Harvest for GBIF nat'l node type records Netherlands Created 11 Jun 11:04

Harvesting Log

[INFO] [2021-06-11 11:04:44] Created harvest instance #4028
[STOP] [2021-06-11 11:04:44] create_harvest_instance
[START] [2021-06-11 11:04:44] fetch_files
[STOP] [2021-06-11 11:04:44] fetch_files
[START] [2021-06-11 11:04:44] validate_each_file
[INFO] [2021-06-11 11:04:44] Looping over 3 formats...
[INFO] [2021-06-11 11:04:44] ...nodes (/app/public/data/gnlntrn/taxon.tab)
[INFO] [2021-06-11 11:04:45] Valid: /app/public/converted_csv/gnlntrn_nodes_4028.csv (16475 lines)
[INFO] [2021-06-11 11:04:45] ...occurrences (/app/public/data/gnlntrn/occurrence.tab)
[INFO] [2021-06-11 11:04:46] Valid: /app/public/converted_csv/gnlntrn_occurrences_4028.csv (26631 lines)
[INFO] [2021-06-11 11:04:46] ...measurements (/app/public/data/gnlntrn/measurement_or_fact.tab)
[INFO] [2021-06-11 11:04:52] Valid: /app/public/converted_csv/gnlntrn_measurements_4028.csv (165872 lines)
[STOP] [2021-06-11 11:04:52] validate_each_file
[START] [2021-06-11 11:04:52] convert_to_csv
[INFO] [2021-06-11 11:04:52] Looping over 3 formats...
[INFO] [2021-06-11 11:04:52] ...nodes (/app/public/data/gnlntrn/taxon.tab)
[CMD] [2021-06-11 11:04:52] /usr/bin/sort /app/public/converted_csv/gnlntrn_nodes_4028.csv > /app/public/converted_csv/gnlntrn_nodes_4028.csv_sorted
[INFO] [2021-06-11 11:04:52] Converted: /app/public/converted_csv/gnlntrn_nodes_4028.csv (16475 lines)
[INFO] [2021-06-11 11:04:52] ...occurrences (/app/public/data/gnlntrn/occurrence.tab)
[CMD] [2021-06-11 11:04:52] /usr/bin/sort /app/public/converted_csv/gnlntrn_occurrences_4028.csv > /app/public/converted_csv/gnlntrn_occurrences_4028.csv_sorted
[INFO] [2021-06-11 11:04:52] Converted: /app/public/converted_csv/gnlntrn_occurrences_4028.csv (26631 lines)
[INFO] [2021-06-11 11:04:52] ...measurements (/app/public/data/gnlntrn/measurement_or_fact.tab)
[CMD] [2021-06-11 11:04:52] /usr/bin/sort /app/public/converted_csv/gnlntrn_measurements_4028.csv > /app/public/converted_csv/gnlntrn_measurements_4028.csv_sorted
[INFO] [2021-06-11 11:04:53] Converted: /app/public/converted_csv/gnlntrn_measurements_4028.csv (165872 lines)
[STOP] [2021-06-11 11:04:53] convert_to_csv
[START] [2021-06-11 11:04:53] calculate_delta
[INFO] [2021-06-11 11:04:53] Looping over 3 formats...
