Stage:
completed
Fetched:
28 Dec 14:13
Validated:
28 Dec 14:13
Deltas Created
28 Dec 14:13
Units Normalized:
28 Dec 14:13
Ancestry Built:
28 Dec 14:13
Nodes Matched:
28 Dec 14:13
Names Parsed:
28 Dec 14:13
New Models Stored:
28 Dec 14:13
Indexed:
28 Dec 14:13
Completed:
28 Dec 14:14
Time to Harvest:
less than a minute
Harvesting Log
(509 lines)
# Logfile created on 2020-12-28 13:45:24 -0500 by logger.rb/v1.4.2
[START] [2020-12-28 13:45:24] logged process: ca5be136aef877c71c74100a42de34a9e7a07645
[START] [2020-12-28 13:45:24] Creating resource from OpenData
[START] [2020-12-28 13:45:25] logged process: ca5be136aef877c71c74100a42de34a9e7a07645
[START] [2020-12-28 13:45:25] Parse meta.xml file and create formats with fields
[STOP] [2020-12-28 13:45:25] Parse meta.xml file and create formats with fields
[STOP] [2020-12-28 13:45:25] Creating resource from OpenData
[INFO] [2020-12-28 13:55:49] ## HARVEST: type = -harvest
[START] [2020-12-28 13:55:49] logged process: ca5be136aef877c71c74100a42de34a9e7a07645
[START] [2020-12-28 13:55:49] create_harvest_instance
[STOP] [2020-12-28 13:55:51] create_harvest_instance
[START] [2020-12-28 13:55:51] fetch_files
[STOP] [2020-12-28 13:55:51] fetch_files
[START] [2020-12-28 13:55:51] validate_each_file
[STOP] [2020-12-28 13:55:51] validate_each_file
[START] [2020-12-28 13:55:51] convert_to_csv
[CMD] [2020-12-28 13:55:51] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__nodes_25879.csv > /app/public/converted_csv/tst_test_of_rep__nodes_25879.csv_sorted
[CMD] [2020-12-28 13:55:51] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__occurrences_25880.csv > /app/public/converted_csv/tst_test_of_rep__occurrences_25880.csv_sorted
[CMD] [2020-12-28 13:55:51] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__assocs_25881.csv > /app/public/converted_csv/tst_test_of_rep__assocs_25881.csv_sorted
[CMD] [2020-12-28 13:55:51] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__measurements_25882.csv > /app/public/converted_csv/tst_test_of_rep__measurements_25882.csv_sorted
[STOP] [2020-12-28 13:55:51] convert_to_csv
[START] [2020-12-28 13:55:51] calculate_delta
[CMD] [2020-12-28 13:55:51] echo "0a" > /app/public/diff/tst_test_of_rep__nodes_25879.diff
[CMD] [2020-12-28 13:55:51] tail -n +1 /app/public/converted_csv/tst_test_of_rep__nodes_25879.csv >> /app/public/diff/tst_test_of_rep__nodes_25879.diff
[CMD] [2020-12-28 13:55:51] echo "." >> /app/public/diff/tst_test_of_rep__nodes_25879.diff
[CMD] [2020-12-28 13:55:51] echo "0a" > /app/public/diff/tst_test_of_rep__occurrences_25880.diff
[CMD] [2020-12-28 13:55:51] tail -n +1 /app/public/converted_csv/tst_test_of_rep__occurrences_25880.csv >> /app/public/diff/tst_test_of_rep__occurrences_25880.diff
[CMD] [2020-12-28 13:55:51] echo "." >> /app/public/diff/tst_test_of_rep__occurrences_25880.diff
[CMD] [2020-12-28 13:55:51] echo "0a" > /app/public/diff/tst_test_of_rep__assocs_25881.diff
[CMD] [2020-12-28 13:55:51] tail -n +1 /app/public/converted_csv/tst_test_of_rep__assocs_25881.csv >> /app/public/diff/tst_test_of_rep__assocs_25881.diff
[CMD] [2020-12-28 13:55:51] echo "." >> /app/public/diff/tst_test_of_rep__assocs_25881.diff
[CMD] [2020-12-28 13:55:51] echo "0a" > /app/public/diff/tst_test_of_rep__measurements_25882.diff
[CMD] [2020-12-28 13:55:51] tail -n +1 /app/public/converted_csv/tst_test_of_rep__measurements_25882.csv >> /app/public/diff/tst_test_of_rep__measurements_25882.diff
[CMD] [2020-12-28 13:55:51] echo "." >> /app/public/diff/tst_test_of_rep__measurements_25882.diff
[STOP] [2020-12-28 13:55:51] calculate_delta
[START] [2020-12-28 13:55:51] parse_diff_and_store
[INFO] [2020-12-28 13:55:51] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-28 13:55:51] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-28 13:55:51] Loading assocs diff file into memory (true lines)...
