Harvest for Fornoff et al 2012 Created 19 Jan 14:57

Stage: completed
Fetched: 19 Jan 14:57
Validated: 19 Jan 14:57
Deltas Created 19 Jan 14:57
Units Normalized: 19 Jan 14:57
Ancestry Built: 19 Jan 14:57
Nodes Matched: 19 Jan 14:57
Names Parsed: 19 Jan 14:57
New Models Stored: 19 Jan 14:57
Indexed: 19 Jan 14:57
Completed: 19 Jan 14:58
Time to Harvest: less than a minute
Harvesting Log

(144 lines)
[INFO] [2023-01-19 14:57:21] Created harvest instance #4263
[STOP] [2023-01-19 14:57:21] create_harvest_instance
[START] [2023-01-19 14:57:21] fetch_files
[STOP] [2023-01-19 14:57:21] fetch_files
[START] [2023-01-19 14:57:21] validate_each_file
[INFO] [2023-01-19 14:57:21] Looping over 3 formats...
[INFO] [2023-01-19 14:57:21] ...nodes (/app/public/data/fornoff_et_al_fo/taxa.txt)
[INFO] [2023-01-19 14:57:21] Valid: /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_nodes_30037.csv (2 lines)
[INFO] [2023-01-19 14:57:21] ...occurrences (/app/public/data/fornoff_et_al_fo/occurrences.txt)
[INFO] [2023-01-19 14:57:21] Valid: /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_occurrences_30038.csv (2 lines)
[INFO] [2023-01-19 14:57:21] ...measurements (/app/public/data/fornoff_et_al_fo/measurementsorfacts.txt)
[INFO] [2023-01-19 14:57:21] Valid: /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_measurements_30039.csv (159 lines)
[STOP] [2023-01-19 14:57:21] validate_each_file
[START] [2023-01-19 14:57:21] convert_to_csv
[INFO] [2023-01-19 14:57:21] Looping over 3 formats...
[INFO] [2023-01-19 14:57:21] ...nodes (/app/public/data/fornoff_et_al_fo/taxa.txt)
[CMD] [2023-01-19 14:57:21] /usr/bin/sort /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_nodes_30037.csv > /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_nodes_30037.csv_sorted
[INFO] [2023-01-19 14:57:21] Converted: /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_nodes_30037.csv (2 lines)
[INFO] [2023-01-19 14:57:21] ...occurrences (/app/public/data/fornoff_et_al_fo/occurrences.txt)
[CMD] [2023-01-19 14:57:21] /usr/bin/sort /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_occurrences_30038.csv > /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_occurrences_30038.csv_sorted
[INFO] [2023-01-19 14:57:21] Converted: /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_occurrences_30038.csv (2 lines)
[INFO] [2023-01-19 14:57:21] ...measurements (/app/public/data/fornoff_et_al_fo/measurementsorfacts.txt)
[CMD] [2023-01-19 14:57:21] /usr/bin/sort /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_measurements_30039.csv > /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_measurements_30039.csv_sorted
[INFO] [2023-01-19 14:57:21] Converted: /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_measurements_30039.csv (159 lines)
[STOP] [2023-01-19 14:57:21] convert_to_csv
[START] [2023-01-19 14:57:21] calculate_delta
[INFO] [2023-01-19 14:57:21] Looping over 3 formats...
