Harvest for AnAge Created 31 Jan 07:56

Stage: completed
Fetched: 31 Jan 07:56
Validated: 31 Jan 07:56
Deltas Created 31 Jan 07:56
Units Normalized: 31 Jan 08:04
Ancestry Built: 31 Jan 07:58
Nodes Matched: 31 Jan 08:02
Names Parsed: 31 Jan 07:58
New Models Stored: 31 Jan 07:57
Indexed: 31 Jan 08:02
Completed: 31 Jan 08:05
Time to Harvest: less than a minute

Harvesting Log

(175 lines)
[INFO] [2023-01-31 07:56:51] Created harvest instance #4283
[STOP] [2023-01-31 07:56:51] create_harvest_instance
[START] [2023-01-31 07:56:51] fetch_files
[STOP] [2023-01-31 07:56:51] fetch_files
[START] [2023-01-31 07:56:51] validate_each_file
[INFO] [2023-01-31 07:56:51] Created new folder: /app/public/converted_csv
[INFO] [2023-01-31 07:56:51] Looping over 4 formats...
[INFO] [2023-01-31 07:56:51] ...nodes (/app/public/data/AnAge/taxon.tab)
[INFO] [2023-01-31 07:56:52] Valid: /app/public/data/AnAge/converted_csv/AnAge_nodes_30138.csv (4205 lines)
[INFO] [2023-01-31 07:56:52] ...vernaculars (/app/public/data/AnAge/vernacular_name.tab)
[INFO] [2023-01-31 07:56:52] Valid: /app/public/data/AnAge/converted_csv/AnAge_vernaculars_30139.csv (4205 lines)
[INFO] [2023-01-31 07:56:52] ...occurrences (/app/public/data/AnAge/occurrence.tab)
[INFO] [2023-01-31 07:56:53] Valid: /app/public/data/AnAge/converted_csv/AnAge_occurrences_30140.csv (29435 lines)
[INFO] [2023-01-31 07:56:53] ...measurements (/app/public/data/AnAge/measurement_or_fact.txt)
[INFO] [2023-01-31 07:56:55] Valid: /app/public/data/AnAge/converted_csv/AnAge_measurements_30141.csv (25332 lines)
[STOP] [2023-01-31 07:56:55] validate_each_file
[START] [2023-01-31 07:56:55] convert_to_csv
[INFO] [2023-01-31 07:56:55] Looping over 4 formats...
[INFO] [2023-01-31 07:56:55] ...nodes (/app/public/data/AnAge/taxon.tab)
[CMD] [2023-01-31 07:56:55] /usr/bin/sort /app/public/data/AnAge/converted_csv/AnAge_nodes_30138.csv > /app/public/data/AnAge/converted_csv/AnAge_nodes_30138.csv_sorted
[INFO] [2023-01-31 07:56:55] Converted: /app/public/data/AnAge/converted_csv/AnAge_nodes_30138.csv (4205 lines)
[INFO] [2023-01-31 07:56:55] ...vernaculars (/app/public/data/AnAge/vernacular_name.tab)
[CMD] [2023-01-31 07:56:55] /usr/bin/sort /app/public/data/AnAge/converted_csv/AnAge_vernaculars_30139.csv > /app/public/data/AnAge/converted_csv/AnAge_vernaculars_30139.csv_sorted
[INFO] [2023-01-31 07:56:55] Converted: /app/public/data/AnAge/converted_csv/AnAge_vernaculars_30139.csv (4205 lines)
[INFO] [2023-01-31 07:56:55] ...occurrences (/app/public/data/AnAge/occurrence.tab)
[CMD] [2023-01-31 07:56:55] /usr/bin/sort /app/public/data/AnAge/converted_csv/AnAge_occurrences_30140.csv > /app/public/data/AnAge/converted_csv/AnAge_occurrences_30140.csv_sorted
[INFO] [2023-01-31 07:56:55] Converted: /app/public/data/AnAge/converted_csv/AnAge_occurrences_30140.csv (29435 lines)
[INFO] [2023-01-31 07:56:55] ...measurements (/app/public/data/AnAge/measurement_or_fact.txt)
[CMD] [2023-01-31 07:56:55] /usr/bin/sort /app/public/data/AnAge/converted_csv/AnAge_measurements_30141.csv > /app/public/data/AnAge/converted_csv/AnAge_measurements_30141.csv_sorted
[INFO] [2023-01-31 07:56:55] Converted: /app/public/data/AnAge/converted_csv/AnAge_measurements_30141.csv (25332 lines)
[STOP] [2023-01-31 07:56:55] convert_to_csv
[START] [2023-01-31 07:56:55] calculate_delta
[INFO] [2023-01-31 07:56:55] Created diff dir: /app/public/diff
[INFO] [2023-01-31 07:56:55] Looping over 4 formats...
