Stage:
completed
Fetched:
30 Jul 14:36
Validated:
30 Jul 14:36
Deltas Created
30 Jul 14:36
Units Normalized:
30 Jul 14:36
Ancestry Built:
30 Jul 14:36
Nodes Matched:
30 Jul 14:36
Names Parsed:
30 Jul 14:36
New Models Stored:
30 Jul 14:36
Indexed:
30 Jul 14:36
Completed:
30 Jul 14:38
Time to Harvest:
less than a minute
Harvesting Log
(533 lines)
# Logfile created on 2020-07-30 12:33:58 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 12:33:58] logged process
[START] [2020-07-30 12:33:58] Creating resource from OpenData
[START] [2020-07-30 12:33:59] logged process
[START] [2020-07-30 12:33:59] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:33:59] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:33:59] Creating resource from OpenData
[INFO] [2020-07-30 12:34:19] ## HARVEST: type = -harvest
[START] [2020-07-30 12:34:21] logged process
[START] [2020-07-30 12:34:21] create_harvest_instance
[STOP] [2020-07-30 12:34:23] create_harvest_instance
[START] [2020-07-30 12:34:23] fetch_files
[STOP] [2020-07-30 12:34:23] fetch_files
[START] [2020-07-30 12:34:23] validate_each_file
[STOP] [2020-07-30 12:34:23] validate_each_file
[START] [2020-07-30 12:34:23] convert_to_csv
[CMD] [2020-07-30 12:34:23] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_refs_22236.csv > /app/public/converted_csv/clark_hermans_cl_refs_22236.csv_sorted
[CMD] [2020-07-30 12:34:23] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_nodes_22237.csv > /app/public/converted_csv/clark_hermans_cl_nodes_22237.csv_sorted
[CMD] [2020-07-30 12:34:23] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_occurrences_22238.csv > /app/public/converted_csv/clark_hermans_cl_occurrences_22238.csv_sorted
[CMD] [2020-07-30 12:34:23] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_measurements_22239.csv > /app/public/converted_csv/clark_hermans_cl_measurements_22239.csv_sorted
[STOP] [2020-07-30 12:34:23] convert_to_csv
[START] [2020-07-30 12:34:23] calculate_delta
[CMD] [2020-07-30 12:34:23] echo "0a" > /app/public/diff/clark_hermans_cl_refs_22236.diff
[CMD] [2020-07-30 12:34:23] tail -n +1 /app/public/converted_csv/clark_hermans_cl_refs_22236.csv >> /app/public/diff/clark_hermans_cl_refs_22236.diff
[CMD] [2020-07-30 12:34:23] echo "." >> /app/public/diff/clark_hermans_cl_refs_22236.diff
[CMD] [2020-07-30 12:34:23] echo "0a" > /app/public/diff/clark_hermans_cl_nodes_22237.diff
[CMD] [2020-07-30 12:34:23] tail -n +1 /app/public/converted_csv/clark_hermans_cl_nodes_22237.csv >> /app/public/diff/clark_hermans_cl_nodes_22237.diff
[CMD] [2020-07-30 12:34:23] echo "." >> /app/public/diff/clark_hermans_cl_nodes_22237.diff
[CMD] [2020-07-30 12:34:23] echo "0a" > /app/public/diff/clark_hermans_cl_occurrences_22238.diff
[CMD] [2020-07-30 12:34:23] tail -n +1 /app/public/converted_csv/clark_hermans_cl_occurrences_22238.csv >> /app/public/diff/clark_hermans_cl_occurrences_22238.diff
[CMD] [2020-07-30 12:34:23] echo "." >> /app/public/diff/clark_hermans_cl_occurrences_22238.diff
[CMD] [2020-07-30 12:34:23] echo "0a" > /app/public/diff/clark_hermans_cl_measurements_22239.diff
[CMD] [2020-07-30 12:34:23] tail -n +1 /app/public/converted_csv/clark_hermans_cl_measurements_22239.csv >> /app/public/diff/clark_hermans_cl_measurements_22239.diff
[CMD] [2020-07-30 12:34:23] echo "." >> /app/public/diff/clark_hermans_cl_measurements_22239.diff
[STOP] [2020-07-30 12:34:23] calculate_delta
[START] [2020-07-30 12:34:23] parse_diff_and_store
[INFO] [2020-07-30 12:34:23] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 12:34:23] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 12:34:23] Loading occurrences diff file into memory (true lines)...