[INFO] [2020-12-28 13:55:51] Loading measurements diff file into memory (true lines)...
[WARN] [2020-12-28 13:55:52] parent trait with resource 578 and id id doesn't exist (for trait 3)
[WARN] [2020-12-28 13:55:52] parent trait with resource 261 and id id doesn't exist (for trait 4)
[WARN] [2020-12-28 13:55:52] parent trait with resource 253 and id id doesn't exist (for trait 5)
[WARN] [2020-12-28 13:55:52] parent trait with resource 344 and id id doesn't exist (for trait 6)
[INFO] [2020-12-28 13:55:52] Storing 2 ScientificNames
[INFO] [2020-12-28 13:55:52] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-28 13:55:52] Average Time: 0.0
[INFO] [2020-12-28 13:55:52] Total Time: 1s
[INFO] [2020-12-28 13:55:52] Storing 2 Nodes
[INFO] [2020-12-28 13:55:52] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-28 13:55:52] Average Time: 0.0
[INFO] [2020-12-28 13:55:52] Total Time: 1s
[INFO] [2020-12-28 13:55:52] Storing 2 Occurrences
[INFO] [2020-12-28 13:55:52] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-28 13:55:52] Average Time: 0.0
[INFO] [2020-12-28 13:55:52] Total Time: 1s
[INFO] [2020-12-28 13:55:52] Storing 6 Traits
[INFO] [2020-12-28 13:55:52] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-28 13:55:52] Average Time: 0.0
[INFO] [2020-12-28 13:55:52] Total Time: 1s
[INFO] [2020-12-28 13:55:52] Storing 1 MetaTraits
[INFO] [2020-12-28 13:55:52] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-28 13:55:52] Average Time: 0.0
[INFO] [2020-12-28 13:55:52] Total Time: 1s
[STOP] [2020-12-28 13:55:52] parse_diff_and_store
[START] [2020-12-28 13:55:52] resolve_keys
[INFO] [2020-12-28 13:55:58] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-28 13:55:58] traits to occurrences...
[INFO] [2020-12-28 13:55:58] traits to nodes (through occurrences)...
[INFO] [2020-12-28 13:55:58] Traits to sex term...
[INFO] [2020-12-28 13:55:58] Traits to lifestage term...
[INFO] [2020-12-28 13:55:58] MetaTraits to traits...
[INFO] [2020-12-28 13:55:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-28 13:55:58] Assocs to occurrences...
[INFO] [2020-12-28 13:55:58] Assocs to nodes...
[INFO] [2020-12-28 13:55:58] Assoc to sex term...
[INFO] [2020-12-28 13:55:58] Assoc to lifestage term...
[INFO] [2020-12-28 13:55:58] MetaAssoc to assocs...
[STOP] [2020-12-28 13:55:58] resolve_keys
[START] [2020-12-28 13:55:58] hold_for_later_1
[STOP] [2020-12-28 13:55:58] hold_for_later_1
[START] [2020-12-28 13:55:58] hold_for_later_2
[STOP] [2020-12-28 13:55:58] hold_for_later_2
[START] [2020-12-28 13:55:58] resolve_missing_parents
[STOP] [2020-12-28 13:55:58] resolve_missing_parents
[START] [2020-12-28 13:55:58] rebuild_nodes
[START] [2020-12-28 13:55:58] Flattener#flatten
[START] [2020-12-28 13:55:58] Flattener#study_resource
[START] [2020-12-28 13:55:58] Flattener#build_ancestry
[STOP] [2020-12-28 13:55:58] Flattener#build_ancestry
[INFO] [2020-12-28 13:55:58] 2 ancestry keys
[START] [2020-12-28 13:55:58] build_node_ancestors
[INFO] [2020-12-28 13:55:58] old ancestors deleted.
[STOP] [2020-12-28 13:55:58] build_node_ancestors
[WARN] [2020-12-28 13:55:58] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-28 13:55:58] Flattener#flatten
[STOP] [2020-12-28 13:55:58] rebuild_nodes
[START] [2020-12-28 13:55:58] resolve_missing_media_owners
[STOP] [2020-12-28 13:55:58] resolve_missing_media_owners
[START] [2020-12-28 13:55:58] sanitize_media_verbatims
[STOP] [2020-12-28 13:55:58] sanitize_media_verbatims
[START] [2020-12-28 13:55:58] queue_downloads
[STOP] [2020-12-28 13:55:58] queue_downloads
[START] [2020-12-28 13:55:58] parse_names
[WARN] [2020-12-28 13:55:58] I see 2 names which still need to be parsed.
