Stage:
completed
Fetched:
01 Mar 17:59
Validated:
01 Mar 17:59
Deltas Created
01 Mar 17:59
Units Normalized:
01 Mar 18:07
Ancestry Built:
01 Mar 18:00
Nodes Matched:
01 Mar 18:06
Names Parsed:
01 Mar 18:00
New Models Stored:
01 Mar 17:59
Indexed:
01 Mar 18:07
Completed:
01 Mar 18:10
Time to Harvest:
less than a minute
Harvesting Log
(353 lines)
# Logfile created on 2019-10-01 16:23:58 -0400 by logger.rb/56815
[START] [2019-10-01 16:23:58] logged process
[START] [2019-10-01 16:23:58] create_harvest_instance
[STOP] [2019-10-01 16:23:58] create_harvest_instance
[START] [2019-10-01 16:23:58] fetch_files
[STOP] [2019-10-01 16:23:58] fetch_files
[START] [2019-10-01 16:23:58] validate_each_file
[STOP] [2019-10-01 16:23:59] validate_each_file
[START] [2019-10-01 16:23:59] convert_to_csv
[CMD] [2019-10-01 16:23:59] /usr/bin/sort /app/public/converted_csv/algeria_sp_list_refs_14758.csv > /app/public/converted_csv/algeria_sp_list_refs_14758.csv_sorted
[CMD] [2019-10-01 16:24:00] /usr/bin/sort /app/public/converted_csv/algeria_sp_list_nodes_14759.csv > /app/public/converted_csv/algeria_sp_list_nodes_14759.csv_sorted
[CMD] [2019-10-01 16:24:02] /usr/bin/sort /app/public/converted_csv/algeria_sp_list_occurrences_14760.csv > /app/public/converted_csv/algeria_sp_list_occurrences_14760.csv_sorted
[CMD] [2019-10-01 16:24:03] /usr/bin/sort /app/public/converted_csv/algeria_sp_list_measurements_14761.csv > /app/public/converted_csv/algeria_sp_list_measurements_14761.csv_sorted
[STOP] [2019-10-01 16:24:05] convert_to_csv
[START] [2019-10-01 16:24:05] calculate_delta
[CMD] [2019-10-01 16:24:05] echo "0a" > /app/public/diff/algeria_sp_list_refs_14758.diff
[CMD] [2019-10-01 16:24:06] tail -n +1 /app/public/converted_csv/algeria_sp_list_refs_14758.csv >> /app/public/diff/algeria_sp_list_refs_14758.diff
[CMD] [2019-10-01 16:24:08] echo "." >> /app/public/diff/algeria_sp_list_refs_14758.diff
[CMD] [2019-10-01 16:24:09] echo "0a" > /app/public/diff/algeria_sp_list_nodes_14759.diff
[CMD] [2019-10-01 16:24:11] tail -n +1 /app/public/converted_csv/algeria_sp_list_nodes_14759.csv >> /app/public/diff/algeria_sp_list_nodes_14759.diff
[CMD] [2019-10-01 16:24:12] echo "." >> /app/public/diff/algeria_sp_list_nodes_14759.diff
[CMD] [2019-10-01 16:24:14] echo "0a" > /app/public/diff/algeria_sp_list_occurrences_14760.diff
[CMD] [2019-10-01 16:24:15] tail -n +1 /app/public/converted_csv/algeria_sp_list_occurrences_14760.csv >> /app/public/diff/algeria_sp_list_occurrences_14760.diff
[CMD] [2019-10-01 16:24:17] echo "." >> /app/public/diff/algeria_sp_list_occurrences_14760.diff
[CMD] [2019-10-01 16:24:18] echo "0a" > /app/public/diff/algeria_sp_list_measurements_14761.diff
[CMD] [2019-10-01 16:24:20] tail -n +1 /app/public/converted_csv/algeria_sp_list_measurements_14761.csv >> /app/public/diff/algeria_sp_list_measurements_14761.diff