[WARN] [2020-07-30 12:34:23] Created lifestage term for 58860!
[WARN] [2020-07-30 12:34:23] Created lifestage term for 58306!
[WARN] [2020-07-30 12:34:23] Created lifestage term for 71623!
[WARN] [2020-07-30 12:34:23] Created lifestage term for 71650!
[INFO] [2020-07-30 12:34:23] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 12:34:23] Storing 4 ScientificNames
[INFO] [2020-07-30 12:34:23] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 12:34:23] Average Time: 0.0
[INFO] [2020-07-30 12:34:23] Total Time: 1s
[INFO] [2020-07-30 12:34:23] Storing 4 Nodes
[INFO] [2020-07-30 12:34:23] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 12:34:23] Average Time: 0.0
[INFO] [2020-07-30 12:34:23] Total Time: 1s
[INFO] [2020-07-30 12:34:23] Storing 4 Occurrences
[INFO] [2020-07-30 12:34:23] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 12:34:23] Average Time: 0.0
[INFO] [2020-07-30 12:34:23] Total Time: 1s
[INFO] [2020-07-30 12:34:23] Storing 8 Traits
[INFO] [2020-07-30 12:34:23] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-30 12:34:23] Average Time: 0.0
[INFO] [2020-07-30 12:34:23] Total Time: 1s
[INFO] [2020-07-30 12:34:23] Storing 8 MetaTraits
[INFO] [2020-07-30 12:34:23] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-30 12:34:23] Average Time: 0.0
[INFO] [2020-07-30 12:34:23] Total Time: 1s
[STOP] [2020-07-30 12:34:23] parse_diff_and_store
[START] [2020-07-30 12:34:23] resolve_keys
[INFO] [2020-07-30 12:34:30] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 12:34:30] traits to occurrences...
[INFO] [2020-07-30 12:34:30] traits to nodes (through occurrences)...
[INFO] [2020-07-30 12:34:30] Traits to sex term...
[INFO] [2020-07-30 12:34:30] Traits to lifestage term...
[INFO] [2020-07-30 12:34:30] MetaTraits to traits...
[INFO] [2020-07-30 12:34:30] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 12:34:30] Assocs to occurrences...
[INFO] [2020-07-30 12:34:30] Assocs to nodes...
[INFO] [2020-07-30 12:34:30] Assoc to sex term...
[INFO] [2020-07-30 12:34:30] Assoc to lifestage term...
[STOP] [2020-07-30 12:34:30] resolve_keys
[START] [2020-07-30 12:34:30] hold_for_later_1
[STOP] [2020-07-30 12:34:30] hold_for_later_1
[START] [2020-07-30 12:34:30] hold_for_later_2
[STOP] [2020-07-30 12:34:30] hold_for_later_2
[START] [2020-07-30 12:34:30] resolve_missing_parents
[STOP] [2020-07-30 12:34:30] resolve_missing_parents
[START] [2020-07-30 12:34:30] rebuild_nodes
[START] [2020-07-30 12:34:30] Flattener#flatten
[START] [2020-07-30 12:34:30] Flattener#study_resource
[START] [2020-07-30 12:34:30] Flattener#build_ancestry
[STOP] [2020-07-30 12:34:30] Flattener#build_ancestry
[INFO] [2020-07-30 12:34:30] 4 ancestry keys
[START] [2020-07-30 12:34:30] build_node_ancestors
[INFO] [2020-07-30 12:34:30] old ancestors deleted.
[STOP] [2020-07-30 12:34:30] build_node_ancestors
[WARN] [2020-07-30 12:34:30] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 12:34:30] Flattener#flatten
[STOP] [2020-07-30 12:34:30] rebuild_nodes
[START] [2020-07-30 12:34:30] resolve_missing_media_owners
[STOP] [2020-07-30 12:34:30] resolve_missing_media_owners
[START] [2020-07-30 12:34:30] sanitize_media_verbatims
[STOP] [2020-07-30 12:34:30] sanitize_media_verbatims
[START] [2020-07-30 12:34:30] queue_downloads
[STOP] [2020-07-30 12:34:30] queue_downloads
[START] [2020-07-30 12:34:30] parse_names
[WARN] [2020-07-30 12:34:30] I see 4 names which still need to be parsed.
