Harvest for Adriatic Sea Species List Created 29 Dec 12:49

Stage: completed
Fetched: 29 Dec 12:49
Validated: 29 Dec 12:49
Deltas Created 29 Dec 12:49
Units Normalized: 29 Dec 13:00
Ancestry Built: 29 Dec 12:50
Nodes Matched: 29 Dec 13:00
Names Parsed: 29 Dec 12:50
New Models Stored: 29 Dec 12:49
Indexed: 29 Dec 13:00
Completed: 29 Dec 13:03
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-12-22 17:13:30 -0500 by logger.rb/56815
[START] [2019-12-22 17:13:30] logged process
[START] [2019-12-22 17:13:30] create_harvest_instance
[STOP] [2019-12-22 17:13:32] create_harvest_instance
[START] [2019-12-22 17:13:32] fetch_files
[STOP] [2019-12-22 17:13:32] fetch_files
[START] [2019-12-22 17:13:32] validate_each_file
[STOP] [2019-12-22 17:13:32] validate_each_file
[START] [2019-12-22 17:13:32] convert_to_csv
[CMD] [2019-12-22 17:13:32] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_refs_18978.csv > /app/public/converted_csv/adriatic_sea_sp2_refs_18978.csv_sorted
[CMD] [2019-12-22 17:13:32] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_nodes_18979.csv > /app/public/converted_csv/adriatic_sea_sp2_nodes_18979.csv_sorted
[CMD] [2019-12-22 17:13:32] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_occurrences_18980.csv > /app/public/converted_csv/adriatic_sea_sp2_occurrences_18980.csv_sorted
[CMD] [2019-12-22 17:13:32] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_measurements_18981.csv > /app/public/converted_csv/adriatic_sea_sp2_measurements_18981.csv_sorted
[STOP] [2019-12-22 17:13:32] convert_to_csv
[START] [2019-12-22 17:13:32] calculate_delta
[CMD] [2019-12-22 17:13:32] echo "0a" > /app/public/diff/adriatic_sea_sp2_refs_18978.diff
[CMD] [2019-12-22 17:13:32] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_refs_18978.csv >> /app/public/diff/adriatic_sea_sp2_refs_18978.diff
[CMD] [2019-12-22 17:13:32] echo "." >> /app/public/diff/adriatic_sea_sp2_refs_18978.diff
[CMD] [2019-12-22 17:13:32] echo "0a" > /app/public/diff/adriatic_sea_sp2_nodes_18979.diff
[CMD] [2019-12-22 17:13:32] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_nodes_18979.csv >> /app/public/diff/adriatic_sea_sp2_nodes_18979.diff
[CMD] [2019-12-22 17:13:32] echo "." >> /app/public/diff/adriatic_sea_sp2_nodes_18979.diff
[CMD] [2019-12-22 17:13:32] echo "0a" > /app/public/diff/adriatic_sea_sp2_occurrences_18980.diff
[CMD] [2019-12-22 17:13:32] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_occurrences_18980.csv >> /app/public/diff/adriatic_sea_sp2_occurrences_18980.diff
[CMD] [2019-12-22 17:13:32] echo "." >> /app/public/diff/adriatic_sea_sp2_occurrences_18980.diff
[CMD] [2019-12-22 17:13:32] echo "0a" > /app/public/diff/adriatic_sea_sp2_measurements_18981.diff
[CMD] [2019-12-22 17:13:32] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_measurements_18981.csv >> /app/public/diff/adriatic_sea_sp2_measurements_18981.diff
[CMD] [2019-12-22 17:13:32] echo "." >> /app/public/diff/adriatic_sea_sp2_measurements_18981.diff
[STOP] [2019-12-22 17:13:32] calculate_delta
[START] [2019-12-22 17:13:32] parse_diff_and_store
