Harvest for Trophic guild data for fungi Created 21 Jun 13:51

Stage: completed
Fetched: 21 Jun 13:51
Validated: 21 Jun 13:51
Deltas Created 21 Jun 13:51
Units Normalized: 21 Jun 13:52
Ancestry Built: 21 Jun 13:52
Nodes Matched: 21 Jun 13:52
Names Parsed: 21 Jun 13:52
New Models Stored: 21 Jun 13:51
Indexed: 21 Jun 13:52
Completed: 21 Jun 13:53
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
[INFO] [2023-06-21 13:51:30] Created harvest instance #4360
[STOP] [2023-06-21 13:51:30] create_harvest_instance
[START] [2023-06-21 13:51:30] fetch_files
[STOP] [2023-06-21 13:51:30] fetch_files
[START] [2023-06-21 13:51:30] validate_each_file
[INFO] [2023-06-21 13:51:30] Looping over 3 formats...
[INFO] [2023-06-21 13:51:30] ...nodes (/app/public/data/trophic_guild_da/taxon.tab)
[INFO] [2023-06-21 13:51:30] Valid: /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_nodes_30394.csv (5017 lines)
[INFO] [2023-06-21 13:51:30] ...occurrences (/app/public/data/trophic_guild_da/occurrence_specific.tab)
[INFO] [2023-06-21 13:51:30] Valid: /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_occurrences_30395.csv (5222 lines)
[INFO] [2023-06-21 13:51:30] ...measurements (/app/public/data/trophic_guild_da/measurement_or_fact_specific.tab)
[INFO] [2023-06-21 13:51:31] Valid: /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_measurements_30396.csv (10380 lines)
[STOP] [2023-06-21 13:51:31] validate_each_file
[START] [2023-06-21 13:51:31] convert_to_csv
[INFO] [2023-06-21 13:51:31] Looping over 3 formats...
[INFO] [2023-06-21 13:51:31] ...nodes (/app/public/data/trophic_guild_da/taxon.tab)
[CMD] [2023-06-21 13:51:31] /usr/bin/sort /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_nodes_30394.csv > /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_nodes_30394.csv_sorted
[INFO] [2023-06-21 13:51:31] Converted: /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_nodes_30394.csv (5017 lines)
[INFO] [2023-06-21 13:51:31] ...occurrences (/app/public/data/trophic_guild_da/occurrence_specific.tab)
[CMD] [2023-06-21 13:51:31] /usr/bin/sort /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_occurrences_30395.csv > /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_occurrences_30395.csv_sorted
[INFO] [2023-06-21 13:51:31] Converted: /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_occurrences_30395.csv (5222 lines)
[INFO] [2023-06-21 13:51:31] ...measurements (/app/public/data/trophic_guild_da/measurement_or_fact_specific.tab)
[CMD] [2023-06-21 13:51:31] /usr/bin/sort /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_measurements_30396.csv > /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_measurements_30396.csv_sorted
[INFO] [2023-06-21 13:51:31] Converted: /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_measurements_30396.csv (10380 lines)
[STOP] [2023-06-21 13:51:31] convert_to_csv
[START] [2023-06-21 13:51:31] calculate_delta
[INFO] [2023-06-21 13:51:31] Looping over 3 formats...
[INFO] [2023-06-21 13:51:31] ...nodes (/app/public/data/trophic_guild_da/taxon.tab)
[CMD] [2023-06-21 13:51:31] echo "0a" > /app/public/data/trophic_guild_da/diff/trophic_guild_da_nodes_30394.diff
[CMD] [2023-06-21 13:51:31] tail -n +1 /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_nodes_30394.csv >> /app/public/data/trophic_guild_da/diff/trophic_guild_da_nodes_30394.diff
[CMD] [2023-06-21 13:51:31] echo "." >> /app/public/data/trophic_guild_da/diff/trophic_guild_da_nodes_30394.diff
[INFO] [2023-06-21 13:51:31] Created diff: /app/public/data/trophic_guild_da/diff/trophic_guild_da_nodes_30394.diff (5019 lines)
[INFO] [2023-06-21 13:51:31] ...occurrences (/app/public/data/trophic_guild_da/occurrence_specific.tab)
[CMD] [2023-06-21 13:51:31] echo "0a" > /app/public/data/trophic_guild_da/diff/trophic_guild_da_occurrences_30395.diff
[CMD] [2023-06-21 13:51:31] tail -n +1 /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_occurrences_30395.csv >> /app/public/data/trophic_guild_da/diff/trophic_guild_da_occurrences_30395.diff
[CMD] [2023-06-21 13:51:31] echo "." >> /app/public/data/trophic_guild_da/diff/trophic_guild_da_occurrences_30395.diff
[INFO] [2023-06-21 13:51:31] Created diff: /app/public/data/trophic_guild_da/diff/trophic_guild_da_occurrences_30395.diff (5224 lines)
[INFO] [2023-06-21 13:51:31] ...measurements (/app/public/data/trophic_guild_da/measurement_or_fact_specific.tab)
[CMD] [2023-06-21 13:51:31] echo "0a" > /app/public/data/trophic_guild_da/diff/trophic_guild_da_measurements_30396.diff
[CMD] [2023-06-21 13:51:31] tail -n +1 /app/public/data/trophic_guild_da/converted_csv/trophic_guild_da_measurements_30396.csv >> /app/public/data/trophic_guild_da/diff/trophic_guild_da_measurements_30396.diff
[CMD] [2023-06-21 13:51:31] echo "." >> /app/public/data/trophic_guild_da/diff/trophic_guild_da_measurements_30396.diff
[INFO] [2023-06-21 13:51:31] Created diff: /app/public/data/trophic_guild_da/diff/trophic_guild_da_measurements_30396.diff (10382 lines)
[STOP] [2023-06-21 13:51:31] calculate_delta
[START] [2023-06-21 13:51:32] parse_diff_and_store
[INFO] [2023-06-21 13:51:32] Handling diff: /app/public/data/trophic_guild_da/diff/trophic_guild_da_nodes_30394.diff (5019 lines)
[INFO] [2023-06-21 13:51:32] Loading nodes diff file into memory (5019 lines)...