[STOP] [2020-07-30 12:34:31] parse_names
[START] [2020-07-30 12:34:31] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 12:34:31] denormalize_canonical_names_to_nodes
[START] [2020-07-30 12:34:31] match_nodes
[START] [2020-07-30 12:34:31] map_all_nodes_to_pages
[STOP] [2020-07-30 12:34:31] map_all_nodes_to_pages
[INFO] [2020-07-30 12:34:31] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2020-07-30 12:34:31] update_nodes
[STOP] [2020-07-30 12:34:31] update_nodes
[STOP] [2020-07-30 12:34:31] match_nodes
[START] [2020-07-30 12:34:31] reindex_search
[STOP] [2020-07-30 12:34:31] reindex_search
[START] [2020-07-30 12:34:31] normalize_units
[STOP] [2020-07-30 12:34:31] normalize_units
[START] [2020-07-30 12:34:31] calculate_statistics
[2020-07-30 12:34:31] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 12:34:31] calculate_statistics
[START] [2020-07-30 12:34:31] complete_harvest_instance
[START] [2020-07-30 12:34:31] overall_tsv_creation
[INFO] [2020-07-30 12:34:31] Processing group of 4 in 1 batches of 10000
[INFO] [2020-07-30 12:35:20] 4 Traits (unfiltered)...
[INFO] [2020-07-30 12:35:57] 4 Traits (filtered)...
[INFO] [2020-07-30 12:35:57] 0 Associations (filtered)...
[INFO] [2020-07-30 12:35:57] 12 metadata added.
[INFO] [2020-07-30 12:35:57] 0 metadata added.
[INFO] [2020-07-30 12:35:57] Average Time: 58.32
[INFO] [2020-07-30 12:35:57] Total Time: 1m26s
[STOP] [2020-07-30 12:35:57] overall_tsv_creation
[INFO] [2020-07-30 12:35:57] Done. Check your files:
[INFO] [2020-07-30 12:35:57] (4 lines) /app/public/data/clark_hermans_cl/publish_nodes.tsv
[INFO] [2020-07-30 12:35:57] (4 lines) /app/public/data/clark_hermans_cl/publish_scientific_names.tsv
[INFO] [2020-07-30 12:35:57] (5 lines) /app/public/data/clark_hermans_cl/publish_traits.tsv
[INFO] [2020-07-30 12:35:57] (5 lines) /app/public/data/clark_hermans_cl/publish_metadata.tsv
[STOP] [2020-07-30 12:35:57] complete_harvest_instance
[START] [2020-07-30 12:35:57] completed
[STOP] [2020-07-30 12:35:57] completed
[STOP] [2020-07-30 12:35:57] logged process, took 95.84
[INFO] [2020-07-30 14:27:03] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-30 14:27:05] ## remove_type: ScientificName
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 4 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.010] Removed 4 Scientificnames
[INFO] [2020-07-30 14:27:05] ## remove_type: Vernacular
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.015] Removed 0 Vernaculars
[INFO] [2020-07-30 14:27:05] ## remove_type: Article
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.018] Removed 0 Articles
[INFO] [2020-07-30 14:27:05] ## remove_type: Medium
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.021] Removed 0 Media
[INFO] [2020-07-30 14:27:05] ## remove_type: Trait
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 8 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.025] Removed 8 Traits
[INFO] [2020-07-30 14:27:05] ## remove_type: MetaTrait
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 8 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.028] Removed 8 Metatraits
[INFO] [2020-07-30 14:27:05] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.031] Removed 0 Occurrencemetadata
[INFO] [2020-07-30 14:27:05] ## remove_type: Assoc
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.034] Removed 0 Assocs
[INFO] [2020-07-30 14:27:05] ## remove_type: MetaAssoc
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.037] Removed 0 Metaassocs
[INFO] [2020-07-30 14:27:05] ## remove_type: Identifier
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.039] Removed 0 Identifiers
[INFO] [2020-07-30 14:27:05] ## remove_type: Reference
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.042] Removed 0 References
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] Starting batch with ID 80634392...
[INFO] [2020-07-30 14:27:05] ## remove_type: Node
[INFO] [2020-07-30 14:27:05] ++ Calling delete_all on 4 instances...
