Harvest for Adriatic Sea Species List Created 09 Jun 11:03

Harvesting Log

[INFO] [2021-06-09 11:03:02] Created harvest instance #4006
[STOP] [2021-06-09 11:03:02] create_harvest_instance
[START] [2021-06-09 11:03:02] fetch_files
[STOP] [2021-06-09 11:03:02] fetch_files
[START] [2021-06-09 11:03:02] validate_each_file
[INFO] [2021-06-09 11:03:02] Looping over 4 formats...
[INFO] [2021-06-09 11:03:02] ...refs (/app/public/data/adriatic_sea_sp_/tb_references.txt)
[INFO] [2021-06-09 11:03:02] Valid: /app/public/converted_csv/adriatic_sea_sp__refs_4006.csv (1 lines)
[INFO] [2021-06-09 11:03:02] ...nodes (/app/public/data/adriatic_sea_sp_/tb_taxon.txt)
[INFO] [2021-06-09 11:03:03] Valid: /app/public/converted_csv/adriatic_sea_sp__nodes_4006.csv (4442 lines)
[INFO] [2021-06-09 11:03:03] ...occurrences (/app/public/data/adriatic_sea_sp_/tb_occurrence.txt)
[INFO] [2021-06-09 11:03:03] Valid: /app/public/converted_csv/adriatic_sea_sp__occurrences_4006.csv (2173 lines)
[INFO] [2021-06-09 11:03:03] ...measurements (/app/public/data/adriatic_sea_sp_/tb_measurement.txt)
[INFO] [2021-06-09 11:03:03] Valid: /app/public/converted_csv/adriatic_sea_sp__measurements_4006.csv (4346 lines)
[STOP] [2021-06-09 11:03:03] validate_each_file
[START] [2021-06-09 11:03:03] convert_to_csv
[INFO] [2021-06-09 11:03:03] Looping over 4 formats...
[INFO] [2021-06-09 11:03:03] ...refs (/app/public/data/adriatic_sea_sp_/tb_references.txt)
[CMD] [2021-06-09 11:03:03] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp__refs_4006.csv > /app/public/converted_csv/adriatic_sea_sp__refs_4006.csv_sorted
[INFO] [2021-06-09 11:03:03] Converted: /app/public/converted_csv/adriatic_sea_sp__refs_4006.csv (1 lines)
[INFO] [2021-06-09 11:03:03] ...nodes (/app/public/data/adriatic_sea_sp_/tb_taxon.txt)
[CMD] [2021-06-09 11:03:03] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp__nodes_4006.csv > /app/public/converted_csv/adriatic_sea_sp__nodes_4006.csv_sorted
[INFO] [2021-06-09 11:03:03] Converted: /app/public/converted_csv/adriatic_sea_sp__nodes_4006.csv (4442 lines)
[INFO] [2021-06-09 11:03:03] ...occurrences (/app/public/data/adriatic_sea_sp_/tb_occurrence.txt)
[CMD] [2021-06-09 11:03:03] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp__occurrences_4006.csv > /app/public/converted_csv/adriatic_sea_sp__occurrences_4006.csv_sorted
[INFO] [2021-06-09 11:03:03] Converted: /app/public/converted_csv/adriatic_sea_sp__occurrences_4006.csv (2173 lines)
[INFO] [2021-06-09 11:03:03] ...measurements (/app/public/data/adriatic_sea_sp_/tb_measurement.txt)
[CMD] [2021-06-09 11:03:03] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp__measurements_4006.csv > /app/public/converted_csv/adriatic_sea_sp__measurements_4006.csv_sorted
[INFO] [2021-06-09 11:03:04] Converted: /app/public/converted_csv/adriatic_sea_sp__measurements_4006.csv (4346 lines)
[STOP] [2021-06-09 11:03:04] convert_to_csv
[START] [2021-06-09 11:03:04] calculate_delta
[INFO] [2021-06-09 11:03:04] Looping over 4 formats...