[INFO] [2023-01-31 07:56:55] ...nodes (/app/public/data/AnAge/taxon.tab)
[CMD] [2023-01-31 07:56:55] echo "0a" > /app/public/data/AnAge/diff/AnAge_nodes_30138.diff
[CMD] [2023-01-31 07:56:55] tail -n +1 /app/public/data/AnAge/converted_csv/AnAge_nodes_30138.csv >> /app/public/data/AnAge/diff/AnAge_nodes_30138.diff
[CMD] [2023-01-31 07:56:55] echo "." >> /app/public/data/AnAge/diff/AnAge_nodes_30138.diff
[INFO] [2023-01-31 07:56:55] Created diff: /app/public/data/AnAge/diff/AnAge_nodes_30138.diff (4207 lines)
[INFO] [2023-01-31 07:56:55] ...vernaculars (/app/public/data/AnAge/vernacular_name.tab)
[CMD] [2023-01-31 07:56:55] echo "0a" > /app/public/data/AnAge/diff/AnAge_vernaculars_30139.diff
[CMD] [2023-01-31 07:56:55] tail -n +1 /app/public/data/AnAge/converted_csv/AnAge_vernaculars_30139.csv >> /app/public/data/AnAge/diff/AnAge_vernaculars_30139.diff
[CMD] [2023-01-31 07:56:55] echo "." >> /app/public/data/AnAge/diff/AnAge_vernaculars_30139.diff
[INFO] [2023-01-31 07:56:55] Created diff: /app/public/data/AnAge/diff/AnAge_vernaculars_30139.diff (4207 lines)
[INFO] [2023-01-31 07:56:55] ...occurrences (/app/public/data/AnAge/occurrence.tab)
[CMD] [2023-01-31 07:56:55] echo "0a" > /app/public/data/AnAge/diff/AnAge_occurrences_30140.diff
[CMD] [2023-01-31 07:56:55] tail -n +1 /app/public/data/AnAge/converted_csv/AnAge_occurrences_30140.csv >> /app/public/data/AnAge/diff/AnAge_occurrences_30140.diff
[CMD] [2023-01-31 07:56:55] echo "." >> /app/public/data/AnAge/diff/AnAge_occurrences_30140.diff
[INFO] [2023-01-31 07:56:55] Created diff: /app/public/data/AnAge/diff/AnAge_occurrences_30140.diff (29437 lines)
[INFO] [2023-01-31 07:56:55] ...measurements (/app/public/data/AnAge/measurement_or_fact.txt)
[CMD] [2023-01-31 07:56:55] echo "0a" > /app/public/data/AnAge/diff/AnAge_measurements_30141.diff
[CMD] [2023-01-31 07:56:56] tail -n +1 /app/public/data/AnAge/converted_csv/AnAge_measurements_30141.csv >> /app/public/data/AnAge/diff/AnAge_measurements_30141.diff
[CMD] [2023-01-31 07:56:56] echo "." >> /app/public/data/AnAge/diff/AnAge_measurements_30141.diff
[INFO] [2023-01-31 07:56:56] Created diff: /app/public/data/AnAge/diff/AnAge_measurements_30141.diff (25334 lines)
[STOP] [2023-01-31 07:56:56] calculate_delta
[START] [2023-01-31 07:56:56] parse_diff_and_store
[INFO] [2023-01-31 07:56:56] Handling diff: /app/public/data/AnAge/diff/AnAge_nodes_30138.diff (4207 lines)
[INFO] [2023-01-31 07:56:56] Loading nodes diff file into memory (4207 lines)...
