Harvest for Desutter Grandcolas 1995 Created 19 Jan 16:39

Stage: completed
Fetched: 19 Jan 16:39
Validated: 19 Jan 16:39
Deltas Created 19 Jan 16:39
Units Normalized: 19 Jan 16:40
Ancestry Built: 19 Jan 16:40
Nodes Matched: 19 Jan 16:40
Names Parsed: 19 Jan 16:40
New Models Stored: 19 Jan 16:39
Indexed: 19 Jan 16:40
Completed: 19 Jan 16:40
Time to Harvest: less than a minute
Harvesting Log

(143 lines)
[INFO] [2023-01-19 16:39:52] Created harvest instance #4268
[STOP] [2023-01-19 16:39:52] create_harvest_instance
[START] [2023-01-19 16:39:52] fetch_files
[STOP] [2023-01-19 16:39:52] fetch_files
[START] [2023-01-19 16:39:52] validate_each_file
[INFO] [2023-01-19 16:39:52] Looping over 3 formats...
[INFO] [2023-01-19 16:39:52] ...nodes (/app/public/data/desutter_grandco/taxa.txt)
[INFO] [2023-01-19 16:39:52] Valid: /app/public/data/desutter_grandco/converted_csv/desutter_grandco_nodes_30052.csv (75 lines)
[INFO] [2023-01-19 16:39:52] ...occurrences (/app/public/data/desutter_grandco/occurrences.txt)
[INFO] [2023-01-19 16:39:52] Valid: /app/public/data/desutter_grandco/converted_csv/desutter_grandco_occurrences_30053.csv (75 lines)
[INFO] [2023-01-19 16:39:52] ...measurements (/app/public/data/desutter_grandco/measurementsorfacts.txt)
[INFO] [2023-01-19 16:39:52] Valid: /app/public/data/desutter_grandco/converted_csv/desutter_grandco_measurements_30054.csv (240 lines)
[STOP] [2023-01-19 16:39:52] validate_each_file
[START] [2023-01-19 16:39:52] convert_to_csv
[INFO] [2023-01-19 16:39:52] Looping over 3 formats...
[INFO] [2023-01-19 16:39:52] ...nodes (/app/public/data/desutter_grandco/taxa.txt)
[CMD] [2023-01-19 16:39:52] /usr/bin/sort /app/public/data/desutter_grandco/converted_csv/desutter_grandco_nodes_30052.csv > /app/public/data/desutter_grandco/converted_csv/desutter_grandco_nodes_30052.csv_sorted
[INFO] [2023-01-19 16:39:52] Converted: /app/public/data/desutter_grandco/converted_csv/desutter_grandco_nodes_30052.csv (75 lines)
[INFO] [2023-01-19 16:39:52] ...occurrences (/app/public/data/desutter_grandco/occurrences.txt)
[CMD] [2023-01-19 16:39:52] /usr/bin/sort /app/public/data/desutter_grandco/converted_csv/desutter_grandco_occurrences_30053.csv > /app/public/data/desutter_grandco/converted_csv/desutter_grandco_occurrences_30053.csv_sorted
[INFO] [2023-01-19 16:39:52] Converted: /app/public/data/desutter_grandco/converted_csv/desutter_grandco_occurrences_30053.csv (75 lines)
[INFO] [2023-01-19 16:39:52] ...measurements (/app/public/data/desutter_grandco/measurementsorfacts.txt)
[CMD] [2023-01-19 16:39:52] /usr/bin/sort /app/public/data/desutter_grandco/converted_csv/desutter_grandco_measurements_30054.csv > /app/public/data/desutter_grandco/converted_csv/desutter_grandco_measurements_30054.csv_sorted
[INFO] [2023-01-19 16:39:52] Converted: /app/public/data/desutter_grandco/converted_csv/desutter_grandco_measurements_30054.csv (240 lines)
[STOP] [2023-01-19 16:39:52] convert_to_csv
[START] [2023-01-19 16:39:52] calculate_delta
[INFO] [2023-01-19 16:39:52] Looping over 3 formats...