[INFO] [2023-01-19 14:57:21] ...nodes (/app/public/data/fornoff_et_al_fo/taxa.txt)
[CMD] [2023-01-19 14:57:21] echo "0a" > /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_nodes_30037.diff
[CMD] [2023-01-19 14:57:21] tail -n +1 /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_nodes_30037.csv >> /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_nodes_30037.diff
[CMD] [2023-01-19 14:57:21] echo "." >> /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_nodes_30037.diff
[INFO] [2023-01-19 14:57:21] Created diff: /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_nodes_30037.diff (4 lines)
[INFO] [2023-01-19 14:57:21] ...occurrences (/app/public/data/fornoff_et_al_fo/occurrences.txt)
[CMD] [2023-01-19 14:57:21] echo "0a" > /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_occurrences_30038.diff
[CMD] [2023-01-19 14:57:21] tail -n +1 /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_occurrences_30038.csv >> /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_occurrences_30038.diff
[CMD] [2023-01-19 14:57:21] echo "." >> /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_occurrences_30038.diff
[INFO] [2023-01-19 14:57:21] Created diff: /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_occurrences_30038.diff (4 lines)
[INFO] [2023-01-19 14:57:21] ...measurements (/app/public/data/fornoff_et_al_fo/measurementsorfacts.txt)
[CMD] [2023-01-19 14:57:21] echo "0a" > /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_measurements_30039.diff
[CMD] [2023-01-19 14:57:21] tail -n +1 /app/public/data/fornoff_et_al_fo/converted_csv/fornoff_et_al_fo_measurements_30039.csv >> /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_measurements_30039.diff
[CMD] [2023-01-19 14:57:21] echo "." >> /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_measurements_30039.diff
[INFO] [2023-01-19 14:57:21] Created diff: /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_measurements_30039.diff (161 lines)
[STOP] [2023-01-19 14:57:21] calculate_delta
[START] [2023-01-19 14:57:21] parse_diff_and_store
[INFO] [2023-01-19 14:57:21] Handling diff: /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_nodes_30037.diff (4 lines)
[INFO] [2023-01-19 14:57:21] Loading nodes diff file into memory (4 lines)...
[INFO] [2023-01-19 14:57:21] Storing 2 ScientificNames (4/2/4)
[INFO] [2023-01-19 14:57:21] Storing 2 Nodes (4/2/4)
[INFO] [2023-01-19 14:57:21] Handling diff: /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_occurrences_30038.diff (4 lines)
[INFO] [2023-01-19 14:57:22] Loading occurrences diff file into memory (4 lines)...
[INFO] [2023-01-19 14:57:22] Storing 2 Occurrences (4/2/4)
[INFO] [2023-01-19 14:57:22] Storing 2 OccurrenceMetadata (4/2/4)
[INFO] [2023-01-19 14:57:22] Handling diff: /app/public/data/fornoff_et_al_fo/diff/fornoff_et_al_fo_measurements_30039.diff (161 lines)
[INFO] [2023-01-19 14:57:22] Loading measurements diff file into memory (161 lines)...
[INFO] [2023-01-19 14:57:22] Storing 159 Traits (161/159/161)
[INFO] [2023-01-19 14:57:22] Storing 2 MetaTraits (161/159/161)
[STOP] [2023-01-19 14:57:22] parse_diff_and_store
[START] [2023-01-19 14:57:22] resolve_keys
[2023-01-19 14:57:22] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-19 14:57:29] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-19 14:57:29] traits to occurrences...
[INFO] [2023-01-19 14:57:29] traits to nodes (through occurrences)...
[INFO] [2023-01-19 14:57:29] Traits to sex term...
[INFO] [2023-01-19 14:57:29] Traits to lifestage term...
[INFO] [2023-01-19 14:57:29] MetaTraits to traits...
[INFO] [2023-01-19 14:57:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-19 14:57:29] Assocs to occurrences...
[INFO] [2023-01-19 14:57:29] Assocs to nodes...
[INFO] [2023-01-19 14:57:29] Assoc to sex term...
[INFO] [2023-01-19 14:57:29] Assoc to lifestage term...
[INFO] [2023-01-19 14:57:29] MetaAssoc to assocs...
[STOP] [2023-01-19 14:57:29] resolve_keys
[START] [2023-01-19 14:57:29] hold_for_later_1
[STOP] [2023-01-19 14:57:29] hold_for_later_1
[START] [2023-01-19 14:57:29] hold_for_later_2
[STOP] [2023-01-19 14:57:29] hold_for_later_2
[START] [2023-01-19 14:57:29] resolve_missing_parents
[STOP] [2023-01-19 14:57:29] resolve_missing_parents
[START] [2023-01-19 14:57:29] rebuild_nodes
[START] [2023-01-19 14:57:29] Flattener#flatten
[START] [2023-01-19 14:57:29] Flattener#study_resource
[START] [2023-01-19 14:57:29] Flattener#build_ancestry
[STOP] [2023-01-19 14:57:29] Flattener#build_ancestry
[INFO] [2023-01-19 14:57:29] 2 ancestry keys
[START] [2023-01-19 14:57:29] build_node_ancestors
[INFO] [2023-01-19 14:57:29] old ancestors deleted.
