Harvest for Gwynne 2001 Created 19 Jan 15:17

Stage: completed
Fetched: 19 Jan 15:17
Validated: 19 Jan 15:17
Deltas Created 19 Jan 15:17
Units Normalized: 19 Jan 15:18
Ancestry Built: 19 Jan 15:18
Nodes Matched: 19 Jan 15:18
Names Parsed: 19 Jan 15:18
New Models Stored: 19 Jan 15:17
Indexed: 19 Jan 15:18
Completed: 19 Jan 15:18
Time to Harvest: less than a minute
Harvesting Log

(144 lines)
[INFO] [2023-01-19 15:17:51] Created harvest instance #4265
[STOP] [2023-01-19 15:17:51] create_harvest_instance
[START] [2023-01-19 15:17:51] fetch_files
[STOP] [2023-01-19 15:17:51] fetch_files
[START] [2023-01-19 15:17:51] validate_each_file
[INFO] [2023-01-19 15:17:51] Looping over 3 formats...
[INFO] [2023-01-19 15:17:51] ...nodes (/app/public/data/gwynne_gwynne_20/taxa.txt)
[INFO] [2023-01-19 15:17:51] Valid: /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_nodes_30043.csv (154 lines)
[INFO] [2023-01-19 15:17:51] ...occurrences (/app/public/data/gwynne_gwynne_20/occurrences.txt)
[INFO] [2023-01-19 15:17:52] Valid: /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_occurrences_30044.csv (154 lines)
[INFO] [2023-01-19 15:17:52] ...measurements (/app/public/data/gwynne_gwynne_20/measurementsorfacts.txt)
[INFO] [2023-01-19 15:17:52] Valid: /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_measurements_30045.csv (574 lines)
[STOP] [2023-01-19 15:17:52] validate_each_file
[START] [2023-01-19 15:17:52] convert_to_csv
[INFO] [2023-01-19 15:17:52] Looping over 3 formats...
[INFO] [2023-01-19 15:17:52] ...nodes (/app/public/data/gwynne_gwynne_20/taxa.txt)
[CMD] [2023-01-19 15:17:52] /usr/bin/sort /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_nodes_30043.csv > /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_nodes_30043.csv_sorted
[INFO] [2023-01-19 15:17:52] Converted: /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_nodes_30043.csv (154 lines)
[INFO] [2023-01-19 15:17:52] ...occurrences (/app/public/data/gwynne_gwynne_20/occurrences.txt)
[CMD] [2023-01-19 15:17:52] /usr/bin/sort /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_occurrences_30044.csv > /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_occurrences_30044.csv_sorted
[INFO] [2023-01-19 15:17:52] Converted: /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_occurrences_30044.csv (154 lines)
[INFO] [2023-01-19 15:17:52] ...measurements (/app/public/data/gwynne_gwynne_20/measurementsorfacts.txt)
[CMD] [2023-01-19 15:17:52] /usr/bin/sort /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_measurements_30045.csv > /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_measurements_30045.csv_sorted
[INFO] [2023-01-19 15:17:52] Converted: /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_measurements_30045.csv (574 lines)
[STOP] [2023-01-19 15:17:52] convert_to_csv
[START] [2023-01-19 15:17:52] calculate_delta
[INFO] [2023-01-19 15:17:52] Looping over 3 formats...
[INFO] [2023-01-19 15:17:52] ...nodes (/app/public/data/gwynne_gwynne_20/taxa.txt)
[CMD] [2023-01-19 15:17:52] echo "0a" > /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_nodes_30043.diff
[CMD] [2023-01-19 15:17:52] tail -n +1 /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_nodes_30043.csv >> /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_nodes_30043.diff
[CMD] [2023-01-19 15:17:52] echo "." >> /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_nodes_30043.diff
[INFO] [2023-01-19 15:17:52] Created diff: /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_nodes_30043.diff (156 lines)
[INFO] [2023-01-19 15:17:52] ...occurrences (/app/public/data/gwynne_gwynne_20/occurrences.txt)
[CMD] [2023-01-19 15:17:52] echo "0a" > /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_occurrences_30044.diff
[CMD] [2023-01-19 15:17:52] tail -n +1 /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_occurrences_30044.csv >> /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_occurrences_30044.diff
[CMD] [2023-01-19 15:17:52] echo "." >> /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_occurrences_30044.diff
[INFO] [2023-01-19 15:17:52] Created diff: /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_occurrences_30044.diff (156 lines)
[INFO] [2023-01-19 15:17:52] ...measurements (/app/public/data/gwynne_gwynne_20/measurementsorfacts.txt)
[CMD] [2023-01-19 15:17:52] echo "0a" > /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_measurements_30045.diff
[CMD] [2023-01-19 15:17:52] tail -n +1 /app/public/data/gwynne_gwynne_20/converted_csv/gwynne_gwynne_20_measurements_30045.csv >> /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_measurements_30045.diff
[CMD] [2023-01-19 15:17:52] echo "." >> /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_measurements_30045.diff
[INFO] [2023-01-19 15:17:52] Created diff: /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_measurements_30045.diff (576 lines)
[STOP] [2023-01-19 15:17:52] calculate_delta
[START] [2023-01-19 15:17:52] parse_diff_and_store
[INFO] [2023-01-19 15:17:52] Handling diff: /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_nodes_30043.diff (156 lines)
[INFO] [2023-01-19 15:17:52] Loading nodes diff file into memory (156 lines)...
