Stage:
completed
Fetched:
01 Feb 15:26
Validated:
01 Feb 15:26
Deltas Created
01 Feb 15:26
Units Normalized:
01 Feb 15:27
Ancestry Built:
01 Feb 15:27
Nodes Matched:
01 Feb 15:27
Names Parsed:
01 Feb 15:27
New Models Stored:
01 Feb 15:26
Indexed:
01 Feb 15:27
Completed:
01 Feb 15:28
Time to Harvest:
less than a minute
Harvesting Log
(144 lines)
[INFO] [2023-02-01 15:26:56] Created harvest instance #4294
[STOP] [2023-02-01 15:26:56] create_harvest_instance
[START] [2023-02-01 15:26:56] fetch_files
[STOP] [2023-02-01 15:26:56] fetch_files
[START] [2023-02-01 15:26:56] validate_each_file
[INFO] [2023-02-01 15:26:56] Looping over 3 formats...
[INFO] [2023-02-01 15:26:56] ...nodes (/app/public/data/bldnab/taxon.tab)
[INFO] [2023-02-01 15:26:56] Valid: /app/public/data/bldnab/converted_csv/bldnab_nodes_30185.csv (508 lines)
[INFO] [2023-02-01 15:26:56] ...occurrences (/app/public/data/bldnab/occurrence_specific.tab)
[INFO] [2023-02-01 15:26:56] Valid: /app/public/data/bldnab/converted_csv/bldnab_occurrences_30186.csv (1040 lines)
[INFO] [2023-02-01 15:26:56] ...measurements (/app/public/data/bldnab/measurement_or_fact_specific.tab)
[INFO] [2023-02-01 15:26:56] Valid: /app/public/data/bldnab/converted_csv/bldnab_measurements_30187.csv (1040 lines)
[STOP] [2023-02-01 15:26:56] validate_each_file
[START] [2023-02-01 15:26:56] convert_to_csv
[INFO] [2023-02-01 15:26:56] Looping over 3 formats...
[INFO] [2023-02-01 15:26:56] ...nodes (/app/public/data/bldnab/taxon.tab)
[CMD] [2023-02-01 15:26:56] /usr/bin/sort /app/public/data/bldnab/converted_csv/bldnab_nodes_30185.csv > /app/public/data/bldnab/converted_csv/bldnab_nodes_30185.csv_sorted
[INFO] [2023-02-01 15:26:56] Converted: /app/public/data/bldnab/converted_csv/bldnab_nodes_30185.csv (508 lines)
[INFO] [2023-02-01 15:26:56] ...occurrences (/app/public/data/bldnab/occurrence_specific.tab)
[CMD] [2023-02-01 15:26:56] /usr/bin/sort /app/public/data/bldnab/converted_csv/bldnab_occurrences_30186.csv > /app/public/data/bldnab/converted_csv/bldnab_occurrences_30186.csv_sorted
[INFO] [2023-02-01 15:26:56] Converted: /app/public/data/bldnab/converted_csv/bldnab_occurrences_30186.csv (1040 lines)
[INFO] [2023-02-01 15:26:56] ...measurements (/app/public/data/bldnab/measurement_or_fact_specific.tab)
[CMD] [2023-02-01 15:26:56] /usr/bin/sort /app/public/data/bldnab/converted_csv/bldnab_measurements_30187.csv > /app/public/data/bldnab/converted_csv/bldnab_measurements_30187.csv_sorted
[INFO] [2023-02-01 15:26:56] Converted: /app/public/data/bldnab/converted_csv/bldnab_measurements_30187.csv (1040 lines)
[STOP] [2023-02-01 15:26:56] convert_to_csv
[START] [2023-02-01 15:26:56] calculate_delta
[INFO] [2023-02-01 15:26:56] Looping over 3 formats...
