Harvest for GANS 1975 Created 14 Oct 08:52

Stage: completed
Fetched: 14 Oct 08:52
Validated: 14 Oct 08:52
Deltas Created 14 Oct 08:52
Units Normalized: 14 Oct 08:52
Ancestry Built: 14 Oct 08:52
Nodes Matched: 14 Oct 08:52
Names Parsed: 14 Oct 08:52
New Models Stored: 14 Oct 08:52
Indexed: 14 Oct 08:52
Completed: 14 Oct 08:53
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2023-10-14 08:52:21] Created harvest instance #4476
[STOP] [2023-10-14 08:52:21] create_harvest_instance
[START] [2023-10-14 08:52:21] fetch_files
[STOP] [2023-10-14 08:52:21] fetch_files
[START] [2023-10-14 08:52:21] validate_each_file
[INFO] [2023-10-14 08:52:21] Looping over 3 formats...
[INFO] [2023-10-14 08:52:21] ...nodes (/app/public/data/gans_1975_gans_1/taxa.txt)
[INFO] [2023-10-14 08:52:21] Valid: /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_nodes_30909.csv (18 lines)
[INFO] [2023-10-14 08:52:21] ...occurrences (/app/public/data/gans_1975_gans_1/occurrences.txt)
[INFO] [2023-10-14 08:52:21] Valid: /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_occurrences_30910.csv (18 lines)
[INFO] [2023-10-14 08:52:21] ...measurements (/app/public/data/gans_1975_gans_1/measurementsorfacts.txt)
[INFO] [2023-10-14 08:52:21] Valid: /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_measurements_30911.csv (57 lines)
[STOP] [2023-10-14 08:52:21] validate_each_file
[START] [2023-10-14 08:52:21] convert_to_csv
[INFO] [2023-10-14 08:52:21] Looping over 3 formats...
[INFO] [2023-10-14 08:52:21] ...nodes (/app/public/data/gans_1975_gans_1/taxa.txt)
[CMD] [2023-10-14 08:52:21] /usr/bin/sort /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_nodes_30909.csv > /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_nodes_30909.csv_sorted
[INFO] [2023-10-14 08:52:22] Converted: /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_nodes_30909.csv (18 lines)
[INFO] [2023-10-14 08:52:22] ...occurrences (/app/public/data/gans_1975_gans_1/occurrences.txt)
[CMD] [2023-10-14 08:52:22] /usr/bin/sort /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_occurrences_30910.csv > /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_occurrences_30910.csv_sorted
[INFO] [2023-10-14 08:52:22] Converted: /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_occurrences_30910.csv (18 lines)
[INFO] [2023-10-14 08:52:22] ...measurements (/app/public/data/gans_1975_gans_1/measurementsorfacts.txt)
[CMD] [2023-10-14 08:52:22] /usr/bin/sort /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_measurements_30911.csv > /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_measurements_30911.csv_sorted
[INFO] [2023-10-14 08:52:22] Converted: /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_measurements_30911.csv (57 lines)
[STOP] [2023-10-14 08:52:22] convert_to_csv
[START] [2023-10-14 08:52:22] calculate_delta
[INFO] [2023-10-14 08:52:22] Looping over 3 formats...