[CMD] [2019-10-01 16:24:21] echo "." >> /app/public/diff/algeria_sp_list_measurements_14761.diff
[STOP] [2019-10-01 16:24:23] calculate_delta
[START] [2019-10-01 16:24:23] parse_diff_and_store
[INFO] [2019-10-01 16:24:24] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-01 16:24:26] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-01 16:24:29] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-01 16:24:31] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-01 16:24:51] Storing 2 References
[INFO] [2019-10-01 16:24:51] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-01 16:24:51] Average Time: 0.0
[INFO] [2019-10-01 16:24:51] Total Time: 1s
[INFO] [2019-10-01 16:24:51] Storing 6498 ScientificNames
[INFO] [2019-10-01 16:24:51] Processing group of 6498 in 7 groups of 1000
[INFO] [2019-10-01 16:24:53] Average Time: 0.329
[INFO] [2019-10-01 16:24:53] Total Time: 3s
[INFO] [2019-10-01 16:24:53] last 3 / first 3: 0.79
[INFO] [2019-10-01 16:24:53] Std.Dev: 0.08366600265340755; Max: 0.43
[INFO] [2019-10-01 16:24:53] Storing 6498 Nodes
[INFO] [2019-10-01 16:24:53] Processing group of 6498 in 7 groups of 1000
[INFO] [2019-10-01 16:24:55] Average Time: 0.263
[INFO] [2019-10-01 16:24:55] Total Time: 2s
[INFO] [2019-10-01 16:24:55] last 3 / first 3: 0.87
[INFO] [2019-10-01 16:24:55] Std.Dev: 0.05477225575051661; Max: 0.31
[INFO] [2019-10-01 16:24:55] Storing 3374 Occurrences
[INFO] [2019-10-01 16:24:55] Processing group of 3374 in 4 groups of 1000
[INFO] [2019-10-01 16:24:55] Average Time: 0.083
[INFO] [2019-10-01 16:24:55] Total Time: 1s
[INFO] [2019-10-01 16:24:55] Storing 7116 TraitsReferences
[INFO] [2019-10-01 16:24:55] Processing group of 7116 in 8 groups of 1000
[INFO] [2019-10-01 16:24:56] Average Time: 0.076
[INFO] [2019-10-01 16:24:56] Total Time: 1s
[INFO] [2019-10-01 16:24:56] last 3 / first 3: 0.69
[INFO] [2019-10-01 16:24:56] Std.Dev: 0.044721359549995794; Max: 0.15
[INFO] [2019-10-01 16:24:56] Storing 7115 Traits
[INFO] [2019-10-01 16:24:56] Processing group of 7115 in 8 groups of 1000
[INFO] [2019-10-01 16:24:58] Average Time: 0.276
[INFO] [2019-10-01 16:24:58] Total Time: 3s
[INFO] [2019-10-01 16:24:58] last 3 / first 3: 0.6
[INFO] [2019-10-01 16:24:58] Std.Dev: 0.10488088481701516; Max: 0.39
[INFO] [2019-10-01 16:24:58] Storing 7105 MetaTraits
[INFO] [2019-10-01 16:24:58] Processing group of 7105 in 8 groups of 1000
[INFO] [2019-10-01 16:24:59] Average Time: 0.121
[INFO] [2019-10-01 16:24:59] Total Time: 2s
[INFO] [2019-10-01 16:24:59] last 3 / first 3: 0.61
[INFO] [2019-10-01 16:24:59] Std.Dev: 0.044721359549995794; Max: 0.16
[STOP] [2019-10-01 16:24:59] parse_diff_and_store
[START] [2019-10-01 16:24:59] resolve_keys
[INFO] [2019-10-01 16:25:27] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-01 16:25:29] traits to occurrences...
[INFO] [2019-10-01 16:25:31] traits to nodes (through occurrences)...
[INFO] [2019-10-01 16:25:31] Traits to sex term...