[INFO] [2023-01-31 07:56:57] Storing 4873 ScientificNames (9746/4205/4207)
[INFO] [2023-01-31 07:56:59] Storing 4873 Nodes (9746/4205/4207)
[INFO] [2023-01-31 07:57:02] Handling diff: /app/public/data/AnAge/diff/AnAge_vernaculars_30139.diff (4207 lines)
[INFO] [2023-01-31 07:57:02] Loading vernaculars diff file into memory (4207 lines)...
[INFO] [2023-01-31 07:57:03] Storing 4205 Vernaculars (4205/4205/4207)
[INFO] [2023-01-31 07:57:04] Handling diff: /app/public/data/AnAge/diff/AnAge_occurrences_30140.diff (29437 lines)
[INFO] [2023-01-31 07:57:04] Loading occurrences diff file into memory (29437 lines)...
[INFO] [2023-01-31 07:57:07] Storing 9999 Occurrences (18580/10000/29437)
[INFO] [2023-01-31 07:57:09] Storing 8581 OccurrenceMetadata (18580/10000/29437)
[WARN] [2023-01-31 07:57:12] SKIPPED 8590 Occurrence metadata (37170/20000/29437) with resource_pks already be in the database!
[INFO] [2023-01-31 07:57:12] Storing 10000 Occurrences (37170/20000/29437)
[INFO] [2023-01-31 07:57:13] Storing 0 OccurrenceMetadata (37170/20000/29437)
[WARN] [2023-01-31 07:57:13] No models to import, skipping!
[WARN] [2023-01-31 07:57:15] SKIPPED 8059 Occurrence metadata (54665/29435/29437) with resource_pks already be in the database!
[INFO] [2023-01-31 07:57:15] Storing 9436 Occurrences (54665/29435/29437)
[INFO] [2023-01-31 07:57:17] Storing 0 OccurrenceMetadata (54665/29435/29437)
[WARN] [2023-01-31 07:57:17] No models to import, skipping!
[INFO] [2023-01-31 07:57:17] Handling diff: /app/public/data/AnAge/diff/AnAge_measurements_30141.diff (25334 lines)
[INFO] [2023-01-31 07:57:17] Loading measurements diff file into memory (25334 lines)...
[INFO] [2023-01-31 07:57:21] Storing 8486 Traits (20844/10000/25334)
[INFO] [2023-01-31 07:57:24] Storing 10845 MetaTraits (20844/10000/25334)
[INFO] [2023-01-31 07:57:25] Storing 1513 OccurrenceMetadata (20844/10000/25334)
[INFO] [2023-01-31 07:57:29] Storing 8155 Traits (41108/20000/25334)
[INFO] [2023-01-31 07:57:32] Storing 10264 MetaTraits (41108/20000/25334)
[INFO] [2023-01-31 07:57:33] Storing 1845 OccurrenceMetadata (41108/20000/25334)
[INFO] [2023-01-31 07:57:35] Storing 4486 Traits (52247/25332/25334)
[INFO] [2023-01-31 07:57:37] Storing 5806 MetaTraits (52247/25332/25334)
[INFO] [2023-01-31 07:57:37] Storing 847 OccurrenceMetadata (52247/25332/25334)
[STOP] [2023-01-31 07:57:37] parse_diff_and_store
[START] [2023-01-31 07:57:37] resolve_keys
[2023-01-31 07:57:40] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-31 07:57:47] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-31 07:57:48] traits to occurrences...