[INFO] [2023-02-01 15:26:56] ...nodes (/app/public/data/bldnab/taxon.tab)
[CMD] [2023-02-01 15:26:56] echo "0a" > /app/public/data/bldnab/diff/bldnab_nodes_30185.diff
[CMD] [2023-02-01 15:26:56] tail -n +1 /app/public/data/bldnab/converted_csv/bldnab_nodes_30185.csv >> /app/public/data/bldnab/diff/bldnab_nodes_30185.diff
[CMD] [2023-02-01 15:26:56] echo "." >> /app/public/data/bldnab/diff/bldnab_nodes_30185.diff
[INFO] [2023-02-01 15:26:56] Created diff: /app/public/data/bldnab/diff/bldnab_nodes_30185.diff (510 lines)
[INFO] [2023-02-01 15:26:56] ...occurrences (/app/public/data/bldnab/occurrence_specific.tab)
[CMD] [2023-02-01 15:26:56] echo "0a" > /app/public/data/bldnab/diff/bldnab_occurrences_30186.diff
[CMD] [2023-02-01 15:26:56] tail -n +1 /app/public/data/bldnab/converted_csv/bldnab_occurrences_30186.csv >> /app/public/data/bldnab/diff/bldnab_occurrences_30186.diff
[CMD] [2023-02-01 15:26:56] echo "." >> /app/public/data/bldnab/diff/bldnab_occurrences_30186.diff
[INFO] [2023-02-01 15:26:56] Created diff: /app/public/data/bldnab/diff/bldnab_occurrences_30186.diff (1042 lines)
[INFO] [2023-02-01 15:26:56] ...measurements (/app/public/data/bldnab/measurement_or_fact_specific.tab)
[CMD] [2023-02-01 15:26:56] echo "0a" > /app/public/data/bldnab/diff/bldnab_measurements_30187.diff
[CMD] [2023-02-01 15:26:56] tail -n +1 /app/public/data/bldnab/converted_csv/bldnab_measurements_30187.csv >> /app/public/data/bldnab/diff/bldnab_measurements_30187.diff
[CMD] [2023-02-01 15:26:56] echo "." >> /app/public/data/bldnab/diff/bldnab_measurements_30187.diff
[INFO] [2023-02-01 15:26:56] Created diff: /app/public/data/bldnab/diff/bldnab_measurements_30187.diff (1042 lines)
[STOP] [2023-02-01 15:26:56] calculate_delta
[START] [2023-02-01 15:26:56] parse_diff_and_store
[INFO] [2023-02-01 15:26:56] Handling diff: /app/public/data/bldnab/diff/bldnab_nodes_30185.diff (510 lines)
[INFO] [2023-02-01 15:26:56] Loading nodes diff file into memory (510 lines)...
[INFO] [2023-02-01 15:26:57] Storing 522 ScientificNames (1044/508/510)
[INFO] [2023-02-01 15:26:57] Storing 522 Nodes (1044/508/510)
[INFO] [2023-02-01 15:26:57] Handling diff: /app/public/data/bldnab/diff/bldnab_occurrences_30186.diff (1042 lines)
[INFO] [2023-02-01 15:26:57] Loading occurrences diff file into memory (1042 lines)...
[INFO] [2023-02-01 15:26:57] Storing 1040 Occurrences (2213/1040/1042)
[INFO] [2023-02-01 15:26:57] Storing 1173 OccurrenceMetadata (2213/1040/1042)
[INFO] [2023-02-01 15:26:57] Handling diff: /app/public/data/bldnab/diff/bldnab_measurements_30187.diff (1042 lines)
[INFO] [2023-02-01 15:26:57] Loading measurements diff file into memory (1042 lines)...
[INFO] [2023-02-01 15:26:58] Storing 1040 Traits (2080/1040/1042)
[INFO] [2023-02-01 15:26:58] Storing 1040 MetaTraits (2080/1040/1042)
[STOP] [2023-02-01 15:26:58] parse_diff_and_store
[START] [2023-02-01 15:26:58] resolve_keys
[2023-02-01 15:26:58] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-02-01 15:27:06] Occurrences to nodes (through scientific_names)...
