Harvest for Genikhovich and Technau 2017 Created 03 Aug 17:05

Harvesting Log

[INFO] [2022-08-03 17:05:02] Created harvest instance #4188
[STOP] [2022-08-03 17:05:02] create_harvest_instance
[START] [2022-08-03 17:05:02] fetch_files
[STOP] [2022-08-03 17:05:02] fetch_files
[START] [2022-08-03 17:05:02] validate_each_file
[INFO] [2022-08-03 17:05:02] Looping over 3 formats...
[INFO] [2022-08-03 17:05:02] ...nodes (/app/public/data/genikhovich_tech/taxa.txt)
[INFO] [2022-08-03 17:05:03] Valid: /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_nodes_29630.csv (4 lines)
[INFO] [2022-08-03 17:05:03] ...occurrences (/app/public/data/genikhovich_tech/occurrences.txt)
[INFO] [2022-08-03 17:05:03] Valid: /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_occurrences_29631.csv (4 lines)
[INFO] [2022-08-03 17:05:03] ...measurements (/app/public/data/genikhovich_tech/measurementOrFact.txt)
[INFO] [2022-08-03 17:05:03] Valid: /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_measurements_29632.csv (8 lines)
[STOP] [2022-08-03 17:05:03] validate_each_file
[START] [2022-08-03 17:05:03] convert_to_csv
[INFO] [2022-08-03 17:05:03] Looping over 3 formats...
[INFO] [2022-08-03 17:05:03] ...nodes (/app/public/data/genikhovich_tech/taxa.txt)
[CMD] [2022-08-03 17:05:03] /usr/bin/sort /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_nodes_29630.csv > /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_nodes_29630.csv_sorted
[INFO] [2022-08-03 17:05:03] Converted: /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_nodes_29630.csv (4 lines)
[INFO] [2022-08-03 17:05:03] ...occurrences (/app/public/data/genikhovich_tech/occurrences.txt)
[CMD] [2022-08-03 17:05:03] /usr/bin/sort /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_occurrences_29631.csv > /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_occurrences_29631.csv_sorted
[INFO] [2022-08-03 17:05:03] Converted: /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_occurrences_29631.csv (4 lines)
[INFO] [2022-08-03 17:05:03] ...measurements (/app/public/data/genikhovich_tech/measurementOrFact.txt)
[CMD] [2022-08-03 17:05:03] /usr/bin/sort /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_measurements_29632.csv > /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_measurements_29632.csv_sorted
[INFO] [2022-08-03 17:05:03] Converted: /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_measurements_29632.csv (8 lines)
[STOP] [2022-08-03 17:05:03] convert_to_csv
[START] [2022-08-03 17:05:03] calculate_delta
[INFO] [2022-08-03 17:05:03] Looping over 3 formats...
[INFO] [2022-08-03 17:05:03] ...nodes (/app/public/data/genikhovich_tech/taxa.txt)
[CMD] [2022-08-03 17:05:03] echo "0a" > /app/public/data/genikhovich_tech/diff/genikhovich_tech_nodes_29630.diff
[CMD] [2022-08-03 17:05:03] tail -n +1 /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_nodes_29630.csv >> /app/public/data/genikhovich_tech/diff/genikhovich_tech_nodes_29630.diff
[CMD] [2022-08-03 17:05:03] echo "." >> /app/public/data/genikhovich_tech/diff/genikhovich_tech_nodes_29630.diff
[INFO] [2022-08-03 17:05:03] Created diff: /app/public/data/genikhovich_tech/diff/genikhovich_tech_nodes_29630.diff (6 lines)
[INFO] [2022-08-03 17:05:03] ...occurrences (/app/public/data/genikhovich_tech/occurrences.txt)
[CMD] [2022-08-03 17:05:03] echo "0a" > /app/public/data/genikhovich_tech/diff/genikhovich_tech_occurrences_29631.diff
[CMD] [2022-08-03 17:05:03] tail -n +1 /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_occurrences_29631.csv >> /app/public/data/genikhovich_tech/diff/genikhovich_tech_occurrences_29631.diff