[INFO] [2021-06-11 11:04:53] ...nodes (/app/public/data/gnlntrn/taxon.tab)
[CMD] [2021-06-11 11:04:53] echo "0a" > /app/public/diff/gnlntrn_nodes_4028.diff
[CMD] [2021-06-11 11:04:53] tail -n +1 /app/public/converted_csv/gnlntrn_nodes_4028.csv >> /app/public/diff/gnlntrn_nodes_4028.diff
[CMD] [2021-06-11 11:04:53] echo "." >> /app/public/diff/gnlntrn_nodes_4028.diff
[INFO] [2021-06-11 11:04:53] Created diff: /app/public/diff/gnlntrn_nodes_4028.diff (16477 lines)
[INFO] [2021-06-11 11:04:53] ...occurrences (/app/public/data/gnlntrn/occurrence.tab)
[CMD] [2021-06-11 11:04:53] echo "0a" > /app/public/diff/gnlntrn_occurrences_4028.diff
[CMD] [2021-06-11 11:04:53] tail -n +1 /app/public/converted_csv/gnlntrn_occurrences_4028.csv >> /app/public/diff/gnlntrn_occurrences_4028.diff
[CMD] [2021-06-11 11:04:53] echo "." >> /app/public/diff/gnlntrn_occurrences_4028.diff
[INFO] [2021-06-11 11:04:53] Created diff: /app/public/diff/gnlntrn_occurrences_4028.diff (26633 lines)
[INFO] [2021-06-11 11:04:53] ...measurements (/app/public/data/gnlntrn/measurement_or_fact.tab)
[CMD] [2021-06-11 11:04:53] echo "0a" > /app/public/diff/gnlntrn_measurements_4028.diff
[CMD] [2021-06-11 11:04:53] tail -n +1 /app/public/converted_csv/gnlntrn_measurements_4028.csv >> /app/public/diff/gnlntrn_measurements_4028.diff
[CMD] [2021-06-11 11:04:53] echo "." >> /app/public/diff/gnlntrn_measurements_4028.diff
[INFO] [2021-06-11 11:04:53] Created diff: /app/public/diff/gnlntrn_measurements_4028.diff (165874 lines)
[STOP] [2021-06-11 11:04:53] calculate_delta
[START] [2021-06-11 11:04:53] parse_diff_and_store
[INFO] [2021-06-11 11:04:53] Handling diff: /app/public/diff/gnlntrn_nodes_4028.diff (16477 lines)
[INFO] [2021-06-11 11:04:53] Loading nodes diff file into memory (16477 /app/public/diff/gnlntrn_nodes_4028.diff lines)...
[WARN] [2021-06-11 11:04:55] Filtered Scientific Name `Charaxes castor Cramer, 1775/76` to `Charaxes castor Cramer, 177576`
[INFO] [2021-06-11 11:04:59] Handling diff: /app/public/diff/gnlntrn_occurrences_4028.diff (26633 lines)
[INFO] [2021-06-11 11:04:59] Loading occurrences diff file into memory (26633 /app/public/diff/gnlntrn_occurrences_4028.diff lines)...
[INFO] [2021-06-11 11:05:08] Handling diff: /app/public/diff/gnlntrn_measurements_4028.diff (165874 lines)
[INFO] [2021-06-11 11:05:08] Loading measurements diff file into memory (165874 /app/public/diff/gnlntrn_measurements_4028.diff lines)...
[INFO] [2021-06-11 11:05:49] Storing 22744 ScientificNames
[INFO] [2021-06-11 11:05:49] Processing group of 22744 in 23 groups of 1000
[INFO] [2021-06-11 11:05:59] Average Time: 0.399
[INFO] [2021-06-11 11:05:59] Total Time: 10s
[INFO] [2021-06-11 11:05:59] last 3 / first 3: 0.33
[INFO] [2021-06-11 11:05:59] Std.Dev: 0.22360679774997896; Max: 1.17
[INFO] [2021-06-11 11:05:59] Storing 22744 Nodes
[INFO] [2021-06-11 11:05:59] Processing group of 22744 in 23 groups of 1000
[INFO] [2021-06-11 11:06:08] Average Time: 0.41
[INFO] [2021-06-11 11:06:08] Total Time: 10s
[INFO] [2021-06-11 11:06:08] last 3 / first 3: 1.47
[INFO] [2021-06-11 11:06:08] Std.Dev: 0.17606816861659008; Max: 0.85
[INFO] [2021-06-11 11:06:08] Storing 26631 Occurrences
[INFO] [2021-06-11 11:06:08] Processing group of 26631 in 27 groups of 1000
[INFO] [2021-06-11 11:06:13] Average Time: 0.162
[INFO] [2021-06-11 11:06:13] Total Time: 5s
[INFO] [2021-06-11 11:06:13] last 3 / first 3: 0.86
[INFO] [2021-06-11 11:06:13] Std.Dev: 0.03162277660168379; Max: 0.3
[INFO] [2021-06-11 11:06:13] Storing 103605 OccurrenceMetadata
[INFO] [2021-06-11 11:06:13] Processing group of 103605 in 104 groups of 1000
[INFO] [2021-06-11 11:06:26] Average Time: 0.125
[INFO] [2021-06-11 11:06:26] Total Time: 14s
[INFO] [2021-06-11 11:06:26] last 3 / first 3: 0.84
[INFO] [2021-06-11 11:06:26] Std.Dev: 0.03162277660168379; Max: 0.24
[INFO] [2021-06-11 11:06:26] Storing 94366 Traits
[INFO] [2021-06-11 11:06:26] Processing group of 94366 in 95 groups of 1000
[INFO] [2021-06-11 11:07:01] Average Time: 0.367
[INFO] [2021-06-11 11:07:01] Total Time: 36s
[INFO] [2021-06-11 11:07:01] last 3 / first 3: 0.54
[INFO] [2021-06-11 11:07:01] Std.Dev: 0.13784048752090222; Max: 1.11
[INFO] [2021-06-11 11:07:01] Storing 5904 MetaTraits
[INFO] [2021-06-11 11:07:01] Processing group of 5904 in 6 groups of 1000
[INFO] [2021-06-11 11:07:02] Average Time: 0.133
[INFO] [2021-06-11 11:07:02] Total Time: 1s
[STOP] [2021-06-11 11:07:02] parse_diff_and_store
[START] [2021-06-11 11:07:02] resolve_keys
[INFO] [2021-06-11 11:07:22] Occurrences to nodes (through scientific_names)...