[INFO] [2019-10-01 16:25:32] Traits to lifestage term...
[INFO] [2019-10-01 16:25:34] MetaTraits to traits...
[INFO] [2019-10-01 16:25:34] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-01 16:25:35] Assocs to occurrences...
[INFO] [2019-10-01 16:25:35] Assocs to nodes...
[INFO] [2019-10-01 16:25:35] Assoc to sex term...
[INFO] [2019-10-01 16:25:35] Assoc to lifestage term...
[STOP] [2019-10-01 16:25:35] resolve_keys
[START] [2019-10-01 16:25:35] hold_for_later_1
[STOP] [2019-10-01 16:25:35] hold_for_later_1
[START] [2019-10-01 16:25:35] hold_for_later_2
[STOP] [2019-10-01 16:25:35] hold_for_later_2
[START] [2019-10-01 16:25:35] resolve_missing_parents
[STOP] [2019-10-01 16:25:49] resolve_missing_parents
[START] [2019-10-01 16:25:49] rebuild_nodes
[START] [2019-10-01 16:25:49] Flattener#flatten
[START] [2019-10-01 16:25:49] Flattener#study_resource
[START] [2019-10-01 16:25:49] Flattener#build_ancestry
[STOP] [2019-10-01 16:25:49] Flattener#build_ancestry
[INFO] [2019-10-01 16:25:49] 6498 ancestry keys
[START] [2019-10-01 16:25:49] build_node_ancestors
[INFO] [2019-10-01 16:25:49] old ancestors deleted.
[STOP] [2019-10-01 16:25:50] build_node_ancestors
[START] [2019-10-01 16:25:51] Flattener#propagate_ancestor_ids
[STOP] [2019-10-01 16:25:52] Flattener#propagate_ancestor_ids
[STOP] [2019-10-01 16:25:52] Flattener#flatten
[STOP] [2019-10-01 16:25:52] rebuild_nodes
[START] [2019-10-01 16:25:52] resolve_missing_media_owners
[STOP] [2019-10-01 16:25:52] resolve_missing_media_owners
[START] [2019-10-01 16:25:52] sanitize_media_verbatims
[STOP] [2019-10-01 16:25:52] sanitize_media_verbatims
[START] [2019-10-01 16:25:52] queue_downloads
[STOP] [2019-10-01 16:25:52] queue_downloads
[START] [2019-10-01 16:25:52] parse_names
[WARN] [2019-10-01 16:25:52] I see 6498 names which still need to be parsed.
[STOP] [2019-10-01 16:25:58] parse_names
[START] [2019-10-01 16:25:58] denormalize_canonical_names_to_nodes
[STOP] [2019-10-01 16:25:58] denormalize_canonical_names_to_nodes
[START] [2019-10-01 16:25:58] match_nodes
[START] [2019-10-01 16:25:58] map_all_nodes_to_pages
[STOP] [2019-10-01 16:31:08] map_all_nodes_to_pages
[INFO] [2019-10-01 16:31:08] 645 Unmatched nodes (of 6498)! That's too many to output. First 10: Triticum rodeti (#47352764); Aegilops bicorne (#47353759); Stipa parviflora (#47353702); Elymus flaccidifolia (#47353052); Elymus scirpeum (#47354298); Puccinellia tenuifolia (#47349753); Helictotrichon macrostachya (#47353839); Thinopyrum flaccidifolia (#47352725); Aristida coerulescens (#47351512); Crypsis schoenoides (#47352487)
[START] [2019-10-01 16:31:08] update_nodes
[STOP] [2019-10-01 16:31:10] update_nodes
[STOP] [2019-10-01 16:31:10] match_nodes
[START] [2019-10-01 16:31:10] reindex_search
[STOP] [2019-10-01 16:31:26] reindex_search
[START] [2019-10-01 16:31:26] normalize_units
[STOP] [2019-10-01 16:31:26] normalize_units
[START] [2019-10-01 16:31:26] calculate_statistics
[STOP] [2019-10-01 16:31:26] calculate_statistics
[START] [2019-10-01 16:31:26] complete_harvest_instance
[START] [2019-10-01 16:31:26] overall_tsv_creation
[INFO] [2019-10-01 16:31:26] Processing group of 6498 in 1 batches of 10000
[INFO] [2019-10-01 16:32:37] 3374 Traits (unfiltered)...
