iplantcollaborativeopensource / python-irodsclient Goto Github PK

When fetching a non-existant resource:

sess.collections.get ('/iplant/home/ZZZ')

raises CollectionDoesNotExist

BUT a non-existant file gets a weird error

sess.data_objects.get ('/iplant/home/ZZZ')

AttributeError: 'iRODSDataObject' object has no attribute 'id'

Expected to get an exception DataObjectDoesNotExist

The README.md claims that this package requires Python 2.7. So I assume it is not compatible with recent Python 3 versions. Are there any plans to provide Python 3 compatibility any soon?

Even if it is not fully clear from the documentation, I'd assume this feature is not yet available.

• Is this a feature to be expected any soon?
• Is there some more exhaustive documentation available I have missed?

When running the Python client on Windows in Python 2.7, a call to

coll = sess.collections.get("...")

yields the following error:

Traceback (most recent call last):
File "", line 1, in
File "C:\Python27\lib\site-packages\irods\resource_manager\collection_manager.py", line 12, in get
result = query.one()
File "C:\Python27\lib\site-packages\irods\query.py", line 132, in one
results = self.execute()
File "C:\Python27\lib\site-packages\irods\query.py", line 118, in execute
with self.sess.pool.get_connection() as conn:
File "C:\Python27\lib\site-packages\irods\pool.py", line 20, in get_connection
conn = Connection(self, self.account)
File "C:\Python27\lib\site-packages\irods\connection.py", line 19, in init
self.connect()
File "C:\Python27\lib\site-packages\irods\connection.py", line 67, in connect
version_msg = self.recv()
File "C:\Python27\lib\site-packages\irods\connection.py", line 37, in recv
msg = iRODSMessage.recv(self.socket)
File "C:\Python27\lib\site-packages\irods\message__init.py", line 23, in recv
rsp_header_size = sock.recv(4, socket.MSG_WAITALL)
AttributeError: 'module' object has no attribute 'MSG_WAITALL'

Perhaps this is a limitation of the socket object on Windows?

I was attempting to use Biopython in combination with the python-irodsclient and ran into an issue when reading sequences from a fasta file. Here is some sample code:
from Bio import SeqIO
from irods.session import iRODSSession

HOST = 'data.iplantcollaborative.org'
PORT = 1247
ZONE = 'iplant'

sess = iRODSSession(host=HOST, port=PORT, user='xxxx', password='xxxx', zone=ZONE)
irods_file = sess.data_objects.get('/iplant/home/dboss/test/POV_SMS_reads.fa')
handle = irods_file.open('r')
print irods_file.id
print irods_file.name
print handle.readline()
handle.close()

The print handle.readline() returns None. The fasta parser in Biopython (http://biopython.org/DIST/docs/api/Bio.SeqIO.FastaIO-pysrc.html) then bails in this line:
if line[0] == ">":
because line is doesn't exist.

is possible to do PAM Authentication?

On line
https://github.com/iPlantCollaborativeOpenSource/python-irodsclient/blob/master/irods/query.py#L51

It has

new_q.limit = self._limit

it should be

new_q._limit = self._limit