Harvest for Saint Vincent and the Grenadines Species List Created 15 Oct 16:30

Stage: completed
Fetched: 15 Oct 16:30
Validated: 15 Oct 16:30
Deltas Created 15 Oct 16:30
Units Normalized: 15 Oct 16:31
Ancestry Built: 15 Oct 16:31
Nodes Matched: 15 Oct 16:31
Names Parsed: 15 Oct 16:31
New Models Stored: 15 Oct 16:30
Indexed: 15 Oct 16:31
Completed: 15 Oct 16:33
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:30:48 -0400 by logger.rb/56815
[START] [2019-10-15 16:30:48] logged process
[START] [2019-10-15 16:30:48] create_harvest_instance
[STOP] [2019-10-15 16:30:49] create_harvest_instance
[START] [2019-10-15 16:30:49] fetch_files
[STOP] [2019-10-15 16:30:49] fetch_files
[START] [2019-10-15 16:30:49] validate_each_file
[STOP] [2019-10-15 16:30:49] validate_each_file
[START] [2019-10-15 16:30:49] convert_to_csv
[CMD] [2019-10-15 16:30:49] /usr/bin/sort /app/public/converted_csv/svgsl_refs_17069.csv > /app/public/converted_csv/svgsl_refs_17069.csv_sorted
[CMD] [2019-10-15 16:30:49] /usr/bin/sort /app/public/converted_csv/svgsl_nodes_17070.csv > /app/public/converted_csv/svgsl_nodes_17070.csv_sorted
[CMD] [2019-10-15 16:30:49] /usr/bin/sort /app/public/converted_csv/svgsl_occurrences_17071.csv > /app/public/converted_csv/svgsl_occurrences_17071.csv_sorted
[CMD] [2019-10-15 16:30:50] /usr/bin/sort /app/public/converted_csv/svgsl_measurements_17072.csv > /app/public/converted_csv/svgsl_measurements_17072.csv_sorted
[STOP] [2019-10-15 16:30:50] convert_to_csv
[START] [2019-10-15 16:30:50] calculate_delta
[CMD] [2019-10-15 16:30:50] echo "0a" > /app/public/diff/svgsl_refs_17069.diff
[CMD] [2019-10-15 16:30:50] tail -n +1 /app/public/converted_csv/svgsl_refs_17069.csv >> /app/public/diff/svgsl_refs_17069.diff
[CMD] [2019-10-15 16:30:51] echo "." >> /app/public/diff/svgsl_refs_17069.diff
[CMD] [2019-10-15 16:30:51] echo "0a" > /app/public/diff/svgsl_nodes_17070.diff
[CMD] [2019-10-15 16:30:51] tail -n +1 /app/public/converted_csv/svgsl_nodes_17070.csv >> /app/public/diff/svgsl_nodes_17070.diff
[CMD] [2019-10-15 16:30:51] echo "." >> /app/public/diff/svgsl_nodes_17070.diff
[CMD] [2019-10-15 16:30:52] echo "0a" > /app/public/diff/svgsl_occurrences_17071.diff
[CMD] [2019-10-15 16:30:52] tail -n +1 /app/public/converted_csv/svgsl_occurrences_17071.csv >> /app/public/diff/svgsl_occurrences_17071.diff
[CMD] [2019-10-15 16:30:52] echo "." >> /app/public/diff/svgsl_occurrences_17071.diff
[CMD] [2019-10-15 16:30:52] echo "0a" > /app/public/diff/svgsl_measurements_17072.diff
[CMD] [2019-10-15 16:30:53] tail -n +1 /app/public/converted_csv/svgsl_measurements_17072.csv >> /app/public/diff/svgsl_measurements_17072.diff
[CMD] [2019-10-15 16:30:53] echo "." >> /app/public/diff/svgsl_measurements_17072.diff
[STOP] [2019-10-15 16:30:53] calculate_delta
[START] [2019-10-15 16:30:53] parse_diff_and_store
[INFO] [2019-10-15 16:30:54] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:30:54] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:30:54] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:30:55] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:30:56] Storing 2 References