[INFO] [2019-10-01 16:32:50] 3374 Traits (filtered)...
[INFO] [2019-10-01 16:32:50] 0 Associations (filtered)...
[INFO] [2019-10-01 16:33:32] 16859 metadata added.
[INFO] [2019-10-01 16:33:32] 0 metadata added.
[INFO] [2019-10-01 16:33:32] Average Time: 99.85
[INFO] [2019-10-01 16:33:32] Total Time: 2m6s
[STOP] [2019-10-01 16:33:32] overall_tsv_creation
[INFO] [2019-10-01 16:33:32] Done. Check your files:
[INFO] [2019-10-01 16:33:33] (6498 lines) /app/public/data/algeria_sp_list/publish_nodes.tsv
[INFO] [2019-10-01 16:33:35] (19795 lines) /app/public/data/algeria_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-01 16:33:36] (6498 lines) /app/public/data/algeria_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-01 16:33:38] (3375 lines) /app/public/data/algeria_sp_list/publish_traits.tsv
[INFO] [2019-10-01 16:33:39] (16860 lines) /app/public/data/algeria_sp_list/publish_metadata.tsv
[STOP] [2019-10-01 16:33:40] complete_harvest_instance
[START] [2019-10-01 16:33:40] completed
[STOP] [2019-10-01 16:33:40] completed
[STOP] [2019-10-01 16:33:40] logged process, took 581.86
[INFO] [2021-03-01 17:59:12] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-03-01 17:59:14] ## remove_type: ScientificName
[INFO] [2021-03-01 17:59:14] ++ Calling delete_all on 6498 instances...
[INFO] [2021-03-01 17:59:16] [17:59:16.444] Removed 6498 Scientificnames
[INFO] [2021-03-01 17:59:16] ## remove_type: Vernacular
[INFO] [2021-03-01 17:59:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-03-01 17:59:16] [17:59:16.447] Removed 0 Vernaculars
[INFO] [2021-03-01 17:59:16] ## remove_type: Article
[INFO] [2021-03-01 17:59:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-03-01 17:59:16] [17:59:16.449] Removed 0 Articles
[INFO] [2021-03-01 17:59:16] ## remove_type: Medium
[INFO] [2021-03-01 17:59:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-03-01 17:59:16] [17:59:16.452] Removed 0 Media
[INFO] [2021-03-01 17:59:16] ## remove_type: Trait
[INFO] [2021-03-01 17:59:16] ++ Calling delete_all on 7115 instances...
[INFO] [2021-03-01 17:59:18] [17:59:18.109] Removed 7115 Traits
[INFO] [2021-03-01 17:59:18] ## remove_type: MetaTrait
[INFO] [2021-03-01 17:59:18] ++ Calling delete_all on 7105 instances...
[INFO] [2021-03-01 17:59:18] [17:59:18.589] Removed 7105 Metatraits
[INFO] [2021-03-01 17:59:18] ## remove_type: OccurrenceMetadatum
[INFO] [2021-03-01 17:59:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-03-01 17:59:18] [17:59:18.622] Removed 0 Occurrencemetadata
[INFO] [2021-03-01 17:59:18] ## remove_type: Assoc
[INFO] [2021-03-01 17:59:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-03-01 17:59:18] [17:59:18.626] Removed 0 Assocs
[INFO] [2021-03-01 17:59:18] ## remove_type: MetaAssoc
[INFO] [2021-03-01 17:59:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-03-01 17:59:18] [17:59:18.650] Removed 0 Metaassocs
[INFO] [2021-03-01 17:59:18] ## remove_type: Identifier
[INFO] [2021-03-01 17:59:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-03-01 17:59:18] [17:59:18.718] Removed 0 Identifiers
[INFO] [2021-03-01 17:59:18] ## remove_type: Reference
[INFO] [2021-03-01 17:59:18] ++ Calling delete_all on 2 instances...