[STOP] [2020-12-28 13:55:59] parse_names
[START] [2020-12-28 13:55:59] denormalize_canonical_names_to_nodes
[STOP] [2020-12-28 13:55:59] denormalize_canonical_names_to_nodes
[START] [2020-12-28 13:55:59] match_nodes
[START] [2020-12-28 13:55:59] map_all_nodes_to_pages
[STOP] [2020-12-28 13:55:59] map_all_nodes_to_pages
[INFO] [2020-12-28 13:55:59] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-12-28 13:55:59] update_nodes
[STOP] [2020-12-28 13:55:59] update_nodes
[STOP] [2020-12-28 13:55:59] match_nodes
[START] [2020-12-28 13:55:59] reindex_search
[STOP] [2020-12-28 13:55:59] reindex_search
[START] [2020-12-28 13:55:59] normalize_units
[STOP] [2020-12-28 13:55:59] normalize_units
[START] [2020-12-28 13:55:59] calculate_statistics
[2020-12-28 13:55:59] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-28 13:55:59] calculate_statistics
[START] [2020-12-28 13:55:59] complete_harvest_instance
[START] [2020-12-28 13:55:59] overall_tsv_creation
[INFO] [2020-12-28 13:55:59] Processing group of 2 in 1 batches of 10000
[INFO] [2020-12-28 13:56:37] 1 Traits (unfiltered)...
[INFO] [2020-12-28 13:57:10] 1 Traits (filtered)...
[INFO] [2020-12-28 13:57:10] 0 Associations (filtered)...
[INFO] [2020-12-28 13:57:10] 2 metadata added.
[INFO] [2020-12-28 13:57:10] 0 metadata added.
[INFO] [2020-12-28 13:57:40] Average Time: 75.72
[INFO] [2020-12-28 13:57:40] Total Time: 1m41s
[STOP] [2020-12-28 13:57:40] overall_tsv_creation
[INFO] [2020-12-28 13:57:40] Done. Check your files:
[INFO] [2020-12-28 13:57:40] (2 lines) /app/public/data/tst_test_of_rep_/publish_nodes.tsv
[INFO] [2020-12-28 13:57:40] (2 lines) /app/public/data/tst_test_of_rep_/publish_scientific_names.tsv
[INFO] [2020-12-28 13:57:40] (2 lines) /app/public/data/tst_test_of_rep_/publish_traits.tsv
[INFO] [2020-12-28 13:57:40] (3 lines) /app/public/data/tst_test_of_rep_/publish_metadata.tsv
[STOP] [2020-12-28 13:57:40] complete_harvest_instance
[START] [2020-12-28 13:57:40] completed
[STOP] [2020-12-28 13:57:40] completed
[STOP] [2020-12-28 13:57:40] logged process, took 110.69
[INFO] [2020-12-28 14:08:15] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-12-28 14:08:17] ## remove_type: ScientificName
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 2 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.096] Removed 2 Scientificnames
[INFO] [2020-12-28 14:08:17] ## remove_type: Vernacular
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.099] Removed 0 Vernaculars
[INFO] [2020-12-28 14:08:17] ## remove_type: Article
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.102] Removed 0 Articles
[INFO] [2020-12-28 14:08:17] ## remove_type: Medium
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.105] Removed 0 Media
[INFO] [2020-12-28 14:08:17] ## remove_type: Trait
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 6 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.109] Removed 6 Traits
[INFO] [2020-12-28 14:08:17] ## remove_type: MetaTrait
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 1 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.112] Removed 1 Metatraits
[INFO] [2020-12-28 14:08:17] ## remove_type: OccurrenceMetadatum
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.115] Removed 0 Occurrencemetadata
[INFO] [2020-12-28 14:08:17] ## remove_type: Assoc
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.118] Removed 0 Assocs
[INFO] [2020-12-28 14:08:17] ## remove_type: MetaAssoc
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.121] Removed 0 Metaassocs
[INFO] [2020-12-28 14:08:17] ## remove_type: Identifier
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.123] Removed 0 Identifiers
[INFO] [2020-12-28 14:08:17] ## remove_type: Reference
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.125] Removed 0 References
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400966...
[INFO] [2020-12-28 14:08:17] Starting batch with ID 87400965...
[INFO] [2020-12-28 14:08:17] ## remove_type: Node
[INFO] [2020-12-28 14:08:17] ++ Calling delete_all on 2 instances...
