Harvest for Nebelsick 1992 Created 13 Oct 13:32

Stage: completed
Fetched: 13 Oct 13:32
Validated: 13 Oct 13:32
Deltas Created 13 Oct 13:32
Units Normalized: 13 Oct 13:32
Ancestry Built: 13 Oct 13:32
Nodes Matched: 13 Oct 13:32
Names Parsed: 13 Oct 13:32
New Models Stored: 13 Oct 13:32
Indexed: 13 Oct 13:32
Completed: 13 Oct 13:33
Time to Harvest: less than a minute
Harvesting Log

(157 lines)
[INFO] [2023-10-13 13:32:34] Created harvest instance #4451
[STOP] [2023-10-13 13:32:34] create_harvest_instance
[START] [2023-10-13 13:32:34] fetch_files
[STOP] [2023-10-13 13:32:34] fetch_files
[START] [2023-10-13 13:32:34] validate_each_file
[INFO] [2023-10-13 13:32:34] Looping over 4 formats...
[INFO] [2023-10-13 13:32:34] ...refs (/app/public/data/nebelsick_nebels/references.txt)
[INFO] [2023-10-13 13:32:34] Valid: /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_refs_30811.csv (1 lines)
[INFO] [2023-10-13 13:32:34] ...nodes (/app/public/data/nebelsick_nebels/taxa.txt)
[INFO] [2023-10-13 13:32:34] Valid: /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_nodes_30808.csv (9 lines)
[INFO] [2023-10-13 13:32:34] ...occurrences (/app/public/data/nebelsick_nebels/occurrences.txt)
[INFO] [2023-10-13 13:32:34] Valid: /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_occurrences_30809.csv (9 lines)
[INFO] [2023-10-13 13:32:34] ...measurements (/app/public/data/nebelsick_nebels/measurementsorfacts.txt)
[INFO] [2023-10-13 13:32:34] Valid: /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_measurements_30810.csv (19 lines)
[STOP] [2023-10-13 13:32:34] validate_each_file
[START] [2023-10-13 13:32:34] convert_to_csv
[INFO] [2023-10-13 13:32:34] Looping over 4 formats...
[INFO] [2023-10-13 13:32:34] ...refs (/app/public/data/nebelsick_nebels/references.txt)
[CMD] [2023-10-13 13:32:34] /usr/bin/sort /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_refs_30811.csv > /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_refs_30811.csv_sorted
[INFO] [2023-10-13 13:32:34] Converted: /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_refs_30811.csv (1 lines)
[INFO] [2023-10-13 13:32:34] ...nodes (/app/public/data/nebelsick_nebels/taxa.txt)
[CMD] [2023-10-13 13:32:34] /usr/bin/sort /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_nodes_30808.csv > /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_nodes_30808.csv_sorted
[INFO] [2023-10-13 13:32:35] Converted: /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_nodes_30808.csv (9 lines)
[INFO] [2023-10-13 13:32:35] ...occurrences (/app/public/data/nebelsick_nebels/occurrences.txt)
[CMD] [2023-10-13 13:32:35] /usr/bin/sort /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_occurrences_30809.csv > /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_occurrences_30809.csv_sorted
[INFO] [2023-10-13 13:32:35] Converted: /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_occurrences_30809.csv (9 lines)
[INFO] [2023-10-13 13:32:35] ...measurements (/app/public/data/nebelsick_nebels/measurementsorfacts.txt)
[CMD] [2023-10-13 13:32:35] /usr/bin/sort /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_measurements_30810.csv > /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_measurements_30810.csv_sorted
[INFO] [2023-10-13 13:32:35] Converted: /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_measurements_30810.csv (19 lines)
[STOP] [2023-10-13 13:32:35] convert_to_csv
[START] [2023-10-13 13:32:35] calculate_delta
[INFO] [2023-10-13 13:32:35] Looping over 4 formats...