[INFO] [2021-03-01 17:59:18] [17:59:18.735] Removed 2 References
[INFO] [2021-03-01 17:59:20] Starting batch with ID 47352112...
[INFO] [2021-03-01 17:59:21] Starting batch with ID 47352112...
[INFO] [2021-03-01 17:59:22] Starting batch with ID 47349112...
[INFO] [2021-03-01 17:59:23] Starting batch with ID 47354424...
[INFO] [2021-03-01 17:59:23] Starting batch with ID 47354424...
[INFO] [2021-03-01 17:59:23] Starting batch with ID 47354424...
[INFO] [2021-03-01 17:59:23] Starting batch with ID 47354424...
[INFO] [2021-03-01 17:59:24] ## remove_type: Node
[INFO] [2021-03-01 17:59:24] ++ Calling delete_all on 6498 instances...
[INFO] [2021-03-01 17:59:24] [17:59:24.682] Removed 6498 Nodes
[START] [2021-03-01 17:59:28] logged process: cdc14cc7e396e8d099dbdcb2b6584e4ad6934982
[START] [2021-03-01 17:59:28] Creating resource from OpenData
[START] [2021-03-01 17:59:28] logged process: cdc14cc7e396e8d099dbdcb2b6584e4ad6934982
[START] [2021-03-01 17:59:28] Parse meta.xml file and create formats with fields
[STOP] [2021-03-01 17:59:28] Parse meta.xml file and create formats with fields
[STOP] [2021-03-01 17:59:28] Creating resource from OpenData
[START] [2021-03-01 17:59:28] logged process: cdc14cc7e396e8d099dbdcb2b6584e4ad6934982
[START] [2021-03-01 17:59:28] create_harvest_instance
[STOP] [2021-03-01 17:59:30] create_harvest_instance
[START] [2021-03-01 17:59:30] fetch_files
[STOP] [2021-03-01 17:59:30] fetch_files
[START] [2021-03-01 17:59:30] validate_each_file
[STOP] [2021-03-01 17:59:30] validate_each_file
[START] [2021-03-01 17:59:30] convert_to_csv
[CMD] [2021-03-01 17:59:30] /usr/bin/sort /app/public/converted_csv/algeria_sp_list_refs_26940.csv > /app/public/converted_csv/algeria_sp_list_refs_26940.csv_sorted
[CMD] [2021-03-01 17:59:30] /usr/bin/sort /app/public/converted_csv/algeria_sp_list_nodes_26941.csv > /app/public/converted_csv/algeria_sp_list_nodes_26941.csv_sorted
[CMD] [2021-03-01 17:59:30] /usr/bin/sort /app/public/converted_csv/algeria_sp_list_occurrences_26942.csv > /app/public/converted_csv/algeria_sp_list_occurrences_26942.csv_sorted
[CMD] [2021-03-01 17:59:30] /usr/bin/sort /app/public/converted_csv/algeria_sp_list_measurements_26943.csv > /app/public/converted_csv/algeria_sp_list_measurements_26943.csv_sorted
[STOP] [2021-03-01 17:59:30] convert_to_csv
[START] [2021-03-01 17:59:30] calculate_delta
[CMD] [2021-03-01 17:59:30] echo "0a" > /app/public/diff/algeria_sp_list_refs_26940.diff
[CMD] [2021-03-01 17:59:30] tail -n +1 /app/public/converted_csv/algeria_sp_list_refs_26940.csv >> /app/public/diff/algeria_sp_list_refs_26940.diff
[CMD] [2021-03-01 17:59:30] echo "." >> /app/public/diff/algeria_sp_list_refs_26940.diff
[CMD] [2021-03-01 17:59:30] echo "0a" > /app/public/diff/algeria_sp_list_nodes_26941.diff