[INFO] [2023-06-21 13:51:33] Storing 5018 ScientificNames (10036/5017/5019)
[INFO] [2023-06-21 13:51:34] Storing 5018 Nodes (10036/5017/5019)
[INFO] [2023-06-21 13:51:36] Handling diff: /app/public/data/trophic_guild_da/diff/trophic_guild_da_occurrences_30395.diff (5224 lines)
[INFO] [2023-06-21 13:51:36] Loading occurrences diff file into memory (5224 lines)...
[INFO] [2023-06-21 13:51:36] Storing 5222 Occurrences (5222/5222/5224)
[INFO] [2023-06-21 13:51:38] Handling diff: /app/public/data/trophic_guild_da/diff/trophic_guild_da_measurements_30396.diff (10382 lines)
[INFO] [2023-06-21 13:51:38] Loading measurements diff file into memory (10382 lines)...
[INFO] [2023-06-21 13:51:42] Storing 9999 Traits (15020/10000/10382)
[INFO] [2023-06-21 13:51:47] Storing 5021 MetaTraits (15020/10000/10382)
[INFO] [2023-06-21 13:51:49] Storing 381 Traits (15602/10380/10382)
[INFO] [2023-06-21 13:51:49] Storing 201 MetaTraits (15602/10380/10382)
[STOP] [2023-06-21 13:51:49] parse_diff_and_store
[START] [2023-06-21 13:51:49] resolve_keys
[2023-06-21 13:51:51] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-06-21 13:51:58] Occurrences to nodes (through scientific_names)...
[INFO] [2023-06-21 13:51:58] traits to occurrences...
[INFO] [2023-06-21 13:52:00] traits to nodes (through occurrences)...
[INFO] [2023-06-21 13:52:00] Traits to sex term...
[INFO] [2023-06-21 13:52:01] Traits to lifestage term...
[INFO] [2023-06-21 13:52:01] MetaTraits to traits...
[INFO] [2023-06-21 13:52:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-06-21 13:52:03] Assocs to occurrences...
[INFO] [2023-06-21 13:52:03] Assocs to nodes...
[INFO] [2023-06-21 13:52:03] Assoc to sex term...
[INFO] [2023-06-21 13:52:03] Assoc to lifestage term...
[INFO] [2023-06-21 13:52:03] MetaAssoc to assocs...
[STOP] [2023-06-21 13:52:03] resolve_keys
[START] [2023-06-21 13:52:03] hold_for_later_1
[STOP] [2023-06-21 13:52:03] hold_for_later_1
[START] [2023-06-21 13:52:03] hold_for_later_2
[STOP] [2023-06-21 13:52:03] hold_for_later_2
[START] [2023-06-21 13:52:03] resolve_missing_parents
[STOP] [2023-06-21 13:52:03] resolve_missing_parents
[START] [2023-06-21 13:52:03] rebuild_nodes
[START] [2023-06-21 13:52:03] Flattener#flatten
[START] [2023-06-21 13:52:03] Flattener#study_resource
[START] [2023-06-21 13:52:03] Flattener#build_ancestry
[STOP] [2023-06-21 13:52:03] Flattener#build_ancestry
[INFO] [2023-06-21 13:52:03] 5018 ancestry keys
[START] [2023-06-21 13:52:03] build_node_ancestors
[INFO] [2023-06-21 13:52:03] old ancestors deleted.