[INFO] [2023-01-19 15:17:52] Storing 158 ScientificNames (316/154/156)
[INFO] [2023-01-19 15:17:52] Storing 158 Nodes (316/154/156)
[INFO] [2023-01-19 15:17:52] Handling diff: /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_occurrences_30044.diff (156 lines)
[INFO] [2023-01-19 15:17:52] Loading occurrences diff file into memory (156 lines)...
[INFO] [2023-01-19 15:17:52] Storing 154 Occurrences (308/154/156)
[INFO] [2023-01-19 15:17:52] Storing 154 OccurrenceMetadata (308/154/156)
[INFO] [2023-01-19 15:17:52] Handling diff: /app/public/data/gwynne_gwynne_20/diff/gwynne_gwynne_20_measurements_30045.diff (576 lines)
[INFO] [2023-01-19 15:17:52] Loading measurements diff file into memory (576 lines)...
[INFO] [2023-01-19 15:17:52] Storing 574 Traits (1150/574/576)
[INFO] [2023-01-19 15:17:53] Storing 576 MetaTraits (1150/574/576)
[STOP] [2023-01-19 15:17:53] parse_diff_and_store
[START] [2023-01-19 15:17:53] resolve_keys
[2023-01-19 15:17:53] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-19 15:18:00] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-19 15:18:00] traits to occurrences...
[INFO] [2023-01-19 15:18:00] traits to nodes (through occurrences)...
[INFO] [2023-01-19 15:18:00] Traits to sex term...
[INFO] [2023-01-19 15:18:00] Traits to lifestage term...
[INFO] [2023-01-19 15:18:00] MetaTraits to traits...
[INFO] [2023-01-19 15:18:00] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-19 15:18:00] Assocs to occurrences...
[INFO] [2023-01-19 15:18:00] Assocs to nodes...
[INFO] [2023-01-19 15:18:00] Assoc to sex term...
[INFO] [2023-01-19 15:18:00] Assoc to lifestage term...
[INFO] [2023-01-19 15:18:00] MetaAssoc to assocs...
[STOP] [2023-01-19 15:18:00] resolve_keys
[START] [2023-01-19 15:18:00] hold_for_later_1
[STOP] [2023-01-19 15:18:00] hold_for_later_1
[START] [2023-01-19 15:18:00] hold_for_later_2
[STOP] [2023-01-19 15:18:00] hold_for_later_2
[START] [2023-01-19 15:18:00] resolve_missing_parents
[STOP] [2023-01-19 15:18:00] resolve_missing_parents
[START] [2023-01-19 15:18:00] rebuild_nodes
[START] [2023-01-19 15:18:00] Flattener#flatten
[START] [2023-01-19 15:18:00] Flattener#study_resource
[START] [2023-01-19 15:18:00] Flattener#build_ancestry
[STOP] [2023-01-19 15:18:00] Flattener#build_ancestry
[INFO] [2023-01-19 15:18:00] 158 ancestry keys
[START] [2023-01-19 15:18:00] build_node_ancestors
[INFO] [2023-01-19 15:18:00] old ancestors deleted.