[INFO] [2019-12-22 17:13:32] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:32] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:34] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:46] Storing 2 References
[INFO] [2019-12-22 17:13:46] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 17:13:46] Average Time: 0.02
[INFO] [2019-12-22 17:13:46] Total Time: 1s
[INFO] [2019-12-22 17:13:46] Storing 4442 ScientificNames
[INFO] [2019-12-22 17:13:46] Processing group of 4442 in 5 groups of 1000
[INFO] [2019-12-22 17:13:48] Average Time: 0.376
[INFO] [2019-12-22 17:13:48] Total Time: 2s
[INFO] [2019-12-22 17:13:48] Storing 4442 Nodes
[INFO] [2019-12-22 17:13:48] Processing group of 4442 in 5 groups of 1000
[INFO] [2019-12-22 17:13:49] Average Time: 0.274
[INFO] [2019-12-22 17:13:49] Total Time: 2s
[INFO] [2019-12-22 17:13:49] Storing 2173 Occurrences
[INFO] [2019-12-22 17:13:49] Processing group of 2173 in 3 groups of 1000
[INFO] [2019-12-22 17:13:50] Average Time: 0.087
[INFO] [2019-12-22 17:13:50] Total Time: 1s
[INFO] [2019-12-22 17:13:50] Storing 4346 TraitsReferences
[INFO] [2019-12-22 17:13:50] Processing group of 4346 in 5 groups of 1000
[INFO] [2019-12-22 17:13:50] Average Time: 0.122
[INFO] [2019-12-22 17:13:50] Total Time: 1s
[INFO] [2019-12-22 17:13:50] Storing 4346 Traits
[INFO] [2019-12-22 17:13:50] Processing group of 4346 in 5 groups of 1000
[INFO] [2019-12-22 17:13:52] Average Time: 0.388
[INFO] [2019-12-22 17:13:52] Total Time: 3s
[INFO] [2019-12-22 17:13:52] Storing 4345 MetaTraits
[INFO] [2019-12-22 17:13:52] Processing group of 4345 in 5 groups of 1000
[INFO] [2019-12-22 17:13:53] Average Time: 0.17
[INFO] [2019-12-22 17:13:53] Total Time: 1s
[STOP] [2019-12-22 17:13:53] parse_diff_and_store
[START] [2019-12-22 17:13:53] resolve_keys
[INFO] [2019-12-22 17:14:14] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 17:14:16] traits to occurrences...
[INFO] [2019-12-22 17:14:18] traits to nodes (through occurrences)...
[INFO] [2019-12-22 17:14:18] Traits to sex term...
[INFO] [2019-12-22 17:14:19] Traits to lifestage term...
[INFO] [2019-12-22 17:14:19] MetaTraits to traits...
[INFO] [2019-12-22 17:14:20] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 17:14:21] Assocs to occurrences...
[INFO] [2019-12-22 17:14:21] Assocs to nodes...
[INFO] [2019-12-22 17:14:21] Assoc to sex term...
[INFO] [2019-12-22 17:14:21] Assoc to lifestage term...
[STOP] [2019-12-22 17:14:21] resolve_keys
[START] [2019-12-22 17:14:21] hold_for_later_1
[STOP] [2019-12-22 17:14:21] hold_for_later_1
[START] [2019-12-22 17:14:21] hold_for_later_2
[STOP] [2019-12-22 17:14:21] hold_for_later_2
[START] [2019-12-22 17:14:21] resolve_missing_parents
[STOP] [2019-12-22 17:14:28] resolve_missing_parents
[START] [2019-12-22 17:14:28] rebuild_nodes
[START] [2019-12-22 17:14:28] Flattener#flatten
[START] [2019-12-22 17:14:28] Flattener#study_resource
[START] [2019-12-22 17:14:28] Flattener#build_ancestry
[STOP] [2019-12-22 17:14:28] Flattener#build_ancestry
[INFO] [2019-12-22 17:14:28] 4442 ancestry keys
[START] [2019-12-22 17:14:28] build_node_ancestors
[INFO] [2019-12-22 17:14:28] old ancestors deleted.