[INFO] [2020-07-30 14:27:05] [14:27:05.722] Removed 4 Nodes
[START] [2020-07-30 14:27:06] logged process
[START] [2020-07-30 14:27:06] Creating resource from OpenData
[START] [2020-07-30 14:27:06] logged process
[START] [2020-07-30 14:27:06] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:27:06] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:27:06] Creating resource from OpenData
[START] [2020-07-30 14:27:06] logged process
[START] [2020-07-30 14:27:06] create_harvest_instance
[STOP] [2020-07-30 14:27:07] create_harvest_instance
[START] [2020-07-30 14:27:07] fetch_files
[STOP] [2020-07-30 14:27:07] fetch_files
[START] [2020-07-30 14:27:07] validate_each_file
[STOP] [2020-07-30 14:27:07] validate_each_file
[START] [2020-07-30 14:27:07] convert_to_csv
[CMD] [2020-07-30 14:27:07] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_refs_22276.csv > /app/public/converted_csv/clark_hermans_cl_refs_22276.csv_sorted
[CMD] [2020-07-30 14:27:07] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_nodes_22277.csv > /app/public/converted_csv/clark_hermans_cl_nodes_22277.csv_sorted
[CMD] [2020-07-30 14:27:07] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_occurrences_22278.csv > /app/public/converted_csv/clark_hermans_cl_occurrences_22278.csv_sorted
[CMD] [2020-07-30 14:27:07] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_measurements_22279.csv > /app/public/converted_csv/clark_hermans_cl_measurements_22279.csv_sorted
[STOP] [2020-07-30 14:27:07] convert_to_csv
[START] [2020-07-30 14:27:07] calculate_delta
[CMD] [2020-07-30 14:27:07] echo "0a" > /app/public/diff/clark_hermans_cl_refs_22276.diff
[CMD] [2020-07-30 14:27:07] tail -n +1 /app/public/converted_csv/clark_hermans_cl_refs_22276.csv >> /app/public/diff/clark_hermans_cl_refs_22276.diff
[CMD] [2020-07-30 14:27:07] echo "." >> /app/public/diff/clark_hermans_cl_refs_22276.diff
[CMD] [2020-07-30 14:27:07] echo "0a" > /app/public/diff/clark_hermans_cl_nodes_22277.diff
[CMD] [2020-07-30 14:27:07] tail -n +1 /app/public/converted_csv/clark_hermans_cl_nodes_22277.csv >> /app/public/diff/clark_hermans_cl_nodes_22277.diff
[CMD] [2020-07-30 14:27:07] echo "." >> /app/public/diff/clark_hermans_cl_nodes_22277.diff
[CMD] [2020-07-30 14:27:07] echo "0a" > /app/public/diff/clark_hermans_cl_occurrences_22278.diff
[CMD] [2020-07-30 14:27:07] tail -n +1 /app/public/converted_csv/clark_hermans_cl_occurrences_22278.csv >> /app/public/diff/clark_hermans_cl_occurrences_22278.diff
[CMD] [2020-07-30 14:27:07] echo "." >> /app/public/diff/clark_hermans_cl_occurrences_22278.diff
[CMD] [2020-07-30 14:27:07] echo "0a" > /app/public/diff/clark_hermans_cl_measurements_22279.diff
[CMD] [2020-07-30 14:27:07] tail -n +1 /app/public/converted_csv/clark_hermans_cl_measurements_22279.csv >> /app/public/diff/clark_hermans_cl_measurements_22279.diff
[CMD] [2020-07-30 14:27:07] echo "." >> /app/public/diff/clark_hermans_cl_measurements_22279.diff
[STOP] [2020-07-30 14:27:07] calculate_delta
[START] [2020-07-30 14:27:07] parse_diff_and_store
[INFO] [2020-07-30 14:27:07] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 14:27:07] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 14:27:07] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 14:27:08] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 14:27:08] Storing 4 ScientificNames
[INFO] [2020-07-30 14:27:08] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 14:27:08] Average Time: 0.0
[INFO] [2020-07-30 14:27:08] Total Time: 1s
[INFO] [2020-07-30 14:27:08] Storing 4 Nodes
[INFO] [2020-07-30 14:27:08] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 14:27:08] Average Time: 0.0
[INFO] [2020-07-30 14:27:08] Total Time: 1s
[INFO] [2020-07-30 14:27:08] Storing 4 Occurrences
[INFO] [2020-07-30 14:27:08] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 14:27:08] Average Time: 0.0
[INFO] [2020-07-30 14:27:08] Total Time: 1s
[INFO] [2020-07-30 14:27:08] Storing 8 Traits
[INFO] [2020-07-30 14:27:08] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-30 14:27:08] Average Time: 0.0
[INFO] [2020-07-30 14:27:08] Total Time: 1s
[INFO] [2020-07-30 14:27:08] Storing 8 MetaTraits
[INFO] [2020-07-30 14:27:08] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-30 14:27:08] Average Time: 0.0
[INFO] [2020-07-30 14:27:08] Total Time: 1s
[STOP] [2020-07-30 14:27:08] parse_diff_and_store
[START] [2020-07-30 14:27:08] resolve_keys
[INFO] [2020-07-30 14:27:14] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 14:27:14] traits to occurrences...