[INFO] [2023-10-14 08:52:22] ...nodes (/app/public/data/gans_1975_gans_1/taxa.txt)
[CMD] [2023-10-14 08:52:22] echo "0a" > /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_nodes_30909.diff
[CMD] [2023-10-14 08:52:22] tail -n +1 /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_nodes_30909.csv >> /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_nodes_30909.diff
[CMD] [2023-10-14 08:52:22] echo "." >> /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_nodes_30909.diff
[INFO] [2023-10-14 08:52:22] Created diff: /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_nodes_30909.diff (20 lines)
[INFO] [2023-10-14 08:52:22] ...occurrences (/app/public/data/gans_1975_gans_1/occurrences.txt)
[CMD] [2023-10-14 08:52:22] echo "0a" > /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_occurrences_30910.diff
[CMD] [2023-10-14 08:52:22] tail -n +1 /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_occurrences_30910.csv >> /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_occurrences_30910.diff
[CMD] [2023-10-14 08:52:22] echo "." >> /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_occurrences_30910.diff
[INFO] [2023-10-14 08:52:22] Created diff: /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_occurrences_30910.diff (20 lines)
[INFO] [2023-10-14 08:52:22] ...measurements (/app/public/data/gans_1975_gans_1/measurementsorfacts.txt)
[CMD] [2023-10-14 08:52:22] echo "0a" > /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_measurements_30911.diff
[CMD] [2023-10-14 08:52:22] tail -n +1 /app/public/data/gans_1975_gans_1/converted_csv/gans_1975_gans_1_measurements_30911.csv >> /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_measurements_30911.diff
[CMD] [2023-10-14 08:52:23] echo "." >> /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_measurements_30911.diff
[INFO] [2023-10-14 08:52:23] Created diff: /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_measurements_30911.diff (59 lines)
[STOP] [2023-10-14 08:52:23] calculate_delta
[START] [2023-10-14 08:52:23] parse_diff_and_store
[INFO] [2023-10-14 08:52:23] Handling diff: /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_nodes_30909.diff (20 lines)
[INFO] [2023-10-14 08:52:23] Loading nodes diff file into memory (20 lines)...
[INFO] [2023-10-14 08:52:23] Storing 18 ScientificNames (36/18/20)
[INFO] [2023-10-14 08:52:23] Storing 18 Nodes (36/18/20)
[INFO] [2023-10-14 08:52:23] Handling diff: /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_occurrences_30910.diff (20 lines)
[INFO] [2023-10-14 08:52:23] Loading occurrences diff file into memory (20 lines)...
[INFO] [2023-10-14 08:52:23] Storing 18 Occurrences (18/18/20)
[INFO] [2023-10-14 08:52:23] Handling diff: /app/public/data/gans_1975_gans_1/diff/gans_1975_gans_1_measurements_30911.diff (59 lines)
[INFO] [2023-10-14 08:52:23] Loading measurements diff file into memory (59 lines)...
[INFO] [2023-10-14 08:52:23] Storing 57 Traits (78/57/59)
[INFO] [2023-10-14 08:52:23] Storing 21 MetaTraits (78/57/59)
[STOP] [2023-10-14 08:52:23] parse_diff_and_store
[START] [2023-10-14 08:52:23] resolve_keys
[2023-10-14 08:52:23] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-14 08:52:31] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-14 08:52:31] traits to occurrences...
[INFO] [2023-10-14 08:52:31] traits to nodes (through occurrences)...
[INFO] [2023-10-14 08:52:31] Traits to sex term...
[INFO] [2023-10-14 08:52:31] Traits to lifestage term...
[INFO] [2023-10-14 08:52:31] MetaTraits to traits...
[INFO] [2023-10-14 08:52:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-14 08:52:31] Assocs to occurrences...
[INFO] [2023-10-14 08:52:31] Assocs to nodes...
[INFO] [2023-10-14 08:52:31] Assoc to sex term...
[INFO] [2023-10-14 08:52:31] Assoc to lifestage term...
[INFO] [2023-10-14 08:52:31] MetaAssoc to assocs...
[STOP] [2023-10-14 08:52:31] resolve_keys
[START] [2023-10-14 08:52:31] hold_for_later_1
[STOP] [2023-10-14 08:52:31] hold_for_later_1
[START] [2023-10-14 08:52:31] hold_for_later_2
[STOP] [2023-10-14 08:52:31] hold_for_later_2
[START] [2023-10-14 08:52:31] resolve_missing_parents
[STOP] [2023-10-14 08:52:31] resolve_missing_parents
[START] [2023-10-14 08:52:31] rebuild_nodes
[START] [2023-10-14 08:52:31] Flattener#flatten
[START] [2023-10-14 08:52:31] Flattener#study_resource
[START] [2023-10-14 08:52:31] Flattener#build_ancestry
[STOP] [2023-10-14 08:52:31] Flattener#build_ancestry
[INFO] [2023-10-14 08:52:31] 18 ancestry keys
[START] [2023-10-14 08:52:31] build_node_ancestors
[INFO] [2023-10-14 08:52:31] old ancestors deleted.