[INFO] [2021-06-09 11:03:04] ...refs (/app/public/data/adriatic_sea_sp_/tb_references.txt)
[CMD] [2021-06-09 11:03:04] echo "0a" > /app/public/diff/adriatic_sea_sp__refs_4006.diff
[CMD] [2021-06-09 11:03:04] tail -n +1 /app/public/converted_csv/adriatic_sea_sp__refs_4006.csv >> /app/public/diff/adriatic_sea_sp__refs_4006.diff
[CMD] [2021-06-09 11:03:04] echo "." >> /app/public/diff/adriatic_sea_sp__refs_4006.diff
[INFO] [2021-06-09 11:03:04] Created diff: /app/public/diff/adriatic_sea_sp__refs_4006.diff (3 lines)
[INFO] [2021-06-09 11:03:04] ...nodes (/app/public/data/adriatic_sea_sp_/tb_taxon.txt)
[CMD] [2021-06-09 11:03:04] echo "0a" > /app/public/diff/adriatic_sea_sp__nodes_4006.diff
[CMD] [2021-06-09 11:03:04] tail -n +1 /app/public/converted_csv/adriatic_sea_sp__nodes_4006.csv >> /app/public/diff/adriatic_sea_sp__nodes_4006.diff
[CMD] [2021-06-09 11:03:04] echo "." >> /app/public/diff/adriatic_sea_sp__nodes_4006.diff
[INFO] [2021-06-09 11:03:04] Created diff: /app/public/diff/adriatic_sea_sp__nodes_4006.diff (4444 lines)
[INFO] [2021-06-09 11:03:04] ...occurrences (/app/public/data/adriatic_sea_sp_/tb_occurrence.txt)
[CMD] [2021-06-09 11:03:04] echo "0a" > /app/public/diff/adriatic_sea_sp__occurrences_4006.diff
[CMD] [2021-06-09 11:03:04] tail -n +1 /app/public/converted_csv/adriatic_sea_sp__occurrences_4006.csv >> /app/public/diff/adriatic_sea_sp__occurrences_4006.diff
[CMD] [2021-06-09 11:03:04] echo "." >> /app/public/diff/adriatic_sea_sp__occurrences_4006.diff
[INFO] [2021-06-09 11:03:04] Created diff: /app/public/diff/adriatic_sea_sp__occurrences_4006.diff (2175 lines)
[INFO] [2021-06-09 11:03:04] ...measurements (/app/public/data/adriatic_sea_sp_/tb_measurement.txt)
[CMD] [2021-06-09 11:03:04] echo "0a" > /app/public/diff/adriatic_sea_sp__measurements_4006.diff
[CMD] [2021-06-09 11:03:05] tail -n +1 /app/public/converted_csv/adriatic_sea_sp__measurements_4006.csv >> /app/public/diff/adriatic_sea_sp__measurements_4006.diff
[CMD] [2021-06-09 11:03:05] echo "." >> /app/public/diff/adriatic_sea_sp__measurements_4006.diff
[INFO] [2021-06-09 11:03:05] Created diff: /app/public/diff/adriatic_sea_sp__measurements_4006.diff (4348 lines)
[STOP] [2021-06-09 11:03:05] calculate_delta
[START] [2021-06-09 11:03:05] parse_diff_and_store
[INFO] [2021-06-09 11:03:05] Handling diff: /app/public/diff/adriatic_sea_sp__refs_4006.diff (3 lines)
[INFO] [2021-06-09 11:03:05] Loading refs diff file into memory (3 /app/public/diff/adriatic_sea_sp__refs_4006.diff lines)...
[INFO] [2021-06-09 11:03:05] Handling diff: /app/public/diff/adriatic_sea_sp__nodes_4006.diff (4444 lines)
[INFO] [2021-06-09 11:03:05] Loading nodes diff file into memory (4444 /app/public/diff/adriatic_sea_sp__nodes_4006.diff lines)...
[INFO] [2021-06-09 11:03:06] Handling diff: /app/public/diff/adriatic_sea_sp__occurrences_4006.diff (2175 lines)
[INFO] [2021-06-09 11:03:06] Loading occurrences diff file into memory (2175 /app/public/diff/adriatic_sea_sp__occurrences_4006.diff lines)...
[INFO] [2021-06-09 11:03:07] Handling diff: /app/public/diff/adriatic_sea_sp__measurements_4006.diff (4348 lines)
[INFO] [2021-06-09 11:03:07] Loading measurements diff file into memory (4348 /app/public/diff/adriatic_sea_sp__measurements_4006.diff lines)...
