Harvest for Fuchs et al 2010 Created 03 Aug 15:54

Stage: completed
Fetched: 03 Aug 15:54
Validated: 03 Aug 15:54
Deltas Created 03 Aug 15:54
Units Normalized: 03 Aug 15:54
Ancestry Built: 03 Aug 15:54
Nodes Matched: 03 Aug 15:54
Names Parsed: 03 Aug 15:54
New Models Stored: 03 Aug 15:54
Indexed: 03 Aug 15:54
Completed: 03 Aug 15:57
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 15:54:50] Created harvest instance #4158
[STOP] [2022-08-03 15:54:50] create_harvest_instance
[START] [2022-08-03 15:54:50] fetch_files
[STOP] [2022-08-03 15:54:50] fetch_files
[START] [2022-08-03 15:54:50] validate_each_file
[INFO] [2022-08-03 15:54:50] Looping over 3 formats...
[INFO] [2022-08-03 15:54:50] ...nodes (/app/public/data/fuchs_et_al_fuch/taxa.txt)
[INFO] [2022-08-03 15:54:50] Valid: /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_nodes_29537.csv (5 lines)
[INFO] [2022-08-03 15:54:50] ...occurrences (/app/public/data/fuchs_et_al_fuch/occurrences.txt)
[INFO] [2022-08-03 15:54:50] Valid: /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_occurrences_29538.csv (5 lines)
[INFO] [2022-08-03 15:54:50] ...measurements (/app/public/data/fuchs_et_al_fuch/measurementOrFact.txt)
[INFO] [2022-08-03 15:54:50] Valid: /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_measurements_29539.csv (10 lines)
[STOP] [2022-08-03 15:54:50] validate_each_file
[START] [2022-08-03 15:54:50] convert_to_csv
[INFO] [2022-08-03 15:54:50] Looping over 3 formats...
[INFO] [2022-08-03 15:54:50] ...nodes (/app/public/data/fuchs_et_al_fuch/taxa.txt)
[CMD] [2022-08-03 15:54:50] /usr/bin/sort /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_nodes_29537.csv > /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_nodes_29537.csv_sorted
[INFO] [2022-08-03 15:54:50] Converted: /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_nodes_29537.csv (5 lines)
[INFO] [2022-08-03 15:54:50] ...occurrences (/app/public/data/fuchs_et_al_fuch/occurrences.txt)
[CMD] [2022-08-03 15:54:50] /usr/bin/sort /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_occurrences_29538.csv > /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_occurrences_29538.csv_sorted
[INFO] [2022-08-03 15:54:50] Converted: /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_occurrences_29538.csv (5 lines)
[INFO] [2022-08-03 15:54:50] ...measurements (/app/public/data/fuchs_et_al_fuch/measurementOrFact.txt)
[CMD] [2022-08-03 15:54:50] /usr/bin/sort /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_measurements_29539.csv > /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_measurements_29539.csv_sorted
[INFO] [2022-08-03 15:54:50] Converted: /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_measurements_29539.csv (10 lines)
[STOP] [2022-08-03 15:54:50] convert_to_csv
[START] [2022-08-03 15:54:50] calculate_delta
[INFO] [2022-08-03 15:54:50] Looping over 3 formats...
