Harvest for Cameron et al 2000 Created 03 Aug 16:06

Stage: completed
Fetched: 03 Aug 16:06
Validated: 03 Aug 16:06
Deltas Created 03 Aug 16:06
Units Normalized: 03 Aug 16:06
Ancestry Built: 03 Aug 16:06
Nodes Matched: 03 Aug 16:06
Names Parsed: 03 Aug 16:06
New Models Stored: 03 Aug 16:06
Indexed: 03 Aug 16:06
Completed: 03 Aug 16:08
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:06:13] Created harvest instance #4162
[STOP] [2022-08-03 16:06:13] create_harvest_instance
[START] [2022-08-03 16:06:13] fetch_files
[STOP] [2022-08-03 16:06:13] fetch_files
[START] [2022-08-03 16:06:13] validate_each_file
[INFO] [2022-08-03 16:06:13] Looping over 3 formats...
[INFO] [2022-08-03 16:06:13] ...nodes (/app/public/data/cameron_et_al_ca/taxa.txt)
[INFO] [2022-08-03 16:06:13] Valid: /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_nodes_29549.csv (2 lines)
[INFO] [2022-08-03 16:06:13] ...occurrences (/app/public/data/cameron_et_al_ca/occurrences.txt)
[INFO] [2022-08-03 16:06:13] Valid: /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_occurrences_29550.csv (2 lines)
[INFO] [2022-08-03 16:06:13] ...measurements (/app/public/data/cameron_et_al_ca/measurementOrFact.txt)
[INFO] [2022-08-03 16:06:13] Valid: /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_measurements_29551.csv (8 lines)
[STOP] [2022-08-03 16:06:13] validate_each_file
[START] [2022-08-03 16:06:13] convert_to_csv
[INFO] [2022-08-03 16:06:13] Looping over 3 formats...
[INFO] [2022-08-03 16:06:13] ...nodes (/app/public/data/cameron_et_al_ca/taxa.txt)
[CMD] [2022-08-03 16:06:13] /usr/bin/sort /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_nodes_29549.csv > /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_nodes_29549.csv_sorted
[INFO] [2022-08-03 16:06:13] Converted: /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_nodes_29549.csv (2 lines)
[INFO] [2022-08-03 16:06:13] ...occurrences (/app/public/data/cameron_et_al_ca/occurrences.txt)
[CMD] [2022-08-03 16:06:13] /usr/bin/sort /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_occurrences_29550.csv > /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_occurrences_29550.csv_sorted
[INFO] [2022-08-03 16:06:13] Converted: /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_occurrences_29550.csv (2 lines)
[INFO] [2022-08-03 16:06:13] ...measurements (/app/public/data/cameron_et_al_ca/measurementOrFact.txt)
[CMD] [2022-08-03 16:06:13] /usr/bin/sort /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_measurements_29551.csv > /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_measurements_29551.csv_sorted
[INFO] [2022-08-03 16:06:13] Converted: /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_measurements_29551.csv (8 lines)
[STOP] [2022-08-03 16:06:13] convert_to_csv
[START] [2022-08-03 16:06:13] calculate_delta
[INFO] [2022-08-03 16:06:13] Looping over 3 formats...