[INFO] [2023-01-19 16:39:52] ...nodes (/app/public/data/desutter_grandco/taxa.txt)
[CMD] [2023-01-19 16:39:52] echo "0a" > /app/public/data/desutter_grandco/diff/desutter_grandco_nodes_30052.diff
[CMD] [2023-01-19 16:39:52] tail -n +1 /app/public/data/desutter_grandco/converted_csv/desutter_grandco_nodes_30052.csv >> /app/public/data/desutter_grandco/diff/desutter_grandco_nodes_30052.diff
[CMD] [2023-01-19 16:39:52] echo "." >> /app/public/data/desutter_grandco/diff/desutter_grandco_nodes_30052.diff
[INFO] [2023-01-19 16:39:52] Created diff: /app/public/data/desutter_grandco/diff/desutter_grandco_nodes_30052.diff (77 lines)
[INFO] [2023-01-19 16:39:52] ...occurrences (/app/public/data/desutter_grandco/occurrences.txt)
[CMD] [2023-01-19 16:39:52] echo "0a" > /app/public/data/desutter_grandco/diff/desutter_grandco_occurrences_30053.diff
[CMD] [2023-01-19 16:39:52] tail -n +1 /app/public/data/desutter_grandco/converted_csv/desutter_grandco_occurrences_30053.csv >> /app/public/data/desutter_grandco/diff/desutter_grandco_occurrences_30053.diff
[CMD] [2023-01-19 16:39:52] echo "." >> /app/public/data/desutter_grandco/diff/desutter_grandco_occurrences_30053.diff
[INFO] [2023-01-19 16:39:52] Created diff: /app/public/data/desutter_grandco/diff/desutter_grandco_occurrences_30053.diff (77 lines)
[INFO] [2023-01-19 16:39:52] ...measurements (/app/public/data/desutter_grandco/measurementsorfacts.txt)
[CMD] [2023-01-19 16:39:52] echo "0a" > /app/public/data/desutter_grandco/diff/desutter_grandco_measurements_30054.diff
[CMD] [2023-01-19 16:39:52] tail -n +1 /app/public/data/desutter_grandco/converted_csv/desutter_grandco_measurements_30054.csv >> /app/public/data/desutter_grandco/diff/desutter_grandco_measurements_30054.diff
[CMD] [2023-01-19 16:39:52] echo "." >> /app/public/data/desutter_grandco/diff/desutter_grandco_measurements_30054.diff
[INFO] [2023-01-19 16:39:52] Created diff: /app/public/data/desutter_grandco/diff/desutter_grandco_measurements_30054.diff (242 lines)
[STOP] [2023-01-19 16:39:52] calculate_delta
[START] [2023-01-19 16:39:52] parse_diff_and_store
[INFO] [2023-01-19 16:39:52] Handling diff: /app/public/data/desutter_grandco/diff/desutter_grandco_nodes_30052.diff (77 lines)
[INFO] [2023-01-19 16:39:53] Loading nodes diff file into memory (77 lines)...
[INFO] [2023-01-19 16:39:53] Storing 75 ScientificNames (150/75/77)
[INFO] [2023-01-19 16:39:53] Storing 75 Nodes (150/75/77)
[INFO] [2023-01-19 16:39:53] Handling diff: /app/public/data/desutter_grandco/diff/desutter_grandco_occurrences_30053.diff (77 lines)
[INFO] [2023-01-19 16:39:53] Loading occurrences diff file into memory (77 lines)...
[INFO] [2023-01-19 16:39:53] Storing 75 Occurrences (150/75/77)
[INFO] [2023-01-19 16:39:53] Storing 75 OccurrenceMetadata (150/75/77)
[INFO] [2023-01-19 16:39:53] Handling diff: /app/public/data/desutter_grandco/diff/desutter_grandco_measurements_30054.diff (242 lines)
[INFO] [2023-01-19 16:39:53] Loading measurements diff file into memory (242 lines)...
[INFO] [2023-01-19 16:39:53] Storing 240 Traits (375/240/242)
[INFO] [2023-01-19 16:39:53] Storing 135 MetaTraits (375/240/242)
[STOP] [2023-01-19 16:39:53] parse_diff_and_store
[START] [2023-01-19 16:39:53] resolve_keys
[2023-01-19 16:39:53] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-19 16:40:00] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-19 16:40:00] traits to occurrences...
[INFO] [2023-01-19 16:40:00] traits to nodes (through occurrences)...
[INFO] [2023-01-19 16:40:00] Traits to sex term...
[INFO] [2023-01-19 16:40:00] Traits to lifestage term...
[INFO] [2023-01-19 16:40:00] MetaTraits to traits...
[INFO] [2023-01-19 16:40:00] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-19 16:40:00] Assocs to occurrences...
[INFO] [2023-01-19 16:40:00] Assocs to nodes...
[INFO] [2023-01-19 16:40:00] Assoc to sex term...
[INFO] [2023-01-19 16:40:00] Assoc to lifestage term...
[INFO] [2023-01-19 16:40:00] MetaAssoc to assocs...
[STOP] [2023-01-19 16:40:00] resolve_keys
[START] [2023-01-19 16:40:00] hold_for_later_1
[STOP] [2023-01-19 16:40:00] hold_for_later_1
[START] [2023-01-19 16:40:00] hold_for_later_2
[STOP] [2023-01-19 16:40:00] hold_for_later_2
[START] [2023-01-19 16:40:00] resolve_missing_parents
[STOP] [2023-01-19 16:40:00] resolve_missing_parents
[START] [2023-01-19 16:40:00] rebuild_nodes
[START] [2023-01-19 16:40:00] Flattener#flatten
[START] [2023-01-19 16:40:00] Flattener#study_resource
[START] [2023-01-19 16:40:00] Flattener#build_ancestry
[STOP] [2023-01-19 16:40:00] Flattener#build_ancestry
[INFO] [2023-01-19 16:40:00] 75 ancestry keys
[START] [2023-01-19 16:40:00] build_node_ancestors
[INFO] [2023-01-19 16:40:00] old ancestors deleted.