[INFO] [2023-10-13 13:32:35] ...refs (/app/public/data/nebelsick_nebels/references.txt)
[CMD] [2023-10-13 13:32:35] echo "0a" > /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_refs_30811.diff
[CMD] [2023-10-13 13:32:35] tail -n +1 /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_refs_30811.csv >> /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_refs_30811.diff
[CMD] [2023-10-13 13:32:35] echo "." >> /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_refs_30811.diff
[INFO] [2023-10-13 13:32:35] Created diff: /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_refs_30811.diff (3 lines)
[INFO] [2023-10-13 13:32:35] ...nodes (/app/public/data/nebelsick_nebels/taxa.txt)
[CMD] [2023-10-13 13:32:35] echo "0a" > /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_nodes_30808.diff
[CMD] [2023-10-13 13:32:35] tail -n +1 /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_nodes_30808.csv >> /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_nodes_30808.diff
[CMD] [2023-10-13 13:32:35] echo "." >> /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_nodes_30808.diff
[INFO] [2023-10-13 13:32:35] Created diff: /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_nodes_30808.diff (11 lines)
[INFO] [2023-10-13 13:32:35] ...occurrences (/app/public/data/nebelsick_nebels/occurrences.txt)
[CMD] [2023-10-13 13:32:35] echo "0a" > /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_occurrences_30809.diff
[CMD] [2023-10-13 13:32:35] tail -n +1 /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_occurrences_30809.csv >> /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_occurrences_30809.diff
[CMD] [2023-10-13 13:32:35] echo "." >> /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_occurrences_30809.diff
[INFO] [2023-10-13 13:32:35] Created diff: /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_occurrences_30809.diff (11 lines)
[INFO] [2023-10-13 13:32:35] ...measurements (/app/public/data/nebelsick_nebels/measurementsorfacts.txt)
[CMD] [2023-10-13 13:32:35] echo "0a" > /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_measurements_30810.diff
[CMD] [2023-10-13 13:32:35] tail -n +1 /app/public/data/nebelsick_nebels/converted_csv/nebelsick_nebels_measurements_30810.csv >> /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_measurements_30810.diff
[CMD] [2023-10-13 13:32:35] echo "." >> /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_measurements_30810.diff
[INFO] [2023-10-13 13:32:36] Created diff: /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_measurements_30810.diff (21 lines)
[STOP] [2023-10-13 13:32:36] calculate_delta
[START] [2023-10-13 13:32:36] parse_diff_and_store
[INFO] [2023-10-13 13:32:36] Handling diff: /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_refs_30811.diff (3 lines)
[INFO] [2023-10-13 13:32:36] Loading refs diff file into memory (3 lines)...
[INFO] [2023-10-13 13:32:36] Storing 1 References (1/1/3)
[INFO] [2023-10-13 13:32:36] Handling diff: /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_nodes_30808.diff (11 lines)
[INFO] [2023-10-13 13:32:36] Loading nodes diff file into memory (11 lines)...
[INFO] [2023-10-13 13:32:36] Storing 9 ScientificNames (18/9/11)
[INFO] [2023-10-13 13:32:36] Storing 9 Nodes (18/9/11)
[INFO] [2023-10-13 13:32:36] Handling diff: /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_occurrences_30809.diff (11 lines)
[INFO] [2023-10-13 13:32:36] Loading occurrences diff file into memory (11 lines)...
[INFO] [2023-10-13 13:32:36] Storing 9 Occurrences (10/9/11)
[INFO] [2023-10-13 13:32:36] Storing 1 OccurrenceMetadata (10/9/11)
[INFO] [2023-10-13 13:32:36] Handling diff: /app/public/data/nebelsick_nebels/diff/nebelsick_nebels_measurements_30810.diff (21 lines)
[INFO] [2023-10-13 13:32:36] Loading measurements diff file into memory (21 lines)...
[INFO] [2023-10-13 13:32:36] Storing 19 Traits (44/19/21)
[INFO] [2023-10-13 13:32:36] Storing 17 MetaTraits (44/19/21)
[INFO] [2023-10-13 13:32:36] Storing 8 TraitsReferences (44/19/21)
[STOP] [2023-10-13 13:32:36] parse_diff_and_store
[START] [2023-10-13 13:32:36] resolve_keys
[2023-10-13 13:32:36] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:32:44] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:32:44] traits to occurrences...
[INFO] [2023-10-13 13:32:44] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:32:44] Traits to sex term...
[INFO] [2023-10-13 13:32:44] Traits to lifestage term...
[INFO] [2023-10-13 13:32:44] MetaTraits to traits...
[INFO] [2023-10-13 13:32:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:32:44] Assocs to occurrences...
[INFO] [2023-10-13 13:32:44] Assocs to nodes...
[INFO] [2023-10-13 13:32:44] Assoc to sex term...
[INFO] [2023-10-13 13:32:44] Assoc to lifestage term...
[INFO] [2023-10-13 13:32:44] MetaAssoc to assocs...