[INFO] [2020-12-28 14:08:17] [14:08:17.713] Removed 2 Nodes
[START] [2020-12-28 14:08:18] logged process: ca5be136aef877c71c74100a42de34a9e7a07645
[START] [2020-12-28 14:08:18] Creating resource from OpenData
[START] [2020-12-28 14:08:18] logged process: ca5be136aef877c71c74100a42de34a9e7a07645
[START] [2020-12-28 14:08:18] Parse meta.xml file and create formats with fields
[STOP] [2020-12-28 14:08:18] Parse meta.xml file and create formats with fields
[STOP] [2020-12-28 14:08:18] Creating resource from OpenData
[START] [2020-12-28 14:08:18] logged process: ca5be136aef877c71c74100a42de34a9e7a07645
[START] [2020-12-28 14:08:18] create_harvest_instance
[STOP] [2020-12-28 14:08:20] create_harvest_instance
[START] [2020-12-28 14:08:20] fetch_files
[STOP] [2020-12-28 14:08:20] fetch_files
[START] [2020-12-28 14:08:20] validate_each_file
[STOP] [2020-12-28 14:08:20] validate_each_file
[START] [2020-12-28 14:08:20] convert_to_csv
[CMD] [2020-12-28 14:08:20] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__nodes_25887.csv > /app/public/converted_csv/tst_test_of_rep__nodes_25887.csv_sorted
[CMD] [2020-12-28 14:08:20] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__occurrences_25888.csv > /app/public/converted_csv/tst_test_of_rep__occurrences_25888.csv_sorted
[CMD] [2020-12-28 14:08:20] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__assocs_25889.csv > /app/public/converted_csv/tst_test_of_rep__assocs_25889.csv_sorted
[CMD] [2020-12-28 14:08:20] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__measurements_25890.csv > /app/public/converted_csv/tst_test_of_rep__measurements_25890.csv_sorted
[STOP] [2020-12-28 14:08:20] convert_to_csv
[START] [2020-12-28 14:08:20] calculate_delta
[CMD] [2020-12-28 14:08:20] echo "0a" > /app/public/diff/tst_test_of_rep__nodes_25887.diff
[CMD] [2020-12-28 14:08:20] tail -n +1 /app/public/converted_csv/tst_test_of_rep__nodes_25887.csv >> /app/public/diff/tst_test_of_rep__nodes_25887.diff
[CMD] [2020-12-28 14:08:20] echo "." >> /app/public/diff/tst_test_of_rep__nodes_25887.diff
[CMD] [2020-12-28 14:08:20] echo "0a" > /app/public/diff/tst_test_of_rep__occurrences_25888.diff
[CMD] [2020-12-28 14:08:20] tail -n +1 /app/public/converted_csv/tst_test_of_rep__occurrences_25888.csv >> /app/public/diff/tst_test_of_rep__occurrences_25888.diff
[CMD] [2020-12-28 14:08:20] echo "." >> /app/public/diff/tst_test_of_rep__occurrences_25888.diff
[CMD] [2020-12-28 14:08:20] echo "0a" > /app/public/diff/tst_test_of_rep__assocs_25889.diff
[CMD] [2020-12-28 14:08:20] tail -n +1 /app/public/converted_csv/tst_test_of_rep__assocs_25889.csv >> /app/public/diff/tst_test_of_rep__assocs_25889.diff
[CMD] [2020-12-28 14:08:20] echo "." >> /app/public/diff/tst_test_of_rep__assocs_25889.diff
[CMD] [2020-12-28 14:08:20] echo "0a" > /app/public/diff/tst_test_of_rep__measurements_25890.diff
[CMD] [2020-12-28 14:08:20] tail -n +1 /app/public/converted_csv/tst_test_of_rep__measurements_25890.csv >> /app/public/diff/tst_test_of_rep__measurements_25890.diff
[CMD] [2020-12-28 14:08:20] echo "." >> /app/public/diff/tst_test_of_rep__measurements_25890.diff
[STOP] [2020-12-28 14:08:20] calculate_delta
[START] [2020-12-28 14:08:20] parse_diff_and_store
[INFO] [2020-12-28 14:08:20] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-28 14:08:20] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-28 14:08:20] Loading assocs diff file into memory (true lines)...
