Harvest for Ladich and Popper 2004 Created 14 Oct 08:29

Stage: completed
Fetched: 14 Oct 08:29
Validated: 14 Oct 08:29
Deltas Created 14 Oct 08:29
Units Normalized: 14 Oct 08:29
Ancestry Built: 14 Oct 08:29
Nodes Matched: 14 Oct 08:29
Names Parsed: 14 Oct 08:29
New Models Stored: 14 Oct 08:29
Indexed: 14 Oct 08:29
Completed: 14 Oct 08:30
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
[INFO] [2023-10-14 08:29:35] Created harvest instance #4470
[STOP] [2023-10-14 08:29:35] create_harvest_instance
[START] [2023-10-14 08:29:35] fetch_files
[STOP] [2023-10-14 08:29:35] fetch_files
[START] [2023-10-14 08:29:35] validate_each_file
[INFO] [2023-10-14 08:29:35] Looping over 4 formats...
[INFO] [2023-10-14 08:29:35] ...refs (/app/public/data/ladich_popper_la/references.txt)
[INFO] [2023-10-14 08:29:35] Valid: /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_refs_30888.csv (8 lines)
[INFO] [2023-10-14 08:29:35] ...nodes (/app/public/data/ladich_popper_la/taxa.txt)
[INFO] [2023-10-14 08:29:35] Valid: /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_nodes_30885.csv (12 lines)
[INFO] [2023-10-14 08:29:35] ...occurrences (/app/public/data/ladich_popper_la/occurrences.txt)
[INFO] [2023-10-14 08:29:35] Valid: /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_occurrences_30886.csv (12 lines)
[INFO] [2023-10-14 08:29:35] ...measurements (/app/public/data/ladich_popper_la/measurementsorfacts.txt)
[INFO] [2023-10-14 08:29:35] Valid: /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_measurements_30887.csv (111 lines)
[STOP] [2023-10-14 08:29:35] validate_each_file
[START] [2023-10-14 08:29:35] convert_to_csv
[INFO] [2023-10-14 08:29:35] Looping over 4 formats...
[INFO] [2023-10-14 08:29:35] ...refs (/app/public/data/ladich_popper_la/references.txt)
[CMD] [2023-10-14 08:29:35] /usr/bin/sort /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_refs_30888.csv > /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_refs_30888.csv_sorted
[INFO] [2023-10-14 08:29:35] Converted: /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_refs_30888.csv (8 lines)
[INFO] [2023-10-14 08:29:35] ...nodes (/app/public/data/ladich_popper_la/taxa.txt)
[CMD] [2023-10-14 08:29:35] /usr/bin/sort /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_nodes_30885.csv > /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_nodes_30885.csv_sorted
[INFO] [2023-10-14 08:29:35] Converted: /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_nodes_30885.csv (12 lines)
[INFO] [2023-10-14 08:29:35] ...occurrences (/app/public/data/ladich_popper_la/occurrences.txt)
[CMD] [2023-10-14 08:29:35] /usr/bin/sort /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_occurrences_30886.csv > /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_occurrences_30886.csv_sorted
[INFO] [2023-10-14 08:29:35] Converted: /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_occurrences_30886.csv (12 lines)
[INFO] [2023-10-14 08:29:35] ...measurements (/app/public/data/ladich_popper_la/measurementsorfacts.txt)
[CMD] [2023-10-14 08:29:35] /usr/bin/sort /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_measurements_30887.csv > /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_measurements_30887.csv_sorted
[INFO] [2023-10-14 08:29:35] Converted: /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_measurements_30887.csv (111 lines)
[STOP] [2023-10-14 08:29:35] convert_to_csv
[START] [2023-10-14 08:29:35] calculate_delta
[INFO] [2023-10-14 08:29:35] Looping over 4 formats...
