Harvest for AmericanInsects Created 31 May 14:13

Stage: completed
Fetched: 31 May 14:13
Validated: 31 May 14:13
Deltas Created 31 May 14:13
Units Normalized: 31 May 14:14
Ancestry Built: 31 May 14:14
Nodes Matched: 31 May 14:14
Names Parsed: 31 May 14:14
New Models Stored: 31 May 14:13
Indexed: 31 May 14:14
Completed: 31 May 14:15
Time to Harvest: less than a minute

Harvesting Log (most recent first)

[INFO] [2021-05-31 14:13:45] Created harvest instance #3928
[STOP] [2021-05-31 14:13:45] create_harvest_instance
[START] [2021-05-31 14:13:45] fetch_files
[STOP] [2021-05-31 14:13:45] fetch_files
[START] [2021-05-31 14:13:45] validate_each_file
[INFO] [2021-05-31 14:13:45] Looping over 4 formats...
[INFO] [2021-05-31 14:13:45] ...refs (/app/public/data/AmericanInsects/reference.tab)
[INFO] [2021-05-31 14:13:45] Valid: /app/public/converted_csv/AmericanInsects_refs_3928.csv (1 lines)
[INFO] [2021-05-31 14:13:45] ...nodes (/app/public/data/AmericanInsects/taxon.tab)
[INFO] [2021-05-31 14:13:45] Valid: /app/public/converted_csv/AmericanInsects_nodes_3928.csv (921 lines)
[INFO] [2021-05-31 14:13:45] ...occurrences (/app/public/data/AmericanInsects/occurrence_specific.tab)
[INFO] [2021-05-31 14:13:45] Valid: /app/public/converted_csv/AmericanInsects_occurrences_3928.csv (978 lines)
[INFO] [2021-05-31 14:13:45] ...measurements (/app/public/data/AmericanInsects/measurement_or_fact_specific.tab)
[INFO] [2021-05-31 14:13:45] Valid: /app/public/converted_csv/AmericanInsects_measurements_3928.csv (979 lines)
[STOP] [2021-05-31 14:13:45] validate_each_file
[START] [2021-05-31 14:13:45] convert_to_csv
[INFO] [2021-05-31 14:13:45] Looping over 4 formats...
[INFO] [2021-05-31 14:13:45] ...refs (/app/public/data/AmericanInsects/reference.tab)
[CMD] [2021-05-31 14:13:45] /usr/bin/sort /app/public/converted_csv/AmericanInsects_refs_3928.csv > /app/public/converted_csv/AmericanInsects_refs_3928.csv_sorted
[INFO] [2021-05-31 14:13:46] Converted: /app/public/converted_csv/AmericanInsects_refs_3928.csv (1 lines)
[INFO] [2021-05-31 14:13:46] ...nodes (/app/public/data/AmericanInsects/taxon.tab)
[CMD] [2021-05-31 14:13:46] /usr/bin/sort /app/public/converted_csv/AmericanInsects_nodes_3928.csv > /app/public/converted_csv/AmericanInsects_nodes_3928.csv_sorted
[INFO] [2021-05-31 14:13:46] Converted: /app/public/converted_csv/AmericanInsects_nodes_3928.csv (921 lines)
[INFO] [2021-05-31 14:13:46] ...occurrences (/app/public/data/AmericanInsects/occurrence_specific.tab)
[CMD] [2021-05-31 14:13:46] /usr/bin/sort /app/public/converted_csv/AmericanInsects_occurrences_3928.csv > /app/public/converted_csv/AmericanInsects_occurrences_3928.csv_sorted
[INFO] [2021-05-31 14:13:46] Converted: /app/public/converted_csv/AmericanInsects_occurrences_3928.csv (978 lines)
[INFO] [2021-05-31 14:13:46] ...measurements (/app/public/data/AmericanInsects/measurement_or_fact_specific.tab)
[CMD] [2021-05-31 14:13:46] /usr/bin/sort /app/public/converted_csv/AmericanInsects_measurements_3928.csv > /app/public/converted_csv/AmericanInsects_measurements_3928.csv_sorted
[INFO] [2021-05-31 14:13:47] Converted: /app/public/converted_csv/AmericanInsects_measurements_3928.csv (979 lines)
[STOP] [2021-05-31 14:13:47] convert_to_csv
[START] [2021-05-31 14:13:47] calculate_delta
[INFO] [2021-05-31 14:13:47] Looping over 4 formats...
