Harvest for Zieger and Meyer Rochow 2008 Created 13 Oct 13:48

Harvesting Log

[INFO] [2023-10-13 13:48:57] Created harvest instance #4458
[STOP] [2023-10-13 13:48:57] create_harvest_instance
[START] [2023-10-13 13:48:57] fetch_files
[STOP] [2023-10-13 13:48:57] fetch_files
[START] [2023-10-13 13:48:57] validate_each_file
[INFO] [2023-10-13 13:48:57] Looping over 4 formats...
[INFO] [2023-10-13 13:48:57] ...refs (/app/public/data/zieger_meyer_roc/references.tsv)
[INFO] [2023-10-13 13:48:57] Valid: /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_refs_30840.csv (2 lines)
[INFO] [2023-10-13 13:48:57] ...nodes (/app/public/data/zieger_meyer_roc/taxa.txt)
[INFO] [2023-10-13 13:48:57] Valid: /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_nodes_30837.csv (9 lines)
[INFO] [2023-10-13 13:48:57] ...occurrences (/app/public/data/zieger_meyer_roc/occurrences.txt)
[INFO] [2023-10-13 13:48:57] Valid: /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_occurrences_30838.csv (9 lines)
[INFO] [2023-10-13 13:48:57] ...measurements (/app/public/data/zieger_meyer_roc/measurementsorfacts.txt)
[INFO] [2023-10-13 13:48:57] Valid: /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_measurements_30839.csv (32 lines)
[STOP] [2023-10-13 13:48:57] validate_each_file
[START] [2023-10-13 13:48:57] convert_to_csv
[INFO] [2023-10-13 13:48:57] Looping over 4 formats...
[INFO] [2023-10-13 13:48:57] ...refs (/app/public/data/zieger_meyer_roc/references.tsv)
[CMD] [2023-10-13 13:48:57] /usr/bin/sort /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_refs_30840.csv > /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_refs_30840.csv_sorted
[INFO] [2023-10-13 13:48:57] Converted: /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_refs_30840.csv (2 lines)
[INFO] [2023-10-13 13:48:57] ...nodes (/app/public/data/zieger_meyer_roc/taxa.txt)
[CMD] [2023-10-13 13:48:57] /usr/bin/sort /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_nodes_30837.csv > /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_nodes_30837.csv_sorted
[INFO] [2023-10-13 13:48:57] Converted: /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_nodes_30837.csv (9 lines)
[INFO] [2023-10-13 13:48:57] ...occurrences (/app/public/data/zieger_meyer_roc/occurrences.txt)
[CMD] [2023-10-13 13:48:57] /usr/bin/sort /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_occurrences_30838.csv > /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_occurrences_30838.csv_sorted
[INFO] [2023-10-13 13:48:57] Converted: /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_occurrences_30838.csv (9 lines)
[INFO] [2023-10-13 13:48:57] ...measurements (/app/public/data/zieger_meyer_roc/measurementsorfacts.txt)
[CMD] [2023-10-13 13:48:57] /usr/bin/sort /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_measurements_30839.csv > /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_measurements_30839.csv_sorted
[INFO] [2023-10-13 13:48:58] Converted: /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_measurements_30839.csv (32 lines)
[STOP] [2023-10-13 13:48:58] convert_to_csv
[START] [2023-10-13 13:48:58] calculate_delta
[INFO] [2023-10-13 13:48:58] Looping over 4 formats...
