Harvest for Choe and Crespi 1997 Created 19 Jan 15:07

Stage: completed
Fetched: 19 Jan 15:07
Validated: 19 Jan 15:07
Deltas Created 19 Jan 15:07
Units Normalized: 19 Jan 15:07
Ancestry Built: 19 Jan 15:07
Nodes Matched: 19 Jan 15:07
Names Parsed: 19 Jan 15:07
New Models Stored: 19 Jan 15:07
Indexed: 19 Jan 15:07
Completed: 19 Jan 15:08
Time to Harvest: less than a minute
Harvesting Log

(143 lines)
[INFO] [2023-01-19 15:07:43] Created harvest instance #4264
[STOP] [2023-01-19 15:07:43] create_harvest_instance
[START] [2023-01-19 15:07:43] fetch_files
[STOP] [2023-01-19 15:07:43] fetch_files
[START] [2023-01-19 15:07:43] validate_each_file
[INFO] [2023-01-19 15:07:43] Looping over 3 formats...
[INFO] [2023-01-19 15:07:43] ...nodes (/app/public/data/choe_crespi_choe/taxa.txt)
[INFO] [2023-01-19 15:07:43] Valid: /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_nodes_30040.csv (5 lines)
[INFO] [2023-01-19 15:07:43] ...occurrences (/app/public/data/choe_crespi_choe/occurrences.txt)
[INFO] [2023-01-19 15:07:43] Valid: /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_occurrences_30041.csv (5 lines)
[INFO] [2023-01-19 15:07:43] ...measurements (/app/public/data/choe_crespi_choe/measurementsorfacts.txt)
[INFO] [2023-01-19 15:07:43] Valid: /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_measurements_30042.csv (15 lines)
[STOP] [2023-01-19 15:07:43] validate_each_file
[START] [2023-01-19 15:07:44] convert_to_csv
[INFO] [2023-01-19 15:07:44] Looping over 3 formats...
[INFO] [2023-01-19 15:07:44] ...nodes (/app/public/data/choe_crespi_choe/taxa.txt)
[CMD] [2023-01-19 15:07:44] /usr/bin/sort /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_nodes_30040.csv > /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_nodes_30040.csv_sorted
[INFO] [2023-01-19 15:07:44] Converted: /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_nodes_30040.csv (5 lines)
[INFO] [2023-01-19 15:07:44] ...occurrences (/app/public/data/choe_crespi_choe/occurrences.txt)
[CMD] [2023-01-19 15:07:44] /usr/bin/sort /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_occurrences_30041.csv > /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_occurrences_30041.csv_sorted
[INFO] [2023-01-19 15:07:44] Converted: /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_occurrences_30041.csv (5 lines)
[INFO] [2023-01-19 15:07:44] ...measurements (/app/public/data/choe_crespi_choe/measurementsorfacts.txt)
[CMD] [2023-01-19 15:07:44] /usr/bin/sort /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_measurements_30042.csv > /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_measurements_30042.csv_sorted
[INFO] [2023-01-19 15:07:44] Converted: /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_measurements_30042.csv (15 lines)
[STOP] [2023-01-19 15:07:44] convert_to_csv
[START] [2023-01-19 15:07:44] calculate_delta
[INFO] [2023-01-19 15:07:44] Looping over 3 formats...
