Stage:
completed
Fetched:
16 Nov 11:20
Validated:
16 Nov 11:24
Deltas Created
16 Nov 11:24
Units Normalized:
19 Nov 02:18
Ancestry Built:
17 Nov 01:30
Nodes Matched:
19 Nov 01:03
Names Parsed:
17 Nov 02:23
New Models Stored:
16 Nov 16:17
Indexed:
19 Nov 02:18
Completed:
19 Nov 08:38
Time to Harvest:
13 minutes
Harvesting Log
(3106 lines)
(showing only the last 1000 lines, see /app/public/data/gbif_classificat/process.log for the full file)
[INFO] [2020-11-16 10:38:21] Starting batch with ID 75069461...
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[INFO] [2020-11-16 10:48:12] ## remove_type: Node
[INFO] [2020-11-16 10:48:13] ++ Batch removal of 3915001 instances...
[INFO] [2020-11-16 10:48:13] [10:48:13.072] Batch 0...
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[INFO] [2020-11-16 10:57:47] [10:57:47.679] Removed 3915001 Nodes
[START] [2020-11-16 11:19:53] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-16 11:19:53] Creating resource from OpenData
[START] [2020-11-16 11:20:10] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-16 11:20:10] Parse meta.xml file and create formats with fields
[STOP] [2020-11-16 11:20:11] Parse meta.xml file and create formats with fields
[STOP] [2020-11-16 11:20:11] Creating resource from OpenData
[START] [2020-11-16 11:20:11] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-16 11:20:11] create_harvest_instance
[STOP] [2020-11-16 11:20:12] create_harvest_instance
[START] [2020-11-16 11:20:12] fetch_files
[STOP] [2020-11-16 11:20:12] fetch_files
[START] [2020-11-16 11:20:12] validate_each_file
[STOP] [2020-11-16 11:24:11] validate_each_file
[START] [2020-11-16 11:24:11] convert_to_csv
[CMD] [2020-11-16 11:24:11] /usr/bin/sort /app/public/converted_csv/gbif_classificat_nodes_24273.csv > /app/public/converted_csv/gbif_classificat_nodes_24273.csv_sorted
[STOP] [2020-11-16 11:24:13] convert_to_csv
[START] [2020-11-16 11:24:13] calculate_delta
[CMD] [2020-11-16 11:24:13] echo "0a" > /app/public/diff/gbif_classificat_nodes_24273.diff
[CMD] [2020-11-16 11:24:13] tail -n +1 /app/public/converted_csv/gbif_classificat_nodes_24273.csv >> /app/public/diff/gbif_classificat_nodes_24273.diff
[CMD] [2020-11-16 11:24:14] echo "." >> /app/public/diff/gbif_classificat_nodes_24273.diff
[STOP] [2020-11-16 11:24:14] calculate_delta
[START] [2020-11-16 11:24:14] parse_diff_and_store
[INFO] [2020-11-16 11:24:17] Loading nodes diff file into memory (true lines)...
[WARN] [2020-11-16 11:24:17] New Taxonomic status: doubtful; treatings as unusable...
[WARN] [2020-11-16 11:24:18] New Taxonomic status: proparte synonym; treatings as unusable...