[INFO] [2022-08-03 15:54:50] ...nodes (/app/public/data/fuchs_et_al_fuch/taxa.txt)
[CMD] [2022-08-03 15:54:50] echo "0a" > /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_nodes_29537.diff
[CMD] [2022-08-03 15:54:50] tail -n +1 /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_nodes_29537.csv >> /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_nodes_29537.diff
[CMD] [2022-08-03 15:54:50] echo "." >> /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_nodes_29537.diff
[INFO] [2022-08-03 15:54:50] Created diff: /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_nodes_29537.diff (7 lines)
[INFO] [2022-08-03 15:54:50] ...occurrences (/app/public/data/fuchs_et_al_fuch/occurrences.txt)
[CMD] [2022-08-03 15:54:50] echo "0a" > /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_occurrences_29538.diff
[CMD] [2022-08-03 15:54:50] tail -n +1 /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_occurrences_29538.csv >> /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_occurrences_29538.diff
[CMD] [2022-08-03 15:54:50] echo "." >> /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_occurrences_29538.diff
[INFO] [2022-08-03 15:54:50] Created diff: /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_occurrences_29538.diff (7 lines)
[INFO] [2022-08-03 15:54:50] ...measurements (/app/public/data/fuchs_et_al_fuch/measurementOrFact.txt)
[CMD] [2022-08-03 15:54:50] echo "0a" > /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_measurements_29539.diff
[CMD] [2022-08-03 15:54:50] tail -n +1 /app/public/data/fuchs_et_al_fuch/converted_csv/fuchs_et_al_fuch_measurements_29539.csv >> /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_measurements_29539.diff
[CMD] [2022-08-03 15:54:50] echo "." >> /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_measurements_29539.diff
[INFO] [2022-08-03 15:54:50] Created diff: /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_measurements_29539.diff (12 lines)
[STOP] [2022-08-03 15:54:50] calculate_delta
[START] [2022-08-03 15:54:50] parse_diff_and_store
[INFO] [2022-08-03 15:54:50] Handling diff: /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_nodes_29537.diff (7 lines)
[INFO] [2022-08-03 15:54:50] Loading nodes diff file into memory (7 lines)...
[INFO] [2022-08-03 15:54:51] Storing 5 ScientificNames (10/5/7)
[INFO] [2022-08-03 15:54:51] Storing 5 Nodes (10/5/7)
[INFO] [2022-08-03 15:54:51] Handling diff: /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_occurrences_29538.diff (7 lines)
[INFO] [2022-08-03 15:54:51] Loading occurrences diff file into memory (7 lines)...
[INFO] [2022-08-03 15:54:51] Storing 5 Occurrences (5/5/7)
[INFO] [2022-08-03 15:54:51] Handling diff: /app/public/data/fuchs_et_al_fuch/diff/fuchs_et_al_fuch_measurements_29539.diff (12 lines)
[INFO] [2022-08-03 15:54:51] Loading measurements diff file into memory (12 lines)...
[INFO] [2022-08-03 15:54:51] Storing 10 Traits (15/10/12)
[INFO] [2022-08-03 15:54:51] Storing 5 MetaTraits (15/10/12)
[STOP] [2022-08-03 15:54:51] parse_diff_and_store
[START] [2022-08-03 15:54:51] resolve_keys
[2022-08-03 15:54:51] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 15:54:58] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 15:54:58] traits to occurrences...
[INFO] [2022-08-03 15:54:58] traits to nodes (through occurrences)...
[INFO] [2022-08-03 15:54:58] Traits to sex term...
[INFO] [2022-08-03 15:54:58] Traits to lifestage term...
[INFO] [2022-08-03 15:54:58] MetaTraits to traits...
[INFO] [2022-08-03 15:54:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 15:54:58] Assocs to occurrences...
[INFO] [2022-08-03 15:54:58] Assocs to nodes...
[INFO] [2022-08-03 15:54:58] Assoc to sex term...
[INFO] [2022-08-03 15:54:58] Assoc to lifestage term...
[INFO] [2022-08-03 15:54:58] MetaAssoc to assocs...
[STOP] [2022-08-03 15:54:58] resolve_keys
[START] [2022-08-03 15:54:58] hold_for_later_1
[STOP] [2022-08-03 15:54:58] hold_for_later_1
[START] [2022-08-03 15:54:58] hold_for_later_2
[STOP] [2022-08-03 15:54:58] hold_for_later_2
[START] [2022-08-03 15:54:58] resolve_missing_parents
[STOP] [2022-08-03 15:54:58] resolve_missing_parents
[START] [2022-08-03 15:54:58] rebuild_nodes
[START] [2022-08-03 15:54:58] Flattener#flatten
[START] [2022-08-03 15:54:58] Flattener#study_resource
[START] [2022-08-03 15:54:58] Flattener#build_ancestry
[STOP] [2022-08-03 15:54:58] Flattener#build_ancestry
[INFO] [2022-08-03 15:54:58] 5 ancestry keys
[START] [2022-08-03 15:54:58] build_node_ancestors
[INFO] [2022-08-03 15:54:58] old ancestors deleted.
