Merge pull request NSLS-II-LIX#4 from hhslepicka/master

Bug fixes. Added configuration file for services connection and others

README.md

@@ -1,2 +1,32 @@
 # lixdc
 User interface for data collection at LIX beam line.
+
+
+## lixdc configuration
+
+Lixdc requires the following configuration information:
+
+```
+amostra_host: localhost
+amostra_port: 7772
+base_path: /Users/hugoslepicka/data
+```
+
+
+This configuration information can live in up to four different places, as
+defined in the docstring of the `load_configuration` function in
+ `lixdc/conf.py`. In order of increasing precedence:
+
+1. The conda environment
+  - CONDA_ENV/etc/{name}.yaml (if CONDA_ETC_env is defined)
+1. At the system level
+  - /etc/{name}.yml
+1. In the user's home directory
+  - ~/.config/{name}/connection.yml
+1. Environmental variables
+  - {PREFIX}_{FIELD}
+
+where
+
+  - {name} is lixdc
+  - {PREFIX} is LIXDC and {FIELD} is one of {amostra_host, amostra_port, base_path}

lixdc/conf.py

@@ -0,0 +1,54 @@
+# no yaml, just python or command line for now
+import os
+import yaml
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+def load_configuration(name, prefix, fields, allow_missing=False):
+    """
+    Load configuration data form a cascading series of locations.
+    The precedence order is (highest priority last):
+    1. CONDA_ENV/etc/{name}.yaml (if CONDA_ETC_ env is defined)
+    2. /etc/{name}.yml
+    3. ~/.config/{name}/connection.yml
+    4. reading {PREFIX}_{FIELD} environmental variables
+    Parameters
+    ----------
+    name : str
+        The expected base-name of the configuration files
+    prefix : str
+        The prefix when looking for environmental variables
+    fields : iterable of strings
+        The required configuration fields
+    Returns
+    ------
+    conf : dict
+        Dictionary keyed on ``fields`` with the values extracted
+    """
+    filenames = [os.path.join('/etc', name + '.yml'),
+                 os.path.join(os.path.expanduser('~'), '.config',
+                              name, 'connection.yml'),
+                ]
+    if 'CONDA_ETC_' in os.environ:
+        filenames.insert(0, os.path.join(os.environ['CONDA_ETC_'],
+                                         name + '.yml'))
+
+    config = {}
+    for filename in filenames:
+        if os.path.isfile(filename):
+            with open(filename) as f:
+                config.update(yaml.load(f))
+            logger.debug("Using db connection specified in config file. \n%r",
+                         config)
+
+    for field in fields:
+        var_name = prefix + '_' + field.upper().replace(' ', '_')
+        config[field] = os.environ.get(var_name, config.get(field, None))
+
+    missing = [k for k, v in config.items() if v is None]
+    if not allow_missing and missing:
+        raise KeyError("The configuration field(s) {0} were not found in any "
+                       "file or environmental variable.".format(missing))
+    return config

lixdc/db/request.py

@@ -1,8 +1,18 @@
 import collections
 import pandas
 import amostra.client.commands as acc
+from lixdc.conf import load_configuration
+
+config_params = {k: v for k, v in load_configuration('lixdc', 'LIXDC',
+                                                     [
+                                                      'amostra_host',
+                                                      'amostra_port',
+                                                     ]
+                                                     ).items() if v is not None}
+
+host, port = config_params['amostra_host'], config_params['amostra_port']
+request_ref = acc.RequestReference(host=host, port=port)
 
-request_ref = acc.RequestReference()
 
 def upsert_request(req_info):
     if 'uid' in req_info:
@@ -16,9 +26,9 @@ def upsert_request(req_info):
 def find_requests(**kwargs):
     return list(request_ref.find(**kwargs))
 
