Harvest for Saint Helena Ascension and Tristan da Cunha Created 15 Oct 16:13

Stage: completed
Fetched: 15 Oct 16:13
Validated: 15 Oct 16:13
Deltas Created 15 Oct 16:13
Units Normalized: 15 Oct 16:15
Ancestry Built: 15 Oct 16:14
Nodes Matched: 15 Oct 16:15
Names Parsed: 15 Oct 16:14
New Models Stored: 15 Oct 16:13
Indexed: 15 Oct 16:15
Completed: 15 Oct 16:17
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:13:32 -0400 by logger.rb/56815
[START] [2019-10-15 16:13:32] logged process
[START] [2019-10-15 16:13:32] create_harvest_instance
[STOP] [2019-10-15 16:13:32] create_harvest_instance
[START] [2019-10-15 16:13:32] fetch_files
[STOP] [2019-10-15 16:13:32] fetch_files
[START] [2019-10-15 16:13:32] validate_each_file
[STOP] [2019-10-15 16:13:33] validate_each_file
[START] [2019-10-15 16:13:33] convert_to_csv
[CMD] [2019-10-15 16:13:33] /usr/bin/sort /app/public/converted_csv/shatdc_refs_17029.csv > /app/public/converted_csv/shatdc_refs_17029.csv_sorted
[CMD] [2019-10-15 16:13:33] /usr/bin/sort /app/public/converted_csv/shatdc_nodes_17030.csv > /app/public/converted_csv/shatdc_nodes_17030.csv_sorted
[CMD] [2019-10-15 16:13:33] /usr/bin/sort /app/public/converted_csv/shatdc_occurrences_17031.csv > /app/public/converted_csv/shatdc_occurrences_17031.csv_sorted
[CMD] [2019-10-15 16:13:33] /usr/bin/sort /app/public/converted_csv/shatdc_measurements_17032.csv > /app/public/converted_csv/shatdc_measurements_17032.csv_sorted
[STOP] [2019-10-15 16:13:34] convert_to_csv
[START] [2019-10-15 16:13:34] calculate_delta
[CMD] [2019-10-15 16:13:34] echo "0a" > /app/public/diff/shatdc_refs_17029.diff
[CMD] [2019-10-15 16:13:34] tail -n +1 /app/public/converted_csv/shatdc_refs_17029.csv >> /app/public/diff/shatdc_refs_17029.diff
[CMD] [2019-10-15 16:13:34] echo "." >> /app/public/diff/shatdc_refs_17029.diff
[CMD] [2019-10-15 16:13:35] echo "0a" > /app/public/diff/shatdc_nodes_17030.diff
[CMD] [2019-10-15 16:13:35] tail -n +1 /app/public/converted_csv/shatdc_nodes_17030.csv >> /app/public/diff/shatdc_nodes_17030.diff
[CMD] [2019-10-15 16:13:35] echo "." >> /app/public/diff/shatdc_nodes_17030.diff
[CMD] [2019-10-15 16:13:35] echo "0a" > /app/public/diff/shatdc_occurrences_17031.diff
[CMD] [2019-10-15 16:13:36] tail -n +1 /app/public/converted_csv/shatdc_occurrences_17031.csv >> /app/public/diff/shatdc_occurrences_17031.diff
[CMD] [2019-10-15 16:13:36] echo "." >> /app/public/diff/shatdc_occurrences_17031.diff
[CMD] [2019-10-15 16:13:36] echo "0a" > /app/public/diff/shatdc_measurements_17032.diff
[CMD] [2019-10-15 16:13:36] tail -n +1 /app/public/converted_csv/shatdc_measurements_17032.csv >> /app/public/diff/shatdc_measurements_17032.diff
[CMD] [2019-10-15 16:13:37] echo "." >> /app/public/diff/shatdc_measurements_17032.diff
[STOP] [2019-10-15 16:13:37] calculate_delta
[START] [2019-10-15 16:13:37] parse_diff_and_store
[INFO] [2019-10-15 16:13:37] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:13:38] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:13:39] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:13:39] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:13:44] Storing 2 References