[CMD] [2021-03-01 17:59:30] tail -n +1 /app/public/converted_csv/algeria_sp_list_nodes_26941.csv >> /app/public/diff/algeria_sp_list_nodes_26941.diff
[CMD] [2021-03-01 17:59:30] echo "." >> /app/public/diff/algeria_sp_list_nodes_26941.diff
[CMD] [2021-03-01 17:59:30] echo "0a" > /app/public/diff/algeria_sp_list_occurrences_26942.diff
[CMD] [2021-03-01 17:59:30] tail -n +1 /app/public/converted_csv/algeria_sp_list_occurrences_26942.csv >> /app/public/diff/algeria_sp_list_occurrences_26942.diff
[CMD] [2021-03-01 17:59:30] echo "." >> /app/public/diff/algeria_sp_list_occurrences_26942.diff
[CMD] [2021-03-01 17:59:30] echo "0a" > /app/public/diff/algeria_sp_list_measurements_26943.diff
[CMD] [2021-03-01 17:59:30] tail -n +1 /app/public/converted_csv/algeria_sp_list_measurements_26943.csv >> /app/public/diff/algeria_sp_list_measurements_26943.diff
[CMD] [2021-03-01 17:59:30] echo "." >> /app/public/diff/algeria_sp_list_measurements_26943.diff
[STOP] [2021-03-01 17:59:30] calculate_delta
[START] [2021-03-01 17:59:30] parse_diff_and_store
[INFO] [2021-03-01 17:59:30] Loading refs diff file into memory (true lines)...
[INFO] [2021-03-01 17:59:31] Loading nodes diff file into memory (true lines)...
[INFO] [2021-03-01 17:59:32] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-03-01 17:59:33] Loading measurements diff file into memory (true lines)...
[INFO] [2021-03-01 17:59:36] Storing 2 References
[INFO] [2021-03-01 17:59:36] Processing group of 2 in 1 groups of 1000
[INFO] [2021-03-01 17:59:36] Average Time: 0.0
[INFO] [2021-03-01 17:59:36] Total Time: 1s
[INFO] [2021-03-01 17:59:36] Storing 6498 ScientificNames
[INFO] [2021-03-01 17:59:36] Processing group of 6498 in 7 groups of 1000
[INFO] [2021-03-01 17:59:38] Average Time: 0.289
[INFO] [2021-03-01 17:59:38] Total Time: 3s
[INFO] [2021-03-01 17:59:38] last 3 / first 3: 0.71
[INFO] [2021-03-01 17:59:38] Std.Dev: 0.07745966692414834; Max: 0.4
[INFO] [2021-03-01 17:59:38] Storing 6498 Nodes
[INFO] [2021-03-01 17:59:38] Processing group of 6498 in 7 groups of 1000
[INFO] [2021-03-01 17:59:40] Average Time: 0.309
[INFO] [2021-03-01 17:59:40] Total Time: 3s
[INFO] [2021-03-01 17:59:40] last 3 / first 3: 0.94
[INFO] [2021-03-01 17:59:40] Std.Dev: 0.09486832980505137; Max: 0.43
[INFO] [2021-03-01 17:59:40] Storing 3374 Occurrences
[INFO] [2021-03-01 17:59:40] Processing group of 3374 in 4 groups of 1000
[INFO] [2021-03-01 17:59:40] Average Time: 0.098
[INFO] [2021-03-01 17:59:40] Total Time: 1s
[INFO] [2021-03-01 17:59:40] Storing 7116 TraitsReferences
[INFO] [2021-03-01 17:59:40] Processing group of 7116 in 8 groups of 1000
[INFO] [2021-03-01 17:59:41] Average Time: 0.104
[INFO] [2021-03-01 17:59:41] Total Time: 1s
[INFO] [2021-03-01 17:59:41] last 3 / first 3: 0.22
[INFO] [2021-03-01 17:59:41] Std.Dev: 0.14491376746189438; Max: 0.46
