Harvest for Ma et al 2010 Created 03 Aug 16:30

Harvesting Log

[INFO] [2022-08-03 16:30:34] Created harvest instance #4172
[STOP] [2022-08-03 16:30:34] create_harvest_instance
[START] [2022-08-03 16:30:34] fetch_files
[STOP] [2022-08-03 16:30:34] fetch_files
[START] [2022-08-03 16:30:34] validate_each_file
[INFO] [2022-08-03 16:30:34] Looping over 3 formats...
[INFO] [2022-08-03 16:30:34] ...nodes (/app/public/data/ma_et_al_ma_et_a/taxa.txt)
[INFO] [2022-08-03 16:30:34] Valid: /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_nodes_29579.csv (1 lines)
[INFO] [2022-08-03 16:30:34] ...occurrences (/app/public/data/ma_et_al_ma_et_a/occurrences.txt)
[INFO] [2022-08-03 16:30:34] Valid: /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_occurrences_29580.csv (1 lines)
[INFO] [2022-08-03 16:30:34] ...measurements (/app/public/data/ma_et_al_ma_et_a/measurementOrFact.txt)
[INFO] [2022-08-03 16:30:34] Valid: /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_measurements_29581.csv (2 lines)
[STOP] [2022-08-03 16:30:34] validate_each_file
[START] [2022-08-03 16:30:34] convert_to_csv
[INFO] [2022-08-03 16:30:34] Looping over 3 formats...
[INFO] [2022-08-03 16:30:34] ...nodes (/app/public/data/ma_et_al_ma_et_a/taxa.txt)
[CMD] [2022-08-03 16:30:34] /usr/bin/sort /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_nodes_29579.csv > /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_nodes_29579.csv_sorted
[INFO] [2022-08-03 16:30:34] Converted: /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_nodes_29579.csv (1 lines)
[INFO] [2022-08-03 16:30:34] ...occurrences (/app/public/data/ma_et_al_ma_et_a/occurrences.txt)
[CMD] [2022-08-03 16:30:34] /usr/bin/sort /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_occurrences_29580.csv > /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_occurrences_29580.csv_sorted
[INFO] [2022-08-03 16:30:34] Converted: /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_occurrences_29580.csv (1 lines)
[INFO] [2022-08-03 16:30:34] ...measurements (/app/public/data/ma_et_al_ma_et_a/measurementOrFact.txt)
[CMD] [2022-08-03 16:30:34] /usr/bin/sort /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_measurements_29581.csv > /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_measurements_29581.csv_sorted
[INFO] [2022-08-03 16:30:34] Converted: /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_measurements_29581.csv (2 lines)
[STOP] [2022-08-03 16:30:34] convert_to_csv
[START] [2022-08-03 16:30:34] calculate_delta
[INFO] [2022-08-03 16:30:34] Looping over 3 formats...
[INFO] [2022-08-03 16:30:34] ...nodes (/app/public/data/ma_et_al_ma_et_a/taxa.txt)
[CMD] [2022-08-03 16:30:34] echo "0a" > /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_nodes_29579.diff
[CMD] [2022-08-03 16:30:34] tail -n +1 /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_nodes_29579.csv >> /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_nodes_29579.diff
[CMD] [2022-08-03 16:30:34] echo "." >> /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_nodes_29579.diff
[INFO] [2022-08-03 16:30:34] Created diff: /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_nodes_29579.diff (3 lines)
[INFO] [2022-08-03 16:30:34] ...occurrences (/app/public/data/ma_et_al_ma_et_a/occurrences.txt)
[CMD] [2022-08-03 16:30:34] echo "0a" > /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_occurrences_29580.diff
[CMD] [2022-08-03 16:30:34] tail -n +1 /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_occurrences_29580.csv >> /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_occurrences_29580.diff
[CMD] [2022-08-03 16:30:34] echo "." >> /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_occurrences_29580.diff
[INFO] [2022-08-03 16:30:34] Created diff: /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_occurrences_29580.diff (3 lines)
[INFO] [2022-08-03 16:30:34] ...measurements (/app/public/data/ma_et_al_ma_et_a/measurementOrFact.txt)
[CMD] [2022-08-03 16:30:34] echo "0a" > /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_measurements_29581.diff
[CMD] [2022-08-03 16:30:34] tail -n +1 /app/public/data/ma_et_al_ma_et_a/converted_csv/ma_et_al_ma_et_a_measurements_29581.csv >> /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_measurements_29581.diff
[CMD] [2022-08-03 16:30:34] echo "." >> /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_measurements_29581.diff
[INFO] [2022-08-03 16:30:34] Created diff: /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_measurements_29581.diff (4 lines)
[STOP] [2022-08-03 16:30:34] calculate_delta
[START] [2022-08-03 16:30:34] parse_diff_and_store
[INFO] [2022-08-03 16:30:35] Handling diff: /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_nodes_29579.diff (3 lines)
[INFO] [2022-08-03 16:30:35] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:30:35] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:30:35] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:30:35] Handling diff: /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_occurrences_29580.diff (3 lines)
