diff --git a/.gitmodules b/.gitmodules
index a95ffcb74fdd76d4a30d84988b24c056baef1ef7..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,9 +0,0 @@
-[submodule "mr_db"]
- path = mr_db
- url = /Users/mdryden/src/mr_db
-[submodule "dstat-interface/mr_db"]
- path = dstat-interface/mr_db
- url = http://microfluidics.utoronto.ca/gitlab/mdryden/mr-db.git
-[submodule "dstat_interface/mr_db"]
- path = dstat_interface/mr_db
- url = http://microfluidics.utoronto.ca/gitlab/mdryden/mr-db.git
diff --git a/CHANGELOG b/CHANGELOG
index f90415d2427dda000d59407b596ba907ea8effa6..0c5a35d10f4a465a4937118f19600b5760e7de8c 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,34 +1,35 @@
-Version 1.0.2
- -Improved logging system: Log messages now print showing where they came from.
- -Implemented gobject IO callbacks for experiments:
- Process will not continuously poll for new data from serial process anymore.
- -Stop button works again
- -Buttons in Photodiode and Calibration modules remain insensitive until ready.
+Version 1.3.3
+ -Bugfix #24: Remove ZODB support until it can be fixed for latest ZODB
-Version 1.0.2a
- -Hotfix #12: Restored measurement ability on Windows
- -Minor logging changes
- -Automatically enable TCS on DStat when measure light sensor button clicked.
+Version 1.3.2
+ -Improves initial connection reliability
+
+Version 1.3.1
+ -Fixed electrochem modes broken when database added
+ -Make metadata keys optional.
-Version 1.0.3
- -Fixed #14: Added support for PMT idle mode
- -Reduced CPU usage when running OCP by reducing polling frequency
+Version 1.3
+ -Fixed a bug related to calibration mode
+ -Added ZODB data storage
+ -Integrated with zmq_plugin
+
+Version 1.2
+ -Old Microdrop interface depreciated
+ -New zmq_plugin based interface
+ -Internal changes to save functionality and plot storage.
-Version 1.0.4
- -Adds support for synchronous electromechanical shutter detection (added in dstat/dstat-firmware@29d4c86)
- -New version string system
+Version 1.1.3
+ -Changed internal storage of experiment data
+ -Added Analysis options:
+ -FFT integral moved there
+ -Basic statistics
-Version 1.0.5
- -Bugfix for saving error introduced by new logging system
-
-Version 1.0.6
- -Automatically integrates shutter FFT peak and saves to data file
- -Adds option to offset start of FFT to avoid PMT startup delay
-
-Version 1.0.7
- -Fixed a few bugs for systems without git
- -Implements mean crossing detection instead of windowing for shutter FFT
+Version 1.1.2
+ -Fixed more critical bugs from refactoring
+Version 1.1.1
+ -Fixed critical bug that made PGA setting change with Gain resistor
+
Version 1.1
-Plot will be prettier if seaborn is installed
-Fixed bug in shutter FFT display
@@ -36,32 +37,35 @@ Version 1.1
-Adds requirement for yaml
-Parameters automatically saved and loaded from last session
-Can manually save and load parameter files
+
+Version 1.0.7
+ -Fixed a few bugs for systems without git
+ -Implements mean crossing detection instead of windowing for shutter FFT
-Version 1.1.1
- -Fixed critical bug that made PGA setting change with Gain resistor
-
-Version 1.1.2
- -Fixed more critical bugs from refactoring
+Version 1.0.6
+ -Automatically integrates shutter FFT peak and saves to data file
+ -Adds option to offset start of FFT to avoid PMT startup delay
-Version 1.1.3
- -Changed internal storage of experiment data
- -Added Analysis options:
- -FFT integral moved there
- -Basic statistics
-Version 1.2
- -Old Microdrop interface depreciated
- -New zmq_plugin based interface
- -Internal changes to save functionality and plot storage.
+Version 1.0.5
+ -Bugfix for saving error introduced by new logging system
-Version 1.3
- -Fixed a bug related to calibration mode
- -Added ZODB data storage
- -Integrated with zmq_plugin
+Version 1.0.4
+ -Adds support for synchronous electromechanical shutter detection (added in dstat/dstat-firmware@29d4c86)
+ -New version string system
-Version 1.3.1
- -Fixed electrochem modes broken when database added
- -Make metadata keys optional.
