD] [2020-07-30 12:23:33] echo "0a" > /app/public/diff/strayer_et_al_st_nodes_22201.diff
[CMD] [2020-07-30 12:23:33] tail -n +1 /app/public/converted_csv/strayer_et_al_st_nodes_22201.csv >> /app/public/diff/strayer_et_al_st_nodes_22201.diff
[CMD] [2020-07-30 12:23:33] echo "." >> /app/public/diff/strayer_et_al_st_nodes_22201.diff
[CMD] [2020-07-30 12:23:33] echo "0a" > /app/public/diff/strayer_et_al_st_occurrences_22202.diff
[CMD] [2020-07-30 12:23:33] tail -n +1 /app/public/converted_csv/strayer_et_al_st_occurrences_22202.csv >> /app/public/diff/strayer_et_al_st_occurrences_22202.diff
[CMD] [2020-07-30 12:23:33] echo "." >> /app/public/diff/strayer_et_al_st_occurrences_22202.diff
[CMD] [2020-07-30 12:23:33] echo "0a" > /app/public/diff/strayer_et_al_st_measurements_22203.diff
[CMD] [2020-07-30 12:23:33] tail -n +1 /app/public/converted_csv/strayer_et_al_st_measurements_22203.csv >> /app/public/diff/strayer_et_al_st_measurements_22203.diff
[CMD] [2020-07-30 12:23:33] echo "." >> /app/public/diff/strayer_et_al_st_measurements_22203.diff
[STOP] [2020-07-30 12:23:33] calculate_delta
[START] [2020-07-30 12:23:33] parse_diff_and_store
[INFO] [2020-07-30 12:23:33] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 12:23:33] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 12:23:33] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 12:23:33] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 12:23:33] Storing 3 ScientificNames
[INFO] [2020-07-30 12:23:33] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-30 12:23:33] Average Time: 0.0
[INFO] [2020-07-30 12:23:33] Total Time: 1s
[INFO] [2020-07-30 12:23:33] Storing 3 Nodes
[INFO] [2020-07-30 12:23:33] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-30 12:23:33] Average Time: 0.0
[INFO] [2020-07-30 12:23:33] Total Time: 1s
[INFO] [2020-07-30 12:23:33] Storing 3 Occurrences
[INFO] [2020-07-30 12:23:33] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-30 12:23:33] Average Time: 0.0
[INFO] [2020-07-30 12:23:33] Total Time: 1s
[INFO] [2020-07-30 12:23:33] Storing 6 Traits
[INFO] [2020-07-30 12:23:33] Processing group of 6 in 1 groups of 1000
[INFO] [2020-07-30 12:23:33] Average Time: 0.0
[INFO] [2020-07-30 12:23:33] Total Time: 1s
[INFO] [2020-07-30 12:23:33] Storing 4 MetaTraits
[INFO] [2020-07-30 12:23:33] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 12:23:33] Average Time: 0.0
[INFO] [2020-07-30 12:23:33] Total Time: 1s
[STOP] [2020-07-30 12:23:33] parse_diff_and_store
[START] [2020-07-30 12:23:33] resolve_keys
[INFO] [2020-07-30 12:23:40] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 12:23:40] traits to occurrences...
[INFO] [2020-07-30 12:23:40] traits to nodes (through occurrences)...
[INFO] [2020-07-30 12:23:40] Traits to sex term...
[INFO] [2020-07-30 12:23:40] Traits to lifestage term...
[INFO] [2020-07-30 12:23:40] MetaTraits to traits...
[INFO] [2020-07-30 12:23:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 12:23:40] Assocs to occurrences...
[INFO] [2020-07-30 12:23:40] Assocs to nodes...
[INFO] [2020-07-30 12:23:40] Assoc to sex term...
[INFO] [2020-07-30 12:23:40] Assoc to lifestage term...