[INFO] [2021-03-01 17:59:41] Storing 7115 Traits
[INFO] [2021-03-01 17:59:41] Processing group of 7115 in 8 groups of 1000
[INFO] [2021-03-01 17:59:44] Average Time: 0.344
[INFO] [2021-03-01 17:59:44] Total Time: 3s
[INFO] [2021-03-01 17:59:44] last 3 / first 3: 0.51
[INFO] [2021-03-01 17:59:44] Std.Dev: 0.16431676725154984; Max: 0.65
[INFO] [2021-03-01 17:59:44] Storing 3558 MetaTraits
[INFO] [2021-03-01 17:59:44] Processing group of 3558 in 4 groups of 1000
[INFO] [2021-03-01 17:59:45] Average Time: 0.115
[INFO] [2021-03-01 17:59:45] Total Time: 1s
[STOP] [2021-03-01 17:59:45] parse_diff_and_store
[START] [2021-03-01 17:59:45] resolve_keys
[INFO] [2021-03-01 18:00:12] Occurrences to nodes (through scientific_names)...
[INFO] [2021-03-01 18:00:13] traits to occurrences...
[INFO] [2021-03-01 18:00:23] traits to nodes (through occurrences)...
[INFO] [2021-03-01 18:00:23] Traits to sex term...
[INFO] [2021-03-01 18:00:25] Traits to lifestage term...
[INFO] [2021-03-01 18:00:26] MetaTraits to traits...
[INFO] [2021-03-01 18:00:26] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-03-01 18:00:27] Assocs to occurrences...
[INFO] [2021-03-01 18:00:27] Assocs to nodes...
[INFO] [2021-03-01 18:00:27] Assoc to sex term...
[INFO] [2021-03-01 18:00:27] Assoc to lifestage term...
[INFO] [2021-03-01 18:00:27] MetaAssoc to assocs...
[STOP] [2021-03-01 18:00:27] resolve_keys
[START] [2021-03-01 18:00:27] hold_for_later_1
[STOP] [2021-03-01 18:00:27] hold_for_later_1
[START] [2021-03-01 18:00:27] hold_for_later_2
[STOP] [2021-03-01 18:00:27] hold_for_later_2
[START] [2021-03-01 18:00:27] resolve_missing_parents
[STOP] [2021-03-01 18:00:30] resolve_missing_parents
[START] [2021-03-01 18:00:30] rebuild_nodes
[START] [2021-03-01 18:00:30] Flattener#flatten
[START] [2021-03-01 18:00:30] Flattener#study_resource
[START] [2021-03-01 18:00:30] Flattener#build_ancestry
[STOP] [2021-03-01 18:00:30] Flattener#build_ancestry
[INFO] [2021-03-01 18:00:30] 6498 ancestry keys
[START] [2021-03-01 18:00:30] build_node_ancestors
[INFO] [2021-03-01 18:00:30] old ancestors deleted.
[STOP] [2021-03-01 18:00:31] build_node_ancestors
[START] [2021-03-01 18:00:32] Flattener#propagate_ancestor_ids
[STOP] [2021-03-01 18:00:33] Flattener#propagate_ancestor_ids
[STOP] [2021-03-01 18:00:33] Flattener#flatten
[STOP] [2021-03-01 18:00:33] rebuild_nodes
[START] [2021-03-01 18:00:33] resolve_missing_media_owners
[STOP] [2021-03-01 18:00:33] resolve_missing_media_owners
[START] [2021-03-01 18:00:33] sanitize_media_verbatims
[STOP] [2021-03-01 18:00:33] sanitize_media_verbatims
[START] [2021-03-01 18:00:33] queue_downloads
[STOP] [2021-03-01 18:00:33] queue_downloads
[START] [2021-03-01 18:00:33] parse_names
[WARN] [2021-03-01 18:00:33] I see 6498 names which still need to be parsed.