[INFO] [2023-01-31 07:57:49] traits to nodes (through occurrences)...
[INFO] [2023-01-31 07:57:55] Traits to sex term...
[INFO] [2023-01-31 07:57:57] Traits to lifestage term...
[INFO] [2023-01-31 07:57:58] MetaTraits to traits...
[INFO] [2023-01-31 07:58:00] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-31 07:58:00] Assocs to occurrences...
[INFO] [2023-01-31 07:58:00] Assocs to nodes...
[INFO] [2023-01-31 07:58:00] Assoc to sex term...
[INFO] [2023-01-31 07:58:00] Assoc to lifestage term...
[INFO] [2023-01-31 07:58:00] MetaAssoc to assocs...
[STOP] [2023-01-31 07:58:00] resolve_keys
[START] [2023-01-31 07:58:00] hold_for_later_1
[STOP] [2023-01-31 07:58:00] hold_for_later_1
[START] [2023-01-31 07:58:00] hold_for_later_2
[STOP] [2023-01-31 07:58:00] hold_for_later_2
[START] [2023-01-31 07:58:00] resolve_missing_parents
[STOP] [2023-01-31 07:58:01] resolve_missing_parents
[START] [2023-01-31 07:58:01] rebuild_nodes
[START] [2023-01-31 07:58:01] Flattener#flatten
[START] [2023-01-31 07:58:01] Flattener#study_resource
[START] [2023-01-31 07:58:01] Flattener#build_ancestry
[STOP] [2023-01-31 07:58:01] Flattener#build_ancestry
[INFO] [2023-01-31 07:58:01] 4873 ancestry keys
[START] [2023-01-31 07:58:01] build_node_ancestors
[INFO] [2023-01-31 07:58:01] old ancestors deleted.
[STOP] [2023-01-31 07:58:02] build_node_ancestors
[START] [2023-01-31 07:58:03] Flattener#propagate_ancestor_ids
[STOP] [2023-01-31 07:58:04] Flattener#propagate_ancestor_ids
[STOP] [2023-01-31 07:58:04] Flattener#flatten
[STOP] [2023-01-31 07:58:04] rebuild_nodes
[START] [2023-01-31 07:58:04] resolve_missing_media_owners
[STOP] [2023-01-31 07:58:04] resolve_missing_media_owners
[START] [2023-01-31 07:58:04] sanitize_media_verbatims
[STOP] [2023-01-31 07:58:04] sanitize_media_verbatims
[START] [2023-01-31 07:58:04] queue_downloads
[STOP] [2023-01-31 07:58:04] queue_downloads
[START] [2023-01-31 07:58:04] parse_names
[WARN] [2023-01-31 07:58:04] I see 4873 names which still need to be parsed.
