Harvest for Bahrain Species List Created 02 Jun 12:11

Harvesting Log

[INFO] [2021-06-02 12:11:58] Created harvest instance #3983
[STOP] [2021-06-02 12:11:58] create_harvest_instance
[START] [2021-06-02 12:11:58] fetch_files
[STOP] [2021-06-02 12:11:58] fetch_files
[START] [2021-06-02 12:11:58] validate_each_file
[INFO] [2021-06-02 12:11:58] Looping over 4 formats...
[INFO] [2021-06-02 12:11:58] ...refs (/app/public/data/bahrain_sp_list/reference.tab)
[INFO] [2021-06-02 12:11:58] Valid: /app/public/converted_csv/bahrain_sp_list_refs_3983.csv (87 lines)
[INFO] [2021-06-02 12:11:58] ...nodes (/app/public/data/bahrain_sp_list/taxon.tab)
[INFO] [2021-06-02 12:11:59] Valid: /app/public/converted_csv/bahrain_sp_list_nodes_3983.csv (1137 lines)
[INFO] [2021-06-02 12:11:59] ...occurrences (/app/public/data/bahrain_sp_list/occurrence_specific.tab)
[INFO] [2021-06-02 12:11:59] Valid: /app/public/converted_csv/bahrain_sp_list_occurrences_3983.csv (1137 lines)
[INFO] [2021-06-02 12:11:59] ...measurements (/app/public/data/bahrain_sp_list/measurement_or_fact_specific.tab)
[INFO] [2021-06-02 12:11:59] Valid: /app/public/converted_csv/bahrain_sp_list_measurements_3983.csv (3676 lines)
[STOP] [2021-06-02 12:11:59] validate_each_file
[START] [2021-06-02 12:11:59] convert_to_csv
[INFO] [2021-06-02 12:11:59] Looping over 4 formats...
[INFO] [2021-06-02 12:11:59] ...refs (/app/public/data/bahrain_sp_list/reference.tab)
[CMD] [2021-06-02 12:11:59] /usr/bin/sort /app/public/converted_csv/bahrain_sp_list_refs_3983.csv > /app/public/converted_csv/bahrain_sp_list_refs_3983.csv_sorted
[INFO] [2021-06-02 12:12:00] Converted: /app/public/converted_csv/bahrain_sp_list_refs_3983.csv (87 lines)
[INFO] [2021-06-02 12:12:00] ...nodes (/app/public/data/bahrain_sp_list/taxon.tab)
[CMD] [2021-06-02 12:12:00] /usr/bin/sort /app/public/converted_csv/bahrain_sp_list_nodes_3983.csv > /app/public/converted_csv/bahrain_sp_list_nodes_3983.csv_sorted
[INFO] [2021-06-02 12:12:01] Converted: /app/public/converted_csv/bahrain_sp_list_nodes_3983.csv (1137 lines)
[INFO] [2021-06-02 12:12:01] ...occurrences (/app/public/data/bahrain_sp_list/occurrence_specific.tab)
[CMD] [2021-06-02 12:12:01] /usr/bin/sort /app/public/converted_csv/bahrain_sp_list_occurrences_3983.csv > /app/public/converted_csv/bahrain_sp_list_occurrences_3983.csv_sorted
[INFO] [2021-06-02 12:12:02] Converted: /app/public/converted_csv/bahrain_sp_list_occurrences_3983.csv (1137 lines)
[INFO] [2021-06-02 12:12:02] ...measurements (/app/public/data/bahrain_sp_list/measurement_or_fact_specific.tab)
[CMD] [2021-06-02 12:12:02] /usr/bin/sort /app/public/converted_csv/bahrain_sp_list_measurements_3983.csv > /app/public/converted_csv/bahrain_sp_list_measurements_3983.csv_sorted
[INFO] [2021-06-02 12:12:03] Converted: /app/public/converted_csv/bahrain_sp_list_measurements_3983.csv (3676 lines)
[STOP] [2021-06-02 12:12:03] convert_to_csv
[START] [2021-06-02 12:12:03] calculate_delta
[INFO] [2021-06-02 12:12:03] Looping over 4 formats...