[STOP] [2023-01-19 15:18:00] build_node_ancestors
[START] [2023-01-19 15:18:00] Flattener#propagate_ancestor_ids
[STOP] [2023-01-19 15:18:00] Flattener#propagate_ancestor_ids
[STOP] [2023-01-19 15:18:00] Flattener#flatten
[STOP] [2023-01-19 15:18:00] rebuild_nodes
[START] [2023-01-19 15:18:00] resolve_missing_media_owners
[STOP] [2023-01-19 15:18:00] resolve_missing_media_owners
[START] [2023-01-19 15:18:00] sanitize_media_verbatims
[STOP] [2023-01-19 15:18:00] sanitize_media_verbatims
[START] [2023-01-19 15:18:00] queue_downloads
[STOP] [2023-01-19 15:18:00] queue_downloads
[START] [2023-01-19 15:18:00] parse_names
[WARN] [2023-01-19 15:18:00] I see 158 names which still need to be parsed.
[WARN] [2023-01-19 15:18:00] Names to parse: 158 formatted: 158 learned: 158 parsed: 158
[STOP] [2023-01-19 15:18:01] parse_names
[START] [2023-01-19 15:18:01] denormalize_canonical_names_to_nodes
[STOP] [2023-01-19 15:18:01] denormalize_canonical_names_to_nodes
[START] [2023-01-19 15:18:01] match_nodes
[START] [2023-01-19 15:18:01] map_all_nodes_to_pages
[STOP] [2023-01-19 15:18:04] map_all_nodes_to_pages
[INFO] [2023-01-19 15:18:04] Unmatched nodes (2 of 158): Canonical: Meconematinae; Node#122416962; ResourceID: Metazoa/Arthropoda/Orthoptera/Meconematinae; Canonical: Speculophlugis; Node#122416963; ResourceID: Speculophlugis
[START] [2023-01-19 15:18:04] update_nodes
[STOP] [2023-01-19 15:18:04] update_nodes
[STOP] [2023-01-19 15:18:04] match_nodes
[START] [2023-01-19 15:18:04] reindex_search
[STOP] [2023-01-19 15:18:04] reindex_search
[START] [2023-01-19 15:18:04] normalize_units
[STOP] [2023-01-19 15:18:04] normalize_units
[START] [2023-01-19 15:18:04] calculate_statistics
[INFO] [2023-01-19 15:18:04] Duplicate page_id count: 2
[STOP] [2023-01-19 15:18:04] calculate_statistics
[START] [2023-01-19 15:18:04] complete_harvest_instance
[START] [2023-01-19 15:18:04] overall_tsv_creation
[INFO] [2023-01-19 15:18:04] Exporting 158 nodes as TSV in batches of 10000...
[INFO] [2023-01-19 15:18:04] Processing group of 158 in 1 batches of 10000
[INFO] [2023-01-19 15:18:05] 288 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-19 15:18:05] Building Traits map for 158 nodes (this can take a while)...
[INFO] [2023-01-19 15:18:05] Mapped 288 traits (576 meta) for 158 nodes.
[INFO] [2023-01-19 15:18:05] Building Associations map (this can take a while)...
[INFO] [2023-01-19 15:18:05] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-19 15:18:05] Adding 288 traits...
[INFO] [2023-01-19 15:18:05] 286 metadata added.
[INFO] [2023-01-19 15:18:05] Adding 0 assocs...
[INFO] [2023-01-19 15:18:05] 0 metadata added.
[INFO] [2023-01-19 15:18:49] Processed 158/158 nodes
[INFO] [2023-01-19 15:18:49] Average Time: 44.49
[INFO] [2023-01-19 15:18:49] Total Time: 45s
[STOP] [2023-01-19 15:18:49] overall_tsv_creation
[INFO] [2023-01-19 15:18:49] Done. Check your files:
[INFO] [2023-01-19 15:18:49] (158 lines) /app/public/data/gwynne_gwynne_20/publish_nodes.tsv
[INFO] [2023-01-19 15:18:49] (10 lines) /app/public/data/gwynne_gwynne_20/publish_node_ancestors.tsv
[INFO] [2023-01-19 15:18:49] (158 lines) /app/public/data/gwynne_gwynne_20/publish_scientific_names.tsv
[INFO] [2023-01-19 15:18:49] (289 lines) /app/public/data/gwynne_gwynne_20/publish_traits.tsv
[INFO] [2023-01-19 15:18:49] (287 lines) /app/public/data/gwynne_gwynne_20/publish_metadata.tsv
[STOP] [2023-01-19 15:18:49] complete_harvest_instance
[START] [2023-01-19 15:18:49] completed
[STOP] [2023-01-19 15:18:49] completed
[STOP] [2023-01-19 15:18:49] logged process, took 57.65
Latest Process

19 Jan 15:17 EXITED currently processing 0