[STOP] [2023-06-21 13:52:03] build_node_ancestors
[START] [2023-06-21 13:52:04] Flattener#propagate_ancestor_ids
[STOP] [2023-06-21 13:52:04] Flattener#propagate_ancestor_ids
[STOP] [2023-06-21 13:52:04] Flattener#flatten
[STOP] [2023-06-21 13:52:04] rebuild_nodes
[START] [2023-06-21 13:52:04] resolve_missing_media_owners
[STOP] [2023-06-21 13:52:04] resolve_missing_media_owners
[START] [2023-06-21 13:52:04] sanitize_media_verbatims
[STOP] [2023-06-21 13:52:04] sanitize_media_verbatims
[START] [2023-06-21 13:52:04] queue_downloads
[STOP] [2023-06-21 13:52:04] queue_downloads
[START] [2023-06-21 13:52:04] parse_names
[WARN] [2023-06-21 13:52:04] I see 5018 names which still need to be parsed.
[WARN] [2023-06-21 13:52:04] Names to parse: 5018 formatted: 5018 learned: 5017 parsed: 5018
[STOP] [2023-06-21 13:52:10] parse_names
[START] [2023-06-21 13:52:10] denormalize_canonical_names_to_nodes
[STOP] [2023-06-21 13:52:10] denormalize_canonical_names_to_nodes
[START] [2023-06-21 13:52:10] match_nodes
[START] [2023-06-21 13:52:10] map_all_nodes_to_pages
[STOP] [2023-06-21 13:52:14] map_all_nodes_to_pages
[INFO] [2023-06-21 13:52:14] ZERO unmatched nodes (of 5018)! Nicely done.
[START] [2023-06-21 13:52:14] update_nodes
[STOP] [2023-06-21 13:52:14] update_nodes
[STOP] [2023-06-21 13:52:14] match_nodes
[START] [2023-06-21 13:52:14] reindex_search
[STOP] [2023-06-21 13:52:18] reindex_search
[START] [2023-06-21 13:52:18] normalize_units
[STOP] [2023-06-21 13:52:18] normalize_units
[START] [2023-06-21 13:52:18] calculate_statistics
[INFO] [2023-06-21 13:52:20] Duplicate page_id count: 0
[STOP] [2023-06-21 13:52:20] calculate_statistics
[START] [2023-06-21 13:52:20] complete_harvest_instance
[START] [2023-06-21 13:52:20] overall_tsv_creation
[INFO] [2023-06-21 13:52:20] Exporting 5018 nodes as TSV in batches of 10000...
[INFO] [2023-06-21 13:52:20] Processing group of 5018 in 1 batches of 10000
[INFO] [2023-06-21 13:52:28] 5222 Traits (unfiltered) and 0 associations...
[INFO] [2023-06-21 13:52:28] Building Traits map for 5018 nodes (this can take a while)...
[INFO] [2023-06-21 13:52:31] Mapped 5222 traits (5222 meta) for 5018 nodes.
[INFO] [2023-06-21 13:52:31] Building Associations map (this can take a while)...
[INFO] [2023-06-21 13:52:33] Done. 0 assocs mapped (0 meta).
[INFO] [2023-06-21 13:52:33] Adding 5222 traits...
[INFO] [2023-06-21 13:52:35] 5158 metadata added.
[INFO] [2023-06-21 13:52:35] Adding 0 assocs...
[INFO] [2023-06-21 13:52:35] 0 metadata added.
[INFO] [2023-06-21 13:53:19] Processed 5018/5018 nodes
[INFO] [2023-06-21 13:53:19] Average Time: 56.82
[INFO] [2023-06-21 13:53:19] Total Time: 59s
[STOP] [2023-06-21 13:53:19] overall_tsv_creation
[INFO] [2023-06-21 13:53:19] Done. Check your files:
[INFO] [2023-06-21 13:53:19] (5017 lines) /app/public/data/trophic_guild_da/publish_nodes.tsv
[INFO] [2023-06-21 13:53:19] (5016 lines) /app/public/data/trophic_guild_da/publish_node_ancestors.tsv
[INFO] [2023-06-21 13:53:19] (5018 lines) /app/public/data/trophic_guild_da/publish_scientific_names.tsv
[INFO] [2023-06-21 13:53:19] (5223 lines) /app/public/data/trophic_guild_da/publish_traits.tsv
[INFO] [2023-06-21 13:53:19] (5159 lines) /app/public/data/trophic_guild_da/publish_metadata.tsv
[STOP] [2023-06-21 13:53:19] complete_harvest_instance
[START] [2023-06-21 13:53:19] completed
[STOP] [2023-06-21 13:53:19] completed
[STOP] [2023-06-21 13:53:19] logged process, took 108.84
Latest Process

21 Jun 13:51 EXITED currently processing 0