[STOP] [2019-12-22 17:14:30] build_node_ancestors
[START] [2019-12-22 17:14:32] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 17:14:33] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 17:14:33] Flattener#flatten
[STOP] [2019-12-22 17:14:33] rebuild_nodes
[START] [2019-12-22 17:14:33] resolve_missing_media_owners
[STOP] [2019-12-22 17:14:33] resolve_missing_media_owners
[START] [2019-12-22 17:14:33] sanitize_media_verbatims
[STOP] [2019-12-22 17:14:33] sanitize_media_verbatims
[START] [2019-12-22 17:14:33] queue_downloads
[STOP] [2019-12-22 17:14:33] queue_downloads
[START] [2019-12-22 17:14:33] parse_names
[WARN] [2019-12-22 17:14:33] I see 4442 names which still need to be parsed.
[STOP] [2019-12-22 17:14:37] parse_names
[START] [2019-12-22 17:14:37] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 17:14:39] denormalize_canonical_names_to_nodes
[START] [2019-12-22 17:14:39] match_nodes
[START] [2019-12-22 17:14:39] map_all_nodes_to_pages
[STOP] [2019-12-22 17:29:30] map_all_nodes_to_pages
[INFO] [2019-12-22 17:29:30] 293 Unmatched nodes (of 4442)! That's too many to output. First 10: Cassidulina crassa (#61647214); Globocassidulina oblonga (#61648424); Cassidulinoides bradyi (#61647365); Elphidium albiumbilicatum (#61647689); Elphidium poeyanum (#61648276); Bolivina subspinescens (#61647377); Cibicides lobatulus (#61647263); Gyroidinoides umbonatus (#61647255); Cancris auriculus (#61650971); Bigenerina nodosaria (#61647249)
[START] [2019-12-22 17:29:30] update_nodes
[STOP] [2019-12-22 17:29:32] update_nodes
[STOP] [2019-12-22 17:29:32] match_nodes
[START] [2019-12-22 17:29:32] reindex_search
[STOP] [2019-12-22 17:29:42] reindex_search
[START] [2019-12-22 17:29:42] normalize_units
[STOP] [2019-12-22 17:29:42] normalize_units
[START] [2019-12-22 17:29:42] calculate_statistics
[STOP] [2019-12-22 17:29:42] calculate_statistics
[START] [2019-12-22 17:29:42] complete_harvest_instance
[START] [2019-12-22 17:29:42] overall_tsv_creation
[INFO] [2019-12-22 17:29:42] Processing group of 4442 in 1 batches of 10000
[INFO] [2019-12-22 17:31:05] 2173 Traits (unfiltered)...
[INFO] [2019-12-22 17:31:18] 2173 Traits (filtered)...
[INFO] [2019-12-22 17:31:18] 0 Associations (filtered)...
[INFO] [2019-12-22 17:32:01] 10864 metadata added.
[INFO] [2019-12-22 17:32:01] 0 metadata added.
[INFO] [2019-12-22 17:32:01] Average Time: 99.12
[INFO] [2019-12-22 17:32:01] Total Time: 2m19s
[STOP] [2019-12-22 17:32:01] overall_tsv_creation
[INFO] [2019-12-22 17:32:01] Done. Check your files:
[INFO] [2019-12-22 17:32:01] (4442 lines) /app/public/data/adriatic_sea_sp2/publish_nodes.tsv
[INFO] [2019-12-22 17:32:01] (21955 lines) /app/public/data/adriatic_sea_sp2/publish_node_ancestors.tsv
[INFO] [2019-12-22 17:32:01] (4442 lines) /app/public/data/adriatic_sea_sp2/publish_scientific_names.tsv
[INFO] [2019-12-22 17:32:01] (2174 lines) /app/public/data/adriatic_sea_sp2/publish_traits.tsv
[INFO] [2019-12-22 17:32:01] (10865 lines) /app/public/data/adriatic_sea_sp2/publish_metadata.tsv
[STOP] [2019-12-22 17:32:01] complete_harvest_instance
[START] [2019-12-22 17:32:01] completed
[STOP] [2019-12-22 17:32:01] completed
[STOP] [2019-12-22 17:32:01] logged process, took 1111.28
[INFO] [2020-12-29 12:49:27] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-12-29 12:49:32] ## remove_type: ScientificName
[INFO] [2020-12-29 12:49:32] ++ Calling delete_all on 4442 instances...
