Stage:
completed
Fetched:
19 Apr 15:33
Validated:
19 Apr 15:33
Deltas Created
19 Apr 15:33
Units Normalized:
19 Apr 15:33
Ancestry Built:
19 Apr 15:33
Nodes Matched:
19 Apr 15:33
Names Parsed:
19 Apr 15:33
New Models Stored:
19 Apr 15:33
Indexed:
19 Apr 15:33
Completed:
19 Apr 15:35
Time to Harvest:
less than a minute
Harvesting Log
(461 lines)
# Logfile created on 2020-08-27 15:42:22 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:42:22] logged process
[START] [2020-08-27 15:42:22] Creating resource from OpenData
[START] [2020-08-27 15:42:23] logged process
[START] [2020-08-27 15:42:23] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:42:23] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:42:23] Creating resource from OpenData
[INFO] [2020-12-03 11:24:29] ## HARVEST: type = -harvest
[START] [2020-12-03 11:24:31] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-03 11:24:31] create_harvest_instance
[STOP] [2020-12-03 11:24:33] create_harvest_instance
[START] [2020-12-03 11:24:33] fetch_files
[STOP] [2020-12-03 11:24:33] fetch_files
[START] [2020-12-03 11:24:33] validate_each_file
[STOP] [2020-12-03 11:24:34] validate_each_file
[START] [2020-12-03 11:24:34] convert_to_csv
[CMD] [2020-12-03 11:24:34] /usr/bin/sort /app/public/converted_csv/mozhm_refs_24812.csv > /app/public/converted_csv/mozhm_refs_24812.csv_sorted
[CMD] [2020-12-03 11:24:34] /usr/bin/sort /app/public/converted_csv/mozhm_nodes_24813.csv > /app/public/converted_csv/mozhm_nodes_24813.csv_sorted
[CMD] [2020-12-03 11:24:34] /usr/bin/sort /app/public/converted_csv/mozhm_occurrences_24814.csv > /app/public/converted_csv/mozhm_occurrences_24814.csv_sorted
[CMD] [2020-12-03 11:24:34] /usr/bin/sort /app/public/converted_csv/mozhm_measurements_24815.csv > /app/public/converted_csv/mozhm_measurements_24815.csv_sorted
[STOP] [2020-12-03 11:24:34] convert_to_csv
[START] [2020-12-03 11:24:34] calculate_delta
[CMD] [2020-12-03 11:24:34] echo "0a" > /app/public/diff/mozhm_refs_24812.diff
[CMD] [2020-12-03 11:24:34] tail -n +1 /app/public/converted_csv/mozhm_refs_24812.csv >> /app/public/diff/mozhm_refs_24812.diff
[CMD] [2020-12-03 11:24:34] echo "." >> /app/public/diff/mozhm_refs_24812.diff
[CMD] [2020-12-03 11:24:34] echo "0a" > /app/public/diff/mozhm_nodes_24813.diff
[CMD] [2020-12-03 11:24:34] tail -n +1 /app/public/converted_csv/mozhm_nodes_24813.csv >> /app/public/diff/mozhm_nodes_24813.diff
[CMD] [2020-12-03 11:24:34] echo "." >> /app/public/diff/mozhm_nodes_24813.diff
[CMD] [2020-12-03 11:24:34] echo "0a" > /app/public/diff/mozhm_occurrences_24814.diff
[CMD] [2020-12-03 11:24:34] tail -n +1 /app/public/converted_csv/mozhm_occurrences_24814.csv >> /app/public/diff/mozhm_occurrences_24814.diff
[CMD] [2020-12-03 11:24:34] echo "." >> /app/public/diff/mozhm_occurrences_24814.diff
[CMD] [2020-12-03 11:24:34] echo "0a" > /app/public/diff/mozhm_measurements_24815.diff
[CMD] [2020-12-03 11:24:34] tail -n +1 /app/public/converted_csv/mozhm_measurements_24815.csv >> /app/public/diff/mozhm_measurements_24815.diff
[CMD] [2020-12-03 11:24:34] echo "." >> /app/public/diff/mozhm_measurements_24815.diff
[STOP] [2020-12-03 11:24:34] calculate_delta
[START] [2020-12-03 11:24:34] parse_diff_and_store
[INFO] [2020-12-03 11:24:34] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:24:34] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:24:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:24:34] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:24:35] Storing 4 ScientificNames
[INFO] [2020-12-03 11:24:35] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 11:24:35] Average Time: 0.01
[INFO] [2020-12-03 11:24:35] Total Time: 1s
[INFO] [2020-12-03 11:24:35] Storing 4 Nodes
[INFO] [2020-12-03 11:24:35] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 11:24:35] Average Time: 0.0
[INFO] [2020-12-03 11:24:35] Total Time: 1s
[INFO] [2020-12-03 11:24:35] Storing 4 Occurrences
[INFO] [2020-12-03 11:24:35] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 11:24:35] Average Time: 0.02
[INFO] [2020-12-03 11:24:35] Total Time: 1s
[INFO] [2020-12-03 11:24:35] Storing 4 Traits
[INFO] [2020-12-03 11:24:35] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 11:24:35] Average Time: 0.01
[INFO] [2020-12-03 11:24:35] Total Time: 1s
[INFO] [2020-12-03 11:24:35] Storing 4 MetaTraits
[INFO] [2020-12-03 11:24:35] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 11:24:35] Average Time: 0.0
[INFO] [2020-12-03 11:24:35] Total Time: 1s
[STOP] [2020-12-03 11:24:35] parse_diff_and_store
[START] [2020-12-03 11:24:35] resolve_keys
[INFO] [2020-12-03 11:24:40] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:24:40] traits to occurrences...