[INFO] [2023-02-01 15:27:06] traits to occurrences...
[INFO] [2023-02-01 15:27:06] traits to nodes (through occurrences)...
[INFO] [2023-02-01 15:27:06] Traits to sex term...
[INFO] [2023-02-01 15:27:06] Traits to lifestage term...
[INFO] [2023-02-01 15:27:06] MetaTraits to traits...
[INFO] [2023-02-01 15:27:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-02-01 15:27:06] Assocs to occurrences...
[INFO] [2023-02-01 15:27:06] Assocs to nodes...
[INFO] [2023-02-01 15:27:06] Assoc to sex term...
[INFO] [2023-02-01 15:27:06] Assoc to lifestage term...
[INFO] [2023-02-01 15:27:06] MetaAssoc to assocs...
[STOP] [2023-02-01 15:27:06] resolve_keys
[START] [2023-02-01 15:27:06] hold_for_later_1
[STOP] [2023-02-01 15:27:06] hold_for_later_1
[START] [2023-02-01 15:27:06] hold_for_later_2
[STOP] [2023-02-01 15:27:06] hold_for_later_2
[START] [2023-02-01 15:27:06] resolve_missing_parents
[STOP] [2023-02-01 15:27:06] resolve_missing_parents
[START] [2023-02-01 15:27:06] rebuild_nodes
[START] [2023-02-01 15:27:06] Flattener#flatten
[START] [2023-02-01 15:27:06] Flattener#study_resource
[START] [2023-02-01 15:27:06] Flattener#build_ancestry
[STOP] [2023-02-01 15:27:06] Flattener#build_ancestry
[INFO] [2023-02-01 15:27:06] 522 ancestry keys
[START] [2023-02-01 15:27:06] build_node_ancestors
[INFO] [2023-02-01 15:27:06] old ancestors deleted.
[STOP] [2023-02-01 15:27:06] build_node_ancestors
[START] [2023-02-01 15:27:06] Flattener#propagate_ancestor_ids
[STOP] [2023-02-01 15:27:06] Flattener#propagate_ancestor_ids
[STOP] [2023-02-01 15:27:06] Flattener#flatten
[STOP] [2023-02-01 15:27:06] rebuild_nodes
[START] [2023-02-01 15:27:06] resolve_missing_media_owners
[STOP] [2023-02-01 15:27:06] resolve_missing_media_owners
[START] [2023-02-01 15:27:06] sanitize_media_verbatims
[STOP] [2023-02-01 15:27:06] sanitize_media_verbatims
[START] [2023-02-01 15:27:06] queue_downloads
[STOP] [2023-02-01 15:27:06] queue_downloads
[START] [2023-02-01 15:27:06] parse_names
[WARN] [2023-02-01 15:27:06] I see 522 names which still need to be parsed.