[STOP] [2022-08-03 15:54:58] build_node_ancestors
[WARN] [2022-08-03 15:54:58] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 15:54:58] Flattener#flatten
[STOP] [2022-08-03 15:54:58] rebuild_nodes
[START] [2022-08-03 15:54:58] resolve_missing_media_owners
[STOP] [2022-08-03 15:54:58] resolve_missing_media_owners
[START] [2022-08-03 15:54:58] sanitize_media_verbatims
[STOP] [2022-08-03 15:54:58] sanitize_media_verbatims
[START] [2022-08-03 15:54:58] queue_downloads
[STOP] [2022-08-03 15:54:58] queue_downloads
[START] [2022-08-03 15:54:58] parse_names
[WARN] [2022-08-03 15:54:58] I see 5 names which still need to be parsed.
[WARN] [2022-08-03 15:54:58] Names to parse: 5 formatted: 5 learned: 5 parsed: 5
[STOP] [2022-08-03 15:54:59] parse_names
[START] [2022-08-03 15:54:59] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 15:54:59] denormalize_canonical_names_to_nodes
[START] [2022-08-03 15:54:59] match_nodes
[START] [2022-08-03 15:54:59] map_all_nodes_to_pages
[STOP] [2022-08-03 15:54:59] map_all_nodes_to_pages
[INFO] [2022-08-03 15:54:59] ZERO unmatched nodes (of 5)! Nicely done.
[START] [2022-08-03 15:54:59] update_nodes
[STOP] [2022-08-03 15:54:59] update_nodes
[STOP] [2022-08-03 15:54:59] match_nodes
[START] [2022-08-03 15:54:59] reindex_search
[STOP] [2022-08-03 15:54:59] reindex_search
[START] [2022-08-03 15:54:59] normalize_units
[STOP] [2022-08-03 15:54:59] normalize_units
[START] [2022-08-03 15:54:59] calculate_statistics
[2022-08-03 15:54:59] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 15:54:59] Duplicate page_id count: 0
[STOP] [2022-08-03 15:54:59] calculate_statistics
[START] [2022-08-03 15:54:59] complete_harvest_instance
[START] [2022-08-03 15:54:59] overall_tsv_creation
[INFO] [2022-08-03 15:54:59] Exporting 5 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 15:54:59] Processing group of 5 in 1 batches of 10000
[INFO] [2022-08-03 15:55:42] 5 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 15:55:42] Building Traits map for 5 nodes (this can take a while)...
[INFO] [2022-08-03 15:56:35] Mapped 5 traits (5 meta) for 5 nodes.
[INFO] [2022-08-03 15:56:35] Building Associations map (this can take a while)...
[INFO] [2022-08-03 15:56:35] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 15:56:35] Adding 5 traits...
[INFO] [2022-08-03 15:56:35] 5 metadata added.
[INFO] [2022-08-03 15:56:35] Adding 0 assocs...
[INFO] [2022-08-03 15:56:35] 0 metadata added.
[INFO] [2022-08-03 15:57:16] Processed 5/5 nodes
[INFO] [2022-08-03 15:57:16] Average Time: 111.09
[INFO] [2022-08-03 15:57:16] Total Time: 2m17s
[STOP] [2022-08-03 15:57:16] overall_tsv_creation
[INFO] [2022-08-03 15:57:16] Done. Check your files:
[INFO] [2022-08-03 15:57:16] (5 lines) /app/public/data/fuchs_et_al_fuch/publish_nodes.tsv
[INFO] [2022-08-03 15:57:16] (5 lines) /app/public/data/fuchs_et_al_fuch/publish_scientific_names.tsv
[INFO] [2022-08-03 15:57:16] (6 lines) /app/public/data/fuchs_et_al_fuch/publish_traits.tsv
[INFO] [2022-08-03 15:57:16] (6 lines) /app/public/data/fuchs_et_al_fuch/publish_metadata.tsv
[STOP] [2022-08-03 15:57:16] complete_harvest_instance
[START] [2022-08-03 15:57:16] completed
[STOP] [2022-08-03 15:57:16] completed
[STOP] [2022-08-03 15:57:16] logged process, took 146.27
Latest Process

03 Aug 15:53 EXITED currently processing 0