Harvest for Budelmann 1992 Created 14 Oct 08:30

Stage: completed
Fetched: 14 Oct 08:30
Validated: 14 Oct 08:30
Deltas Created 14 Oct 08:30
Units Normalized: 14 Oct 08:30
Ancestry Built: 14 Oct 08:30
Nodes Matched: 14 Oct 08:30
Names Parsed: 14 Oct 08:30
New Models Stored: 14 Oct 08:30
Indexed: 14 Oct 08:30
Completed: 14 Oct 08:31
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
[INFO] [2023-10-14 08:30:35] Created harvest instance #4471
[STOP] [2023-10-14 08:30:35] create_harvest_instance
[START] [2023-10-14 08:30:35] fetch_files
[STOP] [2023-10-14 08:30:35] fetch_files
[START] [2023-10-14 08:30:35] validate_each_file
[INFO] [2023-10-14 08:30:35] Looping over 4 formats...
[INFO] [2023-10-14 08:30:35] ...refs (/app/public/data/budelmann_budelm/references.txt)
[INFO] [2023-10-14 08:30:35] Valid: /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_refs_30892.csv (2 lines)
[INFO] [2023-10-14 08:30:35] ...nodes (/app/public/data/budelmann_budelm/taxa.txt)
[INFO] [2023-10-14 08:30:35] Valid: /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_nodes_30889.csv (1 lines)
[INFO] [2023-10-14 08:30:35] ...occurrences (/app/public/data/budelmann_budelm/occurrences.txt)
[INFO] [2023-10-14 08:30:35] Valid: /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_occurrences_30890.csv (1 lines)
[INFO] [2023-10-14 08:30:35] ...measurements (/app/public/data/budelmann_budelm/measurementsorfacts.txt)
[INFO] [2023-10-14 08:30:35] Valid: /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_measurements_30891.csv (11 lines)
[STOP] [2023-10-14 08:30:35] validate_each_file
[START] [2023-10-14 08:30:35] convert_to_csv
[INFO] [2023-10-14 08:30:35] Looping over 4 formats...
[INFO] [2023-10-14 08:30:35] ...refs (/app/public/data/budelmann_budelm/references.txt)
[CMD] [2023-10-14 08:30:35] /usr/bin/sort /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_refs_30892.csv > /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_refs_30892.csv_sorted
[INFO] [2023-10-14 08:30:35] Converted: /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_refs_30892.csv (2 lines)
[INFO] [2023-10-14 08:30:35] ...nodes (/app/public/data/budelmann_budelm/taxa.txt)
[CMD] [2023-10-14 08:30:35] /usr/bin/sort /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_nodes_30889.csv > /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_nodes_30889.csv_sorted
[INFO] [2023-10-14 08:30:35] Converted: /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_nodes_30889.csv (1 lines)
[INFO] [2023-10-14 08:30:35] ...occurrences (/app/public/data/budelmann_budelm/occurrences.txt)
[CMD] [2023-10-14 08:30:35] /usr/bin/sort /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_occurrences_30890.csv > /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_occurrences_30890.csv_sorted
[INFO] [2023-10-14 08:30:35] Converted: /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_occurrences_30890.csv (1 lines)
[INFO] [2023-10-14 08:30:35] ...measurements (/app/public/data/budelmann_budelm/measurementsorfacts.txt)
[CMD] [2023-10-14 08:30:35] /usr/bin/sort /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_measurements_30891.csv > /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_measurements_30891.csv_sorted
[INFO] [2023-10-14 08:30:35] Converted: /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_measurements_30891.csv (11 lines)
[STOP] [2023-10-14 08:30:35] convert_to_csv
[START] [2023-10-14 08:30:35] calculate_delta
[INFO] [2023-10-14 08:30:35] Looping over 4 formats...
