...

pathomx/Pathomx.py

@@ -53,6 +53,7 @@
 
 # Translation (@default context)
 from .translate import tr
+from .runqueue import ExecuteOnly
 
 from distutils.version import StrictVersion
 
@@ -1170,6 +1171,7 @@ def main():
     locale = QLocale.system().name()
     #locale = 'nl'
 
+
     # Load base QT translations from the normal place (does not include _nl, or _it)
     translator_qt = QTranslator()
     if translator_qt.load("qt_%s" % locale, QLibraryInfo.location(QLibraryInfo.TranslationsPath)):
@@ -1191,6 +1193,30 @@ def main():
     notebook_queue.create_user_kernel()
     notebook_queue.create_runners()
     notebook_queue.start_timers()
+    '''
+        exc = ExecuteOnly("""
+    import pip
+    for pkg in [
+        'numpy',ls
+
+        'scipy',
+        'pandas',
+        'matplotlib',
+        'requests',
+        'nmrglue',
+        'gpml2svg',
+        'icoshift',
+        'mplstyler',
+        'pyqtconfig',
+        "pygments",
+        'pydot',
+
+        'jinja2']:
+        pip.main(['install', pkg, '--upgrade'])
+    """)
+    notebook_queue.add_job(exc, {})
+    '''
+
 
     MainWindow()
     logging.info('Ready.')

pathomx/kernel_helpers.py

@@ -48,48 +48,54 @@ def pathomx_notebook_start(varsi, vars):
     for k, v in varsi.items():
         vars[k] = v
 
+    # _keep_input_vars = ['styles']
+    # vars['_pathomx_exclude_input_vars'] = [x for x in varsi.keys() if x not in _keep_input_vars]
+
     # Handle IO magic
-    for k, v in vars['_io']['input'].items():
-        if v in vars:
-            vars[k] = deepcopy(vars[v])
-        else:
-            vars[k] = None
+    if '_io' in vars:
+        for k, v in vars['_io']['input'].items():
+            if v in vars:
+                vars[k] = deepcopy(vars[v])
+            else:
+                vars[k] = None
 
-    global rcParams
-    from matplotlib import rcParams
+    if 'rcParams' in vars:
+        global rcParams
+        from matplotlib import rcParams
 
-    # Block warnings from deprecated rcParams here
-    with warnings.catch_warnings():
-        warnings.simplefilter("ignore")
-        for k, v in vars['rcParams'].items():
-            rcParams[k] = v
+        # Block warnings from deprecated rcParams here
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+            for k, v in vars['rcParams'].items():
+                rcParams[k] = v
 
 
 def pathomx_notebook_stop(vars):
-    # Handle IO magic
-    for k, v in vars['_io']['output'].items():
-        if k in vars:
-            vars[v] = vars[k]
-        else:
-            vars[v] = None
-
     varso = {}
-    for k, v in vars.items():
-        # Check it's an accepted type for passing; and not private (starts with _)
-        if not k.startswith('_') and \
-            not k in vars['_io']['input'].keys():
-
-            if type(v) in MAGIC_TYPES or k in vars['_pathomx_expected_output_vars']:
-                varso[k] = v
-
-            elif hasattr(v, '_repr_html_'):
-                try:
-                    # Check if it is a bound method (not a class definition)
-                    v._repr_html_()
-                except:
-                    pass
-                else:
-                    varso[k] = displayobjects.Html(v)
+    if '_id' in vars:
+        # Handle IO magic
+        for k, v in vars['_io']['output'].items():
+            if k in vars:
+                vars[v] = vars[k]
+            else:
+                vars[v] = None
+
+        for k, v in vars.items():
+            # Check it's an accepted type for passing; and not private (starts with _)
+            if not k.startswith('_') and \
+                not k in vars['_io']['input'].keys():
+
+                if type(v) in MAGIC_TYPES or k in vars['_pathomx_expected_output_vars']:
+                    varso[k] = v
+
+                elif hasattr(v, '_repr_html_'):
+                    try:
+                        # Check if it is a bound method (not a class definition)
+                        v._repr_html_()
+                    except:
+                        pass
+                    else:
+                        varso[k] = displayobjects.Html(v)
 
     vars['varso'] = varso
 

pathomx/plugins.py

@@ -23,6 +23,8 @@
 from .globals import settings, app_launchers, file_handlers, url_handlers, available_tools_by_category, \
                      plugin_categories, plugin_manager, plugin_objects, plugin_metadata, installed_plugin_names
 