[INFO] [2021-06-02 12:12:03] ...refs (/app/public/data/bahrain_sp_list/reference.tab)
[CMD] [2021-06-02 12:12:03] echo "0a" > /app/public/diff/bahrain_sp_list_refs_3983.diff
[CMD] [2021-06-02 12:12:04] tail -n +1 /app/public/converted_csv/bahrain_sp_list_refs_3983.csv >> /app/public/diff/bahrain_sp_list_refs_3983.diff
[CMD] [2021-06-02 12:12:06] echo "." >> /app/public/diff/bahrain_sp_list_refs_3983.diff
[INFO] [2021-06-02 12:12:07] Created diff: /app/public/diff/bahrain_sp_list_refs_3983.diff (89 lines)
[INFO] [2021-06-02 12:12:07] ...nodes (/app/public/data/bahrain_sp_list/taxon.tab)
[CMD] [2021-06-02 12:12:07] echo "0a" > /app/public/diff/bahrain_sp_list_nodes_3983.diff
[CMD] [2021-06-02 12:12:08] tail -n +1 /app/public/converted_csv/bahrain_sp_list_nodes_3983.csv >> /app/public/diff/bahrain_sp_list_nodes_3983.diff
[CMD] [2021-06-02 12:12:09] echo "." >> /app/public/diff/bahrain_sp_list_nodes_3983.diff
[INFO] [2021-06-02 12:12:10] Created diff: /app/public/diff/bahrain_sp_list_nodes_3983.diff (1139 lines)
[INFO] [2021-06-02 12:12:10] ...occurrences (/app/public/data/bahrain_sp_list/occurrence_specific.tab)
[CMD] [2021-06-02 12:12:10] echo "0a" > /app/public/diff/bahrain_sp_list_occurrences_3983.diff
[CMD] [2021-06-02 12:12:11] tail -n +1 /app/public/converted_csv/bahrain_sp_list_occurrences_3983.csv >> /app/public/diff/bahrain_sp_list_occurrences_3983.diff
[CMD] [2021-06-02 12:12:12] echo "." >> /app/public/diff/bahrain_sp_list_occurrences_3983.diff
[INFO] [2021-06-02 12:12:13] Created diff: /app/public/diff/bahrain_sp_list_occurrences_3983.diff (1139 lines)
[INFO] [2021-06-02 12:12:13] ...measurements (/app/public/data/bahrain_sp_list/measurement_or_fact_specific.tab)
[CMD] [2021-06-02 12:12:13] echo "0a" > /app/public/diff/bahrain_sp_list_measurements_3983.diff
[CMD] [2021-06-02 12:12:14] tail -n +1 /app/public/converted_csv/bahrain_sp_list_measurements_3983.csv >> /app/public/diff/bahrain_sp_list_measurements_3983.diff
[CMD] [2021-06-02 12:12:15] echo "." >> /app/public/diff/bahrain_sp_list_measurements_3983.diff
[INFO] [2021-06-02 12:12:16] Created diff: /app/public/diff/bahrain_sp_list_measurements_3983.diff (3678 lines)
[STOP] [2021-06-02 12:12:16] calculate_delta
[START] [2021-06-02 12:12:16] parse_diff_and_store
[INFO] [2021-06-02 12:12:16] Handling diff: /app/public/diff/bahrain_sp_list_refs_3983.diff (89 lines)
[INFO] [2021-06-02 12:12:17] Loading refs diff file into memory (89 /app/public/diff/bahrain_sp_list_refs_3983.diff lines)...
[INFO] [2021-06-02 12:12:18] Handling diff: /app/public/diff/bahrain_sp_list_nodes_3983.diff (1139 lines)
[INFO] [2021-06-02 12:12:20] Loading nodes diff file into memory (1139 /app/public/diff/bahrain_sp_list_nodes_3983.diff lines)...
[INFO] [2021-06-02 12:12:21] Handling diff: /app/public/diff/bahrain_sp_list_occurrences_3983.diff (1139 lines)
[INFO] [2021-06-02 12:12:22] Loading occurrences diff file into memory (1139 /app/public/diff/bahrain_sp_list_occurrences_3983.diff lines)...
[INFO] [2021-06-02 12:12:23] Handling diff: /app/public/diff/bahrain_sp_list_measurements_3983.diff (3678 lines)
[INFO] [2021-06-02 12:12:24] Loading measurements diff file into memory (3678 /app/public/diff/bahrain_sp_list_measurements_3983.diff lines)...
