Harvest for Ruhberg and Hamera 2005 Created 13 Oct 13:50

Stage: completed
Fetched: 13 Oct 13:50
Validated: 13 Oct 13:50
Deltas Created 13 Oct 13:50
Units Normalized: 13 Oct 13:51
Ancestry Built: 13 Oct 13:51
Nodes Matched: 13 Oct 13:51
Names Parsed: 13 Oct 13:51
New Models Stored: 13 Oct 13:50
Indexed: 13 Oct 13:51
Completed: 13 Oct 13:51
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
[INFO] [2023-10-13 13:50:57] Created harvest instance #4460
[STOP] [2023-10-13 13:50:57] create_harvest_instance
[START] [2023-10-13 13:50:57] fetch_files
[STOP] [2023-10-13 13:50:57] fetch_files
[START] [2023-10-13 13:50:57] validate_each_file
[INFO] [2023-10-13 13:50:57] Looping over 4 formats...
[INFO] [2023-10-13 13:50:57] ...refs (/app/public/data/ruhberg_hamera_r/references.tsv)
[INFO] [2023-10-13 13:50:57] Valid: /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_refs_30848.csv (3 lines)
[INFO] [2023-10-13 13:50:57] ...nodes (/app/public/data/ruhberg_hamera_r/taxa.txt)
[INFO] [2023-10-13 13:50:57] Valid: /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_nodes_30845.csv (3 lines)
[INFO] [2023-10-13 13:50:57] ...occurrences (/app/public/data/ruhberg_hamera_r/occurrences.txt)
[INFO] [2023-10-13 13:50:57] Valid: /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_occurrences_30846.csv (3 lines)
[INFO] [2023-10-13 13:50:57] ...measurements (/app/public/data/ruhberg_hamera_r/measurementsorfacts.txt)
[INFO] [2023-10-13 13:50:57] Valid: /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_measurements_30847.csv (3 lines)
[STOP] [2023-10-13 13:50:57] validate_each_file
[START] [2023-10-13 13:50:57] convert_to_csv
[INFO] [2023-10-13 13:50:57] Looping over 4 formats...
[INFO] [2023-10-13 13:50:57] ...refs (/app/public/data/ruhberg_hamera_r/references.tsv)
[CMD] [2023-10-13 13:50:57] /usr/bin/sort /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_refs_30848.csv > /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_refs_30848.csv_sorted
[INFO] [2023-10-13 13:50:57] Converted: /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_refs_30848.csv (3 lines)
[INFO] [2023-10-13 13:50:57] ...nodes (/app/public/data/ruhberg_hamera_r/taxa.txt)
[CMD] [2023-10-13 13:50:57] /usr/bin/sort /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_nodes_30845.csv > /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_nodes_30845.csv_sorted
[INFO] [2023-10-13 13:50:57] Converted: /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_nodes_30845.csv (3 lines)
[INFO] [2023-10-13 13:50:57] ...occurrences (/app/public/data/ruhberg_hamera_r/occurrences.txt)
[CMD] [2023-10-13 13:50:57] /usr/bin/sort /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_occurrences_30846.csv > /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_occurrences_30846.csv_sorted
[INFO] [2023-10-13 13:50:57] Converted: /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_occurrences_30846.csv (3 lines)
[INFO] [2023-10-13 13:50:57] ...measurements (/app/public/data/ruhberg_hamera_r/measurementsorfacts.txt)
[CMD] [2023-10-13 13:50:57] /usr/bin/sort /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_measurements_30847.csv > /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_measurements_30847.csv_sorted
[INFO] [2023-10-13 13:50:57] Converted: /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_measurements_30847.csv (3 lines)
[STOP] [2023-10-13 13:50:57] convert_to_csv
[START] [2023-10-13 13:50:57] calculate_delta
[INFO] [2023-10-13 13:50:57] Looping over 4 formats...