[INFO] [2019-10-15 16:13:44] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:13:44] Average Time: 0.0
[INFO] [2019-10-15 16:13:44] Total Time: 1s
[INFO] [2019-10-15 16:13:44] Storing 1976 ScientificNames
[INFO] [2019-10-15 16:13:44] Processing group of 1976 in 2 groups of 1000
[INFO] [2019-10-15 16:13:45] Average Time: 0.425
[INFO] [2019-10-15 16:13:45] Total Time: 1s
[INFO] [2019-10-15 16:13:45] Storing 1976 Nodes
[INFO] [2019-10-15 16:13:45] Processing group of 1976 in 2 groups of 1000
[INFO] [2019-10-15 16:13:46] Average Time: 0.3
[INFO] [2019-10-15 16:13:46] Total Time: 1s
[INFO] [2019-10-15 16:13:46] Storing 482 Occurrences
[INFO] [2019-10-15 16:13:46] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-15 16:13:46] Average Time: 0.07
[INFO] [2019-10-15 16:13:46] Total Time: 1s
[INFO] [2019-10-15 16:13:46] Storing 1820 TraitsReferences
[INFO] [2019-10-15 16:13:46] Processing group of 1820 in 2 groups of 1000
[INFO] [2019-10-15 16:13:46] Average Time: 0.1
[INFO] [2019-10-15 16:13:46] Total Time: 1s
[INFO] [2019-10-15 16:13:46] Storing 1819 Traits
[INFO] [2019-10-15 16:13:46] Processing group of 1819 in 2 groups of 1000
[INFO] [2019-10-15 16:13:47] Average Time: 0.355
[INFO] [2019-10-15 16:13:47] Total Time: 1s
[INFO] [2019-10-15 16:13:47] Storing 1815 MetaTraits
[INFO] [2019-10-15 16:13:47] Processing group of 1815 in 2 groups of 1000
[INFO] [2019-10-15 16:13:47] Average Time: 0.16
[INFO] [2019-10-15 16:13:47] Total Time: 1s
[STOP] [2019-10-15 16:13:47] parse_diff_and_store
[START] [2019-10-15 16:13:47] resolve_keys
[INFO] [2019-10-15 16:13:58] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:13:58] traits to occurrences...
[INFO] [2019-10-15 16:13:59] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:13:59] Traits to sex term...
[INFO] [2019-10-15 16:13:59] Traits to lifestage term...
[INFO] [2019-10-15 16:14:00] MetaTraits to traits...
[INFO] [2019-10-15 16:14:00] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:14:00] Assocs to occurrences...
[INFO] [2019-10-15 16:14:00] Assocs to nodes...
[INFO] [2019-10-15 16:14:00] Assoc to sex term...
[INFO] [2019-10-15 16:14:00] Assoc to lifestage term...
[STOP] [2019-10-15 16:14:00] resolve_keys
[START] [2019-10-15 16:14:00] hold_for_later_1
[STOP] [2019-10-15 16:14:00] hold_for_later_1
[START] [2019-10-15 16:14:00] hold_for_later_2
[STOP] [2019-10-15 16:14:00] hold_for_later_2
[START] [2019-10-15 16:14:00] resolve_missing_parents
[STOP] [2019-10-15 16:14:03] resolve_missing_parents
[START] [2019-10-15 16:14:03] rebuild_nodes
[START] [2019-10-15 16:14:03] Flattener#flatten
[START] [2019-10-15 16:14:03] Flattener#study_resource
[START] [2019-10-15 16:14:03] Flattener#build_ancestry
[STOP] [2019-10-15 16:14:03] Flattener#build_ancestry
[INFO] [2019-10-15 16:14:03] 1976 ancestry keys
[START] [2019-10-15 16:14:03] build_node_ancestors
[INFO] [2019-10-15 16:14:03] old ancestors deleted.
