Harvest for Shenkar et al 2011 Created 11 Oct 21:13

Harvesting Log

[INFO] [2023-10-11 21:13:25] Created harvest instance #4407
[STOP] [2023-10-11 21:13:25] create_harvest_instance
[START] [2023-10-11 21:13:25] fetch_files
[STOP] [2023-10-11 21:13:25] fetch_files
[START] [2023-10-11 21:13:25] validate_each_file
[INFO] [2023-10-11 21:13:25] Looping over 3 formats...
[INFO] [2023-10-11 21:13:25] ...nodes (/app/public/data/shenkar_et_al_sh/taxa.txt)
[INFO] [2023-10-11 21:13:26] Valid: /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_nodes_30573.csv (62 lines)
[INFO] [2023-10-11 21:13:26] ...occurrences (/app/public/data/shenkar_et_al_sh/occurrences.txt)
[INFO] [2023-10-11 21:13:26] Valid: /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_occurrences_30574.csv (62 lines)
[INFO] [2023-10-11 21:13:26] ...measurements (/app/public/data/shenkar_et_al_sh/measurementOrFact.txt)
[INFO] [2023-10-11 21:13:26] Valid: /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_measurements_30575.csv (125 lines)
[STOP] [2023-10-11 21:13:26] validate_each_file
[START] [2023-10-11 21:13:26] convert_to_csv
[INFO] [2023-10-11 21:13:26] Looping over 3 formats...
[INFO] [2023-10-11 21:13:26] ...nodes (/app/public/data/shenkar_et_al_sh/taxa.txt)
[CMD] [2023-10-11 21:13:26] /usr/bin/sort /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_nodes_30573.csv > /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_nodes_30573.csv_sorted
[INFO] [2023-10-11 21:13:26] Converted: /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_nodes_30573.csv (62 lines)
[INFO] [2023-10-11 21:13:26] ...occurrences (/app/public/data/shenkar_et_al_sh/occurrences.txt)
[CMD] [2023-10-11 21:13:26] /usr/bin/sort /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_occurrences_30574.csv > /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_occurrences_30574.csv_sorted
[INFO] [2023-10-11 21:13:26] Converted: /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_occurrences_30574.csv (62 lines)
[INFO] [2023-10-11 21:13:26] ...measurements (/app/public/data/shenkar_et_al_sh/measurementOrFact.txt)
[CMD] [2023-10-11 21:13:26] /usr/bin/sort /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_measurements_30575.csv > /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_measurements_30575.csv_sorted
[INFO] [2023-10-11 21:13:26] Converted: /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_measurements_30575.csv (125 lines)
[STOP] [2023-10-11 21:13:26] convert_to_csv
[START] [2023-10-11 21:13:26] calculate_delta
[INFO] [2023-10-11 21:13:26] Looping over 3 formats...
[INFO] [2023-10-11 21:13:26] ...nodes (/app/public/data/shenkar_et_al_sh/taxa.txt)
[CMD] [2023-10-11 21:13:26] echo "0a" > /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_nodes_30573.diff
[CMD] [2023-10-11 21:13:26] tail -n +1 /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_nodes_30573.csv >> /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_nodes_30573.diff
[CMD] [2023-10-11 21:13:26] echo "." >> /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_nodes_30573.diff
[INFO] [2023-10-11 21:13:26] Created diff: /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_nodes_30573.diff (64 lines)
[INFO] [2023-10-11 21:13:26] ...occurrences (/app/public/data/shenkar_et_al_sh/occurrences.txt)
[CMD] [2023-10-11 21:13:26] echo "0a" > /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_occurrences_30574.diff
[CMD] [2023-10-11 21:13:26] tail -n +1 /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_occurrences_30574.csv >> /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_occurrences_30574.diff
[CMD] [2023-10-11 21:13:26] echo "." >> /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_occurrences_30574.diff
[INFO] [2023-10-11 21:13:26] Created diff: /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_occurrences_30574.diff (64 lines)
[INFO] [2023-10-11 21:13:26] ...measurements (/app/public/data/shenkar_et_al_sh/measurementOrFact.txt)
[CMD] [2023-10-11 21:13:26] echo "0a" > /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_measurements_30575.diff
[CMD] [2023-10-11 21:13:26] tail -n +1 /app/public/data/shenkar_et_al_sh/converted_csv/shenkar_et_al_sh_measurements_30575.csv >> /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_measurements_30575.diff
[CMD] [2023-10-11 21:13:26] echo "." >> /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_measurements_30575.diff
[INFO] [2023-10-11 21:13:26] Created diff: /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_measurements_30575.diff (127 lines)
[STOP] [2023-10-11 21:13:26] calculate_delta
[START] [2023-10-11 21:13:27] parse_diff_and_store
[INFO] [2023-10-11 21:13:27] Handling diff: /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_nodes_30573.diff (64 lines)
[INFO] [2023-10-11 21:13:27] Loading nodes diff file into memory (64 lines)...