+Version 1.0.3
+ -Fixed #14: Added support for PMT idle mode
+ -Reduced CPU usage when running OCP by reducing polling frequency
+
+Version 1.0.2a
+ -Hotfix #12: Restored measurement ability on Windows
+ -Minor logging changes
+ -Automatically enable TCS on DStat when measure light sensor button clicked.
-Version 1.3.2
- -Improves initial connection reliability
\ No newline at end of file
+Version 1.0.2
+ -Improved logging system: Log messages now print showing where they came from.
+ -Implemented gobject IO callbacks for experiments:
+ Process will not continuously poll for new data from serial process anymore.
+ -Stop button works again
+ -Buttons in Photodiode and Calibration modules remain insensitive until ready.
diff --git a/README.markdown b/README.markdown
index a0157f9408016dfd92d805ff8d3bfc7dc5a73567..c4283474369e404adc878a738d2a9ff272ba8b4b 100644
--- a/README.markdown
+++ b/README.markdown
@@ -38,9 +38,6 @@ Python and related packages needed: (versions listed are tested, older versions
* XQuartz (2.7.7)
* zeromq (4.0.5) and pyzmq (14.6.0)
* pyyaml (3.11)
-* zodb
-* zeo
-* psutil
Optional:
@@ -168,4 +165,4 @@ If the connection failed, unplug the DStat and try again.
3. Set an appropriate potentiostat gain.
4. Click Execute.
-
\ No newline at end of file
+
diff --git a/dstat_interface/db.py b/dstat_interface/db.py
deleted file mode 100644
index 3e1fda80e3c69ec7b85a85162fa412c663ad97b4..0000000000000000000000000000000000000000
--- a/dstat_interface/db.py
+++ /dev/null
@@ -1,194 +0,0 @@
-import logging
-from time import sleep, time
-from os.path import expanduser
-from uuid import uuid4
-
-from BTrees.OOBTree import OOBTree
-
-import mr_db.mr_db as db
-
-logger = logging.getLogger("dstat.db")
-
-current_db = None
-
-def start_db(path=None):
- global current_db
- current_db = Database(data_dir=path)
-
-def restart_db(object, path):
- logger.info("Restarting database")
- global current_db
- if current_db is None:
- logger.info("No database running")
- start_db(path=path)
- else:
- stop_db()
- start_db(path=path)
-
-def stop_db():
- global current_db
- if not current_db is None:
- logger.info("Stopping ZEO")
- current_db.disconnect()
- current_db = None
- db.stop_server()
- else:
- logger.warning("Tried to disconnect ZEO when not connected")
-
-class Database(object):
- def __init__(self, name='dstat', data_dir=None):
- if data_dir is None:
- data_dir = expanduser('~/.mr_db')
- self.connected = False
- self.name = name
-
- self.db_connect(data_dir)
-
- self.db = self.connection.databases
-
- # Make sure database exists
- if not self.db.has_key(name):
- self.db[name] = OOBTree()
- db.transaction.commit()
-
- def disconnect(self):
- if self.connected is True:
- self.connection.db.close()
- else:
- logger.war("Tried to disconnect ZEO when not connected")
-
- def db_connect(self, root_dir):
- """Connects to ZEO process. Starts ZEO if not running. Returns
- connection object.
- """
- if root_dir == '':
- root_dir = None
-
- while self.connected is False:
- try:
- self.connection = db.DbConnection(root_dir=root_dir)
- self.connected = True
- logger.info("Connected to ZEO server")
- except db.ClientStorage.ClientDisconnected:
- db.stop_server()
- logger.info("Starting ZEO server -- root_dir = %s", root_dir)
- db_proc = db.start_server(root_dir=root_dir)
- sleep(3)
-
- def add_results(self, measurement_uuid=None, measurement_name=None,
- experiment_uuid=None, experiment_metadata=None,
- patient_id=None,
- timestamp=None,
- data=None):
-
- """Add a measurement"""
-
- if experiment_metadata is None:
- experiment_metadata = {}
-
- try:
- logger.info("Starting DB transaction")
- db.transaction.begin()
-
- logger.info("Creating Experiment with id: %s", experiment_uuid)
- exp_db, exp_id = self.add_experiment(
- experiment_uuid=experiment_uuid,
- timestamp=timestamp,
- **experiment_metadata)
-
- logger.info("Adding Measurement with id: %s", measurement_uuid)
- name = self.add_dstat_measurement(experiment=exp_db[exp_id],
- measurement_uuid=measurement_uuid,
- name=measurement_name,
- timestamp=timestamp,
- data=data)
-
- if patient_id is not None:
- if not patient_id in self.db['patients']:
- logger.info("Creating patient with id: %s", patient_id)
- patient = db.Patient(pid=patient_id)
- self.db['patients'][patient_id] = patient
-
- if not exp_id in self.db['patients'][patient_id].experiments:
- logger.info("Linking experiment into patient with id: %s",
- patient_id)
- self.db['patients'][patient_id].link_experiment(exp_db,
- exp_id)
-
- logger.info("Committing DB transaction")
- db.transaction.commit()
-
- return name
-
- except:
- logger.error("Aborting DB transaction")
- db.transaction.abort()
- raise
-
- def add_experiment(self, experiment_uuid=None, timestamp=None, **kwargs):
- """Add a new experiment. Will raise KeyExistsError if id is already
- in db to avoid unintended collisions.