[INFO] [2020-12-29 12:49:32] [12:49:32.593] Removed 4442 Scientificnames
[INFO] [2020-12-29 12:49:32] ## remove_type: Vernacular
[INFO] [2020-12-29 12:49:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-29 12:49:32] [12:49:32.596] Removed 0 Vernaculars
[INFO] [2020-12-29 12:49:32] ## remove_type: Article
[INFO] [2020-12-29 12:49:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-29 12:49:32] [12:49:32.599] Removed 0 Articles
[INFO] [2020-12-29 12:49:32] ## remove_type: Medium
[INFO] [2020-12-29 12:49:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-29 12:49:32] [12:49:32.602] Removed 0 Media
[INFO] [2020-12-29 12:49:32] ## remove_type: Trait
[INFO] [2020-12-29 12:49:32] ++ Calling delete_all on 4346 instances...
[INFO] [2020-12-29 12:49:33] [12:49:33.334] Removed 4346 Traits
[INFO] [2020-12-29 12:49:33] ## remove_type: MetaTrait
[INFO] [2020-12-29 12:49:33] ++ Calling delete_all on 4345 instances...
[INFO] [2020-12-29 12:49:33] [12:49:33.587] Removed 4345 Metatraits
[INFO] [2020-12-29 12:49:33] ## remove_type: OccurrenceMetadatum
[INFO] [2020-12-29 12:49:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-29 12:49:33] [12:49:33.674] Removed 0 Occurrencemetadata
[INFO] [2020-12-29 12:49:33] ## remove_type: Assoc
[INFO] [2020-12-29 12:49:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-29 12:49:33] [12:49:33.677] Removed 0 Assocs
[INFO] [2020-12-29 12:49:33] ## remove_type: MetaAssoc
[INFO] [2020-12-29 12:49:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-29 12:49:33] [12:49:33.680] Removed 0 Metaassocs
[INFO] [2020-12-29 12:49:33] ## remove_type: Identifier
[INFO] [2020-12-29 12:49:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-29 12:49:33] [12:49:33.689] Removed 0 Identifiers
[INFO] [2020-12-29 12:49:33] ## remove_type: Reference
[INFO] [2020-12-29 12:49:33] ++ Calling delete_all on 2 instances...
[INFO] [2020-12-29 12:49:33] [12:49:33.693] Removed 2 References
[INFO] [2020-12-29 12:49:34] Starting batch with ID 61648129...
[INFO] [2020-12-29 12:49:35] Starting batch with ID 61648134...
[INFO] [2020-12-29 12:49:35] Starting batch with ID 61648134...
[INFO] [2020-12-29 12:49:36] Starting batch with ID 61648134...
[INFO] [2020-12-29 12:49:36] ## remove_type: Node
[INFO] [2020-12-29 12:49:36] ++ Calling delete_all on 4442 instances...