[INFO] [2020-12-03 11:24:40] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:24:40] Traits to sex term...
[INFO] [2020-12-03 11:24:40] Traits to lifestage term...
[INFO] [2020-12-03 11:24:40] MetaTraits to traits...
[INFO] [2020-12-03 11:24:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:24:40] Assocs to occurrences...
[INFO] [2020-12-03 11:24:40] Assocs to nodes...
[INFO] [2020-12-03 11:24:40] Assoc to sex term...
[INFO] [2020-12-03 11:24:40] Assoc to lifestage term...
[INFO] [2020-12-03 11:24:40] MetaAssoc to assocs...
[STOP] [2020-12-03 11:24:41] resolve_keys
[START] [2020-12-03 11:24:41] hold_for_later_1
[STOP] [2020-12-03 11:24:41] hold_for_later_1
[START] [2020-12-03 11:24:41] hold_for_later_2
[STOP] [2020-12-03 11:24:41] hold_for_later_2
[START] [2020-12-03 11:24:41] resolve_missing_parents
[STOP] [2020-12-03 11:24:41] resolve_missing_parents
[START] [2020-12-03 11:24:41] rebuild_nodes
[START] [2020-12-03 11:24:41] Flattener#flatten
[START] [2020-12-03 11:24:41] Flattener#study_resource
[START] [2020-12-03 11:24:41] Flattener#build_ancestry
[STOP] [2020-12-03 11:24:41] Flattener#build_ancestry
[INFO] [2020-12-03 11:24:41] 4 ancestry keys
[START] [2020-12-03 11:24:41] build_node_ancestors
[INFO] [2020-12-03 11:24:41] old ancestors deleted.
[STOP] [2020-12-03 11:24:41] build_node_ancestors
[WARN] [2020-12-03 11:24:41] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:24:41] Flattener#flatten
[STOP] [2020-12-03 11:24:41] rebuild_nodes
[START] [2020-12-03 11:24:41] resolve_missing_media_owners
[STOP] [2020-12-03 11:24:41] resolve_missing_media_owners
[START] [2020-12-03 11:24:41] sanitize_media_verbatims
[STOP] [2020-12-03 11:24:41] sanitize_media_verbatims
[START] [2020-12-03 11:24:41] queue_downloads
[STOP] [2020-12-03 11:24:41] queue_downloads
[START] [2020-12-03 11:24:41] parse_names
[WARN] [2020-12-03 11:24:41] I see 4 names which still need to be parsed.
[STOP] [2020-12-03 11:24:42] parse_names
[START] [2020-12-03 11:24:42] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:24:42] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:24:42] match_nodes
[START] [2020-12-03 11:24:42] map_all_nodes_to_pages
[STOP] [2020-12-03 11:24:42] map_all_nodes_to_pages
[INFO] [2020-12-03 11:24:42] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2020-12-03 11:24:42] update_nodes
[STOP] [2020-12-03 11:24:42] update_nodes
[STOP] [2020-12-03 11:24:42] match_nodes
[START] [2020-12-03 11:24:42] reindex_search
[STOP] [2020-12-03 11:24:42] reindex_search
[START] [2020-12-03 11:24:42] normalize_units
[STOP] [2020-12-03 11:24:42] normalize_units
[START] [2020-12-03 11:24:42] calculate_statistics
[2020-12-03 11:24:42] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:24:42] calculate_statistics
[START] [2020-12-03 11:24:42] complete_harvest_instance
[START] [2020-12-03 11:24:42] overall_tsv_creation
[INFO] [2020-12-03 11:24:42] Processing group of 4 in 1 batches of 10000
[INFO] [2020-12-03 11:25:21] 4 Traits (unfiltered)...