[STOP] [2023-10-14 08:52:31] build_node_ancestors
[WARN] [2023-10-14 08:52:31] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-14 08:52:31] Flattener#flatten
[STOP] [2023-10-14 08:52:31] rebuild_nodes
[START] [2023-10-14 08:52:31] resolve_missing_media_owners
[STOP] [2023-10-14 08:52:31] resolve_missing_media_owners
[START] [2023-10-14 08:52:31] sanitize_media_verbatims
[STOP] [2023-10-14 08:52:31] sanitize_media_verbatims
[START] [2023-10-14 08:52:31] queue_downloads
[STOP] [2023-10-14 08:52:31] queue_downloads
[START] [2023-10-14 08:52:31] parse_names
[WARN] [2023-10-14 08:52:31] I see 18 names which still need to be parsed.
[WARN] [2023-10-14 08:52:31] Names to parse: 18 formatted: 18 learned: 18 parsed: 18
[STOP] [2023-10-14 08:52:32] parse_names
[START] [2023-10-14 08:52:32] denormalize_canonical_names_to_nodes
[STOP] [2023-10-14 08:52:32] denormalize_canonical_names_to_nodes
[START] [2023-10-14 08:52:32] match_nodes
[START] [2023-10-14 08:52:32] map_all_nodes_to_pages
[STOP] [2023-10-14 08:52:32] map_all_nodes_to_pages
[INFO] [2023-10-14 08:52:32] ZERO unmatched nodes (of 18)! Nicely done.
[START] [2023-10-14 08:52:32] update_nodes
[STOP] [2023-10-14 08:52:32] update_nodes
[STOP] [2023-10-14 08:52:32] match_nodes
[START] [2023-10-14 08:52:32] reindex_search
[STOP] [2023-10-14 08:52:32] reindex_search
[START] [2023-10-14 08:52:32] normalize_units
[STOP] [2023-10-14 08:52:32] normalize_units
[START] [2023-10-14 08:52:32] calculate_statistics
[2023-10-14 08:52:32] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-14 08:52:32] Duplicate page_id count: 0
[STOP] [2023-10-14 08:52:32] calculate_statistics
[START] [2023-10-14 08:52:32] complete_harvest_instance
[START] [2023-10-14 08:52:32] overall_tsv_creation
[INFO] [2023-10-14 08:52:32] Exporting 18 nodes as TSV in batches of 10000...
[INFO] [2023-10-14 08:52:32] Processing group of 18 in 1 batches of 10000
[INFO] [2023-10-14 08:52:33] 21 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-14 08:52:33] Building Traits map for 18 nodes (this can take a while)...
[INFO] [2023-10-14 08:52:33] Mapped 21 traits (21 meta) for 18 nodes.
[INFO] [2023-10-14 08:52:33] Building Associations map (this can take a while)...
[INFO] [2023-10-14 08:52:33] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-14 08:52:33] Adding 21 traits...
[INFO] [2023-10-14 08:52:33] 36 metadata added.
[INFO] [2023-10-14 08:52:33] Adding 0 assocs...
[INFO] [2023-10-14 08:52:33] 0 metadata added.
[INFO] [2023-10-14 08:53:16] Processed 18/18 nodes
[INFO] [2023-10-14 08:53:16] Average Time: 44.0
[INFO] [2023-10-14 08:53:16] Total Time: 45s
[STOP] [2023-10-14 08:53:17] overall_tsv_creation
[INFO] [2023-10-14 08:53:17] Done. Check your files:
[INFO] [2023-10-14 08:53:17] (18 lines) /app/public/data/gans_1975_gans_1/publish_nodes.tsv
[INFO] [2023-10-14 08:53:17] (18 lines) /app/public/data/gans_1975_gans_1/publish_scientific_names.tsv
[INFO] [2023-10-14 08:53:17] (22 lines) /app/public/data/gans_1975_gans_1/publish_traits.tsv
[INFO] [2023-10-14 08:53:17] (37 lines) /app/public/data/gans_1975_gans_1/publish_metadata.tsv
[STOP] [2023-10-14 08:53:17] complete_harvest_instance
[START] [2023-10-14 08:53:17] completed
[STOP] [2023-10-14 08:53:17] completed
[STOP] [2023-10-14 08:53:17] logged process, took 55.64
Latest Process

14 Oct 08:52 EXITED currently processing 0