[INFO] [2023-10-14 08:29:35] ...refs (/app/public/data/ladich_popper_la/references.txt)
[CMD] [2023-10-14 08:29:35] echo "0a" > /app/public/data/ladich_popper_la/diff/ladich_popper_la_refs_30888.diff
[CMD] [2023-10-14 08:29:35] tail -n +1 /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_refs_30888.csv >> /app/public/data/ladich_popper_la/diff/ladich_popper_la_refs_30888.diff
[CMD] [2023-10-14 08:29:35] echo "." >> /app/public/data/ladich_popper_la/diff/ladich_popper_la_refs_30888.diff
[INFO] [2023-10-14 08:29:35] Created diff: /app/public/data/ladich_popper_la/diff/ladich_popper_la_refs_30888.diff (10 lines)
[INFO] [2023-10-14 08:29:35] ...nodes (/app/public/data/ladich_popper_la/taxa.txt)
[CMD] [2023-10-14 08:29:35] echo "0a" > /app/public/data/ladich_popper_la/diff/ladich_popper_la_nodes_30885.diff
[CMD] [2023-10-14 08:29:35] tail -n +1 /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_nodes_30885.csv >> /app/public/data/ladich_popper_la/diff/ladich_popper_la_nodes_30885.diff
[CMD] [2023-10-14 08:29:35] echo "." >> /app/public/data/ladich_popper_la/diff/ladich_popper_la_nodes_30885.diff
[INFO] [2023-10-14 08:29:35] Created diff: /app/public/data/ladich_popper_la/diff/ladich_popper_la_nodes_30885.diff (14 lines)
[INFO] [2023-10-14 08:29:35] ...occurrences (/app/public/data/ladich_popper_la/occurrences.txt)
[CMD] [2023-10-14 08:29:35] echo "0a" > /app/public/data/ladich_popper_la/diff/ladich_popper_la_occurrences_30886.diff
[CMD] [2023-10-14 08:29:36] tail -n +1 /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_occurrences_30886.csv >> /app/public/data/ladich_popper_la/diff/ladich_popper_la_occurrences_30886.diff
[CMD] [2023-10-14 08:29:36] echo "." >> /app/public/data/ladich_popper_la/diff/ladich_popper_la_occurrences_30886.diff
[INFO] [2023-10-14 08:29:36] Created diff: /app/public/data/ladich_popper_la/diff/ladich_popper_la_occurrences_30886.diff (14 lines)
[INFO] [2023-10-14 08:29:36] ...measurements (/app/public/data/ladich_popper_la/measurementsorfacts.txt)
[CMD] [2023-10-14 08:29:36] echo "0a" > /app/public/data/ladich_popper_la/diff/ladich_popper_la_measurements_30887.diff
[CMD] [2023-10-14 08:29:36] tail -n +1 /app/public/data/ladich_popper_la/converted_csv/ladich_popper_la_measurements_30887.csv >> /app/public/data/ladich_popper_la/diff/ladich_popper_la_measurements_30887.diff
[CMD] [2023-10-14 08:29:36] echo "." >> /app/public/data/ladich_popper_la/diff/ladich_popper_la_measurements_30887.diff
[INFO] [2023-10-14 08:29:36] Created diff: /app/public/data/ladich_popper_la/diff/ladich_popper_la_measurements_30887.diff (113 lines)
[STOP] [2023-10-14 08:29:36] calculate_delta
[START] [2023-10-14 08:29:36] parse_diff_and_store
[INFO] [2023-10-14 08:29:36] Handling diff: /app/public/data/ladich_popper_la/diff/ladich_popper_la_refs_30888.diff (10 lines)
[INFO] [2023-10-14 08:29:36] Loading refs diff file into memory (10 lines)...
[INFO] [2023-10-14 08:29:36] Storing 8 References (8/8/10)
[INFO] [2023-10-14 08:29:36] Handling diff: /app/public/data/ladich_popper_la/diff/ladich_popper_la_nodes_30885.diff (14 lines)
[INFO] [2023-10-14 08:29:36] Loading nodes diff file into memory (14 lines)...
[INFO] [2023-10-14 08:29:36] Storing 12 ScientificNames (24/12/14)
[INFO] [2023-10-14 08:29:36] Storing 12 Nodes (24/12/14)
[INFO] [2023-10-14 08:29:36] Handling diff: /app/public/data/ladich_popper_la/diff/ladich_popper_la_occurrences_30886.diff (14 lines)
[INFO] [2023-10-14 08:29:36] Loading occurrences diff file into memory (14 lines)...
[INFO] [2023-10-14 08:29:36] Storing 12 Occurrences (12/12/14)
[INFO] [2023-10-14 08:29:36] Handling diff: /app/public/data/ladich_popper_la/diff/ladich_popper_la_measurements_30887.diff (113 lines)
[INFO] [2023-10-14 08:29:36] Loading measurements diff file into memory (113 lines)...
[INFO] [2023-10-14 08:29:36] Storing 40 TraitsReferences (221/111/113)
[INFO] [2023-10-14 08:29:36] Storing 111 Traits (221/111/113)
[INFO] [2023-10-14 08:29:36] Storing 70 MetaTraits (221/111/113)
[STOP] [2023-10-14 08:29:36] parse_diff_and_store
[START] [2023-10-14 08:29:36] resolve_keys
[2023-10-14 08:29:37] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-14 08:29:44] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-14 08:29:44] traits to occurrences...
[INFO] [2023-10-14 08:29:44] traits to nodes (through occurrences)...
[INFO] [2023-10-14 08:29:44] Traits to sex term...
[INFO] [2023-10-14 08:29:44] Traits to lifestage term...
[INFO] [2023-10-14 08:29:44] MetaTraits to traits...
[INFO] [2023-10-14 08:29:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-14 08:29:44] Assocs to occurrences...
[INFO] [2023-10-14 08:29:44] Assocs to nodes...
[INFO] [2023-10-14 08:29:44] Assoc to sex term...
[INFO] [2023-10-14 08:29:44] Assoc to lifestage term...
[INFO] [2023-10-14 08:29:44] MetaAssoc to assocs...