[INFO] [2020-12-03 11:25:58] 4 Traits (filtered)...
[INFO] [2020-12-03 11:25:58] 0 Associations (filtered)...
[INFO] [2020-12-03 11:25:58] 4 metadata added.
[INFO] [2020-12-03 11:25:58] 0 metadata added.
[INFO] [2020-12-03 11:25:58] Average Time: 53.87
[INFO] [2020-12-03 11:25:58] Total Time: 1m17s
[STOP] [2020-12-03 11:25:58] overall_tsv_creation
[INFO] [2020-12-03 11:25:58] Done. Check your files:
[INFO] [2020-12-03 11:25:59] (4 lines) /app/public/data/mozhm/publish_nodes.tsv
[INFO] [2020-12-03 11:25:59] (4 lines) /app/public/data/mozhm/publish_scientific_names.tsv
[INFO] [2020-12-03 11:25:59] (5 lines) /app/public/data/mozhm/publish_traits.tsv
[INFO] [2020-12-03 11:25:59] (5 lines) /app/public/data/mozhm/publish_metadata.tsv
[STOP] [2020-12-03 11:25:59] complete_harvest_instance
[START] [2020-12-03 11:25:59] completed
[STOP] [2020-12-03 11:25:59] completed
[STOP] [2020-12-03 11:25:59] logged process, took 87.49
[INFO] [2021-04-19 15:17:19] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:33:38] ## remove_type: ScientificName
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.371] Removed 4 Scientificnames
[INFO] [2021-04-19 15:33:38] ## remove_type: Vernacular
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.373] Removed 0 Vernaculars
[INFO] [2021-04-19 15:33:38] ## remove_type: Article
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.374] Removed 0 Articles
[INFO] [2021-04-19 15:33:38] ## remove_type: Medium
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.376] Removed 0 Media
[INFO] [2021-04-19 15:33:38] ## remove_type: Trait
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.378] Removed 4 Traits
[INFO] [2021-04-19 15:33:38] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.380] Removed 4 Metatraits
[INFO] [2021-04-19 15:33:38] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.381] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:33:38] ## remove_type: Assoc
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.382] Removed 0 Assocs
[INFO] [2021-04-19 15:33:38] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.384] Removed 0 Metaassocs
[INFO] [2021-04-19 15:33:38] ## remove_type: Identifier
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.385] Removed 0 Identifiers
[INFO] [2021-04-19 15:33:38] ## remove_type: Reference
[INFO] [2021-04-19 15:33:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:33:38] [15:33:38.386] Removed 0 References
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
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[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
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[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:38] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
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[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
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[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
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[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] Starting batch with ID 86115916...
[INFO] [2021-04-19 15:33:39] ## remove_type: Node
[INFO] [2021-04-19 15:33:39] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 15:33:39] [15:33:39.208] Removed 4 Nodes
[START] [2021-04-19 15:33:39] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:33:39] Creating resource from OpenData
[START] [2021-04-19 15:33:39] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:33:39] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:33:39] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:33:39] Creating resource from OpenData
[START] [2021-04-19 15:33:39] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:33:39] create_harvest_instance
[INFO] [2021-04-19 15:33:39] Created harvest instance #3770
[STOP] [2021-04-19 15:33:39] create_harvest_instance
[START] [2021-04-19 15:33:39] fetch_files
[STOP] [2021-04-19 15:33:39] fetch_files
[START] [2021-04-19 15:33:39] validate_each_file
[INFO] [2021-04-19 15:33:39] Looping over 4 formats...
