import error
Great idea, creating a local database while also working with Entrez. I've hit an error though:
1074 > ncbi-taxonomist collect -n Coronaviridae|ncbi-taxonomist import -db ncbi-taxonomist.db
2020-05-24 11:24:45,724::DEBUG::ncbi-taxonomist.ncbi_taxonomist.collect.collector.Collector::Collect names::1::(['Coronaviridae'])
{"entrezpy.conduit": {"Inquiring": {"query_id": "Xyw_ROeGRba0JruLAKP2Ug==", "function": "esearch"}}}
{"entrezpy.requester.requester": {"settings": {"wait[s]": 0.3333333333333333, "timeout-min[s]": 10, "timeout-max[s]": 60, "timeout-increase[s]": 5, "max-retries": 9}}}
{"entrezpy.esearch.esearcher": {"Parameter": {"db": "taxonomy", "webenv": null, "querykey": 0, "usehistory": true, "term": "\"Coronaviridae\"", "retmode": "json", "uilist": true, "retmax": null, "retstart": 0, "sort": null, "field": null, "datetype": null, "reldate": null, "mindate": null, "maxdate": null, "expected_requsts": 1, "request_size": 100000, "max_request_size": 100000}}}
{"entrezpy.esearch.esearch_request": {"Init": {"id": null, "query-id": null, "retstart": 0, "retmax": 100000}}}
{"entrezpy.esearch.esearch_request": {"POST": {"id": 0, "query-id": "Xyw_ROeGRba0JruLAKP2Ug==", "dump": {"retmax": 100000, "retstart": 0, "retmode": "json", "usehistory": true, "WebEnv": null, "query_key": 0, "sort": null, "field": null, "datetype": null, "reldate": null, "mindate": null, "maxdate": null, "eutil": "esearch.fcgi", "db": "taxonomy", "id": 0, "query_id": "Xyw_ROeGRba0JruLAKP2Ug==", "tool": "entrezpyConduit", "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi", "email": null, "request_error": null, "size": 1, "apikey": null}}}}
{"entrezpy.requester.requester": {"Request": {"try": 0, "req-id": 0, "req-query": "Xyw_ROeGRba0JruLAKP2Ug==", "req-url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi", "qry-url": "email=None&tool=entrezpyConduit&db=taxonomy&term=%22Coronaviridae%22&retmax=100000&retmode=json&usehistory=y"}}}
2020-05-24 11:24:45,726::DEBUG::ncbi-taxonomist.ncbi_taxonomist.db.dbmanager.TaxonomyDb::ncbi-taxonomist.db: Create instance
2020-05-24 11:24:45,726::DEBUG::ncbi-taxonomist.ncbi_taxonomist.db.dbmanager.TaxonomyDb::ncbi-taxonomist.db: Connecting
2020-05-24 11:24:45,727::DEBUG::ncbi-taxonomist.ncbi_taxonomist.db.dbmanager.TaxonomyDb::ncbi-taxonomist.db: Connected
2020-05-24 11:24:45,730::DEBUG::ncbi-taxonomist.ncbi_taxonomist.db.dbmanager.TaxonomyDb::ncbi-taxonomist.db: Database initialized
2020-05-24 11:24:45,730::INFO::ncbi-taxonomist.ncbi_taxonomist.ncbitaxonomist.NcbiTaxonomist::ncbi-taxonomist.db: Successfully connected
{"entrezpy.esearch.esearcher": {"Query status": {"Xyw_ROeGRba0JruLAKP2Ug==": "OK"}}}
Xyw_ROeGRba0JruLAKP2Ug== 0 esearch.fcgi 1 0 0.21260356903076172
{"entrezpy.conduit": {"Inquiring": {"query_id": "K3RGc-cuSPWrOl0IPjW4-w==", "function": "efetch"}}}
{"entrezpy.requester.requester": {"settings": {"wait[s]": 0.3333333333333333, "timeout-min[s]": 10, "timeout-max[s]": 60, "timeout-increase[s]": 5, "max-retries": 9}}}