[INFO] [2021-05-31 14:13:47] ...refs (/app/public/data/AmericanInsects/reference.tab)
[CMD] [2021-05-31 14:13:47] echo "0a" > /app/public/diff/AmericanInsects_refs_3928.diff
[CMD] [2021-05-31 14:13:47] tail -n +1 /app/public/converted_csv/AmericanInsects_refs_3928.csv >> /app/public/diff/AmericanInsects_refs_3928.diff
[CMD] [2021-05-31 14:13:47] echo "." >> /app/public/diff/AmericanInsects_refs_3928.diff
[INFO] [2021-05-31 14:13:48] Created diff: /app/public/diff/AmericanInsects_refs_3928.diff (3 lines)
[INFO] [2021-05-31 14:13:48] ...nodes (/app/public/data/AmericanInsects/taxon.tab)
[CMD] [2021-05-31 14:13:48] echo "0a" > /app/public/diff/AmericanInsects_nodes_3928.diff
[CMD] [2021-05-31 14:13:48] tail -n +1 /app/public/converted_csv/AmericanInsects_nodes_3928.csv >> /app/public/diff/AmericanInsects_nodes_3928.diff
[CMD] [2021-05-31 14:13:49] echo "." >> /app/public/diff/AmericanInsects_nodes_3928.diff
[INFO] [2021-05-31 14:13:49] Created diff: /app/public/diff/AmericanInsects_nodes_3928.diff (923 lines)
[INFO] [2021-05-31 14:13:49] ...occurrences (/app/public/data/AmericanInsects/occurrence_specific.tab)
[CMD] [2021-05-31 14:13:49] echo "0a" > /app/public/diff/AmericanInsects_occurrences_3928.diff
[CMD] [2021-05-31 14:13:49] tail -n +1 /app/public/converted_csv/AmericanInsects_occurrences_3928.csv >> /app/public/diff/AmericanInsects_occurrences_3928.diff
[CMD] [2021-05-31 14:13:50] echo "." >> /app/public/diff/AmericanInsects_occurrences_3928.diff
[INFO] [2021-05-31 14:13:50] Created diff: /app/public/diff/AmericanInsects_occurrences_3928.diff (980 lines)
[INFO] [2021-05-31 14:13:50] ...measurements (/app/public/data/AmericanInsects/measurement_or_fact_specific.tab)
[CMD] [2021-05-31 14:13:50] echo "0a" > /app/public/diff/AmericanInsects_measurements_3928.diff
[CMD] [2021-05-31 14:13:51] tail -n +1 /app/public/converted_csv/AmericanInsects_measurements_3928.csv >> /app/public/diff/AmericanInsects_measurements_3928.diff
[CMD] [2021-05-31 14:13:51] echo "." >> /app/public/diff/AmericanInsects_measurements_3928.diff
[INFO] [2021-05-31 14:13:51] Created diff: /app/public/diff/AmericanInsects_measurements_3928.diff (981 lines)
[STOP] [2021-05-31 14:13:51] calculate_delta
[START] [2021-05-31 14:13:51] parse_diff_and_store
[INFO] [2021-05-31 14:13:51] Handling diff: /app/public/diff/AmericanInsects_refs_3928.diff (3 lines)
[INFO] [2021-05-31 14:13:52] Loading refs diff file into memory (3 /app/public/diff/AmericanInsects_refs_3928.diff lines)...
[INFO] [2021-05-31 14:13:52] Handling diff: /app/public/diff/AmericanInsects_nodes_3928.diff (923 lines)
[INFO] [2021-05-31 14:13:53] Loading nodes diff file into memory (923 /app/public/diff/AmericanInsects_nodes_3928.diff lines)...
[INFO] [2021-05-31 14:13:53] Handling diff: /app/public/diff/AmericanInsects_occurrences_3928.diff (980 lines)
[INFO] [2021-05-31 14:13:54] Loading occurrences diff file into memory (980 /app/public/diff/AmericanInsects_occurrences_3928.diff lines)...
[INFO] [2021-05-31 14:13:54] Handling diff: /app/public/diff/AmericanInsects_measurements_3928.diff (981 lines)
[INFO] [2021-05-31 14:13:54] Loading measurements diff file into memory (981 /app/public/diff/AmericanInsects_measurements_3928.diff lines)...