[INFO] [2021-04-19 15:33:39] ...refs (/app/public/data/mozhm/references.tsv)
[INFO] [2021-04-19 15:33:39] Valid: /app/public/converted_csv/mozhm_refs_3770.csv (0 lines)
[INFO] [2021-04-19 15:33:39] ...nodes (/app/public/data/mozhm/taxa.txt)
[INFO] [2021-04-19 15:33:39] Valid: /app/public/converted_csv/mozhm_nodes_3770.csv (4 lines)
[INFO] [2021-04-19 15:33:39] ...occurrences (/app/public/data/mozhm/occurrences.txt)
[INFO] [2021-04-19 15:33:39] Valid: /app/public/converted_csv/mozhm_occurrences_3770.csv (4 lines)
[INFO] [2021-04-19 15:33:39] ...measurements (/app/public/data/mozhm/measurementsorfacts.txt)
[INFO] [2021-04-19 15:33:39] Valid: /app/public/converted_csv/mozhm_measurements_3770.csv (4 lines)
[STOP] [2021-04-19 15:33:39] validate_each_file
[START] [2021-04-19 15:33:39] convert_to_csv
[INFO] [2021-04-19 15:33:39] Looping over 4 formats...
[INFO] [2021-04-19 15:33:39] ...refs (/app/public/data/mozhm/references.tsv)
[CMD] [2021-04-19 15:33:39] /usr/bin/sort /app/public/converted_csv/mozhm_refs_3770.csv > /app/public/converted_csv/mozhm_refs_3770.csv_sorted
[INFO] [2021-04-19 15:33:39] Converted: /app/public/converted_csv/mozhm_refs_3770.csv (0 lines)
[INFO] [2021-04-19 15:33:39] ...nodes (/app/public/data/mozhm/taxa.txt)
[CMD] [2021-04-19 15:33:39] /usr/bin/sort /app/public/converted_csv/mozhm_nodes_3770.csv > /app/public/converted_csv/mozhm_nodes_3770.csv_sorted
[INFO] [2021-04-19 15:33:39] Converted: /app/public/converted_csv/mozhm_nodes_3770.csv (4 lines)
[INFO] [2021-04-19 15:33:39] ...occurrences (/app/public/data/mozhm/occurrences.txt)
[CMD] [2021-04-19 15:33:39] /usr/bin/sort /app/public/converted_csv/mozhm_occurrences_3770.csv > /app/public/converted_csv/mozhm_occurrences_3770.csv_sorted
[INFO] [2021-04-19 15:33:39] Converted: /app/public/converted_csv/mozhm_occurrences_3770.csv (4 lines)
[INFO] [2021-04-19 15:33:39] ...measurements (/app/public/data/mozhm/measurementsorfacts.txt)
[CMD] [2021-04-19 15:33:39] /usr/bin/sort /app/public/converted_csv/mozhm_measurements_3770.csv > /app/public/converted_csv/mozhm_measurements_3770.csv_sorted
[INFO] [2021-04-19 15:33:39] Converted: /app/public/converted_csv/mozhm_measurements_3770.csv (4 lines)
[STOP] [2021-04-19 15:33:39] convert_to_csv
[START] [2021-04-19 15:33:39] calculate_delta
[INFO] [2021-04-19 15:33:39] Looping over 4 formats...
[INFO] [2021-04-19 15:33:39] ...refs (/app/public/data/mozhm/references.tsv)
[CMD] [2021-04-19 15:33:39] echo "0a" > /app/public/diff/mozhm_refs_3770.diff
[CMD] [2021-04-19 15:33:39] tail -n +1 /app/public/converted_csv/mozhm_refs_3770.csv >> /app/public/diff/mozhm_refs_3770.diff
[CMD] [2021-04-19 15:33:39] echo "." >> /app/public/diff/mozhm_refs_3770.diff
[INFO] [2021-04-19 15:33:39] Created diff: /app/public/diff/mozhm_refs_3770.diff (2 lines)
[INFO] [2021-04-19 15:33:39] ...nodes (/app/public/data/mozhm/taxa.txt)
[CMD] [2021-04-19 15:33:39] echo "0a" > /app/public/diff/mozhm_nodes_3770.diff
[CMD] [2021-04-19 15:33:39] tail -n +1 /app/public/converted_csv/mozhm_nodes_3770.csv >> /app/public/diff/mozhm_nodes_3770.diff
[CMD] [2021-04-19 15:33:39] echo "." >> /app/public/diff/mozhm_nodes_3770.diff
[INFO] [2021-04-19 15:33:39] Created diff: /app/public/diff/mozhm_nodes_3770.diff (6 lines)
[INFO] [2021-04-19 15:33:39] ...occurrences (/app/public/data/mozhm/occurrences.txt)
[CMD] [2021-04-19 15:33:39] echo "0a" > /app/public/diff/mozhm_occurrences_3770.diff