[STOP] [2020-07-30 12:23:40] resolve_keys
[START] [2020-07-30 12:23:40] hold_for_later_1
[STOP] [2020-07-30 12:23:40] hold_for_later_1
[START] [2020-07-30 12:23:40] hold_for_later_2
[STOP] [2020-07-30 12:23:40] hold_for_later_2
[START] [2020-07-30 12:23:40] resolve_missing_parents
[STOP] [2020-07-30 12:23:40] resolve_missing_parents
[START] [2020-07-30 12:23:40] rebuild_nodes
[START] [2020-07-30 12:23:40] Flattener#flatten
[START] [2020-07-30 12:23:40] Flattener#study_resource
[START] [2020-07-30 12:23:40] Flattener#build_ancestry
[STOP] [2020-07-30 12:23:40] Flattener#build_ancestry
[INFO] [2020-07-30 12:23:40] 3 ancestry keys
[START] [2020-07-30 12:23:40] build_node_ancestors
[INFO] [2020-07-30 12:23:40] old ancestors deleted.
[STOP] [2020-07-30 12:23:40] build_node_ancestors
[WARN] [2020-07-30 12:23:40] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 12:23:40] Flattener#flatten
[STOP] [2020-07-30 12:23:40] rebuild_nodes
[START] [2020-07-30 12:23:40] resolve_missing_media_owners
[STOP] [2020-07-30 12:23:40] resolve_missing_media_owners
[START] [2020-07-30 12:23:40] sanitize_media_verbatims
[STOP] [2020-07-30 12:23:40] sanitize_media_verbatims
[START] [2020-07-30 12:23:40] queue_downloads
[STOP] [2020-07-30 12:23:40] queue_downloads
[START] [2020-07-30 12:23:40] parse_names
[WARN] [2020-07-30 12:23:40] I see 3 names which still need to be parsed.
[STOP] [2020-07-30 12:23:42] parse_names
[START] [2020-07-30 12:23:42] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 12:23:42] denormalize_canonical_names_to_nodes
[START] [2020-07-30 12:23:42] match_nodes
[START] [2020-07-30 12:23:42] map_all_nodes_to_pages
[STOP] [2020-07-30 12:23:42] map_all_nodes_to_pages
[INFO] [2020-07-30 12:23:42] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2020-07-30 12:23:42] update_nodes
[STOP] [2020-07-30 12:23:42] update_nodes
[STOP] [2020-07-30 12:23:42] match_nodes
[START] [2020-07-30 12:23:42] reindex_search
[STOP] [2020-07-30 12:23:42] reindex_search
[START] [2020-07-30 12:23:42] normalize_units
[STOP] [2020-07-30 12:23:42] normalize_units
[START] [2020-07-30 12:23:42] calculate_statistics
[2020-07-30 12:23:42] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 12:23:42] calculate_statistics
[START] [2020-07-30 12:23:42] complete_harvest_instance
[START] [2020-07-30 12:23:42] overall_tsv_creation
[INFO] [2020-07-30 12:23:42] Processing group of 3 in 1 batches of 10000
[INFO] [2020-07-30 12:24:37] 3 Traits (unfiltered)...
[INFO] [2020-07-30 12:25:14] 3 Traits (filtered)...
[INFO] [2020-07-30 12:25:14] 0 Associations (filtered)...
[INFO] [2020-07-30 12:25:14] 7 metadata added.
[INFO] [2020-07-30 12:25:14] 0 metadata added.
[INFO] [2020-07-30 12:25:14] Average Time: 58.91
[INFO] [2020-07-30 12:25:14] Total Time: 1m33s
[STOP] [2020-07-30 12:25:14] overall_tsv_creation
[INFO] [2020-07-30 12:25:14] Done. Check your files:
[INFO] [2020-07-30 12:25:14] (3 lines) /app/public/data/strayer_et_al_st/publish_nodes.tsv
[INFO] [2020-07-30 12:25:14] (3 lines) /app/public/data/strayer_et_al_st/publish_scientific_names.tsv
[INFO] [2020-07-30 12:25:15] (4 lines) /app/public/data/strayer_et_al_st/publish_traits.tsv
[INFO] [2020-07-30 12:25:15] (4 lines) /app/public/data/strayer_et_al_st/publish_metadata.tsv
[STOP] [2020-07-30 12:25:15] complete_harvest_instance
[START] [2020-07-30 12:25:15] completed
[STOP] [2020-07-30 12:25:15] completed
[STOP] [2020-07-30 12:25:15] logged process, took 103.06
Latest Process

30 Jul 12:23 EXITED currently processing 0