[INFO] [2020-12-28 14:08:20] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-28 14:08:21] Storing 2 ScientificNames
[INFO] [2020-12-28 14:08:21] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-28 14:08:21] Average Time: 0.0
[INFO] [2020-12-28 14:08:21] Total Time: 1s
[INFO] [2020-12-28 14:08:21] Storing 2 Nodes
[INFO] [2020-12-28 14:08:21] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-28 14:08:21] Average Time: 0.0
[INFO] [2020-12-28 14:08:21] Total Time: 1s
[INFO] [2020-12-28 14:08:21] Storing 2 Occurrences
[INFO] [2020-12-28 14:08:21] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-28 14:08:21] Average Time: 0.0
[INFO] [2020-12-28 14:08:21] Total Time: 1s
[INFO] [2020-12-28 14:08:21] Storing 6 Traits
[INFO] [2020-12-28 14:08:21] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-28 14:08:21] Average Time: 0.0
[INFO] [2020-12-28 14:08:21] Total Time: 1s
[INFO] [2020-12-28 14:08:21] Storing 1 MetaTraits
[INFO] [2020-12-28 14:08:21] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-28 14:08:21] Average Time: 0.0
[INFO] [2020-12-28 14:08:21] Total Time: 1s
[STOP] [2020-12-28 14:08:21] parse_diff_and_store
[START] [2020-12-28 14:08:21] resolve_keys
[INFO] [2020-12-28 14:08:27] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-28 14:08:27] traits to occurrences...
[INFO] [2020-12-28 14:08:27] traits to nodes (through occurrences)...
[INFO] [2020-12-28 14:08:27] Traits to sex term...
[INFO] [2020-12-28 14:08:27] Traits to lifestage term...
[INFO] [2020-12-28 14:08:27] MetaTraits to traits...
[INFO] [2020-12-28 14:08:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-28 14:08:27] Assocs to occurrences...
[INFO] [2020-12-28 14:08:27] Assocs to nodes...
[INFO] [2020-12-28 14:08:27] Assoc to sex term...
[INFO] [2020-12-28 14:08:27] Assoc to lifestage term...
[INFO] [2020-12-28 14:08:27] MetaAssoc to assocs...
[STOP] [2020-12-28 14:08:27] resolve_keys
[START] [2020-12-28 14:08:27] hold_for_later_1
[STOP] [2020-12-28 14:08:27] hold_for_later_1
[START] [2020-12-28 14:08:27] hold_for_later_2
[STOP] [2020-12-28 14:08:27] hold_for_later_2
[START] [2020-12-28 14:08:27] resolve_missing_parents
[STOP] [2020-12-28 14:08:27] resolve_missing_parents
[START] [2020-12-28 14:08:27] rebuild_nodes
[START] [2020-12-28 14:08:27] Flattener#flatten
[START] [2020-12-28 14:08:27] Flattener#study_resource
[START] [2020-12-28 14:08:27] Flattener#build_ancestry
[STOP] [2020-12-28 14:08:27] Flattener#build_ancestry
[INFO] [2020-12-28 14:08:27] 2 ancestry keys
[START] [2020-12-28 14:08:27] build_node_ancestors
[INFO] [2020-12-28 14:08:27] old ancestors deleted.
[STOP] [2020-12-28 14:08:27] build_node_ancestors
[WARN] [2020-12-28 14:08:27] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-28 14:08:27] Flattener#flatten
[STOP] [2020-12-28 14:08:27] rebuild_nodes
[START] [2020-12-28 14:08:27] resolve_missing_media_owners
[STOP] [2020-12-28 14:08:27] resolve_missing_media_owners
[START] [2020-12-28 14:08:27] sanitize_media_verbatims
[STOP] [2020-12-28 14:08:27] sanitize_media_verbatims
[START] [2020-12-28 14:08:27] queue_downloads
[STOP] [2020-12-28 14:08:27] queue_downloads
[START] [2020-12-28 14:08:27] parse_names
[WARN] [2020-12-28 14:08:27] I see 2 names which still need to be parsed.
[STOP] [2020-12-28 14:08:28] parse_names
[START] [2020-12-28 14:08:28] denormalize_canonical_names_to_nodes
[STOP] [2020-12-28 14:08:28] denormalize_canonical_names_to_nodes
[START] [2020-12-28 14:08:28] match_nodes
[START] [2020-12-28 14:08:28] map_all_nodes_to_pages
[STOP] [2020-12-28 14:08:28] map_all_nodes_to_pages
[INFO] [2020-12-28 14:08:28] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-12-28 14:08:28] update_nodes
[STOP] [2020-12-28 14:08:28] update_nodes
[STOP] [2020-12-28 14:08:28] match_nodes
[START] [2020-12-28 14:08:28] reindex_search
[STOP] [2020-12-28 14:08:28] reindex_search
[START] [2020-12-28 14:08:28] normalize_units
[STOP] [2020-12-28 14:08:28] normalize_units
[START] [2020-12-28 14:08:28] calculate_statistics
[2020-12-28 14:08:28] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-28 14:08:28] calculate_statistics
[START] [2020-12-28 14:08:28] complete_harvest_instance
[START] [2020-12-28 14:08:28] overall_tsv_creation
[INFO] [2020-12-28 14:08:28] Processing group of 2 in 1 batches of 10000
[INFO] [2020-12-28 14:09:06] 1 Traits (unfiltered)...