[CMD] [2021-04-19 15:33:39] tail -n +1 /app/public/converted_csv/mozhm_occurrences_3770.csv >> /app/public/diff/mozhm_occurrences_3770.diff
[CMD] [2021-04-19 15:33:39] echo "." >> /app/public/diff/mozhm_occurrences_3770.diff
[INFO] [2021-04-19 15:33:39] Created diff: /app/public/diff/mozhm_occurrences_3770.diff (6 lines)
[INFO] [2021-04-19 15:33:39] ...measurements (/app/public/data/mozhm/measurementsorfacts.txt)
[CMD] [2021-04-19 15:33:39] echo "0a" > /app/public/diff/mozhm_measurements_3770.diff
[CMD] [2021-04-19 15:33:39] tail -n +1 /app/public/converted_csv/mozhm_measurements_3770.csv >> /app/public/diff/mozhm_measurements_3770.diff
[CMD] [2021-04-19 15:33:39] echo "." >> /app/public/diff/mozhm_measurements_3770.diff
[INFO] [2021-04-19 15:33:39] Created diff: /app/public/diff/mozhm_measurements_3770.diff (6 lines)
[STOP] [2021-04-19 15:33:39] calculate_delta
[START] [2021-04-19 15:33:39] parse_diff_and_store
[INFO] [2021-04-19 15:33:39] Handling diff: /app/public/diff/mozhm_refs_3770.diff (2 lines)
[INFO] [2021-04-19 15:33:39] Loading refs diff file into memory (2 /app/public/diff/mozhm_refs_3770.diff lines)...
[INFO] [2021-04-19 15:33:39] Handling diff: /app/public/diff/mozhm_nodes_3770.diff (6 lines)
[INFO] [2021-04-19 15:33:39] Loading nodes diff file into memory (6 /app/public/diff/mozhm_nodes_3770.diff lines)...
[INFO] [2021-04-19 15:33:39] Handling diff: /app/public/diff/mozhm_occurrences_3770.diff (6 lines)
[INFO] [2021-04-19 15:33:39] Loading occurrences diff file into memory (6 /app/public/diff/mozhm_occurrences_3770.diff lines)...
[INFO] [2021-04-19 15:33:39] Handling diff: /app/public/diff/mozhm_measurements_3770.diff (6 lines)
[INFO] [2021-04-19 15:33:39] Loading measurements diff file into memory (6 /app/public/diff/mozhm_measurements_3770.diff lines)...
[INFO] [2021-04-19 15:33:39] Storing 4 ScientificNames
[INFO] [2021-04-19 15:33:39] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 15:33:39] Average Time: 0.0
[INFO] [2021-04-19 15:33:39] Total Time: 1s
[INFO] [2021-04-19 15:33:39] Storing 4 Nodes
[INFO] [2021-04-19 15:33:39] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 15:33:39] Average Time: 0.0
[INFO] [2021-04-19 15:33:39] Total Time: 1s
[INFO] [2021-04-19 15:33:39] Storing 4 Occurrences
[INFO] [2021-04-19 15:33:39] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 15:33:39] Average Time: 0.0
[INFO] [2021-04-19 15:33:39] Total Time: 1s
[INFO] [2021-04-19 15:33:39] Storing 4 Traits
[INFO] [2021-04-19 15:33:39] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 15:33:39] Average Time: 0.0
[INFO] [2021-04-19 15:33:39] Total Time: 1s
[INFO] [2021-04-19 15:33:39] Storing 4 MetaTraits
[INFO] [2021-04-19 15:33:39] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 15:33:39] Average Time: 0.0
[INFO] [2021-04-19 15:33:39] Total Time: 1s
[STOP] [2021-04-19 15:33:39] parse_diff_and_store
[START] [2021-04-19 15:33:39] resolve_keys
[INFO] [2021-04-19 15:33:45] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:33:45] traits to occurrences...
[INFO] [2021-04-19 15:33:45] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:33:45] Traits to sex term...
[INFO] [2021-04-19 15:33:45] Traits to lifestage term...
[INFO] [2021-04-19 15:33:45] MetaTraits to traits...
[INFO] [2021-04-19 15:33:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:33:45] Assocs to occurrences...
[INFO] [2021-04-19 15:33:45] Assocs to nodes...
[INFO] [2021-04-19 15:33:45] Assoc to sex term...
[INFO] [2021-04-19 15:33:45] Assoc to lifestage term...