-def find_request_by_barcode(owner, project, beamline_id, barcode):
+def find_request_by_barcode(owner, proposal_id, beamline_id, barcode):
     try:
-        req_info = list(container_ref.find(owner=owner, project=project,
+        req_info = list(container_ref.find(owner=owner, proposal_id=proposal_id,
                                              beamline_id=beamline_id,
                                              container_barcode=barcode))[0]
     except IndexError:

lixdc/db/sample.py

@@ -3,6 +3,7 @@
 import pandas
 import amostra.client.commands as acc
 import lixdc
+from lixdc.conf import load_configuration
 
 path = os.path.dirname(lixdc.__file__)+"/"
 
@@ -20,8 +21,16 @@
                                 "image": "{}12cells.png".format(path)}
                    }
 
-container_ref = acc.ContainerReference()
-sample_ref = acc.SampleReference()
+config_params = {k: v for k, v in load_configuration('lixdc', 'LIXDC',
+                                                     [
+                                                      'amostra_host',
+                                                      'amostra_port',
+                                                      ]
+                                                     ).items() if v is not None}
+
+host, port = config_params['amostra_host'], config_params['amostra_port']
+container_ref = acc.ContainerReference(host=host, port=port)
+sample_ref = acc.SampleReference(host=host, port=port)
 
 
 def get_container_type_by_id(cont_id):
@@ -34,7 +43,6 @@ def upsert_container(cont_info):
     if 'uid' in cont_info:
         cont = cont_info['uid']
         q = {'uid': cont_info.pop('uid', '')}
-        print('Update Container with: ', cont_info)
         container_ref.update(q, cont_info)
     else:
         cont = container_ref.create(**cont_info)
@@ -51,7 +59,6 @@ def upsert_sample_list(samples):
             result.append(q['uid'])
         else:
             s.pop('uid', '')
-            print('Will Create sample: ', s)
             result.append(sample_ref.create(**s))
 
     return result
@@ -61,9 +68,10 @@ def find_containers(**kwargs):
     return list(container_ref.find(**kwargs))
 
 
-def find_container_by_barcode(owner, project, beamline_id, barcode, fill=True):
+def find_container_by_barcode(owner, proposal_id, beamline_id, barcode, fill=True):
+
     try:
-        cont_info = list(container_ref.find(owner=owner, project=project,
+        cont_info = list(container_ref.find(owner=owner, proposal_id=proposal_id,
                                              beamline_id=beamline_id,
                                              barcode=barcode))[0]
     except IndexError:

lixdc/gui.py

@@ -7,27 +7,36 @@
 from .state.general import State
 from .widgets.main import MainWindow
 from .widgets.login import Login
+from .conf import load_configuration
 
+config_params = {k: v for k, v in load_configuration('lixdc', 'LIXDC',
+                                                     [
+                                                      'amostra_host',
+                                                      'amostra_port',
+                                                      'base_path'
+                                                      ]
+                                                     ).items() if v is not None}
 
 def run():
     app_state = State()
+    app_state.configs = config_params
     app = QtGui.QApplication(sys.argv)
     #print("Styles: ", QtGui.QStyleFactory.keys())
     app.setStyle(QtGui.QStyleFactory.create("Cleanlooks"))
     ### TURNS ON LOGIN SCREEN
     login = Login(app_state=app_state)
     if login.exec_() == QtGui.QDialog.Accepted:
-        #if True:
-        print("After Login App State: ", app_state)
         main = MainWindow(app_state=app_state)
         sys.exit(app.exec_())
 