[INFO] [2021-05-31 14:13:55] Storing 1 References
[INFO] [2021-05-31 14:13:55] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 14:13:55] Average Time: 0.0
[INFO] [2021-05-31 14:13:55] Total Time: 1s
[INFO] [2021-05-31 14:13:55] Storing 921 ScientificNames
[INFO] [2021-05-31 14:13:55] Processing group of 921 in 1 groups of 1000
[INFO] [2021-05-31 14:13:56] Average Time: 0.27
[INFO] [2021-05-31 14:13:56] Total Time: 1s
[INFO] [2021-05-31 14:13:56] Storing 921 Nodes
[INFO] [2021-05-31 14:13:56] Processing group of 921 in 1 groups of 1000
[INFO] [2021-05-31 14:13:56] Average Time: 0.23
[INFO] [2021-05-31 14:13:56] Total Time: 1s
[INFO] [2021-05-31 14:13:56] Storing 978 Occurrences
[INFO] [2021-05-31 14:13:56] Processing group of 978 in 1 groups of 1000
[INFO] [2021-05-31 14:13:56] Average Time: 0.11
[INFO] [2021-05-31 14:13:56] Total Time: 1s
[INFO] [2021-05-31 14:13:56] Storing 978 OccurrenceMetadata
[INFO] [2021-05-31 14:13:56] Processing group of 978 in 1 groups of 1000
[INFO] [2021-05-31 14:13:56] Average Time: 0.11
[INFO] [2021-05-31 14:13:56] Total Time: 1s
[INFO] [2021-05-31 14:13:56] Storing 979 TraitsReferences
[INFO] [2021-05-31 14:13:56] Processing group of 979 in 1 groups of 1000
[INFO] [2021-05-31 14:13:56] Average Time: 0.12
[INFO] [2021-05-31 14:13:56] Total Time: 1s
[INFO] [2021-05-31 14:13:56] Storing 979 Traits
[INFO] [2021-05-31 14:13:56] Processing group of 979 in 1 groups of 1000
[INFO] [2021-05-31 14:13:57] Average Time: 0.3
[INFO] [2021-05-31 14:13:57] Total Time: 1s
[INFO] [2021-05-31 14:13:57] Storing 908 MetaTraits
[INFO] [2021-05-31 14:13:57] Processing group of 908 in 1 groups of 1000
[INFO] [2021-05-31 14:13:57] Average Time: 0.11
[INFO] [2021-05-31 14:13:57] Total Time: 1s
[STOP] [2021-05-31 14:13:57] parse_diff_and_store
[START] [2021-05-31 14:13:57] resolve_keys
[INFO] [2021-05-31 14:14:03] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-31 14:14:03] traits to occurrences...
[INFO] [2021-05-31 14:14:03] traits to nodes (through occurrences)...
[INFO] [2021-05-31 14:14:03] Traits to sex term...
[INFO] [2021-05-31 14:14:03] Traits to lifestage term...
[INFO] [2021-05-31 14:14:03] MetaTraits to traits...
[INFO] [2021-05-31 14:14:03] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-31 14:14:03] Assocs to occurrences...
[INFO] [2021-05-31 14:14:03] Assocs to nodes...
[INFO] [2021-05-31 14:14:03] Assoc to sex term...
[INFO] [2021-05-31 14:14:03] Assoc to lifestage term...
[INFO] [2021-05-31 14:14:03] MetaAssoc to assocs...
[STOP] [2021-05-31 14:14:03] resolve_keys
[START] [2021-05-31 14:14:03] hold_for_later_1
[STOP] [2021-05-31 14:14:03] hold_for_later_1
[START] [2021-05-31 14:14:03] hold_for_later_2
[STOP] [2021-05-31 14:14:03] hold_for_later_2
[START] [2021-05-31 14:14:03] resolve_missing_parents
[STOP] [2021-05-31 14:14:03] resolve_missing_parents
[START] [2021-05-31 14:14:03] rebuild_nodes
[START] [2021-05-31 14:14:03] Flattener#flatten
[START] [2021-05-31 14:14:03] Flattener#study_resource
[START] [2021-05-31 14:14:03] Flattener#build_ancestry
[STOP] [2021-05-31 14:14:03] Flattener#build_ancestry
[INFO] [2021-05-31 14:14:03] 921 ancestry keys
[START] [2021-05-31 14:14:03] build_node_ancestors
[INFO] [2021-05-31 14:14:03] old ancestors deleted.