[INFO] [2020-12-29 12:49:36] [12:49:36.842] Removed 4442 Nodes
[START] [2020-12-29 12:49:39] logged process: ca5be136aef877c71c74100a42de34a9e7a07645

[START] [2020-12-29 12:49:39] Creating resource from OpenData
[START] [2020-12-29 12:49:42] logged process: ca5be136aef877c71c74100a42de34a9e7a07645

[START] [2020-12-29 12:49:42] Parse meta.xml file and create formats with fields
[STOP] [2020-12-29 12:49:42] Parse meta.xml file and create formats with fields
[STOP] [2020-12-29 12:49:42] Creating resource from OpenData
[START] [2020-12-29 12:49:42] logged process: ca5be136aef877c71c74100a42de34a9e7a07645

[START] [2020-12-29 12:49:42] create_harvest_instance
[STOP] [2020-12-29 12:49:44] create_harvest_instance
[START] [2020-12-29 12:49:44] fetch_files
[STOP] [2020-12-29 12:49:44] fetch_files
[START] [2020-12-29 12:49:44] validate_each_file
[STOP] [2020-12-29 12:49:44] validate_each_file
[START] [2020-12-29 12:49:44] convert_to_csv
[CMD] [2020-12-29 12:49:44] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_refs_26002.csv > /app/public/converted_csv/adriatic_sea_sp2_refs_26002.csv_sorted
[CMD] [2020-12-29 12:49:44] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_nodes_26003.csv > /app/public/converted_csv/adriatic_sea_sp2_nodes_26003.csv_sorted
[CMD] [2020-12-29 12:49:44] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_occurrences_26004.csv > /app/public/converted_csv/adriatic_sea_sp2_occurrences_26004.csv_sorted
[CMD] [2020-12-29 12:49:44] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_measurements_26005.csv > /app/public/converted_csv/adriatic_sea_sp2_measurements_26005.csv_sorted
[STOP] [2020-12-29 12:49:44] convert_to_csv
[START] [2020-12-29 12:49:44] calculate_delta
[CMD] [2020-12-29 12:49:44] echo "0a" > /app/public/diff/adriatic_sea_sp2_refs_26002.diff
[CMD] [2020-12-29 12:49:44] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_refs_26002.csv >> /app/public/diff/adriatic_sea_sp2_refs_26002.diff
[CMD] [2020-12-29 12:49:44] echo "." >> /app/public/diff/adriatic_sea_sp2_refs_26002.diff
[CMD] [2020-12-29 12:49:44] echo "0a" > /app/public/diff/adriatic_sea_sp2_nodes_26003.diff
[CMD] [2020-12-29 12:49:44] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_nodes_26003.csv >> /app/public/diff/adriatic_sea_sp2_nodes_26003.diff
[CMD] [2020-12-29 12:49:44] echo "." >> /app/public/diff/adriatic_sea_sp2_nodes_26003.diff
[CMD] [2020-12-29 12:49:44] echo "0a" > /app/public/diff/adriatic_sea_sp2_occurrences_26004.diff
[CMD] [2020-12-29 12:49:44] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_occurrences_26004.csv >> /app/public/diff/adriatic_sea_sp2_occurrences_26004.diff
[CMD] [2020-12-29 12:49:44] echo "." >> /app/public/diff/adriatic_sea_sp2_occurrences_26004.diff
[CMD] [2020-12-29 12:49:44] echo "0a" > /app/public/diff/adriatic_sea_sp2_measurements_26005.diff
[CMD] [2020-12-29 12:49:44] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_measurements_26005.csv >> /app/public/diff/adriatic_sea_sp2_measurements_26005.diff
[CMD] [2020-12-29 12:49:44] echo "." >> /app/public/diff/adriatic_sea_sp2_measurements_26005.diff
[STOP] [2020-12-29 12:49:44] calculate_delta
[START] [2020-12-29 12:49:44] parse_diff_and_store
[INFO] [2020-12-29 12:49:44] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-29 12:49:45] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-29 12:49:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-29 12:49:46] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-29 12:49:48] Storing 2 References
[INFO] [2020-12-29 12:49:48] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-29 12:49:49] Average Time: 0.03