[INFO] [2021-06-11 11:07:32] traits to occurrences...
[INFO] [2021-06-11 11:07:34] traits to nodes (through occurrences)...
[INFO] [2021-06-11 11:07:35] Traits to sex term...
[INFO] [2021-06-11 11:07:36] Traits to lifestage term...
[INFO] [2021-06-11 11:07:36] MetaTraits to traits...
[INFO] [2021-06-11 11:07:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-06-11 11:07:42] Assocs to occurrences...
[INFO] [2021-06-11 11:07:42] Assocs to nodes...
[INFO] [2021-06-11 11:07:42] Assoc to sex term...
[INFO] [2021-06-11 11:07:42] Assoc to lifestage term...
[INFO] [2021-06-11 11:07:42] MetaAssoc to assocs...
[STOP] [2021-06-11 11:07:42] resolve_keys
[START] [2021-06-11 11:07:42] hold_for_later_1
[STOP] [2021-06-11 11:07:42] hold_for_later_1
[START] [2021-06-11 11:07:42] hold_for_later_2
[STOP] [2021-06-11 11:07:42] hold_for_later_2
[START] [2021-06-11 11:07:42] resolve_missing_parents
[STOP] [2021-06-11 11:07:42] resolve_missing_parents
[START] [2021-06-11 11:07:42] rebuild_nodes
[START] [2021-06-11 11:07:42] Flattener#flatten
[START] [2021-06-11 11:07:42] Flattener#study_resource
[START] [2021-06-11 11:07:42] Flattener#build_ancestry
[STOP] [2021-06-11 11:07:44] Flattener#build_ancestry
[INFO] [2021-06-11 11:07:44] 22744 ancestry keys
[START] [2021-06-11 11:07:44] build_node_ancestors
[INFO] [2021-06-11 11:07:44] old ancestors deleted.
[STOP] [2021-06-11 11:07:55] build_node_ancestors
[START] [2021-06-11 11:07:59] Flattener#propagate_ancestor_ids
[STOP] [2021-06-11 11:08:02] Flattener#propagate_ancestor_ids
[STOP] [2021-06-11 11:08:02] Flattener#flatten
[STOP] [2021-06-11 11:08:02] rebuild_nodes
[START] [2021-06-11 11:08:02] resolve_missing_media_owners
[STOP] [2021-06-11 11:08:02] resolve_missing_media_owners
[START] [2021-06-11 11:08:02] sanitize_media_verbatims
[STOP] [2021-06-11 11:08:02] sanitize_media_verbatims
[START] [2021-06-11 11:08:02] queue_downloads
[STOP] [2021-06-11 11:08:02] queue_downloads
[START] [2021-06-11 11:08:02] parse_names
[WARN] [2021-06-11 11:08:02] I see 22744 names which still need to be parsed.
[WARN] [2021-06-11 11:08:19] I see 57 names which still need to be parsed.
[WARN] [2021-06-11 11:08:20] I see 1 names which still need to be parsed.