[WARN] [2020-11-16 11:24:21] Filtered Scientific Name `Motacilla citreola x flava` to `Motacilla citreola x flava`
[WARN] [2020-11-16 11:24:22] Filtered Scientific Name `Sophora yellow stunt alphasatellite 4` to `Sophora yellow stunt alphasatellite 4`
[WARN] [2020-11-16 11:24:26] Filtered Scientific Name `Lentivirus: Visna/maedi virus ICTV` to `Lentivirus: Visnamaedi virus ICTV`
[WARN] [2020-11-16 11:24:28] Filtered Scientific Name `Nephrolepis pendula j smith x undulata` to `Nephrolepis pendula j smith x undulata`
[WARN] [2020-11-16 11:24:34] Filtered Scientific Name `Sophora yellow stunt alphasatellite 5` to `Sophora yellow stunt alphasatellite 5`
[WARN] [2020-11-16 11:24:35] Filtered Scientific Name `Pea necrotic yellow dwarf alphasatellite 1` to `Pea necrotic yellow dwarf alphasatellite 1`
[WARN] [2020-11-16 11:24:39] Filtered Scientific Name `Eleocharis acutangula schultes x e plicarrhachis` to `Eleocharis acutangula schultes x e plicarrhachis`
[WARN] [2020-11-16 11:24:43] Filtered Scientific Name `Inovirus: Enterobacteria phage ZJ/2 ICTV` to `Inovirus: Enterobacteria phage ZJ2 ICTV`
[WARN] [2020-11-16 11:24:50] Filtered Scientific Name `Banana bunchy top alphasatellite 2` to `Banana bunchy top alphasatellite 2`
[WARN] [2020-11-16 11:24:52] Filtered Scientific Name `Turdus atrogularis x eunomus/naumanni` to `Turdus atrogularis x eunomusnaumanni`
[WARN] [2020-11-16 11:24:54] Filtered Scientific Name `Pea necrotic yellow dwarf alphasatellite 2` to `Pea necrotic yellow dwarf alphasatellite 2`
[WARN] [2020-11-16 11:25:13] Filtered Scientific Name `Papilio minor Esper, 1777/79` to `Papilio minor Esper, 177779`
[WARN] [2020-11-16 11:25:13] Filtered Scientific Name `Tortrix tristana Hübner, 1796/99` to `Tortrix tristana Hübner, 179699`
[WARN] [2020-11-16 11:28:49] Filtered Scientific Name `Xyleutes leucolophus Guérin-Meneville, 1829/44` to `Xyleutes leucolophus Guérin-Meneville, 182944`
[WARN] [2020-11-16 11:28:51] Filtered Scientific Name `Phragmataecia terebrifer Fletcher, 1926/27` to `Phragmataecia terebrifer Fletcher, 192627`
[WARN] [2020-11-16 11:28:51] Filtered Scientific Name `Phragmataecia purpureus Fletcher, 1926/27` to `Phragmataecia purpureus Fletcher, 192627`
[WARN] [2020-11-16 11:28:51] Filtered Scientific Name `Gastromega badia Saalmüller, 1877/78` to `Gastromega badia Saalmüller, 187778`
[WARN] [2020-11-16 11:28:53] Filtered Scientific Name `Lechriolepis stumpfi Saalmüller, 1877/78` to `Lechriolepis stumpfi Saalmüller, 187778`
[WARN] [2020-11-16 11:29:04] Filtered Scientific Name `Aterpia charpentierana Hübner, 1822/23` to `Aterpia charpentierana Hübner, 182223`
[WARN] [2020-11-16 11:29:05] Filtered Scientific Name `Bactra lanceolana Hübner, 1796/99` to `Bactra lanceolana Hübner, 179699`
[WARN] [2020-11-16 11:29:05] Filtered Scientific Name `Macroplectra unicolor Moore, 1858/59` to `Macroplectra unicolor Moore, 185859`
[WARN] [2020-11-16 11:29:06] Filtered Scientific Name `Miresa nivaha Moore, 1858/59` to `Miresa nivaha Moore, 185859`
[WARN] [2020-11-16 11:29:06] Filtered Scientific Name `Birthama saturata Kiriakoff, 1946/49` to `Birthama saturata Kiriakoff, 194649`
[WARN] [2020-11-16 11:29:06] Filtered Scientific Name `Tetraclonia dyraspes Druce, 1891/901` to `Tetraclonia dyraspes Druce, 1891901`
[WARN] [2020-11-16 11:29:06] Filtered Scientific Name `Clelea pravata Moore, 1858/59` to `Clelea pravata Moore, 185859`
[WARN] [2020-11-16 11:29:06] Filtered Scientific Name `Seryda basirei Druce, 1891/901` to `Seryda basirei Druce, 1891901`
[WARN] [2020-11-16 11:29:06] Filtered Scientific Name `Phauda mahisa Moore, 1858/59` to `Phauda mahisa Moore, 185859`
[WARN] [2020-11-16 11:29:07] Filtered Scientific Name `Trachea macrophtalma Berio, 1976/77` to `Trachea macrophtalma Berio, 197677`
[WARN] [2020-11-16 11:29:07] Filtered Scientific Name `Trachea bipectinata Berio, 1976/77` to `Trachea bipectinata Berio, 197677`
[WARN] [2020-11-16 11:29:07] (Reached filtered-name limit; supressing further warnings.)