[INFO] [2020-12-29 12:49:49] Total Time: 1s
[INFO] [2020-12-29 12:49:49] Storing 4442 ScientificNames
[INFO] [2020-12-29 12:49:49] Processing group of 4442 in 5 groups of 1000
[INFO] [2020-12-29 12:49:50] Average Time: 0.356
[INFO] [2020-12-29 12:49:50] Total Time: 2s
[INFO] [2020-12-29 12:49:50] Storing 4442 Nodes
[INFO] [2020-12-29 12:49:50] Processing group of 4442 in 5 groups of 1000
[INFO] [2020-12-29 12:49:52] Average Time: 0.32
[INFO] [2020-12-29 12:49:52] Total Time: 2s
[INFO] [2020-12-29 12:49:52] Storing 2173 Occurrences
[INFO] [2020-12-29 12:49:52] Processing group of 2173 in 3 groups of 1000
[INFO] [2020-12-29 12:49:52] Average Time: 0.11
[INFO] [2020-12-29 12:49:52] Total Time: 1s
[INFO] [2020-12-29 12:49:52] Storing 4346 TraitsReferences
[INFO] [2020-12-29 12:49:52] Processing group of 4346 in 5 groups of 1000
[INFO] [2020-12-29 12:49:53] Average Time: 0.142
[INFO] [2020-12-29 12:49:53] Total Time: 1s
[INFO] [2020-12-29 12:49:53] Storing 4346 Traits
[INFO] [2020-12-29 12:49:53] Processing group of 4346 in 5 groups of 1000
[INFO] [2020-12-29 12:49:55] Average Time: 0.364
[INFO] [2020-12-29 12:49:55] Total Time: 2s
[INFO] [2020-12-29 12:49:55] Storing 2173 MetaTraits
[INFO] [2020-12-29 12:49:55] Processing group of 2173 in 3 groups of 1000
[INFO] [2020-12-29 12:49:55] Average Time: 0.083
[INFO] [2020-12-29 12:49:55] Total Time: 1s
[STOP] [2020-12-29 12:49:55] parse_diff_and_store
[START] [2020-12-29 12:49:55] resolve_keys
[INFO] [2020-12-29 12:50:14] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-29 12:50:21] traits to occurrences...
[INFO] [2020-12-29 12:50:21] traits to nodes (through occurrences)...
[INFO] [2020-12-29 12:50:21] Traits to sex term...
[INFO] [2020-12-29 12:50:22] Traits to lifestage term...
[INFO] [2020-12-29 12:50:22] MetaTraits to traits...
[INFO] [2020-12-29 12:50:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-29 12:50:23] Assocs to occurrences...
[INFO] [2020-12-29 12:50:23] Assocs to nodes...
[INFO] [2020-12-29 12:50:23] Assoc to sex term...
[INFO] [2020-12-29 12:50:23] Assoc to lifestage term...
[INFO] [2020-12-29 12:50:23] MetaAssoc to assocs...
[STOP] [2020-12-29 12:50:23] resolve_keys
[START] [2020-12-29 12:50:23] hold_for_later_1
[STOP] [2020-12-29 12:50:23] hold_for_later_1
[START] [2020-12-29 12:50:23] hold_for_later_2
[STOP] [2020-12-29 12:50:23] hold_for_later_2
[START] [2020-12-29 12:50:23] resolve_missing_parents
[STOP] [2020-12-29 12:50:25] resolve_missing_parents
[START] [2020-12-29 12:50:25] rebuild_nodes
[START] [2020-12-29 12:50:25] Flattener#flatten
[START] [2020-12-29 12:50:25] Flattener#study_resource
[START] [2020-12-29 12:50:25] Flattener#build_ancestry
[STOP] [2020-12-29 12:50:25] Flattener#build_ancestry
[INFO] [2020-12-29 12:50:25] 4442 ancestry keys
[START] [2020-12-29 12:50:25] build_node_ancestors
[INFO] [2020-12-29 12:50:25] old ancestors deleted.
[STOP] [2020-12-29 12:50:26] build_node_ancestors
[START] [2020-12-29 12:50:28] Flattener#propagate_ancestor_ids
[STOP] [2020-12-29 12:50:28] Flattener#propagate_ancestor_ids
[STOP] [2020-12-29 12:50:28] Flattener#flatten
[STOP] [2020-12-29 12:50:28] rebuild_nodes
[START] [2020-12-29 12:50:28] resolve_missing_media_owners
[STOP] [2020-12-29 12:50:28] resolve_missing_media_owners
[START] [2020-12-29 12:50:28] sanitize_media_verbatims
[STOP] [2020-12-29 12:50:28] sanitize_media_verbatims
[START] [2020-12-29 12:50:28] queue_downloads
[STOP] [2020-12-29 12:50:28] queue_downloads
[START] [2020-12-29 12:50:28] parse_names
[WARN] [2020-12-29 12:50:28] I see 4442 names which still need to be parsed.
