Error connecting to cryoSPARC patch server

Troubleshooting
1

Hi,

I am trying to import a previous cryosparc project into a new workstation but I got several error while importing. I saw in the forum that are easily fixed after applying a patch however, when I try to check the available patches and install them it crashes giving me this error:

[victor@c105627 cryosparc]$ cryosparcm patch

A cryoSPARC patch is available

Current Version: v3.2.0
Patch Name: 210713
Released On: 2021-07-13 17:55:48
Requires Restart: Yes
Patch Notes:
  • Added: Check Particles job for verifying data integrity of particle stacks
  • Added: Computational batch size parameter in Heterogeneous Refinement job
  • Added: cryosparcm changeport command and related utilities for changing the base port
  • Updated: Local Resolution job now prints local resolution statistics (minimum, median, maximum, 25th percentile, 75th percentile) in job streamlog
  • Updated: CryoSPARC Live Data Management now supports executing a script upon a datatype’s state change. Add “export CRYOSPARC_LIVE_DATA_MANAGEMENT_SCRIPT_ENABLE=true” and “export CRYOSPARC_LIVE_DATA_MANAGEMENT_SCRIPT_PATH=/path/to/script.sh” in cryosparc_master/config.sh to enable this feature
  • Fixed: Import Job/Import Result Group fails with “Unable to find data referenced by cs files” when importing a “mscope_params” result group due to empty fields
  • Fixed: Local Motion correction with EER data
  • Fixed: Jobs no longer wait on cache forever after the cache is unlocked in other jobs
  • Fixed: Restore missing “Use Class Weights” parameter in Deep Picker Train job
  • Fixed: Prevent LD_PRELOAD warning when launching cluster jobs
  • Fixed: ValueError during 3DFSC job’s volume output
  • Fixed: Empty workspaces after importing project
  • Fixed: Prevent error when extracting particles generated by Topaz
  • Fixed: Prevent error in Deep Inference job during plotting
  • Fixed: Prevent error caused by MotionCor2 wrapper outputting incorrect shape
  • Fixed: Improved error messages when reading invalid exposures or particle stacks
  • Fixed: Prevent numeric initialization error in Ab-Initio Reconstruction jobs for some systems
  • Fixed: Prevent numeric error in Inspect Picks job
  • Fixed: Statistic showing the total number of particles being processed by Ab-Initio Reconstruction job in cryoSPARC Live sometimes isn’t updated
  • Fixed: Prevent “mrc_readmic (1) 447: Invalid argument” errors that occur after extracting particles in a pipeline where micrographs were imported multiple times
  • Added: New utility “cryosparcm licensestatus” to verify if a license is valid
  • Added: cryosparcm status now reports patch version
  • Fixed: Prevent I/O exceptions from terminating the cryoSPARC Live Worker while processing exposures
  • Fixed: Allow shell operators during cluster job submission, enabling redirections required for LSF Clusters

Install patch? (y/n): y
Downloading…
Downloading cryosparc_master_patch.tar.gz…
(‘Connection aborted.’, ConnectionResetError(104, ‘Connection reset by peer’))
Traceback (most recent call last):
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 677, in urlopen
chunked=chunked,
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 381, in _make_request
self._validate_conn(conn)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 978, in validate_conn
conn.connect()
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/connection.py”, line 371, in connect
ssl_context=context,
File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/util/ssl.py", line 386, in ssl_wrap_socket
return context.wrap_socket(sock, server_hostname=server_hostname)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/ssl.py”, line 423, in wrap_socket
session=session
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/ssl.py”, line 870, in _create
self.do_handshake()
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/ssl.py”, line 1139, in do_handshake
self._sslobj.do_handshake()
ConnectionResetError: [Errno 104] Connection reset by peer