[STOP] [2021-05-31 14:14:03] build_node_ancestors
[WARN] [2021-05-31 14:14:03] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-05-31 14:14:03] Flattener#flatten
[STOP] [2021-05-31 14:14:03] rebuild_nodes
[START] [2021-05-31 14:14:03] resolve_missing_media_owners
[STOP] [2021-05-31 14:14:03] resolve_missing_media_owners
[START] [2021-05-31 14:14:03] sanitize_media_verbatims
[STOP] [2021-05-31 14:14:03] sanitize_media_verbatims
[START] [2021-05-31 14:14:03] queue_downloads
[STOP] [2021-05-31 14:14:03] queue_downloads
[START] [2021-05-31 14:14:03] parse_names
[WARN] [2021-05-31 14:14:03] I see 921 names which still need to be parsed.
[STOP] [2021-05-31 14:14:05] parse_names
[START] [2021-05-31 14:14:05] denormalize_canonical_names_to_nodes
[STOP] [2021-05-31 14:14:05] denormalize_canonical_names_to_nodes
[START] [2021-05-31 14:14:05] match_nodes
[START] [2021-05-31 14:14:05] map_all_nodes_to_pages
[STOP] [2021-05-31 14:14:15] map_all_nodes_to_pages
[INFO] [2021-05-31 14:14:15] 118 Unmatched nodes (of 921)! That's too many to output. Full list in /app/public/data/AmericanInsects/unmatched_nodes.txt ; First 10: Canonical: Agriphila vulgivagella; Node#95116388; ResourceID: Agriphila_vulgivagella; Canonical: Alobates pennsylvanica; Node#95116392; ResourceID: Alobates_pennsylvanica; Canonical: Amoebaleria helvola; Node#95116395; ResourceID: Amoebaleria_helvola; Canonical: Ampedus areolatus; Node#95116396; ResourceID: Ampedus_areolatus; Canonical: Amphiareus obscuriceps; Node#95116398; ResourceID: Amphiareus_obscuriceps; Canonical: Anthaxia inornatax; Node#95116413; ResourceID: Anthaxia_inornatax; Canonical: Aphodius rusicola; Node#95116421; ResourceID: Aphodius_rusicola; Canonical: Aphodius stercorosus; Node#95116422; ResourceID: Aphodius_stercorosus; Canonical: Aphodius terminalis; Node#95116423; ResourceID: Aphodius_terminalis; Canonical: Apidaurus longistylus; Node#95116424; ResourceID: Apidaurus_longistylus
[START] [2021-05-31 14:14:15] update_nodes
[STOP] [2021-05-31 14:14:15] update_nodes
[STOP] [2021-05-31 14:14:15] match_nodes
[START] [2021-05-31 14:14:15] reindex_search
[STOP] [2021-05-31 14:14:16] reindex_search
[START] [2021-05-31 14:14:16] normalize_units
[STOP] [2021-05-31 14:14:20] normalize_units
[START] [2021-05-31 14:14:20] calculate_statistics
[2021-05-31 14:14:20] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-05-31 14:14:20] calculate_statistics
[START] [2021-05-31 14:14:20] complete_harvest_instance
[START] [2021-05-31 14:14:20] overall_tsv_creation
[INFO] [2021-05-31 14:14:20] Processing group of 921 in 1 batches of 10000
[INFO] [2021-05-31 14:14:56] 979 Traits (unfiltered)...
[INFO] [2021-05-31 14:15:23] 979 Traits (filtered)...
[INFO] [2021-05-31 14:15:23] 0 Associations (filtered)...
[INFO] [2021-05-31 14:15:23] 979 metadata added.
[INFO] [2021-05-31 14:15:23] 0 metadata added.
[INFO] [2021-05-31 14:15:47] Average Time: 63.84
[INFO] [2021-05-31 14:15:47] Total Time: 1m27s
[STOP] [2021-05-31 14:15:47] overall_tsv_creation
[INFO] [2021-05-31 14:15:47] Done. Check your files:
[INFO] [2021-05-31 14:15:47] (921 lines) /app/public/data/AmericanInsects/publish_nodes.tsv
[INFO] [2021-05-31 14:15:47] (921 lines) /app/public/data/AmericanInsects/publish_scientific_names.tsv
[INFO] [2021-05-31 14:15:48] (980 lines) /app/public/data/AmericanInsects/publish_traits.tsv
[INFO] [2021-05-31 14:15:48] (980 lines) /app/public/data/AmericanInsects/publish_metadata.tsv
[STOP] [2021-05-31 14:15:48] complete_harvest_instance
[START] [2021-05-31 14:15:48] completed
[STOP] [2021-05-31 14:15:48] completed
[STOP] [2021-05-31 14:15:48] logged process, took 123.47

Latest Process