[INFO] [2022-08-03 16:30:35] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:30:35] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:30:35] Handling diff: /app/public/data/ma_et_al_ma_et_a/diff/ma_et_al_ma_et_a_measurements_29581.diff (4 lines)
[INFO] [2022-08-03 16:30:35] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 16:30:35] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 16:30:35] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 16:30:35] parse_diff_and_store
[START] [2022-08-03 16:30:35] resolve_keys
[2022-08-03 16:30:35] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:30:42] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:30:42] traits to occurrences...
[INFO] [2022-08-03 16:30:42] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:30:42] Traits to sex term...
[INFO] [2022-08-03 16:30:42] Traits to lifestage term...
[INFO] [2022-08-03 16:30:42] MetaTraits to traits...
[INFO] [2022-08-03 16:30:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:30:42] Assocs to occurrences...
[INFO] [2022-08-03 16:30:42] Assocs to nodes...
[INFO] [2022-08-03 16:30:42] Assoc to sex term...
[INFO] [2022-08-03 16:30:42] Assoc to lifestage term...
[INFO] [2022-08-03 16:30:42] MetaAssoc to assocs...
[STOP] [2022-08-03 16:30:42] resolve_keys
[START] [2022-08-03 16:30:42] hold_for_later_1
[STOP] [2022-08-03 16:30:42] hold_for_later_1
[START] [2022-08-03 16:30:42] hold_for_later_2
[STOP] [2022-08-03 16:30:42] hold_for_later_2
[START] [2022-08-03 16:30:42] resolve_missing_parents
[STOP] [2022-08-03 16:30:42] resolve_missing_parents
[START] [2022-08-03 16:30:42] rebuild_nodes
[START] [2022-08-03 16:30:42] Flattener#flatten
[START] [2022-08-03 16:30:42] Flattener#study_resource
[START] [2022-08-03 16:30:42] Flattener#build_ancestry
[STOP] [2022-08-03 16:30:42] Flattener#build_ancestry
[INFO] [2022-08-03 16:30:42] 1 ancestry keys
[START] [2022-08-03 16:30:42] build_node_ancestors
[INFO] [2022-08-03 16:30:42] old ancestors deleted.
[STOP] [2022-08-03 16:30:42] build_node_ancestors
[WARN] [2022-08-03 16:30:42] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:30:42] Flattener#flatten
[STOP] [2022-08-03 16:30:42] rebuild_nodes
[START] [2022-08-03 16:30:42] resolve_missing_media_owners
[STOP] [2022-08-03 16:30:42] resolve_missing_media_owners
[START] [2022-08-03 16:30:42] sanitize_media_verbatims
[STOP] [2022-08-03 16:30:42] sanitize_media_verbatims
[START] [2022-08-03 16:30:42] queue_downloads
[STOP] [2022-08-03 16:30:42] queue_downloads
[START] [2022-08-03 16:30:42] parse_names
[WARN] [2022-08-03 16:30:42] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:30:42] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:30:43] parse_names
[START] [2022-08-03 16:30:43] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:30:43] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:30:43] match_nodes
[START] [2022-08-03 16:30:43] map_all_nodes_to_pages
[STOP] [2022-08-03 16:30:43] map_all_nodes_to_pages
[INFO] [2022-08-03 16:30:43] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:30:43] update_nodes
[STOP] [2022-08-03 16:30:43] update_nodes
[STOP] [2022-08-03 16:30:43] match_nodes
[START] [2022-08-03 16:30:43] reindex_search
[STOP] [2022-08-03 16:30:43] reindex_search
[START] [2022-08-03 16:30:43] normalize_units
[STOP] [2022-08-03 16:30:43] normalize_units
[START] [2022-08-03 16:30:43] calculate_statistics
[2022-08-03 16:30:43] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:30:43] Duplicate page_id count: 0
[STOP] [2022-08-03 16:30:43] calculate_statistics
[START] [2022-08-03 16:30:43] complete_harvest_instance
[START] [2022-08-03 16:30:43] overall_tsv_creation
[INFO] [2022-08-03 16:30:43] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:30:43] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:31:24] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:31:24] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:32:18] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 16:32:18] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:32:18] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:32:18] Adding 1 traits...
[INFO] [2022-08-03 16:32:18] 1 metadata added.
[INFO] [2022-08-03 16:32:18] Adding 0 assocs...
[INFO] [2022-08-03 16:32:18] 0 metadata added.
[INFO] [2022-08-03 16:33:01] Processed 1/1 nodes
[INFO] [2022-08-03 16:33:01] Average Time: 112.81
[INFO] [2022-08-03 16:33:01] Total Time: 2m18s
[STOP] [2022-08-03 16:33:01] overall_tsv_creation
[INFO] [2022-08-03 16:33:01] Done. Check your files:
[INFO] [2022-08-03 16:33:01] (1 lines) /app/public/data/ma_et_al_ma_et_a/publish_nodes.tsv
[INFO] [2022-08-03 16:33:01] (1 lines) /app/public/data/ma_et_al_ma_et_a/publish_scientific_names.tsv
[INFO] [2022-08-03 16:33:01] (2 lines) /app/public/data/ma_et_al_ma_et_a/publish_traits.tsv
[INFO] [2022-08-03 16:33:01] (2 lines) /app/public/data/ma_et_al_ma_et_a/publish_metadata.tsv
[STOP] [2022-08-03 16:33:01] complete_harvest_instance
[START] [2022-08-03 16:33:01] completed
[STOP] [2022-08-03 16:33:01] completed
[STOP] [2022-08-03 16:33:01] logged process, took 146.99

Latest Process

03 Aug 16:30 EXITED currently processing 0