[INFO] [2023-10-11 21:13:27] Storing 62 ScientificNames (124/62/64)
[INFO] [2023-10-11 21:13:27] Storing 62 Nodes (124/62/64)
[INFO] [2023-10-11 21:13:27] Handling diff: /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_occurrences_30574.diff (64 lines)
[INFO] [2023-10-11 21:13:27] Loading occurrences diff file into memory (64 lines)...
[INFO] [2023-10-11 21:13:27] Storing 62 Occurrences (99/62/64)
[INFO] [2023-10-11 21:13:27] Storing 37 OccurrenceMetadata (99/62/64)
[INFO] [2023-10-11 21:13:27] Handling diff: /app/public/data/shenkar_et_al_sh/diff/shenkar_et_al_sh_measurements_30575.diff (127 lines)
[INFO] [2023-10-11 21:13:27] Loading measurements diff file into memory (127 lines)...
[INFO] [2023-10-11 21:13:27] Storing 125 Traits (187/125/127)
[INFO] [2023-10-11 21:13:27] Storing 62 MetaTraits (187/125/127)
[STOP] [2023-10-11 21:13:27] parse_diff_and_store
[START] [2023-10-11 21:13:27] resolve_keys
[2023-10-11 21:13:27] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-11 21:13:35] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-11 21:13:35] traits to occurrences...
[INFO] [2023-10-11 21:13:35] traits to nodes (through occurrences)...
[INFO] [2023-10-11 21:13:35] Traits to sex term...
[INFO] [2023-10-11 21:13:35] Traits to lifestage term...
[INFO] [2023-10-11 21:13:35] MetaTraits to traits...
[INFO] [2023-10-11 21:13:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-11 21:13:35] Assocs to occurrences...
[INFO] [2023-10-11 21:13:35] Assocs to nodes...
[INFO] [2023-10-11 21:13:35] Assoc to sex term...
[INFO] [2023-10-11 21:13:35] Assoc to lifestage term...
[INFO] [2023-10-11 21:13:35] MetaAssoc to assocs...
[STOP] [2023-10-11 21:13:35] resolve_keys
[START] [2023-10-11 21:13:35] hold_for_later_1
[STOP] [2023-10-11 21:13:35] hold_for_later_1
[START] [2023-10-11 21:13:35] hold_for_later_2
[STOP] [2023-10-11 21:13:35] hold_for_later_2
[START] [2023-10-11 21:13:35] resolve_missing_parents
[STOP] [2023-10-11 21:13:35] resolve_missing_parents
[START] [2023-10-11 21:13:35] rebuild_nodes
[START] [2023-10-11 21:13:35] Flattener#flatten
[START] [2023-10-11 21:13:35] Flattener#study_resource
[START] [2023-10-11 21:13:35] Flattener#build_ancestry
[STOP] [2023-10-11 21:13:35] Flattener#build_ancestry
[INFO] [2023-10-11 21:13:35] 62 ancestry keys
[START] [2023-10-11 21:13:35] build_node_ancestors
[INFO] [2023-10-11 21:13:35] old ancestors deleted.