-def run_ipython(username, project):
-    if username == '' or project == '':
-        raise Exception('Illegal username or project. Please check.')
+def run_ipython(username, proposal, run):
+    if username == '' or proposal == '' or run == '':
+        raise Exception('Illegal username, proposal or run. Please check.')
     app_state = State()
+    app_state.configs = config_params
     app_state.user = username
-    app_state.project = project
+    app_state.proposal_id = proposal
+    app_state.run_id = run
     app_state.login_timestamp = time.time()
     params = {'app_state': app_state}
     main = create_window(MainWindow, **params)

lixdc/state/general.py

@@ -1,13 +1,19 @@
 class State():
     def __init__(self):
         self.user = None
-        self.project = None
+        self.proposal_id = None
+        self.run_id = None
         self.beamline_id = "LIX"
         self.login_timestamp = None
+        self.configs = None
 
     def __str__(self):
-        return "User: {}, Project: {}, Beamline: {}, Login Timestamp: {}".format(self.user, self.project, self.beamline_id, self.login_timestamp)
+        return "User: {}, Proposal: {}, Beamline: {}, Login Timestamp: {}".format(self.user, self.proposal_id, self.beamline_id, self.login_timestamp)
 
     def get_default_fields(self):
-        return {'owner': self.user, 'project': self.project, 'beamline_id':
-                self.beamline_id}
+        return {'owner': self.user, 'proposal_id': self.proposal_id, 'beamline_id':
+                self.beamline_id, 'run_id': self.run_id}
+
+    def get_user_path(self):
+        return "{}/{}/{}/".format(self.configs['base_path'], self.proposal_id,
+                                 self.run_id)

lixdc/utils.py

@@ -1,3 +1,4 @@
+import os
 from PyQt4 import QtGui, QtCore
 
 ANSWER_OK = QtGui.QMessageBox.Ok
@@ -32,3 +33,21 @@ def show_information(text, informative, title):
     msg_box.setStandardButtons(QtGui.QMessageBox.Ok)
     ret = msg_box.exec_()
 
+# xf16id - 5008, lix - 3009
+def makedirs(path, mode=0o777, owner_uid=5008, group=3009):
+    '''Recursively make directories and set permissions'''
+    # Permissions not working with os.makedirs -
+    # See: http://stackoverflow.com/questions/5231901
+    if not path or os.path.exists(path):
+        return []
+
+    head, tail = os.path.split(path)
+    ret = makedirs(head, mode)
+    try:
+        os.mkdir(path)
+    except OSError as ex:
+        if 'File exists' not in str(ex):
+            raise
+    os.chmod(path, mode)
+    ret.append(path)
+    return ret

lixdc/widgets/finder.py

@@ -106,7 +106,7 @@ def filter_containers(self):
         params = dict()
 
         params['owner'] = self.app_state.user
-        params['project'] = self.app_state.project
+        params['proposal_id'] = self.app_state.proposal_id
         params['beamline_id'] = self.app_state.beamline_id
 
         if self.cmb_type.currentText() != '':

lixdc/widgets/login.py

@@ -21,10 +21,16 @@ def init_ui(self):
         self.textPass.setEchoMode(QtGui.QLineEdit.Password)
         self.textPass.setText("lix")
 
-        self.labelProject = QtGui.QLabel(self)
-        self.labelProject.setText("Project: ")
-        self.textProject = QtGui.QLineEdit(self)
-        self.textProject.setText("")
+        self.labelProposal = QtGui.QLabel(self)
+        self.labelProposal.setText("Proposal ID: ")
+        self.textProposal = QtGui.QLineEdit(self)
+        self.textProposal.setText("")
+
+        self.labelRun = QtGui.QLabel(self)
+        self.labelRun.setText("Run #: ")
+        self.textRun = QtGui.QLineEdit(self)
+        self.textRun.setText("{}".format(
+                            time.strftime("%Y%m%d")))
 
         self.buttonLogin = QtGui.QPushButton('Login', self)
         self.buttonLogin.clicked.connect(self.handle_login)
@@ -33,20 +39,22 @@ def init_ui(self):
         form_layout = QtGui.QFormLayout()
         form_layout.addRow(self.labelName, self.textName)
         form_layout.addRow(self.labelPass, self.textPass)
-        form_layout.addRow(self.labelProject, self.textProject)
+        form_layout.addRow(self.labelProposal, self.textProposal)
+        form_layout.addRow(self.labelRun, self.textRun)
         vbox_layout.addLayout(form_layout)
         vbox_layout.addWidget(self.buttonLogin)
 