[INFO] [2022-08-03 16:06:13] ...nodes (/app/public/data/cameron_et_al_ca/taxa.txt)
[CMD] [2022-08-03 16:06:13] echo "0a" > /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_nodes_29549.diff
[CMD] [2022-08-03 16:06:13] tail -n +1 /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_nodes_29549.csv >> /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_nodes_29549.diff
[CMD] [2022-08-03 16:06:13] echo "." >> /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_nodes_29549.diff
[INFO] [2022-08-03 16:06:13] Created diff: /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_nodes_29549.diff (4 lines)
[INFO] [2022-08-03 16:06:13] ...occurrences (/app/public/data/cameron_et_al_ca/occurrences.txt)
[CMD] [2022-08-03 16:06:13] echo "0a" > /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_occurrences_29550.diff
[CMD] [2022-08-03 16:06:13] tail -n +1 /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_occurrences_29550.csv >> /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_occurrences_29550.diff
[CMD] [2022-08-03 16:06:13] echo "." >> /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_occurrences_29550.diff
[INFO] [2022-08-03 16:06:13] Created diff: /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_occurrences_29550.diff (4 lines)
[INFO] [2022-08-03 16:06:13] ...measurements (/app/public/data/cameron_et_al_ca/measurementOrFact.txt)
[CMD] [2022-08-03 16:06:13] echo "0a" > /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_measurements_29551.diff
[CMD] [2022-08-03 16:06:13] tail -n +1 /app/public/data/cameron_et_al_ca/converted_csv/cameron_et_al_ca_measurements_29551.csv >> /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_measurements_29551.diff
[CMD] [2022-08-03 16:06:13] echo "." >> /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_measurements_29551.diff
[INFO] [2022-08-03 16:06:13] Created diff: /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_measurements_29551.diff (10 lines)
[STOP] [2022-08-03 16:06:13] calculate_delta
[START] [2022-08-03 16:06:13] parse_diff_and_store
[INFO] [2022-08-03 16:06:13] Handling diff: /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_nodes_29549.diff (4 lines)
[INFO] [2022-08-03 16:06:13] Loading nodes diff file into memory (4 lines)...
[INFO] [2022-08-03 16:06:13] Storing 2 ScientificNames (4/2/4)
[INFO] [2022-08-03 16:06:13] Storing 2 Nodes (4/2/4)
[INFO] [2022-08-03 16:06:13] Handling diff: /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_occurrences_29550.diff (4 lines)
[INFO] [2022-08-03 16:06:13] Loading occurrences diff file into memory (4 lines)...
[INFO] [2022-08-03 16:06:13] Storing 2 Occurrences (2/2/4)
[INFO] [2022-08-03 16:06:13] Handling diff: /app/public/data/cameron_et_al_ca/diff/cameron_et_al_ca_measurements_29551.diff (10 lines)
[INFO] [2022-08-03 16:06:13] Loading measurements diff file into memory (10 lines)...
[INFO] [2022-08-03 16:06:13] Storing 8 Traits (12/8/10)
[INFO] [2022-08-03 16:06:13] Storing 4 MetaTraits (12/8/10)
[STOP] [2022-08-03 16:06:13] parse_diff_and_store
[START] [2022-08-03 16:06:13] resolve_keys
[2022-08-03 16:06:13] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:06:20] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:06:20] traits to occurrences...
[INFO] [2022-08-03 16:06:20] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:06:20] Traits to sex term...
[INFO] [2022-08-03 16:06:20] Traits to lifestage term...
[INFO] [2022-08-03 16:06:20] MetaTraits to traits...
[INFO] [2022-08-03 16:06:20] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:06:20] Assocs to occurrences...
[INFO] [2022-08-03 16:06:20] Assocs to nodes...
[INFO] [2022-08-03 16:06:20] Assoc to sex term...
[INFO] [2022-08-03 16:06:20] Assoc to lifestage term...
[INFO] [2022-08-03 16:06:20] MetaAssoc to assocs...
[STOP] [2022-08-03 16:06:20] resolve_keys
[START] [2022-08-03 16:06:20] hold_for_later_1
[STOP] [2022-08-03 16:06:20] hold_for_later_1
[START] [2022-08-03 16:06:20] hold_for_later_2
[STOP] [2022-08-03 16:06:20] hold_for_later_2
[START] [2022-08-03 16:06:20] resolve_missing_parents
[STOP] [2022-08-03 16:06:20] resolve_missing_parents
[START] [2022-08-03 16:06:20] rebuild_nodes
[START] [2022-08-03 16:06:20] Flattener#flatten
[START] [2022-08-03 16:06:20] Flattener#study_resource
[START] [2022-08-03 16:06:20] Flattener#build_ancestry
[STOP] [2022-08-03 16:06:20] Flattener#build_ancestry
[INFO] [2022-08-03 16:06:20] 2 ancestry keys
[START] [2022-08-03 16:06:20] build_node_ancestors
[INFO] [2022-08-03 16:06:20] old ancestors deleted.