[INFO] [2023-10-13 13:50:57] ...refs (/app/public/data/ruhberg_hamera_r/references.tsv)
[CMD] [2023-10-13 13:50:57] echo "0a" > /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_refs_30848.diff
[CMD] [2023-10-13 13:50:57] tail -n +1 /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_refs_30848.csv >> /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_refs_30848.diff
[CMD] [2023-10-13 13:50:57] echo "." >> /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_refs_30848.diff
[INFO] [2023-10-13 13:50:58] Created diff: /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_refs_30848.diff (5 lines)
[INFO] [2023-10-13 13:50:58] ...nodes (/app/public/data/ruhberg_hamera_r/taxa.txt)
[CMD] [2023-10-13 13:50:58] echo "0a" > /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_nodes_30845.diff
[CMD] [2023-10-13 13:50:58] tail -n +1 /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_nodes_30845.csv >> /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_nodes_30845.diff
[CMD] [2023-10-13 13:50:58] echo "." >> /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_nodes_30845.diff
[INFO] [2023-10-13 13:50:58] Created diff: /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_nodes_30845.diff (5 lines)
[INFO] [2023-10-13 13:50:58] ...occurrences (/app/public/data/ruhberg_hamera_r/occurrences.txt)
[CMD] [2023-10-13 13:50:58] echo "0a" > /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_occurrences_30846.diff
[CMD] [2023-10-13 13:50:58] tail -n +1 /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_occurrences_30846.csv >> /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_occurrences_30846.diff
[CMD] [2023-10-13 13:50:58] echo "." >> /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_occurrences_30846.diff
[INFO] [2023-10-13 13:50:58] Created diff: /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_occurrences_30846.diff (5 lines)
[INFO] [2023-10-13 13:50:58] ...measurements (/app/public/data/ruhberg_hamera_r/measurementsorfacts.txt)
[CMD] [2023-10-13 13:50:58] echo "0a" > /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_measurements_30847.diff
[CMD] [2023-10-13 13:50:58] tail -n +1 /app/public/data/ruhberg_hamera_r/converted_csv/ruhberg_hamera_r_measurements_30847.csv >> /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_measurements_30847.diff
[CMD] [2023-10-13 13:50:58] echo "." >> /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_measurements_30847.diff
[INFO] [2023-10-13 13:50:58] Created diff: /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_measurements_30847.diff (5 lines)
[STOP] [2023-10-13 13:50:58] calculate_delta
[START] [2023-10-13 13:50:58] parse_diff_and_store
[INFO] [2023-10-13 13:50:58] Handling diff: /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_refs_30848.diff (5 lines)
[INFO] [2023-10-13 13:50:58] Loading refs diff file into memory (5 lines)...
[INFO] [2023-10-13 13:50:58] Storing 3 References (3/3/5)
[INFO] [2023-10-13 13:50:58] Handling diff: /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_nodes_30845.diff (5 lines)
[INFO] [2023-10-13 13:50:58] Loading nodes diff file into memory (5 lines)...
[INFO] [2023-10-13 13:50:58] Storing 3 ScientificNames (6/3/5)
[INFO] [2023-10-13 13:50:58] Storing 3 Nodes (6/3/5)
[INFO] [2023-10-13 13:50:58] Handling diff: /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_occurrences_30846.diff (5 lines)
[INFO] [2023-10-13 13:50:58] Loading occurrences diff file into memory (5 lines)...
[INFO] [2023-10-13 13:50:58] Storing 3 Occurrences (3/3/5)
[INFO] [2023-10-13 13:50:58] Handling diff: /app/public/data/ruhberg_hamera_r/diff/ruhberg_hamera_r_measurements_30847.diff (5 lines)
[INFO] [2023-10-13 13:50:59] Loading measurements diff file into memory (5 lines)...
[INFO] [2023-10-13 13:50:59] Storing 3 TraitsReferences (9/3/5)
[INFO] [2023-10-13 13:50:59] Storing 3 Traits (9/3/5)
[INFO] [2023-10-13 13:50:59] Storing 3 MetaTraits (9/3/5)
[STOP] [2023-10-13 13:50:59] parse_diff_and_store
[START] [2023-10-13 13:50:59] resolve_keys
[2023-10-13 13:50:59] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:51:06] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:51:06] traits to occurrences...
[INFO] [2023-10-13 13:51:06] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:51:06] Traits to sex term...
[INFO] [2023-10-13 13:51:06] Traits to lifestage term...
[INFO] [2023-10-13 13:51:06] MetaTraits to traits...
[INFO] [2023-10-13 13:51:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:51:06] Assocs to occurrences...
[INFO] [2023-10-13 13:51:06] Assocs to nodes...
[INFO] [2023-10-13 13:51:06] Assoc to sex term...
[INFO] [2023-10-13 13:51:06] Assoc to lifestage term...
[INFO] [2023-10-13 13:51:06] MetaAssoc to assocs...