[INFO] [2020-12-28 14:09:42] 1 Traits (filtered)...
[INFO] [2020-12-28 14:09:42] 0 Associations (filtered)...
[INFO] [2020-12-28 14:09:42] 2 metadata added.
[INFO] [2020-12-28 14:09:42] 0 metadata added.
[INFO] [2020-12-28 14:10:13] Average Time: 79.27
[INFO] [2020-12-28 14:10:13] Total Time: 1m45s
[STOP] [2020-12-28 14:10:13] overall_tsv_creation
[INFO] [2020-12-28 14:10:13] Done. Check your files:
[INFO] [2020-12-28 14:10:13] (2 lines) /app/public/data/tst_test_of_rep_/publish_nodes.tsv
[INFO] [2020-12-28 14:10:13] (2 lines) /app/public/data/tst_test_of_rep_/publish_scientific_names.tsv
[INFO] [2020-12-28 14:10:13] (2 lines) /app/public/data/tst_test_of_rep_/publish_traits.tsv
[INFO] [2020-12-28 14:10:13] (7 lines) /app/public/data/tst_test_of_rep_/publish_metadata.tsv
[STOP] [2020-12-28 14:10:13] complete_harvest_instance
[START] [2020-12-28 14:10:13] completed
[STOP] [2020-12-28 14:10:13] completed
[STOP] [2020-12-28 14:10:13] logged process, took 114.62
[INFO] [2020-12-28 14:13:48] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-12-28 14:13:48] ## remove_type: ScientificName
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 2 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.610] Removed 2 Scientificnames
[INFO] [2020-12-28 14:13:48] ## remove_type: Vernacular
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.613] Removed 0 Vernaculars
[INFO] [2020-12-28 14:13:48] ## remove_type: Article
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.616] Removed 0 Articles
[INFO] [2020-12-28 14:13:48] ## remove_type: Medium
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.620] Removed 0 Media
[INFO] [2020-12-28 14:13:48] ## remove_type: Trait
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 6 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.624] Removed 6 Traits
[INFO] [2020-12-28 14:13:48] ## remove_type: MetaTrait
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 1 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.628] Removed 1 Metatraits
[INFO] [2020-12-28 14:13:48] ## remove_type: OccurrenceMetadatum
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.630] Removed 0 Occurrencemetadata
[INFO] [2020-12-28 14:13:48] ## remove_type: Assoc
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.633] Removed 0 Assocs
[INFO] [2020-12-28 14:13:48] ## remove_type: MetaAssoc
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.635] Removed 0 Metaassocs
[INFO] [2020-12-28 14:13:48] ## remove_type: Identifier
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.637] Removed 0 Identifiers
[INFO] [2020-12-28 14:13:48] ## remove_type: Reference
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.640] Removed 0 References
[INFO] [2020-12-28 14:13:48] Starting batch with ID 87400967...
[INFO] [2020-12-28 14:13:48] Starting batch with ID 87400967...
[INFO] [2020-12-28 14:13:48] Starting batch with ID 87400967...
[INFO] [2020-12-28 14:13:48] Starting batch with ID 87400968...
[INFO] [2020-12-28 14:13:48] ## remove_type: Node
[INFO] [2020-12-28 14:13:48] ++ Calling delete_all on 2 instances...