[INFO] [2020-11-16 13:13:44] Storing 3889747 ScientificNames
[INFO] [2020-11-16 13:13:44] Processing group of 3889747 in 3890 groups of 1000
[INFO] [2020-11-16 14:38:14] Average Time: 1.274
[INFO] [2020-11-16 14:38:14] Total Time: 1h24m31s
[INFO] [2020-11-16 14:38:14] last 3 / first 3: 1.01
[INFO] [2020-11-16 14:38:14] Std.Dev: 6.569474864857921; Max: 52.69
[INFO] [2020-11-16 14:38:14] Storing 2959884 Nodes
[INFO] [2020-11-16 14:38:14] Processing group of 2959884 in 2960 groups of 1000
[INFO] [2020-11-16 16:17:37] Average Time: 1.951
[INFO] [2020-11-16 16:17:37] Total Time: 1h39m23s
[INFO] [2020-11-16 16:17:37] last 3 / first 3: 0.79
[INFO] [2020-11-16 16:17:37] Std.Dev: 9.449232773087981; Max: 62.52
[STOP] [2020-11-16 16:17:37] parse_diff_and_store
[START] [2020-11-16 16:17:37] resolve_keys
[INFO] [2020-11-16 16:23:47] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-16 16:23:47] traits to occurrences...
[INFO] [2020-11-16 16:23:47] traits to nodes (through occurrences)...
[INFO] [2020-11-16 16:23:47] Traits to sex term...
[INFO] [2020-11-16 16:23:47] Traits to lifestage term...
[INFO] [2020-11-16 16:23:47] MetaTraits to traits...
[INFO] [2020-11-16 16:23:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-16 16:23:47] Assocs to occurrences...
[INFO] [2020-11-16 16:23:47] Assocs to nodes...
[INFO] [2020-11-16 16:23:47] Assoc to sex term...
[INFO] [2020-11-16 16:23:47] Assoc to lifestage term...
[INFO] [2020-11-16 16:23:47] MetaAssoc to assocs...
[STOP] [2020-11-16 16:23:47] resolve_keys
[START] [2020-11-16 16:23:47] hold_for_later_1
[STOP] [2020-11-16 16:23:47] hold_for_later_1
[START] [2020-11-16 16:23:47] hold_for_later_2
[STOP] [2020-11-16 16:23:47] hold_for_later_2
[START] [2020-11-16 16:23:47] resolve_missing_parents
[STOP] [2020-11-16 16:24:20] resolve_missing_parents
[START] [2020-11-16 16:24:20] rebuild_nodes
[START] [2020-11-16 16:24:20] Flattener#flatten
[START] [2020-11-16 16:24:20] Flattener#study_resource
[START] [2020-11-16 16:25:57] Flattener#build_ancestry
[STOP] [2020-11-17 00:48:35] Flattener#build_ancestry
[INFO] [2020-11-17 00:48:35] 2959884 ancestry keys
[START] [2020-11-17 00:48:35] build_node_ancestors
[INFO] [2020-11-17 00:48:35] old ancestors deleted.
[STOP] [2020-11-17 01:20:26] build_node_ancestors
[START] [2020-11-17 01:20:27] Flattener#propagate_ancestor_ids
[STOP] [2020-11-17 01:30:53] Flattener#propagate_ancestor_ids
[STOP] [2020-11-17 01:30:53] Flattener#flatten
[STOP] [2020-11-17 01:30:53] rebuild_nodes
[START] [2020-11-17 01:30:53] resolve_missing_media_owners
[STOP] [2020-11-17 01:30:53] resolve_missing_media_owners
[START] [2020-11-17 01:30:53] sanitize_media_verbatims
[STOP] [2020-11-17 01:30:53] sanitize_media_verbatims
[START] [2020-11-17 01:30:53] queue_downloads
[STOP] [2020-11-17 01:30:53] queue_downloads
[START] [2020-11-17 01:30:53] parse_names
[WARN] [2020-11-17 01:30:57] I see 3889747 names which still need to be parsed.
[WARN] [2020-11-17 02:22:45] I see 55 names which still need to be parsed.
[WARN] [2020-11-17 02:22:59] I see 4 names which still need to be parsed.
[WARN] [2020-11-17 02:23:13] I see 1 names which still need to be parsed.