+import pip
+
 # Translation (@default context)
 from .translate import tr
 
@@ -64,6 +66,10 @@ def get_available_plugins(plugin_places=None, include_deactivated=False):
 
     available_tools_by_category = defaultdict(list)
 
+    # A list of the packages required for all found plugins (when to install?; via pip)
+    # pip is available since 2.7.9 via ensurepip (and/or we can package)
+    required_packages_all = set()
+
     # Loop round the plugins and print their names.
     for plugin in plugin_manager.getAllPlugins():
         plugin_image = os.path.join(os.path.dirname(plugin.path), 'icon.png')
@@ -76,6 +82,11 @@ def get_available_plugins(plugin_places=None, include_deactivated=False):
         except:
             resource_list = []
 
+        try:
+            required_packages = plugin.details.get('Documentation','Packages').split(',')
+        except:
+            required_packages = []
+
         metadata = {
             'id': type(plugin.plugin_object).__name__,  # __module__,
             'image': plugin_image,
@@ -89,13 +100,20 @@ def get_available_plugins(plugin_places=None, include_deactivated=False):
             'path': os.path.dirname(plugin.path),
             'module': os.path.basename(plugin.path),
             'shortname': os.path.basename(os.path.dirname(plugin.path)),
+            'required_packages': required_packages,
         }
 
+        required_packages_all |= set(required_packages)
+
         plugin_metadata[metadata['shortname']] = metadata
         installed_plugin_names[id(plugin.plugin_object)] = plugin.name
 
         plugin.plugin_object.post_setup(path=os.path.dirname(plugin.path), name=plugin.name, metadata=metadata)
 
+    # Check and import all packages
+    # for pkg_ver in required_packages_all:
+    #    pip.main(['install', pkg_ver, '--upgrade'])
+
 
 class pluginListDelegate(QAbstractItemDelegate):
 

pathomx/plugins/maxquant/maxquant.md

@@ -1,7 +1,7 @@
 MaxQuant
 =======
 
-Import protein quantification from the MaxQuant software.
+Import labelled protein quantification from the MaxQuant software.
 [Martin A. Fitzpatrick][]
 
 Introduction
@@ -13,5 +13,7 @@ are supported. MaxQuant is freely available and can be downloaded from [the webs
 engine Andromeda which is integrated into MaxQuant as well as the Viewer application for inspection of raw data and
 identification and quantification results.
 
+This tool is a first implementation of MaxQuant support, and imports labelled data only.
+
   [Martin A. Fitzpatrick]: http://martinfitzpatrick.name/
   [MaxQuant]: http://www.maxquant.org/

pathomx/plugins/maxquant/maxquant.py

@@ -45,6 +45,7 @@
 
 output_data = df
 df = None
+ds = None
 
 from pathomx.figures import histogram
 Histogram = histogram(output_data)

pathomx/plugins/multivariate/.pathomx-plugin

@@ -7,3 +7,4 @@ Author = Martin Fitzpatrick
 Version = 1.0
 Website = http://martinfitzpatrick.name/
 Description = Multivariate analysis plugins
+Packages = scikit-learn>=0.15, pandas>=0.15, numpy>=1.9

pathomx/plugins/volcano/volcano.py

@@ -1,4 +1,4 @@
-iimport pandas as pd
+import pandas as pd
 import scipy as sp
 import scipy.stats
 import numpy as np

pathomx/runqueue.py

@@ -104,7 +104,7 @@ def run(self, tool, varsi, progress_callback=None, result_callback=None):
         setup_languages(self.e.execute, tool.language)
 
         self.ar = self.e.execute(code)
-        self.e.execute(r'''pathomx_notebook_stop(vars());''')  # This will queue directly above the main code block
+        self.e.execute(r'''pathomx_notebook_stop(vars());''')  # This will queue directly after the main code block
 
     def check_status(self):
         result = {}
@@ -121,7 +121,9 @@ def check_status(self):
                 result['status'] = -1
                 result['traceback'] = '\n'.join(e.render_traceback())
                 result['stdout'] = self.stdout
-                self._result_callback(result)
+                if self._result_callback:
+                    self._result_callback(result)
+
                 self.ar = None
                 self._is_active = False  # Release this kernel
                 self._status = STATUS_ERROR
@@ -141,7 +143,9 @@ def check_status(self):
                 result['traceback'] = '\n'.join(e.render_traceback())
                 result['stdout'] = self.stdout
                 result['varso'] = []
-                self._result_callback(result)
+                if self._result_callback:
+                    self._result_callback(result)
+
                 self.aro = None
                 self._is_active = False  # Release this kernel
                 self._status = STATUS_ERROR
@@ -151,7 +155,9 @@ def check_status(self):
                 result['status'] = 0
                 result['varso'] = varso
                 result['stdout'] = self.stdout
-                self._result_callback(result)
+                if self._result_callback:
+                    self._result_callback(result)
+
                 self._is_active = False  # Release this kernel
                 self._status = STATUS_READY
 