[INFO] [2020-12-28 14:13:48] [14:13:48.704] Removed 2 Nodes
[START] [2020-12-28 14:13:49] logged process: ca5be136aef877c71c74100a42de34a9e7a07645
[START] [2020-12-28 14:13:49] Creating resource from OpenData
[START] [2020-12-28 14:13:49] logged process: ca5be136aef877c71c74100a42de34a9e7a07645
[START] [2020-12-28 14:13:49] Parse meta.xml file and create formats with fields
[STOP] [2020-12-28 14:13:49] Parse meta.xml file and create formats with fields
[STOP] [2020-12-28 14:13:49] Creating resource from OpenData
[START] [2020-12-28 14:13:49] logged process: ca5be136aef877c71c74100a42de34a9e7a07645
[START] [2020-12-28 14:13:49] create_harvest_instance
[STOP] [2020-12-28 14:13:51] create_harvest_instance
[START] [2020-12-28 14:13:51] fetch_files
[STOP] [2020-12-28 14:13:51] fetch_files
[START] [2020-12-28 14:13:51] validate_each_file
[STOP] [2020-12-28 14:13:51] validate_each_file
[START] [2020-12-28 14:13:51] convert_to_csv
[CMD] [2020-12-28 14:13:51] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__nodes_25895.csv > /app/public/converted_csv/tst_test_of_rep__nodes_25895.csv_sorted
[CMD] [2020-12-28 14:13:51] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__occurrences_25896.csv > /app/public/converted_csv/tst_test_of_rep__occurrences_25896.csv_sorted
[CMD] [2020-12-28 14:13:51] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__assocs_25897.csv > /app/public/converted_csv/tst_test_of_rep__assocs_25897.csv_sorted
[CMD] [2020-12-28 14:13:51] /usr/bin/sort /app/public/converted_csv/tst_test_of_rep__measurements_25898.csv > /app/public/converted_csv/tst_test_of_rep__measurements_25898.csv_sorted
[STOP] [2020-12-28 14:13:51] convert_to_csv
[START] [2020-12-28 14:13:51] calculate_delta
[CMD] [2020-12-28 14:13:51] echo "0a" > /app/public/diff/tst_test_of_rep__nodes_25895.diff
[CMD] [2020-12-28 14:13:51] tail -n +1 /app/public/converted_csv/tst_test_of_rep__nodes_25895.csv >> /app/public/diff/tst_test_of_rep__nodes_25895.diff
[CMD] [2020-12-28 14:13:51] echo "." >> /app/public/diff/tst_test_of_rep__nodes_25895.diff
[CMD] [2020-12-28 14:13:51] echo "0a" > /app/public/diff/tst_test_of_rep__occurrences_25896.diff
[CMD] [2020-12-28 14:13:51] tail -n +1 /app/public/converted_csv/tst_test_of_rep__occurrences_25896.csv >> /app/public/diff/tst_test_of_rep__occurrences_25896.diff
[CMD] [2020-12-28 14:13:51] echo "." >> /app/public/diff/tst_test_of_rep__occurrences_25896.diff
[CMD] [2020-12-28 14:13:51] echo "0a" > /app/public/diff/tst_test_of_rep__assocs_25897.diff
[CMD] [2020-12-28 14:13:51] tail -n +1 /app/public/converted_csv/tst_test_of_rep__assocs_25897.csv >> /app/public/diff/tst_test_of_rep__assocs_25897.diff
[CMD] [2020-12-28 14:13:51] echo "." >> /app/public/diff/tst_test_of_rep__assocs_25897.diff
[CMD] [2020-12-28 14:13:51] echo "0a" > /app/public/diff/tst_test_of_rep__measurements_25898.diff
[CMD] [2020-12-28 14:13:51] tail -n +1 /app/public/converted_csv/tst_test_of_rep__measurements_25898.csv >> /app/public/diff/tst_test_of_rep__measurements_25898.diff
[CMD] [2020-12-28 14:13:51] echo "." >> /app/public/diff/tst_test_of_rep__measurements_25898.diff
[STOP] [2020-12-28 14:13:51] calculate_delta
[START] [2020-12-28 14:13:51] parse_diff_and_store
[INFO] [2020-12-28 14:13:51] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-28 14:13:51] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-28 14:13:51] Loading assocs diff file into memory (true lines)...
[INFO] [2020-12-28 14:13:51] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-28 14:13:51] Storing 2 ScientificNames
[INFO] [2020-12-28 14:13:51] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-28 14:13:51] Average Time: 0.0
[INFO] [2020-12-28 14:13:51] Total Time: 1s
[INFO] [2020-12-28 14:13:51] Storing 2 Nodes
[INFO] [2020-12-28 14:13:51] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-28 14:13:51] Average Time: 0.0
[INFO] [2020-12-28 14:13:51] Total Time: 1s
[INFO] [2020-12-28 14:13:51] Storing 2 Occurrences
[INFO] [2020-12-28 14:13:51] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-28 14:13:51] Average Time: 0.0
[INFO] [2020-12-28 14:13:51] Total Time: 1s
[STOP] [2020-12-28 14:13:51] parse_diff_and_store
[START] [2020-12-28 14:13:51] resolve_keys
[INFO] [2020-12-28 14:13:57] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-28 14:13:57] traits to occurrences...
[INFO] [2020-12-28 14:13:57] traits to nodes (through occurrences)...