[INFO] [2019-10-15 16:30:56] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:30:56] Average Time: 0.0
[INFO] [2019-10-15 16:30:56] Total Time: 1s
[INFO] [2019-10-15 16:30:56] Storing 660 ScientificNames
[INFO] [2019-10-15 16:30:56] Processing group of 660 in 1 groups of 1000
[INFO] [2019-10-15 16:30:56] Average Time: 0.32
[INFO] [2019-10-15 16:30:56] Total Time: 1s
[INFO] [2019-10-15 16:30:56] Storing 660 Nodes
[INFO] [2019-10-15 16:30:56] Processing group of 660 in 1 groups of 1000
[INFO] [2019-10-15 16:30:57] Average Time: 0.19
[INFO] [2019-10-15 16:30:57] Total Time: 1s
[INFO] [2019-10-15 16:30:57] Storing 244 Occurrences
[INFO] [2019-10-15 16:30:57] Processing group of 244 in 1 groups of 1000
[INFO] [2019-10-15 16:30:57] Average Time: 0.05
[INFO] [2019-10-15 16:30:57] Total Time: 1s
[INFO] [2019-10-15 16:30:57] Storing 488 TraitsReferences
[INFO] [2019-10-15 16:30:57] Processing group of 488 in 1 groups of 1000
[INFO] [2019-10-15 16:30:57] Average Time: 0.12
[INFO] [2019-10-15 16:30:57] Total Time: 1s
[INFO] [2019-10-15 16:30:57] Storing 488 Traits
[INFO] [2019-10-15 16:30:57] Processing group of 488 in 1 groups of 1000
[INFO] [2019-10-15 16:30:57] Average Time: 0.27
[INFO] [2019-10-15 16:30:57] Total Time: 1s
[INFO] [2019-10-15 16:30:57] Storing 488 MetaTraits
[INFO] [2019-10-15 16:30:57] Processing group of 488 in 1 groups of 1000
[INFO] [2019-10-15 16:30:57] Average Time: 0.09
[INFO] [2019-10-15 16:30:57] Total Time: 1s
[STOP] [2019-10-15 16:30:57] parse_diff_and_store
[START] [2019-10-15 16:30:57] resolve_keys
[INFO] [2019-10-15 16:31:02] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:31:02] traits to occurrences...
[INFO] [2019-10-15 16:31:02] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:31:02] Traits to sex term...
[INFO] [2019-10-15 16:31:02] Traits to lifestage term...
[INFO] [2019-10-15 16:31:03] MetaTraits to traits...
[INFO] [2019-10-15 16:31:03] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:31:03] Assocs to occurrences...
[INFO] [2019-10-15 16:31:03] Assocs to nodes...
[INFO] [2019-10-15 16:31:03] Assoc to sex term...
[INFO] [2019-10-15 16:31:03] Assoc to lifestage term...
[STOP] [2019-10-15 16:31:03] resolve_keys
[START] [2019-10-15 16:31:03] hold_for_later_1
[STOP] [2019-10-15 16:31:03] hold_for_later_1
[START] [2019-10-15 16:31:03] hold_for_later_2
[STOP] [2019-10-15 16:31:03] hold_for_later_2
[START] [2019-10-15 16:31:03] resolve_missing_parents
[STOP] [2019-10-15 16:31:03] resolve_missing_parents
[START] [2019-10-15 16:31:03] rebuild_nodes
[START] [2019-10-15 16:31:03] Flattener#flatten
[START] [2019-10-15 16:31:03] Flattener#study_resource
[START] [2019-10-15 16:31:03] Flattener#build_ancestry
[STOP] [2019-10-15 16:31:03] Flattener#build_ancestry
[INFO] [2019-10-15 16:31:03] 660 ancestry keys
[START] [2019-10-15 16:31:03] build_node_ancestors
[INFO] [2019-10-15 16:31:03] old ancestors deleted.