[INFO] [2020-07-30 14:27:14] traits to nodes (through occurrences)...
[INFO] [2020-07-30 14:27:14] Traits to sex term...
[INFO] [2020-07-30 14:27:14] Traits to lifestage term...
[INFO] [2020-07-30 14:27:14] MetaTraits to traits...
[INFO] [2020-07-30 14:27:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 14:27:14] Assocs to occurrences...
[INFO] [2020-07-30 14:27:14] Assocs to nodes...
[INFO] [2020-07-30 14:27:14] Assoc to sex term...
[INFO] [2020-07-30 14:27:14] Assoc to lifestage term...
[STOP] [2020-07-30 14:27:14] resolve_keys
[START] [2020-07-30 14:27:14] hold_for_later_1
[STOP] [2020-07-30 14:27:14] hold_for_later_1
[START] [2020-07-30 14:27:14] hold_for_later_2
[STOP] [2020-07-30 14:27:14] hold_for_later_2
[START] [2020-07-30 14:27:14] resolve_missing_parents
[STOP] [2020-07-30 14:27:14] resolve_missing_parents
[START] [2020-07-30 14:27:14] rebuild_nodes
[START] [2020-07-30 14:27:14] Flattener#flatten
[START] [2020-07-30 14:27:14] Flattener#study_resource
[START] [2020-07-30 14:27:14] Flattener#build_ancestry
[STOP] [2020-07-30 14:27:14] Flattener#build_ancestry
[INFO] [2020-07-30 14:27:14] 4 ancestry keys
[START] [2020-07-30 14:27:14] build_node_ancestors
[INFO] [2020-07-30 14:27:14] old ancestors deleted.
[STOP] [2020-07-30 14:27:14] build_node_ancestors
[WARN] [2020-07-30 14:27:14] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 14:27:14] Flattener#flatten
[STOP] [2020-07-30 14:27:14] rebuild_nodes
[START] [2020-07-30 14:27:14] resolve_missing_media_owners
[STOP] [2020-07-30 14:27:14] resolve_missing_media_owners
[START] [2020-07-30 14:27:14] sanitize_media_verbatims
[STOP] [2020-07-30 14:27:14] sanitize_media_verbatims
[START] [2020-07-30 14:27:14] queue_downloads
[STOP] [2020-07-30 14:27:14] queue_downloads
[START] [2020-07-30 14:27:14] parse_names
[WARN] [2020-07-30 14:27:14] I see 4 names which still need to be parsed.
[STOP] [2020-07-30 14:27:16] parse_names
[START] [2020-07-30 14:27:16] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 14:27:16] denormalize_canonical_names_to_nodes
[START] [2020-07-30 14:27:16] match_nodes
[START] [2020-07-30 14:27:16] map_all_nodes_to_pages
[STOP] [2020-07-30 14:27:16] map_all_nodes_to_pages
[INFO] [2020-07-30 14:27:16] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2020-07-30 14:27:16] update_nodes
[STOP] [2020-07-30 14:27:16] update_nodes
[STOP] [2020-07-30 14:27:16] match_nodes
[START] [2020-07-30 14:27:16] reindex_search
[STOP] [2020-07-30 14:27:16] reindex_search
[START] [2020-07-30 14:27:16] normalize_units
[STOP] [2020-07-30 14:27:16] normalize_units
[START] [2020-07-30 14:27:16] calculate_statistics
[2020-07-30 14:27:16] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 14:27:16] calculate_statistics
[START] [2020-07-30 14:27:16] complete_harvest_instance
[START] [2020-07-30 14:27:16] overall_tsv_creation
[INFO] [2020-07-30 14:27:16] Processing group of 4 in 1 batches of 10000
[INFO] [2020-07-30 14:28:04] 4 Traits (unfiltered)...
[INFO] [2020-07-30 14:28:41] 4 Traits (filtered)...
[INFO] [2020-07-30 14:28:41] 0 Associations (filtered)...
[INFO] [2020-07-30 14:28:41] 12 metadata added.