[STOP] [2023-10-14 08:29:44] resolve_keys
[START] [2023-10-14 08:29:44] hold_for_later_1
[STOP] [2023-10-14 08:29:44] hold_for_later_1
[START] [2023-10-14 08:29:44] hold_for_later_2
[STOP] [2023-10-14 08:29:44] hold_for_later_2
[START] [2023-10-14 08:29:44] resolve_missing_parents
[STOP] [2023-10-14 08:29:44] resolve_missing_parents
[START] [2023-10-14 08:29:44] rebuild_nodes
[START] [2023-10-14 08:29:44] Flattener#flatten
[START] [2023-10-14 08:29:44] Flattener#study_resource
[START] [2023-10-14 08:29:44] Flattener#build_ancestry
[STOP] [2023-10-14 08:29:44] Flattener#build_ancestry
[INFO] [2023-10-14 08:29:44] 12 ancestry keys
[START] [2023-10-14 08:29:44] build_node_ancestors
[INFO] [2023-10-14 08:29:44] old ancestors deleted.
[STOP] [2023-10-14 08:29:44] build_node_ancestors
[WARN] [2023-10-14 08:29:44] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-14 08:29:44] Flattener#flatten
[STOP] [2023-10-14 08:29:44] rebuild_nodes
[START] [2023-10-14 08:29:44] resolve_missing_media_owners
[STOP] [2023-10-14 08:29:44] resolve_missing_media_owners
[START] [2023-10-14 08:29:44] sanitize_media_verbatims
[STOP] [2023-10-14 08:29:44] sanitize_media_verbatims
[START] [2023-10-14 08:29:44] queue_downloads
[STOP] [2023-10-14 08:29:44] queue_downloads
[START] [2023-10-14 08:29:44] parse_names
[WARN] [2023-10-14 08:29:44] I see 12 names which still need to be parsed.
[WARN] [2023-10-14 08:29:45] Names to parse: 12 formatted: 12 learned: 12 parsed: 12
[STOP] [2023-10-14 08:29:46] parse_names
[START] [2023-10-14 08:29:46] denormalize_canonical_names_to_nodes
[STOP] [2023-10-14 08:29:46] denormalize_canonical_names_to_nodes
[START] [2023-10-14 08:29:46] match_nodes
[START] [2023-10-14 08:29:46] map_all_nodes_to_pages
[STOP] [2023-10-14 08:29:46] map_all_nodes_to_pages
[INFO] [2023-10-14 08:29:46] ZERO unmatched nodes (of 12)! Nicely done.
[START] [2023-10-14 08:29:46] update_nodes
[STOP] [2023-10-14 08:29:46] update_nodes
[STOP] [2023-10-14 08:29:46] match_nodes
[START] [2023-10-14 08:29:46] reindex_search
[STOP] [2023-10-14 08:29:46] reindex_search
[START] [2023-10-14 08:29:46] normalize_units
[STOP] [2023-10-14 08:29:46] normalize_units
[START] [2023-10-14 08:29:46] calculate_statistics
[2023-10-14 08:29:46] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-14 08:29:46] Duplicate page_id count: 0
[STOP] [2023-10-14 08:29:46] calculate_statistics
[START] [2023-10-14 08:29:46] complete_harvest_instance
[START] [2023-10-14 08:29:46] overall_tsv_creation
[INFO] [2023-10-14 08:29:46] Exporting 12 nodes as TSV in batches of 10000...
[INFO] [2023-10-14 08:29:46] Processing group of 12 in 1 batches of 10000
[INFO] [2023-10-14 08:29:46] 39 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-14 08:29:46] Building Traits map for 12 nodes (this can take a while)...
[INFO] [2023-10-14 08:29:46] Mapped 39 traits (70 meta) for 12 nodes.
[INFO] [2023-10-14 08:29:46] Building Associations map (this can take a while)...
[INFO] [2023-10-14 08:29:46] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-14 08:29:46] Adding 39 traits...
[INFO] [2023-10-14 08:29:46] 112 metadata added.
[INFO] [2023-10-14 08:29:46] Adding 0 assocs...
[INFO] [2023-10-14 08:29:46] 0 metadata added.
[INFO] [2023-10-14 08:30:30] Processed 12/12 nodes
[INFO] [2023-10-14 08:30:30] Average Time: 43.98
[INFO] [2023-10-14 08:30:30] Total Time: 45s
[STOP] [2023-10-14 08:30:30] overall_tsv_creation
[INFO] [2023-10-14 08:30:30] Done. Check your files:
[INFO] [2023-10-14 08:30:30] (12 lines) /app/public/data/ladich_popper_la/publish_nodes.tsv
[INFO] [2023-10-14 08:30:30] (12 lines) /app/public/data/ladich_popper_la/publish_scientific_names.tsv
[INFO] [2023-10-14 08:30:31] (40 lines) /app/public/data/ladich_popper_la/publish_traits.tsv
[INFO] [2023-10-14 08:30:31] (113 lines) /app/public/data/ladich_popper_la/publish_metadata.tsv
[STOP] [2023-10-14 08:30:31] complete_harvest_instance
[START] [2023-10-14 08:30:31] completed
[STOP] [2023-10-14 08:30:31] completed
[STOP] [2023-10-14 08:30:31] logged process, took 56.09
Latest Process

14 Oct 08:29 EXITED currently processing 0