[STOP] [2023-10-13 13:32:44] resolve_keys
[START] [2023-10-13 13:32:44] hold_for_later_1
[STOP] [2023-10-13 13:32:44] hold_for_later_1
[START] [2023-10-13 13:32:44] hold_for_later_2
[STOP] [2023-10-13 13:32:44] hold_for_later_2
[START] [2023-10-13 13:32:44] resolve_missing_parents
[STOP] [2023-10-13 13:32:44] resolve_missing_parents
[START] [2023-10-13 13:32:44] rebuild_nodes
[START] [2023-10-13 13:32:44] Flattener#flatten
[START] [2023-10-13 13:32:44] Flattener#study_resource
[START] [2023-10-13 13:32:44] Flattener#build_ancestry
[STOP] [2023-10-13 13:32:44] Flattener#build_ancestry
[INFO] [2023-10-13 13:32:44] 9 ancestry keys
[START] [2023-10-13 13:32:44] build_node_ancestors
[INFO] [2023-10-13 13:32:44] old ancestors deleted.
[STOP] [2023-10-13 13:32:44] build_node_ancestors
[WARN] [2023-10-13 13:32:44] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:32:44] Flattener#flatten
[STOP] [2023-10-13 13:32:44] rebuild_nodes
[START] [2023-10-13 13:32:44] resolve_missing_media_owners
[STOP] [2023-10-13 13:32:44] resolve_missing_media_owners
[START] [2023-10-13 13:32:44] sanitize_media_verbatims
[STOP] [2023-10-13 13:32:44] sanitize_media_verbatims
[START] [2023-10-13 13:32:44] queue_downloads
[STOP] [2023-10-13 13:32:44] queue_downloads
[START] [2023-10-13 13:32:44] parse_names
[WARN] [2023-10-13 13:32:44] I see 9 names which still need to be parsed.
[WARN] [2023-10-13 13:32:44] Names to parse: 9 formatted: 9 learned: 5 parsed: 9
[STOP] [2023-10-13 13:32:45] parse_names
[START] [2023-10-13 13:32:45] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:32:45] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:32:45] match_nodes
[START] [2023-10-13 13:32:45] map_all_nodes_to_pages
[STOP] [2023-10-13 13:32:45] map_all_nodes_to_pages
[INFO] [2023-10-13 13:32:45] ZERO unmatched nodes (of 9)! Nicely done.
[START] [2023-10-13 13:32:45] update_nodes
[STOP] [2023-10-13 13:32:45] update_nodes
[STOP] [2023-10-13 13:32:45] match_nodes
[START] [2023-10-13 13:32:45] reindex_search
[STOP] [2023-10-13 13:32:45] reindex_search
[START] [2023-10-13 13:32:45] normalize_units
[STOP] [2023-10-13 13:32:45] normalize_units
[START] [2023-10-13 13:32:45] calculate_statistics
[2023-10-13 13:32:45] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:32:45] Duplicate page_id count: 8
[STOP] [2023-10-13 13:32:45] calculate_statistics
[START] [2023-10-13 13:32:45] complete_harvest_instance
[START] [2023-10-13 13:32:45] overall_tsv_creation
[INFO] [2023-10-13 13:32:45] Exporting 9 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:32:45] Processing group of 9 in 1 batches of 10000
[INFO] [2023-10-13 13:32:45] 9 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:32:45] Building Traits map for 9 nodes (this can take a while)...
[INFO] [2023-10-13 13:32:45] Mapped 9 traits (17 meta) for 9 nodes.
[INFO] [2023-10-13 13:32:45] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:32:45] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:32:45] Adding 9 traits...
[INFO] [2023-10-13 13:32:45] 18 metadata added.
[INFO] [2023-10-13 13:32:45] Adding 0 assocs...
[INFO] [2023-10-13 13:32:45] 0 metadata added.
[INFO] [2023-10-13 13:33:29] Processed 9/9 nodes
[INFO] [2023-10-13 13:33:29] Average Time: 43.87
[INFO] [2023-10-13 13:33:29] Total Time: 44s
[STOP] [2023-10-13 13:33:29] overall_tsv_creation
[INFO] [2023-10-13 13:33:29] Done. Check your files:
[INFO] [2023-10-13 13:33:29] (5 lines) /app/public/data/nebelsick_nebels/publish_nodes.tsv
[INFO] [2023-10-13 13:33:29] (9 lines) /app/public/data/nebelsick_nebels/publish_scientific_names.tsv
[INFO] [2023-10-13 13:33:29] (10 lines) /app/public/data/nebelsick_nebels/publish_traits.tsv
[INFO] [2023-10-13 13:33:29] (19 lines) /app/public/data/nebelsick_nebels/publish_metadata.tsv
[STOP] [2023-10-13 13:33:29] complete_harvest_instance
[START] [2023-10-13 13:33:29] completed
[STOP] [2023-10-13 13:33:29] completed
[STOP] [2023-10-13 13:33:29] logged process, took 55.16
Latest Process

13 Oct 13:32 EXITED currently processing 0