[STOP] [2020-12-29 12:50:33] parse_names
[START] [2020-12-29 12:50:33] denormalize_canonical_names_to_nodes
[STOP] [2020-12-29 12:50:33] denormalize_canonical_names_to_nodes
[START] [2020-12-29 12:50:33] match_nodes
[START] [2020-12-29 12:50:33] map_all_nodes_to_pages
[STOP] [2020-12-29 13:00:45] map_all_nodes_to_pages
[INFO] [2020-12-29 13:00:45] 321 Unmatched nodes (of 4442)! That's too many to output. Full list in /app/public/data/adriatic_sea_sp2/unmatched_nodes.txt ; First 10: Cassidulina crassa (#87418615); Globocassidulina oblonga (#87419825); Cassidulinoides bradyi (#87418766); Elphidium albiumbilicatum (#87419090); Elphidium poeyanum (#87419677); Bolivina subspinescens (#87418778); Cibicides lobatulus (#87418664); Gyroidinoides umbonatus (#87418656); Cancris auriculus (#87422372); Bigenerina nodosaria (#87418650)
[START] [2020-12-29 13:00:45] update_nodes
[STOP] [2020-12-29 13:00:46] update_nodes
[STOP] [2020-12-29 13:00:46] match_nodes
[START] [2020-12-29 13:00:46] reindex_search
[STOP] [2020-12-29 13:00:54] reindex_search
[START] [2020-12-29 13:00:54] normalize_units
[STOP] [2020-12-29 13:00:54] normalize_units
[START] [2020-12-29 13:00:54] calculate_statistics
[STOP] [2020-12-29 13:00:54] calculate_statistics
[START] [2020-12-29 13:00:54] complete_harvest_instance
[START] [2020-12-29 13:00:54] overall_tsv_creation
[INFO] [2020-12-29 13:00:54] Processing group of 4442 in 1 batches of 10000
[INFO] [2020-12-29 13:02:14] 2173 Traits (unfiltered)...
[INFO] [2020-12-29 13:02:57] 2173 Traits (filtered)...
[INFO] [2020-12-29 13:02:57] 0 Associations (filtered)...
[INFO] [2020-12-29 13:02:58] 8692 metadata added.
[INFO] [2020-12-29 13:02:58] 0 metadata added.
[INFO] [2020-12-29 13:03:28] Average Time: 102.88
[INFO] [2020-12-29 13:03:28] Total Time: 2m34s
[STOP] [2020-12-29 13:03:28] overall_tsv_creation
[INFO] [2020-12-29 13:03:28] Done. Check your files:
[INFO] [2020-12-29 13:03:28] (4442 lines) /app/public/data/adriatic_sea_sp2/publish_nodes.tsv
[INFO] [2020-12-29 13:03:28] (21955 lines) /app/public/data/adriatic_sea_sp2/publish_node_ancestors.tsv
[INFO] [2020-12-29 13:03:28] (4442 lines) /app/public/data/adriatic_sea_sp2/publish_scientific_names.tsv
[INFO] [2020-12-29 13:03:28] (2174 lines) /app/public/data/adriatic_sea_sp2/publish_traits.tsv
[INFO] [2020-12-29 13:03:28] (8693 lines) /app/public/data/adriatic_sea_sp2/publish_metadata.tsv
[STOP] [2020-12-29 13:03:28] complete_harvest_instance
[START] [2020-12-29 13:03:28] completed
[STOP] [2020-12-29 13:03:28] completed
[STOP] [2020-12-29 13:03:28] logged process, took 825.96

Latest Process