[INFO] [2023-01-19 15:07:44] ...nodes (/app/public/data/choe_crespi_choe/taxa.txt)
[CMD] [2023-01-19 15:07:44] echo "0a" > /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_nodes_30040.diff
[CMD] [2023-01-19 15:07:44] tail -n +1 /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_nodes_30040.csv >> /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_nodes_30040.diff
[CMD] [2023-01-19 15:07:44] echo "." >> /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_nodes_30040.diff
[INFO] [2023-01-19 15:07:44] Created diff: /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_nodes_30040.diff (7 lines)
[INFO] [2023-01-19 15:07:44] ...occurrences (/app/public/data/choe_crespi_choe/occurrences.txt)
[CMD] [2023-01-19 15:07:44] echo "0a" > /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_occurrences_30041.diff
[CMD] [2023-01-19 15:07:44] tail -n +1 /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_occurrences_30041.csv >> /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_occurrences_30041.diff
[CMD] [2023-01-19 15:07:44] echo "." >> /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_occurrences_30041.diff
[INFO] [2023-01-19 15:07:44] Created diff: /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_occurrences_30041.diff (7 lines)
[INFO] [2023-01-19 15:07:44] ...measurements (/app/public/data/choe_crespi_choe/measurementsorfacts.txt)
[CMD] [2023-01-19 15:07:44] echo "0a" > /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_measurements_30042.diff
[CMD] [2023-01-19 15:07:44] tail -n +1 /app/public/data/choe_crespi_choe/converted_csv/choe_crespi_choe_measurements_30042.csv >> /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_measurements_30042.diff
[CMD] [2023-01-19 15:07:44] echo "." >> /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_measurements_30042.diff
[INFO] [2023-01-19 15:07:44] Created diff: /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_measurements_30042.diff (17 lines)
[STOP] [2023-01-19 15:07:44] calculate_delta
[START] [2023-01-19 15:07:44] parse_diff_and_store
[INFO] [2023-01-19 15:07:44] Handling diff: /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_nodes_30040.diff (7 lines)
[INFO] [2023-01-19 15:07:44] Loading nodes diff file into memory (7 lines)...
[INFO] [2023-01-19 15:07:44] Storing 5 ScientificNames (10/5/7)
[INFO] [2023-01-19 15:07:44] Storing 5 Nodes (10/5/7)
[INFO] [2023-01-19 15:07:44] Handling diff: /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_occurrences_30041.diff (7 lines)
[INFO] [2023-01-19 15:07:44] Loading occurrences diff file into memory (7 lines)...
[INFO] [2023-01-19 15:07:44] Storing 5 Occurrences (10/5/7)
[INFO] [2023-01-19 15:07:44] Storing 5 OccurrenceMetadata (10/5/7)
[INFO] [2023-01-19 15:07:44] Handling diff: /app/public/data/choe_crespi_choe/diff/choe_crespi_choe_measurements_30042.diff (17 lines)
[INFO] [2023-01-19 15:07:44] Loading measurements diff file into memory (17 lines)...
[INFO] [2023-01-19 15:07:44] Storing 15 Traits (23/15/17)
[INFO] [2023-01-19 15:07:44] Storing 8 MetaTraits (23/15/17)
[STOP] [2023-01-19 15:07:44] parse_diff_and_store
[START] [2023-01-19 15:07:44] resolve_keys
[2023-01-19 15:07:44] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-19 15:07:51] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-19 15:07:51] traits to occurrences...
[INFO] [2023-01-19 15:07:51] traits to nodes (through occurrences)...
[INFO] [2023-01-19 15:07:51] Traits to sex term...
[INFO] [2023-01-19 15:07:51] Traits to lifestage term...
[INFO] [2023-01-19 15:07:51] MetaTraits to traits...
[INFO] [2023-01-19 15:07:51] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-19 15:07:51] Assocs to occurrences...
[INFO] [2023-01-19 15:07:51] Assocs to nodes...
[INFO] [2023-01-19 15:07:51] Assoc to sex term...
[INFO] [2023-01-19 15:07:51] Assoc to lifestage term...
[INFO] [2023-01-19 15:07:51] MetaAssoc to assocs...
[STOP] [2023-01-19 15:07:51] resolve_keys
[START] [2023-01-19 15:07:51] hold_for_later_1
[STOP] [2023-01-19 15:07:51] hold_for_later_1
[START] [2023-01-19 15:07:51] hold_for_later_2
[STOP] [2023-01-19 15:07:51] hold_for_later_2
[START] [2023-01-19 15:07:51] resolve_missing_parents
[STOP] [2023-01-19 15:07:51] resolve_missing_parents
[START] [2023-01-19 15:07:51] rebuild_nodes
[START] [2023-01-19 15:07:51] Flattener#flatten
[START] [2023-01-19 15:07:51] Flattener#study_resource
[START] [2023-01-19 15:07:51] Flattener#build_ancestry
[STOP] [2023-01-19 15:07:51] Flattener#build_ancestry
[INFO] [2023-01-19 15:07:51] 5 ancestry keys
[START] [2023-01-19 15:07:51] build_node_ancestors
[INFO] [2023-01-19 15:07:51] old ancestors deleted.