[CMD] [2022-08-03 17:05:03] echo "." >> /app/public/data/genikhovich_tech/diff/genikhovich_tech_occurrences_29631.diff
[INFO] [2022-08-03 17:05:03] Created diff: /app/public/data/genikhovich_tech/diff/genikhovich_tech_occurrences_29631.diff (6 lines)
[INFO] [2022-08-03 17:05:03] ...measurements (/app/public/data/genikhovich_tech/measurementOrFact.txt)
[CMD] [2022-08-03 17:05:03] echo "0a" > /app/public/data/genikhovich_tech/diff/genikhovich_tech_measurements_29632.diff
[CMD] [2022-08-03 17:05:03] tail -n +1 /app/public/data/genikhovich_tech/converted_csv/genikhovich_tech_measurements_29632.csv >> /app/public/data/genikhovich_tech/diff/genikhovich_tech_measurements_29632.diff
[CMD] [2022-08-03 17:05:03] echo "." >> /app/public/data/genikhovich_tech/diff/genikhovich_tech_measurements_29632.diff
[INFO] [2022-08-03 17:05:03] Created diff: /app/public/data/genikhovich_tech/diff/genikhovich_tech_measurements_29632.diff (10 lines)
[STOP] [2022-08-03 17:05:03] calculate_delta
[START] [2022-08-03 17:05:03] parse_diff_and_store
[INFO] [2022-08-03 17:05:03] Handling diff: /app/public/data/genikhovich_tech/diff/genikhovich_tech_nodes_29630.diff (6 lines)
[INFO] [2022-08-03 17:05:03] Loading nodes diff file into memory (6 lines)...
[INFO] [2022-08-03 17:05:03] Storing 4 ScientificNames (8/4/6)
[INFO] [2022-08-03 17:05:03] Storing 4 Nodes (8/4/6)
[INFO] [2022-08-03 17:05:03] Handling diff: /app/public/data/genikhovich_tech/diff/genikhovich_tech_occurrences_29631.diff (6 lines)
[INFO] [2022-08-03 17:05:03] Loading occurrences diff file into memory (6 lines)...
[INFO] [2022-08-03 17:05:03] Storing 4 Occurrences (4/4/6)
[INFO] [2022-08-03 17:05:03] Handling diff: /app/public/data/genikhovich_tech/diff/genikhovich_tech_measurements_29632.diff (10 lines)
[INFO] [2022-08-03 17:05:03] Loading measurements diff file into memory (10 lines)...
[INFO] [2022-08-03 17:05:03] Storing 8 Traits (12/8/10)
[INFO] [2022-08-03 17:05:03] Storing 4 MetaTraits (12/8/10)
[STOP] [2022-08-03 17:05:03] parse_diff_and_store
[START] [2022-08-03 17:05:03] resolve_keys
[2022-08-03 17:05:03] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:05:10] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:05:10] traits to occurrences...
[INFO] [2022-08-03 17:05:10] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:05:10] Traits to sex term...
[INFO] [2022-08-03 17:05:10] Traits to lifestage term...
[INFO] [2022-08-03 17:05:10] MetaTraits to traits...
[INFO] [2022-08-03 17:05:10] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:05:10] Assocs to occurrences...
[INFO] [2022-08-03 17:05:10] Assocs to nodes...
[INFO] [2022-08-03 17:05:10] Assoc to sex term...
[INFO] [2022-08-03 17:05:10] Assoc to lifestage term...
[INFO] [2022-08-03 17:05:10] MetaAssoc to assocs...
[STOP] [2022-08-03 17:05:10] resolve_keys
[START] [2022-08-03 17:05:10] hold_for_later_1
[STOP] [2022-08-03 17:05:10] hold_for_later_1
[START] [2022-08-03 17:05:10] hold_for_later_2
[STOP] [2022-08-03 17:05:10] hold_for_later_2
[START] [2022-08-03 17:05:10] resolve_missing_parents
[STOP] [2022-08-03 17:05:10] resolve_missing_parents
[START] [2022-08-03 17:05:10] rebuild_nodes
[START] [2022-08-03 17:05:10] Flattener#flatten
[START] [2022-08-03 17:05:10] Flattener#study_resource
[START] [2022-08-03 17:05:10] Flattener#build_ancestry
[STOP] [2022-08-03 17:05:10] Flattener#build_ancestry
[INFO] [2022-08-03 17:05:10] 4 ancestry keys
[START] [2022-08-03 17:05:10] build_node_ancestors
[INFO] [2022-08-03 17:05:10] old ancestors deleted.