[STOP] [2019-10-15 16:14:04] build_node_ancestors
[START] [2019-10-15 16:14:04] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:14:04] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:14:04] Flattener#flatten
[STOP] [2019-10-15 16:14:04] rebuild_nodes
[START] [2019-10-15 16:14:04] resolve_missing_media_owners
[STOP] [2019-10-15 16:14:04] resolve_missing_media_owners
[START] [2019-10-15 16:14:04] sanitize_media_verbatims
[STOP] [2019-10-15 16:14:04] sanitize_media_verbatims
[START] [2019-10-15 16:14:04] queue_downloads
[STOP] [2019-10-15 16:14:04] queue_downloads
[START] [2019-10-15 16:14:04] parse_names
[WARN] [2019-10-15 16:14:04] I see 1976 names which still need to be parsed.
[STOP] [2019-10-15 16:14:07] parse_names
[START] [2019-10-15 16:14:07] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:14:07] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:14:07] match_nodes
[START] [2019-10-15 16:14:07] map_all_nodes_to_pages
[STOP] [2019-10-15 16:15:52] map_all_nodes_to_pages
[INFO] [2019-10-15 16:15:52] 115 Unmatched nodes (of 1976)! That's too many to output. First 10: Protosteliales (#51750197); Protosteliaceae (#51750196); Protostelium pyriforme (#51750219); Cavosteliaceae (#51750252); Agrostis carmichaeli (#51750225); Agrostis tenuis (#51751114); Spartina (#51750738); Isolepis sulcatus (#51751416); Rostkovia tristanensis (#51752132); Diachea leucopoda (#51750590)
[START] [2019-10-15 16:15:52] update_nodes
[STOP] [2019-10-15 16:15:52] update_nodes
[STOP] [2019-10-15 16:15:52] match_nodes
[START] [2019-10-15 16:15:52] reindex_search
[STOP] [2019-10-15 16:15:56] reindex_search
[START] [2019-10-15 16:15:56] normalize_units
[STOP] [2019-10-15 16:15:56] normalize_units
[START] [2019-10-15 16:15:56] calculate_statistics
[STOP] [2019-10-15 16:15:56] calculate_statistics
[START] [2019-10-15 16:15:56] complete_harvest_instance
[START] [2019-10-15 16:15:56] overall_tsv_creation
[INFO] [2019-10-15 16:15:56] Processing group of 1976 in 1 batches of 10000
[INFO] [2019-10-15 16:16:50] 482 Traits (unfiltered)...
[INFO] [2019-10-15 16:17:04] 482 Traits (filtered)...
[INFO] [2019-10-15 16:17:04] 0 Associations (filtered)...
[INFO] [2019-10-15 16:17:43] 2408 metadata added.
[INFO] [2019-10-15 16:17:43] 0 metadata added.
[INFO] [2019-10-15 16:17:43] Average Time: 83.68
[INFO] [2019-10-15 16:17:43] Total Time: 1m47s
[STOP] [2019-10-15 16:17:43] overall_tsv_creation
[INFO] [2019-10-15 16:17:43] Done. Check your files:
[INFO] [2019-10-15 16:17:43] (1976 lines) /app/public/data/shatdc/publish_nodes.tsv
[INFO] [2019-10-15 16:17:43] (3272 lines) /app/public/data/shatdc/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:17:44] (1976 lines) /app/public/data/shatdc/publish_scientific_names.tsv
[INFO] [2019-10-15 16:17:44] (483 lines) /app/public/data/shatdc/publish_traits.tsv
[INFO] [2019-10-15 16:17:44] (2409 lines) /app/public/data/shatdc/publish_metadata.tsv
[STOP] [2019-10-15 16:17:44] complete_harvest_instance
[START] [2019-10-15 16:17:44] completed
[STOP] [2019-10-15 16:17:44] completed
[STOP] [2019-10-15 16:17:44] logged process, took 252.39
Latest Process

15 Oct 16:13 EXITED currently processing 0