- ----
- Arguments:
- id: experiment id---UUID will be generated if not supplied
- timestamp: current time---Will be generated if not supplied
- kwargs: additional keyword arguments that will be saved in experiment.
- """
-
- if experiment_uuid is None:
- experiment_uuid = uuid4().hex
- if timestamp is None:
- timestamp = time()
-
- kwargs.update({'id':experiment_uuid, 'timestamp':timestamp})
-
- if not experiment_uuid in self.db[self.name]:
- self.db[self.name][experiment_uuid] = db.PersistentMapping()
- else:
- logger.info("Experiment already exists, appending")
-
- self.db[self.name][experiment_uuid].update(kwargs)
-
- return (self.db[self.name], experiment_uuid)
-
- def add_dstat_measurement(self, experiment, measurement_uuid=None,
- data=None, timestamp=None, name=None):
-
- if measurement_uuid is None:
- measurement_uuid = uuid4().hex
- if timestamp is None:
- timestamp = time()
- if data is None:
- data = {}
-
- if not 'measurements' in experiment:
- experiment['measurements'] = db.PersistentMapping()
- if not 'measurements_by_name' in experiment:
- experiment['measurements_by_name'] = db.PersistentMapping()
-
- if measurement_uuid in experiment['measurements']:
- raise db.KeyExistsError(measurement_uuid,
- "Measurement ID already exists. Access directly to update")
-
- data['timestamp'] = timestamp
- data['id'] = measurement_uuid
-
- if name is not None:
- data['name'] = name
-
- experiment['measurements'][measurement_uuid] = data
-
- if name is not None:
- while name in experiment['measurements_by_name']:
- first, sep, last = name.rpartition('-')
-
- if last.isdigit():
- index = int(last)
- index += 1
- name = sep.join((first,str(index)))
- else:
- name += '-1'
-
- experiment['measurements_by_name'][name] = data
-
- return name
\ No newline at end of file
diff --git a/dstat_interface/interface/dstatinterface.glade b/dstat_interface/interface/dstatinterface.glade
index 345ab09706c9af5db2e3a6c58fa6e6add4c47739..02aab91f98344971444470fc676593c4e7e46437 100644
--- a/dstat_interface/interface/dstatinterface.glade
+++ b/dstat_interface/interface/dstatinterface.glade
@@ -689,11 +689,6 @@ Thanks to Christian Fobel for help with Dropbot Plugin</property>
<property name="can_focus">False</property>
<property name="stock">gtk-preferences</property>
</object>
- <object class="GtkImage" id="image7">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="stock">gtk-info</property>
- </object>
<object class="GtkImage" id="image8">
<property name="visible">True</property>
<property name="can_focus">False</property>
@@ -841,28 +836,6 @@ Thanks to Christian Fobel for help with Dropbot Plugin</property>
</child>
</object>
</child>
- <child>
- <object class="GtkMenuItem" id="menu_database">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Database</property>
- <child type="submenu">
- <object class="GtkMenu" id="menu5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkImageMenuItem" id="menu_database_options">
- <property name="label" translatable="yes">Database Options</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="image">image7</property>
- <property name="use_stock">False</property>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
<child>
<object class="GtkMenuItem" id="menuitem4">
<property name="visible">True</property>
diff --git a/dstat_interface/main.py b/dstat_interface/main.py
index 274d2bbc6acb01b796952b905ef1baf63b394ecc..c4b65beec26ff99f22a9e2a68c52e3ab7f8fb1dc 100755
--- a/dstat_interface/main.py
+++ b/dstat_interface/main.py
@@ -48,7 +48,6 @@ os.chdir(os.path.dirname(os.path.abspath(sys.argv[0])))
from version import getVersion
import interface.save as save