[INFO] [2021-06-09 11:03:08] Storing 1 References
[INFO] [2021-06-09 11:03:08] Processing group of 1 in 1 groups of 1000
[INFO] [2021-06-09 11:03:08] Average Time: 0.0
[INFO] [2021-06-09 11:03:08] Total Time: 1s
[INFO] [2021-06-09 11:03:08] Storing 4442 ScientificNames
[INFO] [2021-06-09 11:03:08] Processing group of 4442 in 5 groups of 1000
[INFO] [2021-06-09 11:03:10] Average Time: 0.342
[INFO] [2021-06-09 11:03:10] Total Time: 2s
[INFO] [2021-06-09 11:03:10] Storing 4442 Nodes
[INFO] [2021-06-09 11:03:10] Processing group of 4442 in 5 groups of 1000
[INFO] [2021-06-09 11:03:12] Average Time: 0.396
[INFO] [2021-06-09 11:03:12] Total Time: 3s
[INFO] [2021-06-09 11:03:12] Storing 2173 Occurrences
[INFO] [2021-06-09 11:03:12] Processing group of 2173 in 3 groups of 1000
[INFO] [2021-06-09 11:03:14] Average Time: 0.643
[INFO] [2021-06-09 11:03:14] Total Time: 2s
[INFO] [2021-06-09 11:03:14] Storing 4346 Traits
[INFO] [2021-06-09 11:03:14] Processing group of 4346 in 5 groups of 1000
[INFO] [2021-06-09 11:03:16] Average Time: 0.304
[INFO] [2021-06-09 11:03:16] Total Time: 2s
[INFO] [2021-06-09 11:03:16] Storing 4346 TraitsReferences
[INFO] [2021-06-09 11:03:16] Processing group of 4346 in 5 groups of 1000
[INFO] [2021-06-09 11:03:16] Average Time: 0.052
[INFO] [2021-06-09 11:03:16] Total Time: 1s
[STOP] [2021-06-09 11:03:16] parse_diff_and_store
[START] [2021-06-09 11:03:16] resolve_keys
[INFO] [2021-06-09 11:03:34] Occurrences to nodes (through scientific_names)...
[INFO] [2021-06-09 11:03:42] traits to occurrences...
[INFO] [2021-06-09 11:03:43] traits to nodes (through occurrences)...
[INFO] [2021-06-09 11:03:43] Traits to sex term...
[INFO] [2021-06-09 11:03:44] Traits to lifestage term...
[INFO] [2021-06-09 11:03:45] MetaTraits to traits...
[INFO] [2021-06-09 11:03:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-06-09 11:03:45] Assocs to occurrences...
[INFO] [2021-06-09 11:03:45] Assocs to nodes...
[INFO] [2021-06-09 11:03:45] Assoc to sex term...
[INFO] [2021-06-09 11:03:45] Assoc to lifestage term...
[INFO] [2021-06-09 11:03:45] MetaAssoc to assocs...
[STOP] [2021-06-09 11:03:45] resolve_keys
[START] [2021-06-09 11:03:45] hold_for_later_1
[STOP] [2021-06-09 11:03:45] hold_for_later_1
[START] [2021-06-09 11:03:45] hold_for_later_2
[STOP] [2021-06-09 11:03:45] hold_for_later_2
[START] [2021-06-09 11:03:45] resolve_missing_parents
[STOP] [2021-06-09 11:03:47] resolve_missing_parents
[START] [2021-06-09 11:03:47] rebuild_nodes
[START] [2021-06-09 11:03:47] Flattener#flatten
[START] [2021-06-09 11:03:47] Flattener#study_resource
[START] [2021-06-09 11:03:47] Flattener#build_ancestry
[STOP] [2021-06-09 11:03:47] Flattener#build_ancestry
[INFO] [2021-06-09 11:03:47] 4442 ancestry keys
[START] [2021-06-09 11:03:47] build_node_ancestors
[INFO] [2021-06-09 11:03:47] old ancestors deleted.
[STOP] [2021-06-09 11:03:48] build_node_ancestors
[START] [2021-06-09 11:03:49] Flattener#propagate_ancestor_ids
[STOP] [2021-06-09 11:03:50] Flattener#propagate_ancestor_ids
[STOP] [2021-06-09 11:03:50] Flattener#flatten
[STOP] [2021-06-09 11:03:50] rebuild_nodes
[START] [2021-06-09 11:03:50] resolve_missing_media_owners
[STOP] [2021-06-09 11:03:50] resolve_missing_media_owners
[START] [2021-06-09 11:03:50] sanitize_media_verbatims
[STOP] [2021-06-09 11:03:50] sanitize_media_verbatims
[START] [2021-06-09 11:03:50] queue_downloads
[STOP] [2021-06-09 11:03:50] queue_downloads
[START] [2021-06-09 11:03:50] parse_names
[WARN] [2021-06-09 11:03:50] I see 4442 names which still need to be parsed.