[STOP] [2023-01-19 14:57:29] build_node_ancestors
[WARN] [2023-01-19 14:57:29] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-19 14:57:29] Flattener#flatten
[STOP] [2023-01-19 14:57:29] rebuild_nodes
[START] [2023-01-19 14:57:29] resolve_missing_media_owners
[STOP] [2023-01-19 14:57:29] resolve_missing_media_owners
[START] [2023-01-19 14:57:29] sanitize_media_verbatims
[STOP] [2023-01-19 14:57:29] sanitize_media_verbatims
[START] [2023-01-19 14:57:29] queue_downloads
[STOP] [2023-01-19 14:57:29] queue_downloads
[START] [2023-01-19 14:57:29] parse_names
[WARN] [2023-01-19 14:57:29] I see 2 names which still need to be parsed.
[WARN] [2023-01-19 14:57:29] Names to parse: 2 formatted: 2 learned: 2 parsed: 2
[STOP] [2023-01-19 14:57:30] parse_names
[START] [2023-01-19 14:57:30] denormalize_canonical_names_to_nodes
[STOP] [2023-01-19 14:57:30] denormalize_canonical_names_to_nodes
[START] [2023-01-19 14:57:30] match_nodes
[START] [2023-01-19 14:57:30] map_all_nodes_to_pages
[STOP] [2023-01-19 14:57:30] map_all_nodes_to_pages
[INFO] [2023-01-19 14:57:30] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2023-01-19 14:57:30] update_nodes
[STOP] [2023-01-19 14:57:30] update_nodes
[STOP] [2023-01-19 14:57:30] match_nodes
[START] [2023-01-19 14:57:30] reindex_search
[STOP] [2023-01-19 14:57:30] reindex_search
[START] [2023-01-19 14:57:30] normalize_units
[STOP] [2023-01-19 14:57:30] normalize_units
[START] [2023-01-19 14:57:30] calculate_statistics
[2023-01-19 14:57:30] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-19 14:57:30] Duplicate page_id count: 0
[STOP] [2023-01-19 14:57:30] calculate_statistics
[START] [2023-01-19 14:57:30] complete_harvest_instance
[START] [2023-01-19 14:57:30] overall_tsv_creation
[INFO] [2023-01-19 14:57:30] Exporting 2 nodes as TSV in batches of 10000...
[INFO] [2023-01-19 14:57:30] Processing group of 2 in 1 batches of 10000
[INFO] [2023-01-19 14:57:30] 2 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-19 14:57:30] Building Traits map for 2 nodes (this can take a while)...
[INFO] [2023-01-19 14:57:30] Mapped 2 traits (2 meta) for 2 nodes.
[INFO] [2023-01-19 14:57:30] Building Associations map (this can take a while)...
[INFO] [2023-01-19 14:57:30] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-19 14:57:30] Adding 2 traits...
[INFO] [2023-01-19 14:57:30] Trait #285042809 in key 285042809 has 158 metadata... that seems high?
[INFO] [2023-01-19 14:57:30] 157 metadata added.
[INFO] [2023-01-19 14:57:30] Adding 0 assocs...
[INFO] [2023-01-19 14:57:30] 0 metadata added.
[INFO] [2023-01-19 14:58:14] Processed 2/2 nodes
[INFO] [2023-01-19 14:58:14] Average Time: 43.91
[INFO] [2023-01-19 14:58:14] Total Time: 44s
[STOP] [2023-01-19 14:58:14] overall_tsv_creation
[INFO] [2023-01-19 14:58:14] Done. Check your files:
[INFO] [2023-01-19 14:58:14] (2 lines) /app/public/data/fornoff_et_al_fo/publish_nodes.tsv
[INFO] [2023-01-19 14:58:14] (2 lines) /app/public/data/fornoff_et_al_fo/publish_scientific_names.tsv
[INFO] [2023-01-19 14:58:14] (3 lines) /app/public/data/fornoff_et_al_fo/publish_traits.tsv
[INFO] [2023-01-19 14:58:14] (158 lines) /app/public/data/fornoff_et_al_fo/publish_metadata.tsv
[STOP] [2023-01-19 14:58:14] complete_harvest_instance
[START] [2023-01-19 14:58:14] completed
[STOP] [2023-01-19 14:58:14] completed
[STOP] [2023-01-19 14:58:14] logged process, took 53.23
Latest Process

19 Jan 14:57 EXITED currently processing 0