[INFO] [2021-06-02 12:12:27] Storing 87 References
[INFO] [2021-06-02 12:12:27] Processing group of 87 in 1 groups of 1000
[INFO] [2021-06-02 12:12:27] Average Time: 0.03
[INFO] [2021-06-02 12:12:27] Total Time: 1s
[INFO] [2021-06-02 12:12:27] Storing 2409 ScientificNames
[INFO] [2021-06-02 12:12:27] Processing group of 2409 in 3 groups of 1000
[INFO] [2021-06-02 12:12:27] Average Time: 0.23
[INFO] [2021-06-02 12:12:27] Total Time: 1s
[INFO] [2021-06-02 12:12:27] Storing 2409 Nodes
[INFO] [2021-06-02 12:12:27] Processing group of 2409 in 3 groups of 1000
[INFO] [2021-06-02 12:12:28] Average Time: 0.21
[INFO] [2021-06-02 12:12:28] Total Time: 1s
[INFO] [2021-06-02 12:12:28] Storing 1137 Occurrences
[INFO] [2021-06-02 12:12:28] Processing group of 1137 in 2 groups of 1000
[INFO] [2021-06-02 12:12:28] Average Time: 0.07
[INFO] [2021-06-02 12:12:28] Total Time: 1s
[INFO] [2021-06-02 12:12:28] Storing 3676 Traits
[INFO] [2021-06-02 12:12:28] Processing group of 3676 in 4 groups of 1000
[INFO] [2021-06-02 12:12:30] Average Time: 0.303
[INFO] [2021-06-02 12:12:30] Total Time: 2s
[INFO] [2021-06-02 12:12:30] Storing 1402 TraitsReferences
[INFO] [2021-06-02 12:12:30] Processing group of 1402 in 2 groups of 1000
[INFO] [2021-06-02 12:12:30] Average Time: 0.05
[INFO] [2021-06-02 12:12:30] Total Time: 1s
[INFO] [2021-06-02 12:12:30] Storing 1137 MetaTraits
[INFO] [2021-06-02 12:12:30] Processing group of 1137 in 2 groups of 1000
[INFO] [2021-06-02 12:12:30] Average Time: 0.07
[INFO] [2021-06-02 12:12:30] Total Time: 1s
[STOP] [2021-06-02 12:12:30] parse_diff_and_store
[START] [2021-06-02 12:12:30] resolve_keys
[INFO] [2021-06-02 12:12:39] Occurrences to nodes (through scientific_names)...
[INFO] [2021-06-02 12:12:40] traits to occurrences...
[INFO] [2021-06-02 12:12:40] traits to nodes (through occurrences)...
[INFO] [2021-06-02 12:12:40] Traits to sex term...
[INFO] [2021-06-02 12:12:40] Traits to lifestage term...
[INFO] [2021-06-02 12:12:40] MetaTraits to traits...
[INFO] [2021-06-02 12:12:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-06-02 12:12:41] Assocs to occurrences...
[INFO] [2021-06-02 12:12:41] Assocs to nodes...
[INFO] [2021-06-02 12:12:41] Assoc to sex term...
[INFO] [2021-06-02 12:12:41] Assoc to lifestage term...
[INFO] [2021-06-02 12:12:41] MetaAssoc to assocs...
[STOP] [2021-06-02 12:12:41] resolve_keys
[START] [2021-06-02 12:12:41] hold_for_later_1
[STOP] [2021-06-02 12:12:41] hold_for_later_1
[START] [2021-06-02 12:12:41] hold_for_later_2
[STOP] [2021-06-02 12:12:41] hold_for_later_2
[START] [2021-06-02 12:12:41] resolve_missing_parents
[STOP] [2021-06-02 12:12:41] resolve_missing_parents
[START] [2021-06-02 12:12:41] rebuild_nodes
[START] [2021-06-02 12:12:41] Flattener#flatten
[START] [2021-06-02 12:12:41] Flattener#study_resource
[START] [2021-06-02 12:12:41] Flattener#build_ancestry
[STOP] [2021-06-02 12:12:41] Flattener#build_ancestry
[INFO] [2021-06-02 12:12:41] 2409 ancestry keys
[START] [2021-06-02 12:12:41] build_node_ancestors
[INFO] [2021-06-02 12:12:41] old ancestors deleted.
[STOP] [2021-06-02 12:12:41] build_node_ancestors
[START] [2021-06-02 12:12:42] Flattener#propagate_ancestor_ids
[STOP] [2021-06-02 12:12:42] Flattener#propagate_ancestor_ids
[STOP] [2021-06-02 12:12:42] Flattener#flatten
[STOP] [2021-06-02 12:12:42] rebuild_nodes
[START] [2021-06-02 12:12:42] resolve_missing_media_owners
[STOP] [2021-06-02 12:12:42] resolve_missing_media_owners
[START] [2021-06-02 12:12:42] sanitize_media_verbatims
[STOP] [2021-06-02 12:12:42] sanitize_media_verbatims
[START] [2021-06-02 12:12:42] queue_downloads
[STOP] [2021-06-02 12:12:42] queue_downloads
[START] [2021-06-02 12:12:42] parse_names
[WARN] [2021-06-02 12:12:42] I see 2409 names which still need to be parsed.