[STOP] [2022-08-03 17:05:10] build_node_ancestors
[WARN] [2022-08-03 17:05:10] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:05:10] Flattener#flatten
[STOP] [2022-08-03 17:05:10] rebuild_nodes
[START] [2022-08-03 17:05:10] resolve_missing_media_owners
[STOP] [2022-08-03 17:05:10] resolve_missing_media_owners
[START] [2022-08-03 17:05:10] sanitize_media_verbatims
[STOP] [2022-08-03 17:05:10] sanitize_media_verbatims
[START] [2022-08-03 17:05:10] queue_downloads
[STOP] [2022-08-03 17:05:10] queue_downloads
[START] [2022-08-03 17:05:10] parse_names
[WARN] [2022-08-03 17:05:10] I see 4 names which still need to be parsed.
[WARN] [2022-08-03 17:05:10] Names to parse: 4 formatted: 4 learned: 4 parsed: 4
[STOP] [2022-08-03 17:05:11] parse_names
[START] [2022-08-03 17:05:11] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:05:11] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:05:11] match_nodes
[START] [2022-08-03 17:05:11] map_all_nodes_to_pages
[STOP] [2022-08-03 17:05:12] map_all_nodes_to_pages
[INFO] [2022-08-03 17:05:12] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2022-08-03 17:05:12] update_nodes
[STOP] [2022-08-03 17:05:12] update_nodes
[STOP] [2022-08-03 17:05:12] match_nodes
[START] [2022-08-03 17:05:12] reindex_search
[STOP] [2022-08-03 17:05:12] reindex_search
[START] [2022-08-03 17:05:12] normalize_units
[STOP] [2022-08-03 17:05:12] normalize_units
[START] [2022-08-03 17:05:12] calculate_statistics
[2022-08-03 17:05:12] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:05:12] Duplicate page_id count: 0
[STOP] [2022-08-03 17:05:12] calculate_statistics
[START] [2022-08-03 17:05:12] complete_harvest_instance
[START] [2022-08-03 17:05:12] overall_tsv_creation
[INFO] [2022-08-03 17:05:12] Exporting 4 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:05:12] Processing group of 4 in 1 batches of 10000
[INFO] [2022-08-03 17:05:54] 4 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:05:54] Building Traits map for 4 nodes (this can take a while)...
[INFO] [2022-08-03 17:06:49] Mapped 4 traits (4 meta) for 4 nodes.
[INFO] [2022-08-03 17:06:49] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:06:49] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:06:49] Adding 4 traits...
[INFO] [2022-08-03 17:06:49] 4 metadata added.
[INFO] [2022-08-03 17:06:49] Adding 0 assocs...
[INFO] [2022-08-03 17:06:49] 0 metadata added.
[INFO] [2022-08-03 17:07:31] Processed 4/4 nodes
[INFO] [2022-08-03 17:07:31] Average Time: 113.79
[INFO] [2022-08-03 17:07:31] Total Time: 2m20s
[STOP] [2022-08-03 17:07:31] overall_tsv_creation
[INFO] [2022-08-03 17:07:31] Done. Check your files:
[INFO] [2022-08-03 17:07:31] (4 lines) /app/public/data/genikhovich_tech/publish_nodes.tsv
[INFO] [2022-08-03 17:07:31] (4 lines) /app/public/data/genikhovich_tech/publish_scientific_names.tsv
[INFO] [2022-08-03 17:07:31] (5 lines) /app/public/data/genikhovich_tech/publish_traits.tsv
[INFO] [2022-08-03 17:07:31] (5 lines) /app/public/data/genikhovich_tech/publish_metadata.tsv
[STOP] [2022-08-03 17:07:31] complete_harvest_instance
[START] [2022-08-03 17:07:31] completed
[STOP] [2022-08-03 17:07:31] completed
[STOP] [2022-08-03 17:07:31] logged process, took 148.5

Latest Process

03 Aug 17:05 EXITED currently processing 0