[STOP] [2023-01-19 15:07:51] build_node_ancestors
[WARN] [2023-01-19 15:07:51] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-19 15:07:51] Flattener#flatten
[STOP] [2023-01-19 15:07:51] rebuild_nodes
[START] [2023-01-19 15:07:51] resolve_missing_media_owners
[STOP] [2023-01-19 15:07:51] resolve_missing_media_owners
[START] [2023-01-19 15:07:51] sanitize_media_verbatims
[STOP] [2023-01-19 15:07:51] sanitize_media_verbatims
[START] [2023-01-19 15:07:51] queue_downloads
[STOP] [2023-01-19 15:07:51] queue_downloads
[START] [2023-01-19 15:07:51] parse_names
[WARN] [2023-01-19 15:07:51] I see 5 names which still need to be parsed.
[WARN] [2023-01-19 15:07:51] Names to parse: 5 formatted: 5 learned: 5 parsed: 5
[STOP] [2023-01-19 15:07:52] parse_names
[START] [2023-01-19 15:07:52] denormalize_canonical_names_to_nodes
[STOP] [2023-01-19 15:07:52] denormalize_canonical_names_to_nodes
[START] [2023-01-19 15:07:52] match_nodes
[START] [2023-01-19 15:07:52] map_all_nodes_to_pages
[STOP] [2023-01-19 15:07:52] map_all_nodes_to_pages
[INFO] [2023-01-19 15:07:52] ZERO unmatched nodes (of 5)! Nicely done.
[START] [2023-01-19 15:07:52] update_nodes
[STOP] [2023-01-19 15:07:52] update_nodes
[STOP] [2023-01-19 15:07:52] match_nodes
[START] [2023-01-19 15:07:52] reindex_search
[STOP] [2023-01-19 15:07:53] reindex_search
[START] [2023-01-19 15:07:53] normalize_units
[STOP] [2023-01-19 15:07:53] normalize_units
[START] [2023-01-19 15:07:53] calculate_statistics
[2023-01-19 15:07:53] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-19 15:07:53] Duplicate page_id count: 0
[STOP] [2023-01-19 15:07:53] calculate_statistics
[START] [2023-01-19 15:07:53] complete_harvest_instance
[START] [2023-01-19 15:07:53] overall_tsv_creation
[INFO] [2023-01-19 15:07:53] Exporting 5 nodes as TSV in batches of 10000...
[INFO] [2023-01-19 15:07:53] Processing group of 5 in 1 batches of 10000
[INFO] [2023-01-19 15:07:53] 8 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-19 15:07:53] Building Traits map for 5 nodes (this can take a while)...
[INFO] [2023-01-19 15:07:53] Mapped 8 traits (8 meta) for 5 nodes.
[INFO] [2023-01-19 15:07:53] Building Associations map (this can take a while)...
[INFO] [2023-01-19 15:07:53] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-19 15:07:53] Adding 8 traits...
[INFO] [2023-01-19 15:07:53] 7 metadata added.
[INFO] [2023-01-19 15:07:53] Adding 0 assocs...
[INFO] [2023-01-19 15:07:53] 0 metadata added.
[INFO] [2023-01-19 15:08:37] Processed 5/5 nodes
[INFO] [2023-01-19 15:08:37] Average Time: 44.01
[INFO] [2023-01-19 15:08:37] Total Time: 45s
[STOP] [2023-01-19 15:08:37] overall_tsv_creation
[INFO] [2023-01-19 15:08:37] Done. Check your files:
[INFO] [2023-01-19 15:08:37] (5 lines) /app/public/data/choe_crespi_choe/publish_nodes.tsv
[INFO] [2023-01-19 15:08:37] (5 lines) /app/public/data/choe_crespi_choe/publish_scientific_names.tsv
[INFO] [2023-01-19 15:08:37] (9 lines) /app/public/data/choe_crespi_choe/publish_traits.tsv
[INFO] [2023-01-19 15:08:37] (8 lines) /app/public/data/choe_crespi_choe/publish_metadata.tsv
[STOP] [2023-01-19 15:08:37] complete_harvest_instance
[START] [2023-01-19 15:08:37] completed
[STOP] [2023-01-19 15:08:37] completed
[STOP] [2023-01-19 15:08:37] logged process, took 53.62
Latest Process

19 Jan 15:07 EXITED currently processing 0