[STOP] [2021-06-09 11:03:55] parse_names
[START] [2021-06-09 11:03:55] denormalize_canonical_names_to_nodes
[STOP] [2021-06-09 11:03:55] denormalize_canonical_names_to_nodes
[START] [2021-06-09 11:03:55] match_nodes
[START] [2021-06-09 11:03:55] map_all_nodes_to_pages
[STOP] [2021-06-09 11:07:37] map_all_nodes_to_pages
[INFO] [2021-06-09 11:07:37] 278 Unmatched nodes (of 4442)! That's too many to output. Full list in /app/public/data/adriatic_sea_sp_/unmatched_nodes.txt ; First 10: Canonical: Cassidulina crassa; Node#95867827; ResourceID: T100090; Canonical: Globocassidulina oblonga; Node#95869037; ResourceID: T101311; Canonical: Cassidulinoides bradyi; Node#95867978; ResourceID: T100241; Canonical: Elphidium albiumbilicatum; Node#95868302; ResourceID: T100570; Canonical: Elphidium poeyanum; Node#95868889; ResourceID: T101163; Canonical: Bolivina subspinescens; Node#95867990; ResourceID: T100253; Canonical: Cibicides lobatulus; Node#95867876; ResourceID: T100139; Canonical: Gyroidinoides umbonatus; Node#95867868; ResourceID: T100131; Canonical: Cancris auriculus; Node#95871584; ResourceID: T103879; Canonical: Bigenerina nodosaria; Node#95867862; ResourceID: T100125
[START] [2021-06-09 11:07:37] update_nodes
[STOP] [2021-06-09 11:07:39] update_nodes
[STOP] [2021-06-09 11:07:39] match_nodes
[START] [2021-06-09 11:07:39] reindex_search
[STOP] [2021-06-09 11:07:43] reindex_search
[START] [2021-06-09 11:07:43] normalize_units
[STOP] [2021-06-09 11:07:43] normalize_units
[START] [2021-06-09 11:07:43] calculate_statistics
[STOP] [2021-06-09 11:07:43] calculate_statistics
[START] [2021-06-09 11:07:43] complete_harvest_instance
[START] [2021-06-09 11:07:43] overall_tsv_creation
[INFO] [2021-06-09 11:07:43] Processing group of 4442 in 1 batches of 10000
[INFO] [2021-06-09 11:08:31] 2173 Traits (unfiltered)...
[INFO] [2021-06-09 11:09:20] 2173 Traits (filtered)...
[INFO] [2021-06-09 11:09:22] 0 Associations (filtered)...
[INFO] [2021-06-09 11:09:23] 2173 metadata added.
[INFO] [2021-06-09 11:09:23] 0 metadata added.
[INFO] [2021-06-09 11:09:50] Average Time: 102.31
[INFO] [2021-06-09 11:09:50] Total Time: 2m8s
[STOP] [2021-06-09 11:09:50] overall_tsv_creation
[INFO] [2021-06-09 11:09:50] Done. Check your files:
[INFO] [2021-06-09 11:09:50] (4442 lines) /app/public/data/adriatic_sea_sp_/publish_nodes.tsv
[INFO] [2021-06-09 11:09:51] (21955 lines) /app/public/data/adriatic_sea_sp_/publish_node_ancestors.tsv
[INFO] [2021-06-09 11:09:51] (4442 lines) /app/public/data/adriatic_sea_sp_/publish_scientific_names.tsv
[INFO] [2021-06-09 11:09:51] (2174 lines) /app/public/data/adriatic_sea_sp_/publish_traits.tsv
[INFO] [2021-06-09 11:09:51] (2174 lines) /app/public/data/adriatic_sea_sp_/publish_metadata.tsv
[STOP] [2021-06-09 11:09:51] complete_harvest_instance
[START] [2021-06-09 11:09:51] completed
[STOP] [2021-06-09 11:09:51] completed
[STOP] [2021-06-09 11:09:51] logged process, took 408.75

Latest Process

09 Jun 11:03 EXITED currently processing 0