     def handle_login(self):
         # TODO: Implement real authentication
-        if self.textProject.text() == '':
-            QtGui.QMessageBox.warning(self, 'Error', 'Project is required.')
+        if self.textProposal.text() == '' or self.textRun.text() == '':
+            QtGui.QMessageBox.warning(self, 'Error', 'Proposal and Run Number are required.')
             return
 
         if self.textName.text() != '' and self.textPass.text() == 'lix':
             self.app_state.user = self.textName.text()
-            self.app_state.project = self.textProject.text()
             self.app_state.login_timestamp = time.time()
+            self.app_state.proposal_id = self.textProposal.text()
+            self.app_state.run_id = self.textRun.text()
             self.accept()
         else:
             QtGui.QMessageBox.warning(self, 'Error', 'Bad user or password')

lixdc/widgets/main.py

@@ -20,12 +20,12 @@ def init_ui(self):
         self.setStatusBar(self.status_bar)
 
         self.lbl_user_data = QtGui.QLabel()
-        user_data_str = "Logged in at: {} as {} | Project: {}"
+        user_data_str = "Logged in at: {} as {} | Proposal: {}"
         fmt_date = datetime.fromtimestamp(self.app_state.login_timestamp)
         fmt_date = fmt_date.strftime("%D %H:%M:%S")
         self.lbl_user_data.text = user_data_str.format(fmt_date,
                                                        self.app_state.user,
-                                                       self.app_state.project)
+                                                       self.app_state.proposal_id)
         self.status_bar.addWidget(self.lbl_user_data,1)
 
 

lixdc/widgets/sample_manager.py

@@ -139,7 +139,7 @@ def filter_containers(self):
         params = dict()
 
         params['owner'] = self.app_state.user
-        params['project'] = self.app_state.project
+        params['proposal_id'] = self.app_state.proposal_id
         params['beamline_id'] = self.app_state.beamline_id
 
         if self.cmb_type.currentText() != '':
@@ -445,7 +445,7 @@ def read_import_file(self, fname):
                 plate_info = {
                     "uid": None,
                     "owner": self.app_state.user,
-                    "project": self.app_state.project,
+                    "proposal_id": self.app_state.proposal_id,
                     "beamline_id": self.app_state.beamline_id,
                     "kind": kind,
                     "name": name,
@@ -460,7 +460,7 @@ def read_import_file(self, fname):
             s_temperature = line[1][9]
             sample_info = {
                     "uid": None,
-                    "project": self.app_state.project,
+                    "proposal_id": self.app_state.proposal_id,
                     "beamline_id": self.app_state.beamline_id,
                     "owner": self.app_state.user,
                     "name": s_name,

lixdc/widgets/tab_hplc_setup.py

@@ -185,7 +185,7 @@ def gen_batch(self):
         self.create_request()
         fname = self.compose_file()
         utils.show_information('Batch file created.',
-         'Now copy the file located at: {} to the HPLC computer and execute the batch.'.format(fname),
+         'Now copy the file located at:\n\t{}\n\nTo the HPLC computer and execute the batch.'.format(fname),
          'Success')
 
     def create_request(self):
@@ -220,7 +220,9 @@ def compose_file(self):
                                     plate['name'])
         prefix = 'TBD'
         sep = '\r\n'
-        with open(fname, 'w') as f:
+        utils.makedirs(self.app_state.get_user_path())
+        full_file_path = "{}{}".format(self.app_state.get_user_path(),fname) 
+        with open(full_file_path, 'w') as f:
             f.write(''+sep)
             f.write('[Header]'+sep)
             f.write('Batch File Name\t{}\{}'.format(batch_path, fname)+sep)
@@ -381,4 +383,4 @@ def compose_file(self):
                         multi_injection, barcode, sampler_file, conc_overrides
                     )
                 )
-        return fname
+        return full_file_path