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/requests/adapters.py”, line 449, in send
timeout=timeout
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 727, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/util/retry.py”, line 410, in increment
raise six.reraise(type(error), error, _stacktrace)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/packages/six.py”, line 734, in reraise
raise value.with_traceback(tb)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 677, in urlopen
chunked=chunked,
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 381, in _make_request
self._validate_conn(conn)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 978, in validate_conn
conn.connect()
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/connection.py”, line 371, in connect
ssl_context=context,
File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/urllib3/util/ssl.py", line 386, in ssl_wrap_socket
return context.wrap_socket(sock, server_hostname=server_hostname)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/ssl.py”, line 423, in wrap_socket
session=session
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/ssl.py”, line 870, in _create
self.do_handshake()
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/ssl.py”, line 1139, in do_handshake
self._sslobj.do_handshake()
urllib3.exceptions.ProtocolError: (‘Connection aborted.’, ConnectionResetError(104, ‘Connection reset by peer’))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/victor/cryosparc/cryosparc_master/patch.py”, line 69, in download_file
r = requests.get(url, stream=True, verify=VERIFY_HTTPS_REQUESTS)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/requests/api.py”, line 76, in get
return request(‘get’, url, params=params, **kwargs)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/requests/api.py”, line 61, in request
return session.request(method=method, url=url, **kwargs)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/requests/sessions.py”, line 530, in request
resp = self.send(prep, **send_kwargs)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/requests/sessions.py”, line 665, in send
history = [resp for resp in gen]
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/requests/sessions.py”, line 665, in
history = [resp for resp in gen]
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/requests/sessions.py”, line 245, in resolve_redirects
**adapter_kwargs
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/requests/sessions.py”, line 643, in send
r = adapter.send(request, **kwargs)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/requests/adapters.py”, line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: (‘Connection aborted.’, ConnectionResetError(104, ‘Connection reset by peer’))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/runpy.py”, line 193, in _run_module_as_main
“main”, mod_spec)
File “/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/runpy.py”, line 85, in _run_code
exec(code, run_globals)
File “/home/victor/cryosparc/cryosparc_master/patch.py”, line 403, in
exit(main())
File “/home/victor/cryosparc/cryosparc_master/patch.py”, line 388, in main
master_patch_file, worker_patch_file = download_patch(latest_patch)
File “/home/victor/cryosparc/cryosparc_master/patch.py”, line 230, in download_patch
download_file(url, dest)
File “/home/victor/cryosparc/cryosparc_master/patch.py”, line 72, in download_file
assert False, “Error connecting to cryoSPARC patch server.”
AssertionError: Error connecting to cryoSPARC patch server.

Here cryosparc status:

[victor@c105627 cryosparc]$ cryosparcm status

CryoSPARC System master node installed at
/home/victor/cryosparc/cryosparc_master
Current cryoSPARC version: v3.2.0

CryoSPARC process status:

app RUNNING pid 75222, uptime 16:22:35
app_dev STOPPED Not started
command_core RUNNING pid 75106, uptime 16:22:45
command_rtp RUNNING pid 75172, uptime 16:22:41
command_vis RUNNING pid 75136, uptime 16:22:42
database RUNNING pid 75031, uptime 16:22:47
liveapp RUNNING pid 75242, uptime 16:22:33
liveapp_dev STOPPED Not started
webapp RUNNING pid 75198, uptime 16:22:37
webapp_dev STOPPED Not started

global config variables:

export CRYOSPARC_LICENSE_ID=“xxxxxxxxx”
export CRYOSPARC_MASTER_HOSTNAME=“xxxxxx.dhcp.swmed.org”
export CRYOSPARC_DB_PATH="/home/victor/cryosparc/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false
export CRYOSPARC_CLICK_WRAP=true

export no_proxy=localhost,127.0.0.1,localaddress,.localdomain.com,swmed.org,swmed.edu,.swmed.org,.swmed.edu,swlxnexpose.swmed.org,129.112.7.*
export NO_PROXY=localhost,127.0.0.1,localaddress,.localdomain.com,swmed.org,swmed.edu,.swmed.org,.swmed.edu,swlxnexpose.swmed.org,129.112.7.*

I added last two entries defining no proxy as it was the only way I found to fix the proxy issue on this workstation connected to the institutional network (issue posted here)

Thank you!