[INFO] [2023-10-14 08:30:35] ...refs (/app/public/data/budelmann_budelm/references.txt)
[CMD] [2023-10-14 08:30:35] echo "0a" > /app/public/data/budelmann_budelm/diff/budelmann_budelm_refs_30892.diff
[CMD] [2023-10-14 08:30:35] tail -n +1 /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_refs_30892.csv >> /app/public/data/budelmann_budelm/diff/budelmann_budelm_refs_30892.diff
[CMD] [2023-10-14 08:30:35] echo "." >> /app/public/data/budelmann_budelm/diff/budelmann_budelm_refs_30892.diff
[INFO] [2023-10-14 08:30:35] Created diff: /app/public/data/budelmann_budelm/diff/budelmann_budelm_refs_30892.diff (4 lines)
[INFO] [2023-10-14 08:30:35] ...nodes (/app/public/data/budelmann_budelm/taxa.txt)
[CMD] [2023-10-14 08:30:35] echo "0a" > /app/public/data/budelmann_budelm/diff/budelmann_budelm_nodes_30889.diff
[CMD] [2023-10-14 08:30:36] tail -n +1 /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_nodes_30889.csv >> /app/public/data/budelmann_budelm/diff/budelmann_budelm_nodes_30889.diff
[CMD] [2023-10-14 08:30:36] echo "." >> /app/public/data/budelmann_budelm/diff/budelmann_budelm_nodes_30889.diff
[INFO] [2023-10-14 08:30:36] Created diff: /app/public/data/budelmann_budelm/diff/budelmann_budelm_nodes_30889.diff (3 lines)
[INFO] [2023-10-14 08:30:36] ...occurrences (/app/public/data/budelmann_budelm/occurrences.txt)
[CMD] [2023-10-14 08:30:36] echo "0a" > /app/public/data/budelmann_budelm/diff/budelmann_budelm_occurrences_30890.diff
[CMD] [2023-10-14 08:30:36] tail -n +1 /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_occurrences_30890.csv >> /app/public/data/budelmann_budelm/diff/budelmann_budelm_occurrences_30890.diff
[CMD] [2023-10-14 08:30:36] echo "." >> /app/public/data/budelmann_budelm/diff/budelmann_budelm_occurrences_30890.diff
[INFO] [2023-10-14 08:30:36] Created diff: /app/public/data/budelmann_budelm/diff/budelmann_budelm_occurrences_30890.diff (3 lines)
[INFO] [2023-10-14 08:30:36] ...measurements (/app/public/data/budelmann_budelm/measurementsorfacts.txt)
[CMD] [2023-10-14 08:30:36] echo "0a" > /app/public/data/budelmann_budelm/diff/budelmann_budelm_measurements_30891.diff
[CMD] [2023-10-14 08:30:36] tail -n +1 /app/public/data/budelmann_budelm/converted_csv/budelmann_budelm_measurements_30891.csv >> /app/public/data/budelmann_budelm/diff/budelmann_budelm_measurements_30891.diff
[CMD] [2023-10-14 08:30:36] echo "." >> /app/public/data/budelmann_budelm/diff/budelmann_budelm_measurements_30891.diff
[INFO] [2023-10-14 08:30:36] Created diff: /app/public/data/budelmann_budelm/diff/budelmann_budelm_measurements_30891.diff (13 lines)
[STOP] [2023-10-14 08:30:36] calculate_delta
[START] [2023-10-14 08:30:36] parse_diff_and_store
[INFO] [2023-10-14 08:30:36] Handling diff: /app/public/data/budelmann_budelm/diff/budelmann_budelm_refs_30892.diff (4 lines)
[INFO] [2023-10-14 08:30:36] Loading refs diff file into memory (4 lines)...
[INFO] [2023-10-14 08:30:36] Storing 2 References (2/2/4)
[INFO] [2023-10-14 08:30:36] Handling diff: /app/public/data/budelmann_budelm/diff/budelmann_budelm_nodes_30889.diff (3 lines)
[INFO] [2023-10-14 08:30:36] Loading nodes diff file into memory (3 lines)...
[INFO] [2023-10-14 08:30:36] Storing 1 ScientificNames (2/1/3)
[INFO] [2023-10-14 08:30:36] Storing 1 Nodes (2/1/3)
[INFO] [2023-10-14 08:30:36] Handling diff: /app/public/data/budelmann_budelm/diff/budelmann_budelm_occurrences_30890.diff (3 lines)
[INFO] [2023-10-14 08:30:36] Loading occurrences diff file into memory (3 lines)...
[INFO] [2023-10-14 08:30:36] Storing 1 Occurrences (1/1/3)
[INFO] [2023-10-14 08:30:36] Handling diff: /app/public/data/budelmann_budelm/diff/budelmann_budelm_measurements_30891.diff (13 lines)
[INFO] [2023-10-14 08:30:36] Loading measurements diff file into memory (13 lines)...
[INFO] [2023-10-14 08:30:37] Storing 8 TraitsReferences (27/11/13)
[INFO] [2023-10-14 08:30:37] Storing 11 Traits (27/11/13)
[INFO] [2023-10-14 08:30:37] Storing 8 MetaTraits (27/11/13)
[STOP] [2023-10-14 08:30:37] parse_diff_and_store
[START] [2023-10-14 08:30:37] resolve_keys
[2023-10-14 08:30:37] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-14 08:30:44] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-14 08:30:44] traits to occurrences...
[INFO] [2023-10-14 08:30:44] traits to nodes (through occurrences)...
[INFO] [2023-10-14 08:30:44] Traits to sex term...
[INFO] [2023-10-14 08:30:44] Traits to lifestage term...
[INFO] [2023-10-14 08:30:44] MetaTraits to traits...
[INFO] [2023-10-14 08:30:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-14 08:30:44] Assocs to occurrences...
[INFO] [2023-10-14 08:30:44] Assocs to nodes...
[INFO] [2023-10-14 08:30:44] Assoc to sex term...
[INFO] [2023-10-14 08:30:44] Assoc to lifestage term...
[INFO] [2023-10-14 08:30:44] MetaAssoc to assocs...