{"entrezpy.efetch.efetcher": {"Parameter": {"db": "taxonomy", "WebEnv": "NCID_1_462497162_130.14.22.76_9001_1590337485_701483012_0MetA0_S_MegaStore", "query_key": 1, "uids": ["11118"], "retmode": "xml", "rettype": null, "retstart": 0, "retmax": 1, "strand": null, "seqstart": null, "seqstop": null, "complexity": null, "request_size": 10000, "expected_requets": 1}}}
{"entrezpy.requester.requester": {"Request": {"try": 0, "req-id": 0, "req-query": "K3RGc-cuSPWrOl0IPjW4-w==", "req-url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi", "qry-url": "email=None&tool=entrezpyConduit&db=taxonomy&retmode=xml&WebEnv=NCID_1_462497162_130.14.22.76_9001_1590337485_701483012_0MetA0_S_MegaStore&query_key=1&retstart=0&retmax=1"}}}
K3RGc-cuSPWrOl0IPjW4-w== 0 0 1 0 0.4417545795440674
{"entrezpy.efetch.efetcher": {"Query status": {"K3RGc-cuSPWrOl0IPjW4-w==": "OK"}}}
{"taxon_id":10239,"rank":"superkingdom","names":{"Viruses":"scientific_name"},"parent_id":null,"name":"Viruses"}
{"taxon_id":2559587,"rank":"NA","names":{"Riboviria":"scientific_name"},"parent_id":10239,"name":"Riboviria"}
{"taxon_id":2732396,"rank":"kingdom","names":{"Orthornavirae":"scientific_name"},"parent_id":2559587,"name":"Orthornavirae"}
{"taxon_id":2732408,"rank":"phylum","names":{"Pisuviricota":"scientific_name"},"parent_id":2732396,"name":"Pisuviricota"}
{"taxon_id":2732506,"rank":"class","names":{"Pisoniviricetes":"scientific_name"},"parent_id":2732408,"name":"Pisoniviricetes"}
{"taxon_id":76804,"rank":"order","names":{"Nidovirales":"scientific_name"},"parent_id":2732506,"name":"Nidovirales"}
{"taxon_id":2499399,"rank":"suborder","names":{"Cornidovirineae":"scientific_name"},"parent_id":76804,"name":"Cornidovirineae"}
{"taxon_id":11118,"rank":"family","names":{"Coronaviridae":"scientific_name"},"parent_id":2499399,"name":"Coronaviridae"}
Traceback (most recent call last):
File "/home1/04769/bosborne/.local/bin/ncbi-taxonomist", line 114, in <module>
main()
File "/home1/04769/bosborne/.local/bin/ncbi-taxonomist", line 59, in main
nt.import_to_db(args.filter)
File "/home1/04769/bosborne/.local/lib/python3.7/site-packages/ncbi_taxonomist/ncbitaxonomist.py", line 105, in import_to_db
dbimporter.import_stdin(self.db, out_attrib)
File "/home1/04769/bosborne/.local/lib/python3.7/site-packages/ncbi_taxonomist/db/dbimporter.py", line 90, in import_stdin
commit(db, taxa, names)
File "/home1/04769/bosborne/.local/lib/python3.7/site-packages/ncbi_taxonomist/db/dbimporter.py", line 43, in commit
db.add_taxa(taxa)
File "/home1/04769/bosborne/.local/lib/python3.7/site-packages/ncbi_taxonomist/db/dbmanager.py", line 60, in add_taxa
self.taxatbl.insert(self.connection, taxa)
File "/home1/04769/bosborne/.local/lib/python3.7/site-packages/ncbi_taxonomist/db/table/taxa.py", line 38, in insert
connection.cursor().executemany(stmt, taxavalues)
sqlite3.OperationalError: near "ON": syntax error
This is with Python 3.7.0.
Edited by jpb