[INFO] [2023-10-13 13:48:58] ...refs (/app/public/data/zieger_meyer_roc/references.tsv)
[CMD] [2023-10-13 13:48:58] echo "0a" > /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_refs_30840.diff
[CMD] [2023-10-13 13:48:58] tail -n +1 /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_refs_30840.csv >> /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_refs_30840.diff
[CMD] [2023-10-13 13:48:58] echo "." >> /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_refs_30840.diff
[INFO] [2023-10-13 13:48:58] Created diff: /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_refs_30840.diff (4 lines)
[INFO] [2023-10-13 13:48:58] ...nodes (/app/public/data/zieger_meyer_roc/taxa.txt)
[CMD] [2023-10-13 13:48:58] echo "0a" > /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_nodes_30837.diff
[CMD] [2023-10-13 13:48:58] tail -n +1 /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_nodes_30837.csv >> /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_nodes_30837.diff
[CMD] [2023-10-13 13:48:58] echo "." >> /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_nodes_30837.diff
[INFO] [2023-10-13 13:48:58] Created diff: /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_nodes_30837.diff (11 lines)
[INFO] [2023-10-13 13:48:58] ...occurrences (/app/public/data/zieger_meyer_roc/occurrences.txt)
[CMD] [2023-10-13 13:48:58] echo "0a" > /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_occurrences_30838.diff
[CMD] [2023-10-13 13:48:58] tail -n +1 /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_occurrences_30838.csv >> /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_occurrences_30838.diff
[CMD] [2023-10-13 13:48:58] echo "." >> /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_occurrences_30838.diff
[INFO] [2023-10-13 13:48:58] Created diff: /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_occurrences_30838.diff (11 lines)
[INFO] [2023-10-13 13:48:58] ...measurements (/app/public/data/zieger_meyer_roc/measurementsorfacts.txt)
[CMD] [2023-10-13 13:48:58] echo "0a" > /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_measurements_30839.diff
[CMD] [2023-10-13 13:48:58] tail -n +1 /app/public/data/zieger_meyer_roc/converted_csv/zieger_meyer_roc_measurements_30839.csv >> /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_measurements_30839.diff
[CMD] [2023-10-13 13:48:58] echo "." >> /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_measurements_30839.diff
[INFO] [2023-10-13 13:48:58] Created diff: /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_measurements_30839.diff (34 lines)
[STOP] [2023-10-13 13:48:58] calculate_delta
[START] [2023-10-13 13:48:58] parse_diff_and_store
[INFO] [2023-10-13 13:48:58] Handling diff: /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_refs_30840.diff (4 lines)
[INFO] [2023-10-13 13:48:59] Loading refs diff file into memory (4 lines)...
[INFO] [2023-10-13 13:48:59] Storing 2 References (2/2/4)
[INFO] [2023-10-13 13:48:59] Handling diff: /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_nodes_30837.diff (11 lines)
[INFO] [2023-10-13 13:48:59] Loading nodes diff file into memory (11 lines)...
[INFO] [2023-10-13 13:48:59] Storing 9 ScientificNames (18/9/11)
[INFO] [2023-10-13 13:48:59] Storing 9 Nodes (18/9/11)
[INFO] [2023-10-13 13:48:59] Handling diff: /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_occurrences_30838.diff (11 lines)
[INFO] [2023-10-13 13:48:59] Loading occurrences diff file into memory (11 lines)...
[INFO] [2023-10-13 13:48:59] Storing 9 Occurrences (9/9/11)
[INFO] [2023-10-13 13:48:59] Handling diff: /app/public/data/zieger_meyer_roc/diff/zieger_meyer_roc_measurements_30839.diff (34 lines)
[INFO] [2023-10-13 13:48:59] Loading measurements diff file into memory (34 lines)...
[INFO] [2023-10-13 13:48:59] Storing 32 Traits (50/32/34)
[INFO] [2023-10-13 13:48:59] Storing 16 MetaTraits (50/32/34)
[INFO] [2023-10-13 13:48:59] Storing 2 TraitsReferences (50/32/34)
[STOP] [2023-10-13 13:48:59] parse_diff_and_store
[START] [2023-10-13 13:48:59] resolve_keys
[2023-10-13 13:48:59] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:49:07] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:49:07] traits to occurrences...
[INFO] [2023-10-13 13:49:07] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:49:07] Traits to sex term...
[INFO] [2023-10-13 13:49:07] Traits to lifestage term...
[INFO] [2023-10-13 13:49:07] MetaTraits to traits...
[INFO] [2023-10-13 13:49:07] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:49:07] Assocs to occurrences...
[INFO] [2023-10-13 13:49:07] Assocs to nodes...
[INFO] [2023-10-13 13:49:07] Assoc to sex term...
[INFO] [2023-10-13 13:49:07] Assoc to lifestage term...
[INFO] [2023-10-13 13:49:07] MetaAssoc to assocs...
[STOP] [2023-10-13 13:49:07] resolve_keys
[START] [2023-10-13 13:49:07] hold_for_later_1
[STOP] [2023-10-13 13:49:07] hold_for_later_1
[START] [2023-10-13 13:49:07] hold_for_later_2
[STOP] [2023-10-13 13:49:07] hold_for_later_2
[START] [2023-10-13 13:49:07] resolve_missing_parents
[STOP] [2023-10-13 13:49:07] resolve_missing_parents
[START] [2023-10-13 13:49:07] rebuild_nodes
[START] [2023-10-13 13:49:07] Flattener#flatten
[START] [2023-10-13 13:49:07] Flattener#study_resource
[START] [2023-10-13 13:49:07] Flattener#build_ancestry
[STOP] [2023-10-13 13:49:07] Flattener#build_ancestry
[INFO] [2023-10-13 13:49:07] 9 ancestry keys
[START] [2023-10-13 13:49:07] build_node_ancestors
[INFO] [2023-10-13 13:49:07] old ancestors deleted.