-from interface.db import DB_Window
import dstat_comm as comm
import experiments as exp
import interface.exp_window as exp_window
@@ -59,7 +58,6 @@ import params
import parameter_test
import analysis
import zmq
-import db
from errors import InputError
from plugin import DstatPlugin, get_hub_uri
@@ -101,12 +99,6 @@ class Main(object):
self.exp_window = exp_window.Experiments(self.builder)
self.analysis_opt_window = analysis.AnalysisOptions(self.builder)
-
- self.db_window = DB_Window()
- self.builder.get_object('menu_database_options').connect_object(
- 'activate', DB_Window.show, self.db_window
- )
- self.db_window.connect('db_reset', db.restart_db)
# Setup Autosave
self.autosave_checkbox = self.builder.get_object('autosave_checkbutton')
@@ -191,7 +183,6 @@ class Main(object):
params.save_params(self, 'last_params.yml')
self.on_serial_disconnect_clicked()
- db.stop_db()
mainloop.quit()
def on_gtk_about_activate(self, menuitem, data=None):
@@ -412,13 +403,7 @@ class Main(object):
self.metadata = metadata
if self.metadata is not None:
- logger.info("Loading external metadata")
- self.db_window.update_from_metadata(self.metadata)
- elif self.db_window.params['exp_id_entry'] is None:
- logger.info("DB exp_id field blank, autogenerating")
- self.db_window.on_exp_id_autogen_button_clicked()
-
- self.db_window.params = {'measure_id_entry':experiment_id.hex}
+ logger.info("Loading external metadata")
def exceptions():
""" Cleans up after errors """
@@ -704,33 +689,6 @@ class Main(object):
self.autosavedir_button.get_filename(),
self.autosavename.get_text()
)
- # Database output
- if self.current_exp.parameters['db_enable_checkbutton']:
- meta = {}
-
- if self.current_exp.parameters['metadata'] is not None:
- metadata = self.current_exp.parameters['metadata']
- exp_metakeys = ['experiment_uuid', 'patient_id', 'name']
- meta.update(
- {k: metadata[k]
- for k in metadata
- if k not in exp_metakeys
- }
- )
-
- name = self.current_exp.parameters['measure_name_entry']
-
- newname = db.current_db.add_results(
- measurement_uuid=self.active_experiment_id.hex,
- measurement_name=name,
- experiment_uuid=self.current_exp.parameters['exp_id_entry'],
- experiment_metadata=meta,
- patient_id=self.current_exp.parameters['patient_id_entry'],
- timestamp=None,
- data=self.current_exp.export()
- )
-
- self.db_window.params = {'measure_name_entry':newname}
# uDrop
# UI stuff
diff --git a/dstat_interface/params.py b/dstat_interface/params.py
index 1bf6db84b2cf76a539b17f766b6bf330105078c2..6d384e6c806a47526d100377e3cac627a050e202 100755
--- a/dstat_interface/params.py
+++ b/dstat_interface/params.py
@@ -43,8 +43,7 @@ def get_params(window):
logger.info("No gain selected.")
parameters.update(window.exp_window.get_params(selection))
parameters.update(window.analysis_opt_window.params)
- parameters.update(window.db_window.persistent_params)
-
+
return parameters
def save_params(window, path):
@@ -74,6 +73,5 @@ def set_params(window, params):
window.exp_window.set_params(params['experiment_index'], params)
window.analysis_opt_window.params = params
- window.db_window.params = params
window.params_loaded = True
diff --git a/pavement.py b/pavement.py
index bf1f907e0cfac6ff06845920459077722865df40..0aea7f58afe84674e34958f65404241569de2066 100644
--- a/pavement.py
+++ b/pavement.py
@@ -18,8 +18,7 @@ setup(name='dstat_interface',
license='GPLv3',
packages=['dstat_interface', ],
install_requires=['matplotlib', 'numpy', 'pyserial', 'pyzmq',
- 'pyyaml','seaborn', 'zmq-plugin>=0.2.post2', 'zodb',
- 'zeo', 'psutil'],
+ 'pyyaml','seaborn', 'zmq-plugin>=0.2.post2'],
# Install data listed in `MANIFEST.in`
include_package_data=True)