[INFO] [2020-07-30 14:28:41] 0 metadata added.
[INFO] [2020-07-30 14:28:41] Average Time: 58.3
[INFO] [2020-07-30 14:28:41] Total Time: 1m26s
[STOP] [2020-07-30 14:28:41] overall_tsv_creation
[INFO] [2020-07-30 14:28:41] Done. Check your files:
[INFO] [2020-07-30 14:28:41] (4 lines) /app/public/data/clark_hermans_cl/publish_nodes.tsv
[INFO] [2020-07-30 14:28:41] (4 lines) /app/public/data/clark_hermans_cl/publish_scientific_names.tsv
[INFO] [2020-07-30 14:28:41] (5 lines) /app/public/data/clark_hermans_cl/publish_traits.tsv
[INFO] [2020-07-30 14:28:41] (5 lines) /app/public/data/clark_hermans_cl/publish_metadata.tsv
[STOP] [2020-07-30 14:28:41] complete_harvest_instance
[START] [2020-07-30 14:28:41] completed
[STOP] [2020-07-30 14:28:41] completed
[STOP] [2020-07-30 14:28:41] logged process, took 95.11
[INFO] [2020-07-30 14:36:39] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-30 14:36:44] ## remove_type: ScientificName
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 4 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.119] Removed 4 Scientificnames
[INFO] [2020-07-30 14:36:44] ## remove_type: Vernacular
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.122] Removed 0 Vernaculars
[INFO] [2020-07-30 14:36:44] ## remove_type: Article
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.125] Removed 0 Articles
[INFO] [2020-07-30 14:36:44] ## remove_type: Medium
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.129] Removed 0 Media
[INFO] [2020-07-30 14:36:44] ## remove_type: Trait
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 8 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.133] Removed 8 Traits
[INFO] [2020-07-30 14:36:44] ## remove_type: MetaTrait
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 8 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.136] Removed 8 Metatraits
[INFO] [2020-07-30 14:36:44] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.139] Removed 0 Occurrencemetadata
[INFO] [2020-07-30 14:36:44] ## remove_type: Assoc
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.142] Removed 0 Assocs
[INFO] [2020-07-30 14:36:44] ## remove_type: MetaAssoc
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.145] Removed 0 Metaassocs
[INFO] [2020-07-30 14:36:44] ## remove_type: Identifier
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.147] Removed 0 Identifiers
[INFO] [2020-07-30 14:36:44] ## remove_type: Reference
[INFO] [2020-07-30 14:36:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:36:44] [14:36:44.150] Removed 0 References
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:44] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:45] Starting batch with ID 80634404...
[INFO] [2020-07-30 14:36:45] ## remove_type: Node
[INFO] [2020-07-30 14:36:45] ++ Calling delete_all on 4 instances...
[INFO] [2020-07-30 14:36:45] [14:36:45.174] Removed 4 Nodes
[START] [2020-07-30 14:36:45] logged process
[START] [2020-07-30 14:36:45] Creating resource from OpenData
[START] [2020-07-30 14:36:45] logged process
[START] [2020-07-30 14:36:45] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:36:45] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:36:45] Creating resource from OpenData
[START] [2020-07-30 14:36:45] logged process
[START] [2020-07-30 14:36:45] create_harvest_instance
[STOP] [2020-07-30 14:36:47] create_harvest_instance
[START] [2020-07-30 14:36:47] fetch_files
[STOP] [2020-07-30 14:36:47] fetch_files
[START] [2020-07-30 14:36:47] validate_each_file
[STOP] [2020-07-30 14:36:47] validate_each_file
[START] [2020-07-30 14:36:47] convert_to_csv
[CMD] [2020-07-30 14:36:47] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_refs_22292.csv > /app/public/converted_csv/clark_hermans_cl_refs_22292.csv_sorted
[CMD] [2020-07-30 14:36:47] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_nodes_22293.csv > /app/public/converted_csv/clark_hermans_cl_nodes_22293.csv_sorted