[WARN] [2021-06-02 12:12:45] I see 16 names which still need to be parsed.
[STOP] [2021-06-02 12:12:46] parse_names
[START] [2021-06-02 12:12:46] denormalize_canonical_names_to_nodes
[STOP] [2021-06-02 12:12:46] denormalize_canonical_names_to_nodes
[START] [2021-06-02 12:12:46] match_nodes
[START] [2021-06-02 12:12:46] map_all_nodes_to_pages
[STOP] [2021-06-02 12:14:41] map_all_nodes_to_pages
[INFO] [2021-06-02 12:14:41] 146 Unmatched nodes (of 2409)! That's too many to output. Full list in /app/public/data/bahrain_sp_list/unmatched_nodes.txt ; First 10: Canonical: Biflustra; Node#95610416; ResourceID: 1007713; Canonical: Stylopoma; Node#95610420; ResourceID: 1010088; Canonical: Amathia; Node#95610423; ResourceID: 1010211; Canonical: Porites; Node#95611898; ResourceID: 3250147; Canonical: Acropora; Node#95612637; ResourceID: 7673664; Canonical: BOLD:AAW9878; Node#95610434; ResourceID: 10355799; Canonical: Chroicocephalus genei; Node#95612480; ResourceID: 6065810; Canonical: Xenus cinereus; Node#95611365; ResourceID: 2481703; Canonical: Lymnocryptes minimus; Node#95611389; ResourceID: 2481835; Canonical: Circus macrourus; Node#95611306; ResourceID: 2480491
[START] [2021-06-02 12:14:41] update_nodes
[STOP] [2021-06-02 12:14:42] update_nodes
[STOP] [2021-06-02 12:14:42] match_nodes
[START] [2021-06-02 12:14:42] reindex_search
[STOP] [2021-06-02 12:14:44] reindex_search
[START] [2021-06-02 12:14:44] normalize_units
[STOP] [2021-06-02 12:14:44] normalize_units
[START] [2021-06-02 12:14:44] calculate_statistics
[STOP] [2021-06-02 12:14:44] calculate_statistics
[START] [2021-06-02 12:14:44] complete_harvest_instance
[START] [2021-06-02 12:14:44] overall_tsv_creation
[INFO] [2021-06-02 12:14:44] Processing group of 2409 in 1 batches of 10000
[INFO] [2021-06-02 12:15:28] 1137 Traits (unfiltered)...
[INFO] [2021-06-02 12:16:07] 1137 Traits (filtered)...
[INFO] [2021-06-02 12:16:07] 0 Associations (filtered)...
[INFO] [2021-06-02 12:16:07] 2804 metadata added.
[INFO] [2021-06-02 12:16:07] 0 metadata added.
[INFO] [2021-06-02 12:16:33] Average Time: 82.19
[INFO] [2021-06-02 12:16:33] Total Time: 1m50s
[STOP] [2021-06-02 12:16:33] overall_tsv_creation
[INFO] [2021-06-02 12:16:33] Done. Check your files:
[INFO] [2021-06-02 12:16:34] (2409 lines) /app/public/data/bahrain_sp_list/publish_nodes.tsv
[INFO] [2021-06-02 12:16:35] (11961 lines) /app/public/data/bahrain_sp_list/publish_node_ancestors.tsv
[INFO] [2021-06-02 12:16:36] (2409 lines) /app/public/data/bahrain_sp_list/publish_scientific_names.tsv
[INFO] [2021-06-02 12:16:37] (1138 lines) /app/public/data/bahrain_sp_list/publish_traits.tsv
[INFO] [2021-06-02 12:16:38] (2805 lines) /app/public/data/bahrain_sp_list/publish_metadata.tsv
[STOP] [2021-06-02 12:16:39] complete_harvest_instance
[START] [2021-06-02 12:16:39] completed
[STOP] [2021-06-02 12:16:39] completed
[STOP] [2021-06-02 12:16:39] logged process, took 281.29

Latest Process

02 Jun 12:11 EXITED currently processing 0