obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

URI decoding: fixed reading a taxonomy before any view

Browse Source
This commit is contained in:
mercierc
2021-05-31 16:57:20 +12:00
parent c884615522
commit da91ffc2c7
1 changed files with 9 additions and 8 deletions
Download Patch File Download Diff File Expand all files Collapse all files

7
python/obitools3/uri/decode.pyx
View File

@ -210,11 +210,12 @@ def open_uri(uri,
error = None
if urib != b"-" and \
if b'/taxonomy/' in urib or \
(urib != b"-" and \
(scheme==b"dms" or \
(scheme==b"" and \
(((not input) and "outputformat" not in config["obi"]) or \
(input and "inputformat" not in config["obi"])))): # TODO maybe not best way
(input and "inputformat" not in config["obi"]))))): # TODO maybe not best way
if default_dms is not None and b"/" not in urip.path: # assuming view to open in default DMS (TODO discuss)
dms=(default_dms, urip.path)
@ -464,7 +465,7 @@ def open_uri(uri,
if format is not None:
if seqtype==b"nuc":
objclass = Nuc_Seq # Nuc_Seq_Stored? TODO
if format==b"fasta" or format==b"silva":
if format==b"fasta" or format==b"silva" or format==b"rdp":
if input:
iseq = fastaNucIterator(file,
skip=skip,