[CMD] [2020-07-30 14:36:47] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_occurrences_22294.csv > /app/public/converted_csv/clark_hermans_cl_occurrences_22294.csv_sorted
[CMD] [2020-07-30 14:36:47] /usr/bin/sort /app/public/converted_csv/clark_hermans_cl_measurements_22295.csv > /app/public/converted_csv/clark_hermans_cl_measurements_22295.csv_sorted
[STOP] [2020-07-30 14:36:47] convert_to_csv
[START] [2020-07-30 14:36:47] calculate_delta
[CMD] [2020-07-30 14:36:47] echo "0a" > /app/public/diff/clark_hermans_cl_refs_22292.diff
[CMD] [2020-07-30 14:36:47] tail -n +1 /app/public/converted_csv/clark_hermans_cl_refs_22292.csv >> /app/public/diff/clark_hermans_cl_refs_22292.diff
[CMD] [2020-07-30 14:36:47] echo "." >> /app/public/diff/clark_hermans_cl_refs_22292.diff
[CMD] [2020-07-30 14:36:47] echo "0a" > /app/public/diff/clark_hermans_cl_nodes_22293.diff
[CMD] [2020-07-30 14:36:47] tail -n +1 /app/public/converted_csv/clark_hermans_cl_nodes_22293.csv >> /app/public/diff/clark_hermans_cl_nodes_22293.diff
[CMD] [2020-07-30 14:36:47] echo "." >> /app/public/diff/clark_hermans_cl_nodes_22293.diff
[CMD] [2020-07-30 14:36:47] echo "0a" > /app/public/diff/clark_hermans_cl_occurrences_22294.diff
[CMD] [2020-07-30 14:36:47] tail -n +1 /app/public/converted_csv/clark_hermans_cl_occurrences_22294.csv >> /app/public/diff/clark_hermans_cl_occurrences_22294.diff
[CMD] [2020-07-30 14:36:47] echo "." >> /app/public/diff/clark_hermans_cl_occurrences_22294.diff
[CMD] [2020-07-30 14:36:47] echo "0a" > /app/public/diff/clark_hermans_cl_measurements_22295.diff
[CMD] [2020-07-30 14:36:47] tail -n +1 /app/public/converted_csv/clark_hermans_cl_measurements_22295.csv >> /app/public/diff/clark_hermans_cl_measurements_22295.diff
[CMD] [2020-07-30 14:36:47] echo "." >> /app/public/diff/clark_hermans_cl_measurements_22295.diff
[STOP] [2020-07-30 14:36:47] calculate_delta
[START] [2020-07-30 14:36:47] parse_diff_and_store
[INFO] [2020-07-30 14:36:47] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 14:36:47] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 14:36:47] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 14:36:47] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 14:36:47] Storing 4 ScientificNames
[INFO] [2020-07-30 14:36:47] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 14:36:47] Average Time: 0.0
[INFO] [2020-07-30 14:36:47] Total Time: 1s
[INFO] [2020-07-30 14:36:47] Storing 4 Nodes
[INFO] [2020-07-30 14:36:47] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 14:36:47] Average Time: 0.0
[INFO] [2020-07-30 14:36:47] Total Time: 1s
[INFO] [2020-07-30 14:36:47] Storing 4 Occurrences
[INFO] [2020-07-30 14:36:47] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 14:36:47] Average Time: 0.0
[INFO] [2020-07-30 14:36:47] Total Time: 1s
[INFO] [2020-07-30 14:36:47] Storing 8 Traits
[INFO] [2020-07-30 14:36:47] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-30 14:36:47] Average Time: 0.0
[INFO] [2020-07-30 14:36:47] Total Time: 1s
[INFO] [2020-07-30 14:36:47] Storing 8 MetaTraits
[INFO] [2020-07-30 14:36:47] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-30 14:36:47] Average Time: 0.0
[INFO] [2020-07-30 14:36:47] Total Time: 1s
[STOP] [2020-07-30 14:36:47] parse_diff_and_store
[START] [2020-07-30 14:36:47] resolve_keys
[INFO] [2020-07-30 14:36:54] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 14:36:54] traits to occurrences...
[INFO] [2020-07-30 14:36:54] traits to nodes (through occurrences)...
[INFO] [2020-07-30 14:36:54] Traits to sex term...
[INFO] [2020-07-30 14:36:54] Traits to lifestage term...
[INFO] [2020-07-30 14:36:54] MetaTraits to traits...
[INFO] [2020-07-30 14:36:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 14:36:54] Assocs to occurrences...
[INFO] [2020-07-30 14:36:54] Assocs to nodes...
[INFO] [2020-07-30 14:36:54] Assoc to sex term...
[INFO] [2020-07-30 14:36:54] Assoc to lifestage term...