[STOP] [2022-08-03 16:06:20] build_node_ancestors
[WARN] [2022-08-03 16:06:20] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:06:20] Flattener#flatten
[STOP] [2022-08-03 16:06:20] rebuild_nodes
[START] [2022-08-03 16:06:20] resolve_missing_media_owners
[STOP] [2022-08-03 16:06:20] resolve_missing_media_owners
[START] [2022-08-03 16:06:21] sanitize_media_verbatims
[STOP] [2022-08-03 16:06:21] sanitize_media_verbatims
[START] [2022-08-03 16:06:21] queue_downloads
[STOP] [2022-08-03 16:06:21] queue_downloads
[START] [2022-08-03 16:06:21] parse_names
[WARN] [2022-08-03 16:06:21] I see 2 names which still need to be parsed.
[WARN] [2022-08-03 16:06:21] Names to parse: 2 formatted: 2 learned: 2 parsed: 2
[STOP] [2022-08-03 16:06:22] parse_names
[START] [2022-08-03 16:06:22] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:06:22] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:06:22] match_nodes
[START] [2022-08-03 16:06:22] map_all_nodes_to_pages
[STOP] [2022-08-03 16:06:22] map_all_nodes_to_pages
[INFO] [2022-08-03 16:06:22] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2022-08-03 16:06:22] update_nodes
[STOP] [2022-08-03 16:06:22] update_nodes
[STOP] [2022-08-03 16:06:22] match_nodes
[START] [2022-08-03 16:06:22] reindex_search
[STOP] [2022-08-03 16:06:22] reindex_search
[START] [2022-08-03 16:06:22] normalize_units
[STOP] [2022-08-03 16:06:22] normalize_units
[START] [2022-08-03 16:06:22] calculate_statistics
[2022-08-03 16:06:22] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:06:22] Duplicate page_id count: 0
[STOP] [2022-08-03 16:06:22] calculate_statistics
[START] [2022-08-03 16:06:22] complete_harvest_instance
[START] [2022-08-03 16:06:22] overall_tsv_creation
[INFO] [2022-08-03 16:06:22] Exporting 2 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:06:22] Processing group of 2 in 1 batches of 10000
[INFO] [2022-08-03 16:07:04] 4 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:07:04] Building Traits map for 2 nodes (this can take a while)...
[INFO] [2022-08-03 16:07:56] Mapped 4 traits (4 meta) for 2 nodes.
[INFO] [2022-08-03 16:07:56] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:07:56] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:07:56] Adding 4 traits...
[INFO] [2022-08-03 16:07:56] 4 metadata added.
[INFO] [2022-08-03 16:07:56] Adding 0 assocs...
[INFO] [2022-08-03 16:07:56] 0 metadata added.
[INFO] [2022-08-03 16:08:38] Processed 2/2 nodes
[INFO] [2022-08-03 16:08:38] Average Time: 110.63
[INFO] [2022-08-03 16:08:38] Total Time: 2m16s
[STOP] [2022-08-03 16:08:38] overall_tsv_creation
[INFO] [2022-08-03 16:08:38] Done. Check your files:
[INFO] [2022-08-03 16:08:38] (2 lines) /app/public/data/cameron_et_al_ca/publish_nodes.tsv
[INFO] [2022-08-03 16:08:38] (2 lines) /app/public/data/cameron_et_al_ca/publish_scientific_names.tsv
[INFO] [2022-08-03 16:08:38] (5 lines) /app/public/data/cameron_et_al_ca/publish_traits.tsv
[INFO] [2022-08-03 16:08:38] (5 lines) /app/public/data/cameron_et_al_ca/publish_metadata.tsv
[STOP] [2022-08-03 16:08:38] complete_harvest_instance
[START] [2022-08-03 16:08:38] completed
[STOP] [2022-08-03 16:08:38] completed
[STOP] [2022-08-03 16:08:38] logged process, took 145.03
Latest Process

03 Aug 16:01 EXITED currently processing 0