[STOP] [2021-03-01 18:00:39] parse_names
[START] [2021-03-01 18:00:39] denormalize_canonical_names_to_nodes
[STOP] [2021-03-01 18:00:39] denormalize_canonical_names_to_nodes
[START] [2021-03-01 18:00:39] match_nodes
[START] [2021-03-01 18:00:39] map_all_nodes_to_pages
[STOP] [2021-03-01 18:06:52] map_all_nodes_to_pages
[INFO] [2021-03-01 18:06:52] 705 Unmatched nodes (of 6498)! That's too many to output. Full list in /app/public/data/algeria_sp_list/unmatched_nodes.txt ; First 10: Triticum rodeti (#89280569); Aegilops bicorne (#89281564); Pennisetum (#89276458); Stipa parviflora (#89281507); Rostraria michelii (#89276931); Elymus elongatum (#89279055); Elymus junceum (#89279965); Elymus flaccidifolia (#89280857); Elymus scirpeum (#89282103); Aira tenorii (#89281468)
[START] [2021-03-01 18:06:52] update_nodes
[STOP] [2021-03-01 18:06:55] update_nodes
[STOP] [2021-03-01 18:06:55] match_nodes
[START] [2021-03-01 18:06:55] reindex_search
[STOP] [2021-03-01 18:07:02] reindex_search
[START] [2021-03-01 18:07:03] normalize_units
[STOP] [2021-03-01 18:07:03] normalize_units
[START] [2021-03-01 18:07:03] calculate_statistics
[STOP] [2021-03-01 18:07:04] calculate_statistics
[START] [2021-03-01 18:07:04] complete_harvest_instance
[START] [2021-03-01 18:07:04] overall_tsv_creation
[INFO] [2021-03-01 18:07:04] Processing group of 6498 in 1 batches of 10000
[INFO] [2021-03-01 18:09:23] 3374 Traits (unfiltered)...
[INFO] [2021-03-01 18:10:18] 3374 Traits (filtered)...
[INFO] [2021-03-01 18:10:18] 0 Associations (filtered)...
[INFO] [2021-03-01 18:10:19] 10122 metadata added.
[INFO] [2021-03-01 18:10:19] 0 metadata added.
[INFO] [2021-03-01 18:10:47] Average Time: 122.2
[INFO] [2021-03-01 18:10:47] Total Time: 3m44s
[STOP] [2021-03-01 18:10:47] overall_tsv_creation
[INFO] [2021-03-01 18:10:47] Done. Check your files:
[INFO] [2021-03-01 18:10:47] (6498 lines) /app/public/data/algeria_sp_list/publish_nodes.tsv
[INFO] [2021-03-01 18:10:47] (19795 lines) /app/public/data/algeria_sp_list/publish_node_ancestors.tsv
[INFO] [2021-03-01 18:10:47] (6498 lines) /app/public/data/algeria_sp_list/publish_scientific_names.tsv
[INFO] [2021-03-01 18:10:47] (3375 lines) /app/public/data/algeria_sp_list/publish_traits.tsv
[INFO] [2021-03-01 18:10:47] (10123 lines) /app/public/data/algeria_sp_list/publish_metadata.tsv
[STOP] [2021-03-01 18:10:47] complete_harvest_instance
[START] [2021-03-01 18:10:47] completed
[STOP] [2021-03-01 18:10:47] completed
[STOP] [2021-03-01 18:10:47] logged process, took 678.79
[START] [2021-03-23 12:41:21] logged process: bf5ef5e3f6f21085920392f11ae91bba0127737c
[START] [2021-03-23 12:41:21] Parse meta.xml file and create formats with fields
[STOP] [2021-03-23 12:41:21] Parse meta.xml file and create formats with fields
Latest Process