[STOP] [2020-07-30 14:36:54] resolve_keys
[START] [2020-07-30 14:36:54] hold_for_later_1
[STOP] [2020-07-30 14:36:54] hold_for_later_1
[START] [2020-07-30 14:36:54] hold_for_later_2
[STOP] [2020-07-30 14:36:54] hold_for_later_2
[START] [2020-07-30 14:36:54] resolve_missing_parents
[STOP] [2020-07-30 14:36:54] resolve_missing_parents
[START] [2020-07-30 14:36:54] rebuild_nodes
[START] [2020-07-30 14:36:54] Flattener#flatten
[START] [2020-07-30 14:36:54] Flattener#study_resource
[START] [2020-07-30 14:36:54] Flattener#build_ancestry
[STOP] [2020-07-30 14:36:54] Flattener#build_ancestry
[INFO] [2020-07-30 14:36:54] 4 ancestry keys
[START] [2020-07-30 14:36:54] build_node_ancestors
[INFO] [2020-07-30 14:36:54] old ancestors deleted.
[STOP] [2020-07-30 14:36:54] build_node_ancestors
[WARN] [2020-07-30 14:36:54] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 14:36:54] Flattener#flatten
[STOP] [2020-07-30 14:36:54] rebuild_nodes
[START] [2020-07-30 14:36:54] resolve_missing_media_owners
[STOP] [2020-07-30 14:36:54] resolve_missing_media_owners
[START] [2020-07-30 14:36:54] sanitize_media_verbatims
[STOP] [2020-07-30 14:36:54] sanitize_media_verbatims
[START] [2020-07-30 14:36:54] queue_downloads
[STOP] [2020-07-30 14:36:54] queue_downloads
[START] [2020-07-30 14:36:54] parse_names
[WARN] [2020-07-30 14:36:54] I see 4 names which still need to be parsed.
[STOP] [2020-07-30 14:36:55] parse_names
[START] [2020-07-30 14:36:55] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 14:36:55] denormalize_canonical_names_to_nodes
[START] [2020-07-30 14:36:55] match_nodes
[START] [2020-07-30 14:36:55] map_all_nodes_to_pages
[STOP] [2020-07-30 14:36:55] map_all_nodes_to_pages
[INFO] [2020-07-30 14:36:55] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2020-07-30 14:36:55] update_nodes
[STOP] [2020-07-30 14:36:55] update_nodes
[STOP] [2020-07-30 14:36:55] match_nodes
[START] [2020-07-30 14:36:55] reindex_search
[STOP] [2020-07-30 14:36:55] reindex_search
[START] [2020-07-30 14:36:55] normalize_units
[STOP] [2020-07-30 14:36:55] normalize_units
[START] [2020-07-30 14:36:55] calculate_statistics
[2020-07-30 14:36:55] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 14:36:55] calculate_statistics
[START] [2020-07-30 14:36:55] complete_harvest_instance
[START] [2020-07-30 14:36:55] overall_tsv_creation
[INFO] [2020-07-30 14:36:55] Processing group of 4 in 1 batches of 10000
[INFO] [2020-07-30 14:37:44] 4 Traits (unfiltered)...
[INFO] [2020-07-30 14:38:20] 4 Traits (filtered)...
[INFO] [2020-07-30 14:38:20] 0 Associations (filtered)...
[INFO] [2020-07-30 14:38:20] 12 metadata added.
[INFO] [2020-07-30 14:38:20] 0 metadata added.
[INFO] [2020-07-30 14:38:20] Average Time: 57.68
[INFO] [2020-07-30 14:38:20] Total Time: 1m25s
[STOP] [2020-07-30 14:38:20] overall_tsv_creation
[INFO] [2020-07-30 14:38:20] Done. Check your files:
[INFO] [2020-07-30 14:38:20] (4 lines) /app/public/data/clark_hermans_cl/publish_nodes.tsv
[INFO] [2020-07-30 14:38:20] (4 lines) /app/public/data/clark_hermans_cl/publish_scientific_names.tsv
[INFO] [2020-07-30 14:38:20] (5 lines) /app/public/data/clark_hermans_cl/publish_traits.tsv
[INFO] [2020-07-30 14:38:20] (5 lines) /app/public/data/clark_hermans_cl/publish_metadata.tsv
[STOP] [2020-07-30 14:38:20] complete_harvest_instance
[START] [2020-07-30 14:38:20] completed
[STOP] [2020-07-30 14:38:20] completed
[STOP] [2020-07-30 14:38:20] logged process, took 94.45
Latest Process