@@ -557,35 +563,37 @@ def run(self):
             self.jobs.insert(0, (tool, varsi, progress_callback, result_callback))
             return False
 
-        varsi['_pathomx_expected_output_vars'] = tool.data.o.keys()
+        if hasattr(tool, 'data'):
+            # We can run code without an associated tool (e.g. for central-setup)
+            varsi['_pathomx_expected_output_vars'] = tool.data.o.keys()
 
-        # Build the IO magic
-        # - if the source did not run on the current runner we'll need to push the data over
-        io = {'input': {}, 'output': {}, }
-        for i, sm in tool.data.i.items():
-            if sm:
-                mo, mi = sm
-                io['input'][i] = "_%s_%s" % (mi, id(mo.v))
+            # Build the IO magic
+            # - if the source did not run on the current runner we'll need to push the data over
+            io = {'input': {}, 'output': {}, }
+            for i, sm in tool.data.i.items():
+                if sm:
+                    mo, mi = sm
+                    io['input'][i] = "_%s_%s" % (mi, id(mo.v))
 
-                # Check if the last run of this occurred on the selected runner
-                if id(mo.v) in self.run_metadata and \
-                    self.run_metadata[id(mo.v)]['last_runner'] != id(runner):
+                    # Check if the last run of this occurred on the selected runner
+                    if id(mo.v) in self.run_metadata and \
+                        self.run_metadata[id(mo.v)]['last_runner'] != id(runner):
 
-                    # We need to push the actual data; this should do it?
-                    varsi['_%s_%s' % (mi, id(mo.v))] = tool.data.get(i)
-            else:
-                io['input'][i] = None
+                        # We need to push the actual data; this should do it?
+                        varsi['_%s_%s' % (mi, id(mo.v))] = tool.data.get(i)
+                else:
+                    io['input'][i] = None
 
-        for o in tool.data.o.keys():
-            io['output'][o] = "_%s_%s" % (o, id(tool))
+            for o in tool.data.o.keys():
+                io['output'][o] = "_%s_%s" % (o, id(tool))
 
-        varsi['_io'] = io
+            varsi['_io'] = io
 
-        self.run_metadata[id(tool)] = {
-            'last_runner': id(runner)
-        }
+            self.run_metadata[id(tool)] = {
+                'last_runner': id(runner)
+            }
 
-        tool.logger.info("Starting job....")
+            tool.logger.info("Starting job....")
 
         # Result callback gets the varso dict
         runner.run(tool, varsi, progress_callback=progress_callback, result_callback=result_callback)
@@ -625,7 +633,7 @@ def create_runners(self):
 
         if self.p is None:
             # Use the in-process runner for now
-            self.runners = [self.in_process_runner]
+            # self.runners = [self.in_process_runner]
             self.start_cluster()
 
         elif self.p.poll() is None:
@@ -640,7 +648,7 @@ def create_runners(self):
             for e in self.client:
                 found = False
                 for r in self.runners:
-                    if r is not self.in_process_runner and e.targets == r.e.targets:
+                    if e.targets == r.e.targets:
                         found = True
 
                 if not found:
@@ -649,12 +657,6 @@ def create_runners(self):
                     runner.e.execute('%matplotlib inline')
                     self.runners.append(runner)
 
-            if len(self.runners) > 1:
-                # We've got a running cluster
-                # remove the in-process kernel from the queue
-                if self.in_process_runner in self.runners:
-                    self.runners.remove(self.in_process_runner)
-
         else:
             # We've got a -value for poll; it's terminated this will trigger restart on next poll
             self.stop_cluster()
@@ -665,3 +667,11 @@ def create_user_kernel(self):
         self.in_process_runner = InProcessRunner()
         self.in_process_runner.kernel_client.execute('%reset -f')
         #self.in_process_runner.kernel_client.execute('%matplotlib inline')
+
+
+class ExecuteOnly(object):
+    language = 'python'
+
+    def __init__(self, code):
+        self.code = code
+