cytoscape / py4cytoscape

Python library for calling Cytoscape Automation via CyREST
https://Py4Cytoscape.readthedocs.io
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get_installed_apps() fails #67

Closed kozo2 closed 2 years ago

kozo2 commented 3 years ago

The versions:

import py4cytoscape as p4c
p4c.cytoscape_version_info()
{'apiVersion': 'v1',
 'cytoscapeVersion': '3.8.2',
 'automationAPIVersion': '1.3.0',
 'py4cytoscapeVersion': '0.0.11'}

How to invoke the error:

p4c.install_app('MCODE')
for app in p4c.get_installed_apps():
    if app['appName'] == 'MCODE':
        print(app['version'])
In commands_post(): {'status': 500, 'type': 'urn:cytoscape:ci:cyrest-core:v1:handle-json-command:errors:3', 'message': 'Task returned invalid json.', 'link': 'file:/C:/Users/kozo2/CytoscapeConfiguration/3/framework-cytoscape.log'}
---------------------------------------------------------------------------
CyError                                   Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_17368/1103263763.py in <module>
----> 1 for app in p4c.get_installed_apps():
      2     if app['appName'] == 'MCODE':
      3         print(app['version'])

~\mambaforge\lib\site-packages\py4cytoscape-0.0.11-py3.9.egg\py4cytoscape\py4cytoscape_logger.py in wrapper_log(*args, **kwargs)
    131             return log_return(func, value)
    132         except Exception as e:
--> 133             log_exception(func, e)
    134         finally:
    135             log_finally()

~\mambaforge\lib\site-packages\py4cytoscape-0.0.11-py3.9.egg\py4cytoscape\py4cytoscape_logger.py in wrapper_log(*args, **kwargs)
    128         log_incoming(func, *args, **kwargs)
    129         try:
--> 130             value = func(*args, **kwargs) # Call function being logged
    131             return log_return(func, value)
    132         except Exception as e:

~\mambaforge\lib\site-packages\py4cytoscape-0.0.11-py3.9.egg\py4cytoscape\apps.py in get_installed_apps(base_url)
    205     """
    206     verify_supported_versions(1, 3.7, base_url=base_url)
--> 207     res = commands.commands_post('apps list installed', base_url=base_url)
    208     return res
    209 

~\mambaforge\lib\site-packages\py4cytoscape-0.0.11-py3.9.egg\py4cytoscape\py4cytoscape_logger.py in wrapper_log(*args, **kwargs)
    131             return log_return(func, value)
    132         except Exception as e:
--> 133             log_exception(func, e)
    134         finally:
    135             log_finally()

~\mambaforge\lib\site-packages\py4cytoscape-0.0.11-py3.9.egg\py4cytoscape\py4cytoscape_logger.py in wrapper_log(*args, **kwargs)
    128         log_incoming(func, *args, **kwargs)
    129         try:
--> 130             value = func(*args, **kwargs) # Call function being logged
    131             return log_return(func, value)
    132         except Exception as e:

~\mambaforge\lib\site-packages\py4cytoscape-0.0.11-py3.9.egg\py4cytoscape\commands.py in commands_post(cmd, base_url)
    391         res = json.loads(r.text)
    392         if len(res['errors']):
--> 393             raise CyError(str(res['errors'][0]))
    394         return res['data']
    395     except requests.exceptions.RequestException as e:

CyError: In commands_post(): {'status': 500, 'type': 'urn:cytoscape:ci:cyrest-core:v1:handle-json-command:errors:3', 'message': 'Task returned invalid json.', 'link': 'file:/C:/Users/kozo2/CytoscapeConfiguration/3/framework-cytoscape.log'}
bdemchak commented 2 years ago

This appears to be a CyREST issue ... in 3.9.1, I can't duplicate this, so I'll close this issue for now. Feel free to reopen it if you find it's still a problem.