[STOP] [2023-10-14 08:30:44] resolve_keys
[START] [2023-10-14 08:30:44] hold_for_later_1
[STOP] [2023-10-14 08:30:44] hold_for_later_1
[START] [2023-10-14 08:30:44] hold_for_later_2
[STOP] [2023-10-14 08:30:44] hold_for_later_2
[START] [2023-10-14 08:30:44] resolve_missing_parents
[STOP] [2023-10-14 08:30:44] resolve_missing_parents
[START] [2023-10-14 08:30:44] rebuild_nodes
[START] [2023-10-14 08:30:44] Flattener#flatten
[START] [2023-10-14 08:30:44] Flattener#study_resource
[START] [2023-10-14 08:30:44] Flattener#build_ancestry
[STOP] [2023-10-14 08:30:44] Flattener#build_ancestry
[INFO] [2023-10-14 08:30:44] 1 ancestry keys
[START] [2023-10-14 08:30:44] build_node_ancestors
[INFO] [2023-10-14 08:30:44] old ancestors deleted.
[STOP] [2023-10-14 08:30:44] build_node_ancestors
[WARN] [2023-10-14 08:30:44] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-14 08:30:44] Flattener#flatten
[STOP] [2023-10-14 08:30:44] rebuild_nodes
[START] [2023-10-14 08:30:44] resolve_missing_media_owners
[STOP] [2023-10-14 08:30:44] resolve_missing_media_owners
[START] [2023-10-14 08:30:44] sanitize_media_verbatims
[STOP] [2023-10-14 08:30:44] sanitize_media_verbatims
[START] [2023-10-14 08:30:44] queue_downloads
[STOP] [2023-10-14 08:30:44] queue_downloads
[START] [2023-10-14 08:30:44] parse_names
[WARN] [2023-10-14 08:30:44] I see 1 names which still need to be parsed.
[WARN] [2023-10-14 08:30:44] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2023-10-14 08:30:45] parse_names
[START] [2023-10-14 08:30:45] denormalize_canonical_names_to_nodes
[STOP] [2023-10-14 08:30:45] denormalize_canonical_names_to_nodes
[START] [2023-10-14 08:30:45] match_nodes
[START] [2023-10-14 08:30:46] map_all_nodes_to_pages
[STOP] [2023-10-14 08:30:46] map_all_nodes_to_pages
[INFO] [2023-10-14 08:30:46] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2023-10-14 08:30:46] update_nodes
[STOP] [2023-10-14 08:30:46] update_nodes
[STOP] [2023-10-14 08:30:46] match_nodes
[START] [2023-10-14 08:30:46] reindex_search
[STOP] [2023-10-14 08:30:46] reindex_search
[START] [2023-10-14 08:30:46] normalize_units
[STOP] [2023-10-14 08:30:46] normalize_units
[START] [2023-10-14 08:30:46] calculate_statistics
[2023-10-14 08:30:46] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-14 08:30:46] Duplicate page_id count: 0
[STOP] [2023-10-14 08:30:46] calculate_statistics
[START] [2023-10-14 08:30:46] complete_harvest_instance
[START] [2023-10-14 08:30:46] overall_tsv_creation
[INFO] [2023-10-14 08:30:46] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2023-10-14 08:30:46] Processing group of 1 in 1 batches of 10000
[INFO] [2023-10-14 08:30:46] 4 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-14 08:30:46] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2023-10-14 08:30:46] Mapped 4 traits (8 meta) for 1 nodes.
[INFO] [2023-10-14 08:30:46] Building Associations map (this can take a while)...
[INFO] [2023-10-14 08:30:46] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-14 08:30:46] Adding 4 traits...
[INFO] [2023-10-14 08:30:46] 15 metadata added.
[INFO] [2023-10-14 08:30:46] Adding 0 assocs...
[INFO] [2023-10-14 08:30:46] 0 metadata added.
[INFO] [2023-10-14 08:31:29] Processed 1/1 nodes
[INFO] [2023-10-14 08:31:29] Average Time: 43.8
[INFO] [2023-10-14 08:31:29] Total Time: 44s
[STOP] [2023-10-14 08:31:29] overall_tsv_creation
[INFO] [2023-10-14 08:31:29] Done. Check your files:
[INFO] [2023-10-14 08:31:30] (1 lines) /app/public/data/budelmann_budelm/publish_nodes.tsv
[INFO] [2023-10-14 08:31:30] (1 lines) /app/public/data/budelmann_budelm/publish_scientific_names.tsv
[INFO] [2023-10-14 08:31:30] (5 lines) /app/public/data/budelmann_budelm/publish_traits.tsv
[INFO] [2023-10-14 08:31:30] (16 lines) /app/public/data/budelmann_budelm/publish_metadata.tsv
[STOP] [2023-10-14 08:31:30] complete_harvest_instance
[START] [2023-10-14 08:31:30] completed
[STOP] [2023-10-14 08:31:30] completed
[STOP] [2023-10-14 08:31:30] logged process, took 55.04
Latest Process

14 Oct 08:30 EXITED currently processing 0