[INFO] [2021-04-19 15:33:45] MetaAssoc to assocs...
[STOP] [2021-04-19 15:33:45] resolve_keys
[START] [2021-04-19 15:33:45] hold_for_later_1
[STOP] [2021-04-19 15:33:45] hold_for_later_1
[START] [2021-04-19 15:33:45] hold_for_later_2
[STOP] [2021-04-19 15:33:45] hold_for_later_2
[START] [2021-04-19 15:33:45] resolve_missing_parents
[STOP] [2021-04-19 15:33:45] resolve_missing_parents
[START] [2021-04-19 15:33:45] rebuild_nodes
[START] [2021-04-19 15:33:45] Flattener#flatten
[START] [2021-04-19 15:33:45] Flattener#study_resource
[START] [2021-04-19 15:33:45] Flattener#build_ancestry
[STOP] [2021-04-19 15:33:45] Flattener#build_ancestry
[INFO] [2021-04-19 15:33:45] 4 ancestry keys
[START] [2021-04-19 15:33:45] build_node_ancestors
[INFO] [2021-04-19 15:33:45] old ancestors deleted.
[STOP] [2021-04-19 15:33:45] build_node_ancestors
[WARN] [2021-04-19 15:33:45] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:33:45] Flattener#flatten
[STOP] [2021-04-19 15:33:45] rebuild_nodes
[START] [2021-04-19 15:33:45] resolve_missing_media_owners
[STOP] [2021-04-19 15:33:45] resolve_missing_media_owners
[START] [2021-04-19 15:33:45] sanitize_media_verbatims
[STOP] [2021-04-19 15:33:45] sanitize_media_verbatims
[START] [2021-04-19 15:33:45] queue_downloads
[STOP] [2021-04-19 15:33:45] queue_downloads
[START] [2021-04-19 15:33:45] parse_names
[WARN] [2021-04-19 15:33:45] I see 4 names which still need to be parsed.
[STOP] [2021-04-19 15:33:46] parse_names
[START] [2021-04-19 15:33:46] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:33:46] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:33:46] match_nodes
[START] [2021-04-19 15:33:46] map_all_nodes_to_pages
[STOP] [2021-04-19 15:33:47] map_all_nodes_to_pages
[INFO] [2021-04-19 15:33:47] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2021-04-19 15:33:47] update_nodes
[STOP] [2021-04-19 15:33:47] update_nodes
[STOP] [2021-04-19 15:33:47] match_nodes
[START] [2021-04-19 15:33:47] reindex_search
[STOP] [2021-04-19 15:33:47] reindex_search
[START] [2021-04-19 15:33:47] normalize_units
[STOP] [2021-04-19 15:33:47] normalize_units
[START] [2021-04-19 15:33:47] calculate_statistics
[2021-04-19 15:33:47] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:33:47] calculate_statistics
[START] [2021-04-19 15:33:47] complete_harvest_instance
[START] [2021-04-19 15:33:47] overall_tsv_creation
[INFO] [2021-04-19 15:33:47] Processing group of 4 in 1 batches of 10000
[INFO] [2021-04-19 15:34:22] 4 Traits (unfiltered)...
[INFO] [2021-04-19 15:34:56] 4 Traits (filtered)...
[INFO] [2021-04-19 15:34:56] 0 Associations (filtered)...
[INFO] [2021-04-19 15:34:56] 0 metadata added.
[INFO] [2021-04-19 15:34:56] 0 metadata added.
[INFO] [2021-04-19 15:35:22] Average Time: 71.34
[INFO] [2021-04-19 15:35:22] Total Time: 1m36s
[STOP] [2021-04-19 15:35:22] overall_tsv_creation
[INFO] [2021-04-19 15:35:22] Done. Check your files:
[INFO] [2021-04-19 15:35:22] (4 lines) /app/public/data/mozhm/publish_nodes.tsv
[INFO] [2021-04-19 15:35:22] (4 lines) /app/public/data/mozhm/publish_scientific_names.tsv
[INFO] [2021-04-19 15:35:22] (5 lines) /app/public/data/mozhm/publish_traits.tsv
[INFO] [2021-04-19 15:35:22] (1 lines) /app/public/data/mozhm/publish_metadata.tsv
[STOP] [2021-04-19 15:35:22] complete_harvest_instance
[START] [2021-04-19 15:35:22] completed
[STOP] [2021-04-19 15:35:22] completed
[STOP] [2021-04-19 15:35:22] logged process, took 102.67
Latest Process