[INFO] [2020-12-28 14:13:57] Traits to sex term...
[INFO] [2020-12-28 14:13:57] Traits to lifestage term...
[INFO] [2020-12-28 14:13:57] MetaTraits to traits...
[INFO] [2020-12-28 14:13:57] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-28 14:13:57] Assocs to occurrences...
[INFO] [2020-12-28 14:13:57] Assocs to nodes...
[INFO] [2020-12-28 14:13:57] Assoc to sex term...
[INFO] [2020-12-28 14:13:57] Assoc to lifestage term...
[INFO] [2020-12-28 14:13:57] MetaAssoc to assocs...
[STOP] [2020-12-28 14:13:57] resolve_keys
[START] [2020-12-28 14:13:57] hold_for_later_1
[STOP] [2020-12-28 14:13:57] hold_for_later_1
[START] [2020-12-28 14:13:57] hold_for_later_2
[STOP] [2020-12-28 14:13:57] hold_for_later_2
[START] [2020-12-28 14:13:57] resolve_missing_parents
[STOP] [2020-12-28 14:13:57] resolve_missing_parents
[START] [2020-12-28 14:13:57] rebuild_nodes
[START] [2020-12-28 14:13:57] Flattener#flatten
[START] [2020-12-28 14:13:57] Flattener#study_resource
[START] [2020-12-28 14:13:57] Flattener#build_ancestry
[STOP] [2020-12-28 14:13:57] Flattener#build_ancestry
[INFO] [2020-12-28 14:13:57] 2 ancestry keys
[START] [2020-12-28 14:13:57] build_node_ancestors
[INFO] [2020-12-28 14:13:57] old ancestors deleted.
[STOP] [2020-12-28 14:13:57] build_node_ancestors
[WARN] [2020-12-28 14:13:57] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-28 14:13:57] Flattener#flatten
[STOP] [2020-12-28 14:13:57] rebuild_nodes
[START] [2020-12-28 14:13:57] resolve_missing_media_owners
[STOP] [2020-12-28 14:13:57] resolve_missing_media_owners
[START] [2020-12-28 14:13:57] sanitize_media_verbatims
[STOP] [2020-12-28 14:13:57] sanitize_media_verbatims
[START] [2020-12-28 14:13:57] queue_downloads
[STOP] [2020-12-28 14:13:57] queue_downloads
[START] [2020-12-28 14:13:57] parse_names
[WARN] [2020-12-28 14:13:57] I see 2 names which still need to be parsed.
[STOP] [2020-12-28 14:13:58] parse_names
[START] [2020-12-28 14:13:58] denormalize_canonical_names_to_nodes
[STOP] [2020-12-28 14:13:58] denormalize_canonical_names_to_nodes
[START] [2020-12-28 14:13:58] match_nodes
[START] [2020-12-28 14:13:58] map_all_nodes_to_pages
[STOP] [2020-12-28 14:13:58] map_all_nodes_to_pages
[INFO] [2020-12-28 14:13:58] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-12-28 14:13:58] update_nodes
[STOP] [2020-12-28 14:13:58] update_nodes
[STOP] [2020-12-28 14:13:58] match_nodes
[START] [2020-12-28 14:13:58] reindex_search
[STOP] [2020-12-28 14:13:58] reindex_search
[START] [2020-12-28 14:13:58] normalize_units
[STOP] [2020-12-28 14:13:58] normalize_units
[START] [2020-12-28 14:13:58] calculate_statistics
[2020-12-28 14:13:58] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-28 14:13:58] calculate_statistics
[START] [2020-12-28 14:13:58] complete_harvest_instance
[START] [2020-12-28 14:13:58] overall_tsv_creation
[INFO] [2020-12-28 14:13:58] Processing group of 2 in 1 batches of 10000
[INFO] [2020-12-28 14:14:29] Average Time: 6.46
[INFO] [2020-12-28 14:14:29] Total Time: 32s
[STOP] [2020-12-28 14:14:29] overall_tsv_creation
[INFO] [2020-12-28 14:14:29] Done. Check your files:
[INFO] [2020-12-28 14:14:29] (2 lines) /app/public/data/tst_test_of_rep_/publish_nodes.tsv
[INFO] [2020-12-28 14:14:29] (2 lines) /app/public/data/tst_test_of_rep_/publish_scientific_names.tsv
[STOP] [2020-12-28 14:14:29] complete_harvest_instance
[START] [2020-12-28 14:14:29] completed
[STOP] [2020-12-28 14:14:29] completed
[STOP] [2020-12-28 14:14:29] logged process, took 40.41
Latest Process