[STOP] [2019-10-15 16:31:03] build_node_ancestors
[START] [2019-10-15 16:31:04] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:31:04] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:31:04] Flattener#flatten
[STOP] [2019-10-15 16:31:04] rebuild_nodes
[START] [2019-10-15 16:31:04] resolve_missing_media_owners
[STOP] [2019-10-15 16:31:04] resolve_missing_media_owners
[START] [2019-10-15 16:31:04] sanitize_media_verbatims
[STOP] [2019-10-15 16:31:04] sanitize_media_verbatims
[START] [2019-10-15 16:31:04] queue_downloads
[STOP] [2019-10-15 16:31:04] queue_downloads
[START] [2019-10-15 16:31:04] parse_names
[WARN] [2019-10-15 16:31:04] I see 660 names which still need to be parsed.
[STOP] [2019-10-15 16:31:05] parse_names
[START] [2019-10-15 16:31:05] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:31:05] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:31:05] match_nodes
[START] [2019-10-15 16:31:05] map_all_nodes_to_pages
[STOP] [2019-10-15 16:31:55] map_all_nodes_to_pages
[INFO] [2019-10-15 16:31:55] 24 Unmatched nodes (of 660)! That's too many to output. First 10: Coerebidae (#51756194); Thalaseus (#51756738); Thalaseus maximus (#51756737); Arcos cephalus (#51756376); Strabomantidae (#51756474); Marattiopsida (#51756282); Blechnum ryani (#51756422); Callipteris ambiguum (#51756450); Lycopodiella cernuum (#51756591); Palhinhaea cernuum (#51756792)
[START] [2019-10-15 16:31:55] update_nodes
[STOP] [2019-10-15 16:31:56] update_nodes
[STOP] [2019-10-15 16:31:56] match_nodes
[START] [2019-10-15 16:31:56] reindex_search
[STOP] [2019-10-15 16:31:57] reindex_search
[START] [2019-10-15 16:31:57] normalize_units
[STOP] [2019-10-15 16:31:57] normalize_units
[START] [2019-10-15 16:31:57] calculate_statistics
[STOP] [2019-10-15 16:31:57] calculate_statistics
[START] [2019-10-15 16:31:57] complete_harvest_instance
[START] [2019-10-15 16:31:57] overall_tsv_creation
[INFO] [2019-10-15 16:31:57] Processing group of 660 in 1 batches of 10000
[INFO] [2019-10-15 16:32:45] 244 Traits (unfiltered)...
[INFO] [2019-10-15 16:32:58] 244 Traits (filtered)...
[INFO] [2019-10-15 16:32:58] 0 Associations (filtered)...
[INFO] [2019-10-15 16:33:38] 1220 metadata added.
[INFO] [2019-10-15 16:33:38] 0 metadata added.
[INFO] [2019-10-15 16:33:38] Average Time: 79.21
[INFO] [2019-10-15 16:33:38] Total Time: 1m41s
[STOP] [2019-10-15 16:33:38] overall_tsv_creation
[INFO] [2019-10-15 16:33:38] Done. Check your files:
[INFO] [2019-10-15 16:33:38] (660 lines) /app/public/data/svgsl/publish_nodes.tsv
[INFO] [2019-10-15 16:33:39] (3132 lines) /app/public/data/svgsl/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:33:39] (660 lines) /app/public/data/svgsl/publish_scientific_names.tsv
[INFO] [2019-10-15 16:33:39] (245 lines) /app/public/data/svgsl/publish_traits.tsv
[INFO] [2019-10-15 16:33:39] (1221 lines) /app/public/data/svgsl/publish_metadata.tsv
[STOP] [2019-10-15 16:33:39] complete_harvest_instance
[START] [2019-10-15 16:33:39] completed
[STOP] [2019-10-15 16:33:39] completed
[STOP] [2019-10-15 16:33:39] logged process, took 171.35
Latest Process

15 Oct 16:30 EXITED currently processing 0