[STOP] [2023-10-13 13:51:06] resolve_keys
[START] [2023-10-13 13:51:06] hold_for_later_1
[STOP] [2023-10-13 13:51:06] hold_for_later_1
[START] [2023-10-13 13:51:06] hold_for_later_2
[STOP] [2023-10-13 13:51:06] hold_for_later_2
[START] [2023-10-13 13:51:06] resolve_missing_parents
[STOP] [2023-10-13 13:51:06] resolve_missing_parents
[START] [2023-10-13 13:51:06] rebuild_nodes
[START] [2023-10-13 13:51:06] Flattener#flatten
[START] [2023-10-13 13:51:06] Flattener#study_resource
[START] [2023-10-13 13:51:06] Flattener#build_ancestry
[STOP] [2023-10-13 13:51:06] Flattener#build_ancestry
[INFO] [2023-10-13 13:51:06] 3 ancestry keys
[START] [2023-10-13 13:51:06] build_node_ancestors
[INFO] [2023-10-13 13:51:06] old ancestors deleted.
[STOP] [2023-10-13 13:51:06] build_node_ancestors
[WARN] [2023-10-13 13:51:06] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:51:06] Flattener#flatten
[STOP] [2023-10-13 13:51:06] rebuild_nodes
[START] [2023-10-13 13:51:06] resolve_missing_media_owners
[STOP] [2023-10-13 13:51:06] resolve_missing_media_owners
[START] [2023-10-13 13:51:06] sanitize_media_verbatims
[STOP] [2023-10-13 13:51:06] sanitize_media_verbatims
[START] [2023-10-13 13:51:06] queue_downloads
[STOP] [2023-10-13 13:51:06] queue_downloads
[START] [2023-10-13 13:51:06] parse_names
[WARN] [2023-10-13 13:51:06] I see 3 names which still need to be parsed.
[WARN] [2023-10-13 13:51:06] Names to parse: 3 formatted: 3 learned: 3 parsed: 3
[STOP] [2023-10-13 13:51:07] parse_names
[START] [2023-10-13 13:51:07] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:51:07] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:51:07] match_nodes
[START] [2023-10-13 13:51:07] map_all_nodes_to_pages
[STOP] [2023-10-13 13:51:08] map_all_nodes_to_pages
[INFO] [2023-10-13 13:51:08] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2023-10-13 13:51:08] update_nodes
[STOP] [2023-10-13 13:51:08] update_nodes
[STOP] [2023-10-13 13:51:08] match_nodes
[START] [2023-10-13 13:51:08] reindex_search
[STOP] [2023-10-13 13:51:08] reindex_search
[START] [2023-10-13 13:51:08] normalize_units
[STOP] [2023-10-13 13:51:08] normalize_units
[START] [2023-10-13 13:51:08] calculate_statistics
[2023-10-13 13:51:08] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:51:08] Duplicate page_id count: 0
[STOP] [2023-10-13 13:51:08] calculate_statistics
[START] [2023-10-13 13:51:08] complete_harvest_instance
[START] [2023-10-13 13:51:08] overall_tsv_creation
[INFO] [2023-10-13 13:51:08] Exporting 3 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:51:08] Processing group of 3 in 1 batches of 10000
[INFO] [2023-10-13 13:51:08] 3 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:51:08] Building Traits map for 3 nodes (this can take a while)...
[INFO] [2023-10-13 13:51:08] Mapped 3 traits (3 meta) for 3 nodes.
[INFO] [2023-10-13 13:51:08] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:51:08] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:51:08] Adding 3 traits...
[INFO] [2023-10-13 13:51:08] 3 metadata added.
[INFO] [2023-10-13 13:51:08] Adding 0 assocs...
[INFO] [2023-10-13 13:51:08] 0 metadata added.
[INFO] [2023-10-13 13:51:51] Processed 3/3 nodes
[INFO] [2023-10-13 13:51:51] Average Time: 43.83
[INFO] [2023-10-13 13:51:51] Total Time: 44s
[STOP] [2023-10-13 13:51:51] overall_tsv_creation
[INFO] [2023-10-13 13:51:51] Done. Check your files:
[INFO] [2023-10-13 13:51:52] (3 lines) /app/public/data/ruhberg_hamera_r/publish_nodes.tsv
[INFO] [2023-10-13 13:51:52] (3 lines) /app/public/data/ruhberg_hamera_r/publish_scientific_names.tsv
[INFO] [2023-10-13 13:51:52] (4 lines) /app/public/data/ruhberg_hamera_r/publish_traits.tsv
[INFO] [2023-10-13 13:51:52] (4 lines) /app/public/data/ruhberg_hamera_r/publish_metadata.tsv
[STOP] [2023-10-13 13:51:52] complete_harvest_instance
[START] [2023-10-13 13:51:52] completed
[STOP] [2023-10-13 13:51:52] completed
[STOP] [2023-10-13 13:51:52] logged process, took 54.99
Latest Process

13 Oct 13:50 EXITED currently processing 0