[STOP] [2020-11-17 02:23:27] parse_names
[START] [2020-11-17 02:23:27] denormalize_canonical_names_to_nodes
[STOP] [2020-11-17 02:24:11] denormalize_canonical_names_to_nodes
[START] [2020-11-17 02:24:11] match_nodes
[START] [2020-11-17 02:24:15] map_all_nodes_to_pages
[INFO] [2020-11-18 19:07:09] ## HARVEST: type = resume_-harvest
[START] [2020-11-18 19:07:10] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[ERR] [2020-11-18 19:07:10][hdls] *****
[ERR] [2020-11-18 19:07:10][hdls] ***** HARVEST ATTEMPT FAILED: This resource is locked; assuming it is already running. Remove lock if not.
[ERR] [2020-11-18 19:07:10][hdls] *****
[INFO] [2020-11-18 19:25:31] ## HARVEST: type = resume_-harvest
[START] [2020-11-18 19:25:32] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[INFO] [2020-11-18 19:25:32] Already completed stage create_harvest_instance, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage fetch_files, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage validate_each_file, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage convert_to_csv, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage calculate_delta, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage parse_diff_and_store, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage resolve_keys, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage hold_for_later_1, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage hold_for_later_2, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage resolve_missing_parents, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage rebuild_nodes, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage resolve_missing_media_owners, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage sanitize_media_verbatims, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage queue_downloads, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage parse_names, skipping...
[INFO] [2020-11-18 19:25:32] Already completed stage denormalize_canonical_names_to_nodes, skipping...
[START] [2020-11-18 19:25:32] match_nodes
[START] [2020-11-18 19:25:35] map_all_nodes_to_pages
[STOP] [2020-11-19 01:03:18] map_all_nodes_to_pages
[INFO] [2020-11-19 01:03:18] 54279 Unmatched nodes (of 2959884)! That's too many to output. First 10: Dicliptera roxburghiana roxburghiana (#83703459); Dicliptera riparia riparia (#84039290); Dicliptera paniculata paniculata (#83918474); Dicliptera foetida foetida (#83709622); Dicliptera obtusifolia obtusifolia (#83663726); Dicliptera moritziana moritziana (#83663733); Dicliptera sebastinei sebastinei (#84390228); Dicliptera caerulea (#83921894); Dicliptera horsfieldii (#84031863); Dicliptera retorta (#84121113)
[START] [2020-11-19 01:03:18] update_nodes
[STOP] [2020-11-19 01:03:25] update_nodes
[STOP] [2020-11-19 01:03:25] match_nodes
[START] [2020-11-19 01:03:25] reindex_search
[STOP] [2020-11-19 02:18:52] reindex_search
[START] [2020-11-19 02:18:52] normalize_units
[STOP] [2020-11-19 02:18:52] normalize_units
[START] [2020-11-19 02:18:52] calculate_statistics
[STOP] [2020-11-19 02:18:56] calculate_statistics
[START] [2020-11-19 02:18:56] complete_harvest_instance
[START] [2020-11-19 02:18:56] overall_tsv_creation
[INFO] [2020-11-19 02:18:59] Processing group of 2959884 in 296 batches of 10000
[INFO] [2020-11-19 08:38:29] Average Time: 48.85
[INFO] [2020-11-19 08:38:29] Total Time: 6h19m31s
[INFO] [2020-11-19 08:38:29] last 3 / first 3: 1.04
[INFO] [2020-11-19 08:38:29] Std.Dev: 6.065228767326093; Max: 84.89
[STOP] [2020-11-19 08:38:29] overall_tsv_creation
[INFO] [2020-11-19 08:38:29] Done. Check your files:
[INFO] [2020-11-19 08:38:29] (2959884 lines) /app/public/data/gbif_classificat/publish_nodes.tsv
[INFO] [2020-11-19 08:38:29] (17201175 lines) /app/public/data/gbif_classificat/publish_node_ancestors.tsv
[INFO] [2020-11-19 08:38:30] (3872512 lines) /app/public/data/gbif_classificat/publish_scientific_names.tsv
[STOP] [2020-11-19 08:38:34] complete_harvest_instance
[START] [2020-11-19 08:38:34] completed
[STOP] [2020-11-19 08:38:34] completed
[STOP] [2020-11-19 08:38:34] logged process, took 47581.97
Latest Process