[STOP] [2023-10-13 13:49:07] build_node_ancestors
[WARN] [2023-10-13 13:49:07] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:49:07] Flattener#flatten
[STOP] [2023-10-13 13:49:07] rebuild_nodes
[START] [2023-10-13 13:49:07] resolve_missing_media_owners
[STOP] [2023-10-13 13:49:07] resolve_missing_media_owners
[START] [2023-10-13 13:49:07] sanitize_media_verbatims
[STOP] [2023-10-13 13:49:07] sanitize_media_verbatims
[START] [2023-10-13 13:49:07] queue_downloads
[STOP] [2023-10-13 13:49:07] queue_downloads
[START] [2023-10-13 13:49:07] parse_names
[WARN] [2023-10-13 13:49:07] I see 9 names which still need to be parsed.
[WARN] [2023-10-13 13:49:07] Names to parse: 9 formatted: 9 learned: 9 parsed: 9
[STOP] [2023-10-13 13:49:08] parse_names
[START] [2023-10-13 13:49:08] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:49:08] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:49:08] match_nodes
[START] [2023-10-13 13:49:08] map_all_nodes_to_pages
[STOP] [2023-10-13 13:49:08] map_all_nodes_to_pages
[INFO] [2023-10-13 13:49:08] ZERO unmatched nodes (of 9)! Nicely done.
[START] [2023-10-13 13:49:08] update_nodes
[STOP] [2023-10-13 13:49:08] update_nodes
[STOP] [2023-10-13 13:49:08] match_nodes
[START] [2023-10-13 13:49:08] reindex_search
[STOP] [2023-10-13 13:49:08] reindex_search
[START] [2023-10-13 13:49:08] normalize_units
[STOP] [2023-10-13 13:49:08] normalize_units
[START] [2023-10-13 13:49:08] calculate_statistics
[2023-10-13 13:49:08] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:49:08] Duplicate page_id count: 0
[STOP] [2023-10-13 13:49:08] calculate_statistics
[START] [2023-10-13 13:49:08] complete_harvest_instance
[START] [2023-10-13 13:49:08] overall_tsv_creation
[INFO] [2023-10-13 13:49:08] Exporting 9 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:49:08] Processing group of 9 in 1 batches of 10000
[INFO] [2023-10-13 13:49:08] 9 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:49:08] Building Traits map for 9 nodes (this can take a while)...
[INFO] [2023-10-13 13:49:08] Mapped 9 traits (16 meta) for 9 nodes.
[INFO] [2023-10-13 13:49:08] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:49:08] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:49:08] Adding 9 traits...
[INFO] [2023-10-13 13:49:08] 25 metadata added.
[INFO] [2023-10-13 13:49:08] Adding 0 assocs...
[INFO] [2023-10-13 13:49:08] 0 metadata added.
[INFO] [2023-10-13 13:49:52] Processed 9/9 nodes
[INFO] [2023-10-13 13:49:52] Average Time: 43.87
[INFO] [2023-10-13 13:49:52] Total Time: 44s
[STOP] [2023-10-13 13:49:52] overall_tsv_creation
[INFO] [2023-10-13 13:49:52] Done. Check your files:
[INFO] [2023-10-13 13:49:52] (9 lines) /app/public/data/zieger_meyer_roc/publish_nodes.tsv
[INFO] [2023-10-13 13:49:52] (9 lines) /app/public/data/zieger_meyer_roc/publish_scientific_names.tsv
[INFO] [2023-10-13 13:49:52] (10 lines) /app/public/data/zieger_meyer_roc/publish_traits.tsv
[INFO] [2023-10-13 13:49:52] (26 lines) /app/public/data/zieger_meyer_roc/publish_metadata.tsv
[STOP] [2023-10-13 13:49:52] complete_harvest_instance
[START] [2023-10-13 13:49:52] completed
[STOP] [2023-10-13 13:49:52] completed
[STOP] [2023-10-13 13:49:52] logged process, took 55.23

Latest Process

13 Oct 13:48 EXITED currently processing 0