[WARN] [2023-01-31 07:58:04] Names to parse: 4873 formatted: 4873 learned: 4873 parsed: 4873
[STOP] [2023-01-31 07:58:08] parse_names
[START] [2023-01-31 07:58:08] denormalize_canonical_names_to_nodes
[STOP] [2023-01-31 07:58:08] denormalize_canonical_names_to_nodes
[START] [2023-01-31 07:58:08] match_nodes
[START] [2023-01-31 07:58:08] map_all_nodes_to_pages
[STOP] [2023-01-31 08:02:50] map_all_nodes_to_pages
[INFO] [2023-01-31 08:02:50] 156 Unmatched nodes (of 4873)! That's too many to output. Full list in /app/public/data/AnAge/unmatched_nodes.txt ; First 10: Canonical: Sylvia melanocephala; Node#122865223; ResourceID: 006f03d4f12fe7138012e84cf0506e7a; Canonical: Sylvia curruca; Node#122865274; ResourceID: 01adbabd3d0820730acff7da383c1dfa; Canonical: Sylvia communis; Node#122867289; ResourceID: 62dedd6f58dc884ca9a33ec18bf2e72f; Canonical: Sylvia nisoria; Node#122868457; ResourceID: a55be95b1c129656e84bef61ede5995b; Canonical: Turdoides striatus; Node#122868710; ResourceID: b4e25e1802626a002ca462f962e5cc72; Canonical: Dendroica palmarum; Node#122865231; ResourceID: 008c5a8c6447630fd46760c7d2d95cee; Canonical: Dendroica kirtlandii; Node#122865273; ResourceID: 019a410be9ceb33e35136b20a70984ec; Canonical: Dendroica coronata; Node#122865559; ResourceID: 0d1b2e5a1814d8a07ac347efad73334f; Canonical: Parula americana; Node#122866418; ResourceID: 36ee8918cf887ac4c2e4fc65e805140b; Canonical: Dendroica occidentalis; Node#122866565; ResourceID: 3f0e27d98994bc55c99e13ead7aad574
[START] [2023-01-31 08:02:50] update_nodes
[STOP] [2023-01-31 08:02:52] update_nodes
[STOP] [2023-01-31 08:02:52] match_nodes
[START] [2023-01-31 08:02:52] reindex_search
[STOP] [2023-01-31 08:02:58] reindex_search
[START] [2023-01-31 08:02:58] normalize_units
[STOP] [2023-01-31 08:04:03] normalize_units
[START] [2023-01-31 08:04:03] calculate_statistics
[INFO] [2023-01-31 08:04:23] Duplicate page_id count: 0
[STOP] [2023-01-31 08:04:23] calculate_statistics
[START] [2023-01-31 08:04:23] complete_harvest_instance
[START] [2023-01-31 08:04:23] overall_tsv_creation
[INFO] [2023-01-31 08:04:23] Exporting 4873 nodes as TSV in batches of 10000...
[INFO] [2023-01-31 08:04:23] Processing group of 4873 in 1 batches of 10000
[INFO] [2023-01-31 08:04:33] 21127 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-31 08:04:33] Building Traits map for 4873 nodes (this can take a while)...
[INFO] [2023-01-31 08:04:43] Mapped 21127 traits (26915 meta) for 4873 nodes.
[INFO] [2023-01-31 08:04:43] Building Associations map (this can take a while)...
[INFO] [2023-01-31 08:04:51] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-31 08:04:51] Adding 21127 traits...
[INFO] [2023-01-31 08:04:54] 5055 metadata added.
[INFO] [2023-01-31 08:04:54] Adding 0 assocs...
[INFO] [2023-01-31 08:04:54] 0 metadata added.
[INFO] [2023-01-31 08:05:42] Processed 4873/4873 nodes
[INFO] [2023-01-31 08:05:42] Average Time: 76.01
[INFO] [2023-01-31 08:05:42] Total Time: 1m19s
[STOP] [2023-01-31 08:05:42] overall_tsv_creation
[INFO] [2023-01-31 08:05:42] Done. Check your files:
[INFO] [2023-01-31 08:05:42] (4873 lines) /app/public/data/AnAge/publish_nodes.tsv
[INFO] [2023-01-31 08:05:42] (23488 lines) /app/public/data/AnAge/publish_node_ancestors.tsv
[INFO] [2023-01-31 08:05:42] (4873 lines) /app/public/data/AnAge/publish_scientific_names.tsv
[INFO] [2023-01-31 08:05:42] (4205 lines) /app/public/data/AnAge/publish_vernaculars.tsv
[INFO] [2023-01-31 08:05:42] (21128 lines) /app/public/data/AnAge/publish_traits.tsv
[INFO] [2023-01-31 08:05:42] (5056 lines) /app/public/data/AnAge/publish_metadata.tsv
[STOP] [2023-01-31 08:05:42] complete_harvest_instance
[START] [2023-01-31 08:05:42] completed
[STOP] [2023-01-31 08:05:42] completed
[STOP] [2023-01-31 08:05:42] logged process, took 531.35

Latest Process