[STOP] [2021-06-11 11:08:21] parse_names
[START] [2021-06-11 11:08:21] denormalize_canonical_names_to_nodes
[STOP] [2021-06-11 11:08:21] denormalize_canonical_names_to_nodes
[START] [2021-06-11 11:08:21] match_nodes
[START] [2021-06-11 11:08:21] map_all_nodes_to_pages
[STOP] [2021-06-11 11:17:42] map_all_nodes_to_pages
[INFO] [2021-06-11 11:17:42] 2224 Unmatched nodes (of 22744)! That's too many to output. Full list in /app/public/data/gnlntrn/unmatched_nodes.txt ; First 10: Canonical: Heterosporicola; Node#95984935; ResourceID: Heterosporicola; Canonical: Alternaria; Node#95975222; ResourceID: Alternaria; Canonical: Alternaria calendulae; Node#95975254; ResourceID: Alternaria_calendulae; Canonical: Alternaria; Node#95975223; ResourceID: Alternaria; Canonical: Phoma opuntiae; Node#95991057; ResourceID: Phoma_opuntiae; Canonical: Neoconiothyrium; Node#95980564; ResourceID: Neoconiothyrium; Canonical: Massaria conspurcata; Node#95987115; ResourceID: Massaria_conspurcata; Canonical: Massaria ulmi; Node#95987122; ResourceID: Massaria_ulmi; Canonical: Periconiaceae; Node#95989017; ResourceID: Periconiaceae; Canonical: Pseudopyrenochaetaceae; Node#95992547; ResourceID: Pseudopyrenochaetaceae
[START] [2021-06-11 11:17:42] update_nodes
[STOP] [2021-06-11 11:17:52] update_nodes
[STOP] [2021-06-11 11:17:52] match_nodes
[START] [2021-06-11 11:17:52] reindex_search
[STOP] [2021-06-11 11:18:13] reindex_search
[START] [2021-06-11 11:18:13] normalize_units
[STOP] [2021-06-11 11:18:14] normalize_units
[START] [2021-06-11 11:18:14] calculate_statistics
[STOP] [2021-06-11 11:18:15] calculate_statistics
[START] [2021-06-11 11:18:15] complete_harvest_instance
[START] [2021-06-11 11:18:15] overall_tsv_creation
[INFO] [2021-06-11 11:18:15] Processing group of 22744 in 3 batches of 10000
[INFO] [2021-06-11 11:20:56] 10917 Traits (unfiltered)...
[INFO] [2021-06-11 11:22:37] 10917 Traits (filtered)...
[INFO] [2021-06-11 11:22:41] 0 Associations (filtered)...
[INFO] [2021-06-11 11:22:47] 67847 metadata added.
[INFO] [2021-06-11 11:22:47] 0 metadata added.
[INFO] [2021-06-11 11:24:38] 11383 Traits (unfiltered)...
[INFO] [2021-06-11 11:26:26] 11383 Traits (filtered)...
[INFO] [2021-06-11 11:26:29] 0 Associations (filtered)...
[INFO] [2021-06-11 11:26:36] 72545 metadata added.
[INFO] [2021-06-11 11:26:36] 0 metadata added.
[INFO] [2021-06-11 11:27:52] 4331 Traits (unfiltered)...
[INFO] [2021-06-11 11:28:53] 4331 Traits (filtered)...
[INFO] [2021-06-11 11:28:53] 0 Associations (filtered)...
[INFO] [2021-06-11 11:28:56] 30839 metadata added.
[INFO] [2021-06-11 11:28:56] 0 metadata added.
[INFO] [2021-06-11 11:29:24] Average Time: 162.663
[INFO] [2021-06-11 11:29:24] Total Time: 11m10s
[STOP] [2021-06-11 11:29:24] overall_tsv_creation
[INFO] [2021-06-11 11:29:24] Done. Check your files:
[INFO] [2021-06-11 11:29:24] (22225 lines) /app/public/data/gnlntrn/publish_nodes.tsv
[INFO] [2021-06-11 11:29:25] (122508 lines) /app/public/data/gnlntrn/publish_node_ancestors.tsv
[INFO] [2021-06-11 11:29:25] (22744 lines) /app/public/data/gnlntrn/publish_scientific_names.tsv
[INFO] [2021-06-11 11:29:25] (26632 lines) /app/public/data/gnlntrn/publish_traits.tsv
[INFO] [2021-06-11 11:29:25] (171232 lines) /app/public/data/gnlntrn/publish_metadata.tsv
[STOP] [2021-06-11 11:29:25] complete_harvest_instance
[START] [2021-06-11 11:29:25] completed
[STOP] [2021-06-11 11:29:25] completed
[STOP] [2021-06-11 11:29:25] logged process, took 1480.63

Latest Process

11 Jun 11:04 EXITED currently processing 0