[STOP] [2023-10-11 21:13:35] build_node_ancestors
[WARN] [2023-10-11 21:13:35] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-11 21:13:35] Flattener#flatten
[STOP] [2023-10-11 21:13:35] rebuild_nodes
[START] [2023-10-11 21:13:35] resolve_missing_media_owners
[STOP] [2023-10-11 21:13:35] resolve_missing_media_owners
[START] [2023-10-11 21:13:35] sanitize_media_verbatims
[STOP] [2023-10-11 21:13:35] sanitize_media_verbatims
[START] [2023-10-11 21:13:35] queue_downloads
[STOP] [2023-10-11 21:13:35] queue_downloads
[START] [2023-10-11 21:13:35] parse_names
[WARN] [2023-10-11 21:13:35] I see 62 names which still need to be parsed.
[WARN] [2023-10-11 21:13:35] Names to parse: 62 formatted: 62 learned: 62 parsed: 62
[STOP] [2023-10-11 21:13:36] parse_names
[START] [2023-10-11 21:13:36] denormalize_canonical_names_to_nodes
[STOP] [2023-10-11 21:13:36] denormalize_canonical_names_to_nodes
[START] [2023-10-11 21:13:36] match_nodes
[START] [2023-10-11 21:13:36] map_all_nodes_to_pages
[STOP] [2023-10-11 21:13:36] map_all_nodes_to_pages
[INFO] [2023-10-11 21:13:36] ZERO unmatched nodes (of 62)! Nicely done.
[START] [2023-10-11 21:13:36] update_nodes
[STOP] [2023-10-11 21:13:36] update_nodes
[STOP] [2023-10-11 21:13:36] match_nodes
[START] [2023-10-11 21:13:36] reindex_search
[STOP] [2023-10-11 21:13:36] reindex_search
[START] [2023-10-11 21:13:36] normalize_units
[STOP] [2023-10-11 21:13:36] normalize_units
[START] [2023-10-11 21:13:36] calculate_statistics
[2023-10-11 21:13:36] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-11 21:13:36] Duplicate page_id count: 0
[STOP] [2023-10-11 21:13:36] calculate_statistics
[START] [2023-10-11 21:13:36] complete_harvest_instance
[START] [2023-10-11 21:13:36] overall_tsv_creation
[INFO] [2023-10-11 21:13:36] Exporting 62 nodes as TSV in batches of 10000...
[INFO] [2023-10-11 21:13:36] Processing group of 62 in 1 batches of 10000
[INFO] [2023-10-11 21:13:36] 62 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-11 21:13:36] Building Traits map for 62 nodes (this can take a while)...
[INFO] [2023-10-11 21:13:37] Mapped 62 traits (62 meta) for 62 nodes.
[INFO] [2023-10-11 21:13:37] Building Associations map (this can take a while)...
[INFO] [2023-10-11 21:13:37] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-11 21:13:37] Adding 62 traits...
[INFO] [2023-10-11 21:13:37] 63 metadata added.
[INFO] [2023-10-11 21:13:37] Adding 0 assocs...
[INFO] [2023-10-11 21:13:37] 0 metadata added.
[INFO] [2023-10-11 21:14:21] Processed 62/62 nodes
[INFO] [2023-10-11 21:14:21] Average Time: 44.52
[INFO] [2023-10-11 21:14:21] Total Time: 45s
[STOP] [2023-10-11 21:14:21] overall_tsv_creation
[INFO] [2023-10-11 21:14:21] Done. Check your files:
[INFO] [2023-10-11 21:14:21] (62 lines) /app/public/data/shenkar_et_al_sh/publish_nodes.tsv
[INFO] [2023-10-11 21:14:21] (62 lines) /app/public/data/shenkar_et_al_sh/publish_scientific_names.tsv
[INFO] [2023-10-11 21:14:21] (63 lines) /app/public/data/shenkar_et_al_sh/publish_traits.tsv
[INFO] [2023-10-11 21:14:21] (64 lines) /app/public/data/shenkar_et_al_sh/publish_metadata.tsv
[STOP] [2023-10-11 21:14:21] complete_harvest_instance
[START] [2023-10-11 21:14:21] completed
[STOP] [2023-10-11 21:14:21] completed
[STOP] [2023-10-11 21:14:21] logged process, took 56.62

Latest Process

11 Oct 21:13 EXITED currently processing 0