[WARN] [2023-02-01 15:27:07] Names to parse: 522 formatted: 522 learned: 522 parsed: 522
[STOP] [2023-02-01 15:27:08] parse_names
[START] [2023-02-01 15:27:08] denormalize_canonical_names_to_nodes
[STOP] [2023-02-01 15:27:08] denormalize_canonical_names_to_nodes
[START] [2023-02-01 15:27:08] match_nodes
[START] [2023-02-01 15:27:08] map_all_nodes_to_pages
[STOP] [2023-02-01 15:27:31] map_all_nodes_to_pages
[INFO] [2023-02-01 15:27:31] 44 Unmatched nodes (of 522)! That's too many to output. Full list in /app/public/data/bldnab/unmatched_nodes.txt ; First 10: Canonical: Agrilus bilineatus bilineatus; Node#122870232; ResourceID: Agrilus_bilineatus_bilineatus; Canonical: Agrilus bilineatus carpini; Node#122870233; ResourceID: Agrilus_bilineatus_carpini; Canonical: Eupristocerus cognitans; Node#122870471; ResourceID: Eupristocerus_cognitans; Canonical: Haplanthaxia cyanella; Node#122870476; ResourceID: Haplanthaxia_cyanella; Canonical: Haplanthaxia deleta; Node#122870477; ResourceID: Haplanthaxia_deleta; Canonical: Haplanthaxia fisheri; Node#122870478; ResourceID: Haplanthaxia_fisheri; Canonical: Haplanthaxia pseudotsugae; Node#122870479; ResourceID: Haplanthaxia_pseudotsugae; Canonical: Haplanthaxia quercata; Node#122870480; ResourceID: Haplanthaxia_quercata; Canonical: Haplanthaxia quercicola; Node#122870481; ResourceID: Haplanthaxia_quercicola; Canonical: Haplanthaxia viridicornis; Node#122870482; ResourceID: Haplanthaxia_viridicornis
[START] [2023-02-01 15:27:31] update_nodes
[STOP] [2023-02-01 15:27:31] update_nodes
[STOP] [2023-02-01 15:27:31] match_nodes
[START] [2023-02-01 15:27:31] reindex_search
[STOP] [2023-02-01 15:27:31] reindex_search
[START] [2023-02-01 15:27:31] normalize_units
[STOP] [2023-02-01 15:27:35] normalize_units
[START] [2023-02-01 15:27:35] calculate_statistics
[INFO] [2023-02-01 15:27:35] Duplicate page_id count: 6
[STOP] [2023-02-01 15:27:35] calculate_statistics
[START] [2023-02-01 15:27:35] complete_harvest_instance
[START] [2023-02-01 15:27:35] overall_tsv_creation
[INFO] [2023-02-01 15:27:35] Exporting 522 nodes as TSV in batches of 10000...
[INFO] [2023-02-01 15:27:35] Processing group of 522 in 1 batches of 10000
[INFO] [2023-02-01 15:27:36] 1040 Traits (unfiltered) and 0 associations...
[INFO] [2023-02-01 15:27:36] Building Traits map for 522 nodes (this can take a while)...
[INFO] [2023-02-01 15:27:36] Mapped 1040 traits (1040 meta) for 522 nodes.
[INFO] [2023-02-01 15:27:36] Building Associations map (this can take a while)...
[INFO] [2023-02-01 15:27:36] Done. 0 assocs mapped (0 meta).
[INFO] [2023-02-01 15:27:36] Adding 1040 traits...
[INFO] [2023-02-01 15:27:36] 0 metadata added.
[INFO] [2023-02-01 15:27:36] Adding 0 assocs...
[INFO] [2023-02-01 15:27:36] 0 metadata added.
[INFO] [2023-02-01 15:28:21] Processed 522/522 nodes
[INFO] [2023-02-01 15:28:21] Average Time: 45.39
[INFO] [2023-02-01 15:28:21] Total Time: 46s
[STOP] [2023-02-01 15:28:21] overall_tsv_creation
[INFO] [2023-02-01 15:28:21] Done. Check your files:
[INFO] [2023-02-01 15:28:21] (522 lines) /app/public/data/bldnab/publish_nodes.tsv
[INFO] [2023-02-01 15:28:21] (1549 lines) /app/public/data/bldnab/publish_node_ancestors.tsv
[INFO] [2023-02-01 15:28:21] (522 lines) /app/public/data/bldnab/publish_scientific_names.tsv
[INFO] [2023-02-01 15:28:21] (1041 lines) /app/public/data/bldnab/publish_traits.tsv
[INFO] [2023-02-01 15:28:21] (1 lines) /app/public/data/bldnab/publish_metadata.tsv
[STOP] [2023-02-01 15:28:21] complete_harvest_instance
[START] [2023-02-01 15:28:21] completed
[STOP] [2023-02-01 15:28:21] completed
[STOP] [2023-02-01 15:28:21] logged process, took 84.87
Latest Process