[STOP] [2023-01-19 16:40:00] build_node_ancestors
[WARN] [2023-01-19 16:40:00] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-19 16:40:00] Flattener#flatten
[STOP] [2023-01-19 16:40:00] rebuild_nodes
[START] [2023-01-19 16:40:00] resolve_missing_media_owners
[STOP] [2023-01-19 16:40:00] resolve_missing_media_owners
[START] [2023-01-19 16:40:00] sanitize_media_verbatims
[STOP] [2023-01-19 16:40:00] sanitize_media_verbatims
[START] [2023-01-19 16:40:00] queue_downloads
[STOP] [2023-01-19 16:40:00] queue_downloads
[START] [2023-01-19 16:40:00] parse_names
[WARN] [2023-01-19 16:40:00] I see 75 names which still need to be parsed.
[WARN] [2023-01-19 16:40:00] Names to parse: 75 formatted: 75 learned: 75 parsed: 75
[STOP] [2023-01-19 16:40:01] parse_names
[START] [2023-01-19 16:40:01] denormalize_canonical_names_to_nodes
[STOP] [2023-01-19 16:40:01] denormalize_canonical_names_to_nodes
[START] [2023-01-19 16:40:01] match_nodes
[START] [2023-01-19 16:40:01] map_all_nodes_to_pages
[STOP] [2023-01-19 16:40:02] map_all_nodes_to_pages
[INFO] [2023-01-19 16:40:02] Unmatched nodes (2 of 75): Canonical: Isecksohniella; Node#122417031; ResourceID: Isecksohniella; Canonical: Tairona; Node#122417075; ResourceID: Tairona
[START] [2023-01-19 16:40:02] update_nodes
[STOP] [2023-01-19 16:40:02] update_nodes
[STOP] [2023-01-19 16:40:02] match_nodes
[START] [2023-01-19 16:40:02] reindex_search
[STOP] [2023-01-19 16:40:02] reindex_search
[START] [2023-01-19 16:40:02] normalize_units
[STOP] [2023-01-19 16:40:02] normalize_units
[START] [2023-01-19 16:40:02] calculate_statistics
[2023-01-19 16:40:02] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-19 16:40:02] Duplicate page_id count: 2
[STOP] [2023-01-19 16:40:02] calculate_statistics
[START] [2023-01-19 16:40:02] complete_harvest_instance
[START] [2023-01-19 16:40:02] overall_tsv_creation
[INFO] [2023-01-19 16:40:02] Exporting 75 nodes as TSV in batches of 10000...
[INFO] [2023-01-19 16:40:02] Processing group of 75 in 1 batches of 10000
[INFO] [2023-01-19 16:40:02] 121 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-19 16:40:02] Building Traits map for 75 nodes (this can take a while)...
[INFO] [2023-01-19 16:40:02] Mapped 121 traits (135 meta) for 75 nodes.
[INFO] [2023-01-19 16:40:02] Building Associations map (this can take a while)...
[INFO] [2023-01-19 16:40:02] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-19 16:40:02] Adding 121 traits...
[INFO] [2023-01-19 16:40:02] 119 metadata added.
[INFO] [2023-01-19 16:40:02] Adding 0 assocs...
[INFO] [2023-01-19 16:40:02] 0 metadata added.
[INFO] [2023-01-19 16:40:46] Processed 75/75 nodes
[INFO] [2023-01-19 16:40:46] Average Time: 43.73
[INFO] [2023-01-19 16:40:46] Total Time: 44s
[STOP] [2023-01-19 16:40:46] overall_tsv_creation
[INFO] [2023-01-19 16:40:46] Done. Check your files:
[INFO] [2023-01-19 16:40:46] (75 lines) /app/public/data/desutter_grandco/publish_nodes.tsv
[INFO] [2023-01-19 16:40:46] (75 lines) /app/public/data/desutter_grandco/publish_scientific_names.tsv
[INFO] [2023-01-19 16:40:46] (122 lines) /app/public/data/desutter_grandco/publish_traits.tsv
[INFO] [2023-01-19 16:40:46] (120 lines) /app/public/data/desutter_grandco/publish_metadata.tsv
[STOP] [2023-01-19 16:40:46] complete_harvest_instance
[START] [2023-01-19 16:40:46] completed
[STOP] [2023-01-19 16:40:46] completed
[STOP] [2023-01-19 16:40:46] logged process, took 53.81
Latest Process

19 Jan 16:39 EXITED currently processing 0