From bae7254ff3214305a1d6d352bfd389f195986546 Mon Sep 17 00:00:00 2001
From: Michael DM Dryden <mdryden@chem.utoronto.ca>
Date: Tue, 14 Mar 2017 19:20:19 -0400
Subject: [PATCH] Remove ZODB support until newest version can be integrated
properly. Fixes #24
---
.gitmodules | 9 -
dstat_interface/db.py | 194 ----------------
dstat_interface/interface/db.glade | 219 ------------------
.../interface/dstatinterface.glade | 27 ---
dstat_interface/main.py | 52 +----
dstat_interface/params.py | 4 +-
pavement.py | 3 +-
7 files changed, 4 insertions(+), 504 deletions(-)
delete mode 100644 dstat_interface/db.py
delete mode 100644 dstat_interface/interface/db.glade
diff --git a/.gitmodules b/.gitmodules
index a95ffcb..e69de29 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/dstat_interface/db.py b/dstat_interface/db.py
deleted file mode 100644
index 3e1fda8..0000000
--- 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/db.glade b/dstat_interface/interface/db.glade
deleted file mode 100644
index 20a833a..0000000
--- a/dstat_interface/interface/db.glade
+++ /dev/null
@@ -1,219 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<interface>
- <requires lib="gtk+" version="2.24"/>
- <!-- interface-naming-policy project-wide -->
- <object class="GtkWindow" id="db_window">
- <property name="can_focus">False</property>
- <property name="title" translatable="yes">Database</property>
- <property name="window_position">center-on-parent</property>
- <property name="destroy_with_parent">True</property>
- <child>
- <object class="GtkVBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkCheckButton" id="db_enable_checkbutton">
- <property name="label" translatable="yes">Enable Database saving</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="active">True</property>
- <property name="draw_indicator">True</property>
- <signal name="toggled" handler="on_db_enable_checkbutton_toggled" swapped="no"/>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkTable" id="db_control_table">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="n_rows">5</property>
- <property name="n_columns">3</property>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <object class="GtkLabel" id="label3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Measurement ID</property>
- </object>
- <packing>
- <property name="top_attach">1</property>
- <property name="bottom_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Experiment ID</property>
- </object>
- </child>
- <child>
- <object class="GtkEntry" id="exp_id_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- <property name="primary_icon_sensitive">True</property>
- <property name="secondary_icon_sensitive">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="right_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="measure_id_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="editable">False</property>
- <property name="invisible_char">â—</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- <property name="primary_icon_sensitive">True</property>
- <property name="secondary_icon_sensitive">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="right_attach">2</property>
- <property name="top_attach">1</property>
- <property name="bottom_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="patient_id_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="editable">False</property>
- <property name="invisible_char">â—</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- <property name="primary_icon_sensitive">True</property>
- <property name="secondary_icon_sensitive">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="right_attach">2</property>
- <property name="top_attach">3</property>
- <property name="bottom_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Patient ID</property>
- </object>
- <packing>
- <property name="top_attach">3</property>
- <property name="bottom_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="exp_id_autogen_button">
- <property name="label" translatable="yes">Generate New</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <signal name="clicked" handler="on_exp_id_autogen_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="right_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">DB Path</property>
- </object>
- <packing>
- <property name="top_attach">4</property>
- <property name="bottom_attach">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="db_path_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- <property name="primary_icon_sensitive">True</property>
- <property name="secondary_icon_sensitive">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="right_attach">2</property>
- <property name="top_attach">4</property>
- <property name="bottom_attach">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="db_apply_button">
- <property name="label" translatable="yes">Apply</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <signal name="clicked" handler="on_db_apply_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="right_attach">3</property>
- <property name="top_attach">4</property>
- <property name="bottom_attach">5</property>
- </packing>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <object class="GtkLabel" id="label5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Measurement Name</property>
- </object>
- <packing>
- <property name="top_attach">2</property>
- <property name="bottom_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="measure_name_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- <property name="primary_icon_sensitive">True</property>
- <property name="secondary_icon_sensitive">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="right_attach">2</property>
- <property name="top_attach">2</property>
- <property name="bottom_attach">3</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/interface/dstatinterface.glade b/dstat_interface/interface/dstatinterface.glade
index 6503660..8ae7a00 100644
--- a/dstat_interface/interface/dstatinterface.glade
+++ b/dstat_interface/interface/dstatinterface.glade
@@ -749,11 +749,6 @@ 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="GtkListStore" id="serial_liststore">
<columns>
<!-- column-name serial -->
@@ -897,28 +892,6 @@ 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">View…</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 a7e05d1..6b72172 100755
--- a/dstat_interface/main.py
+++ b/dstat_interface/main.py
@@ -50,7 +50,6 @@ 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 interface.exp_window as exp_window
import interface.adc_pot as adc_pot
@@ -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
@@ -105,12 +103,6 @@ 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')
@@ -209,7 +201,6 @@ class Main(object):
params.save_params(self, 'last_params.yml')
self.on_serial_disconnect_clicked()
- db.stop_db()
gtk.main_quit()
def on_gtk_about_activate(self, menuitem, data=None):
@@ -438,13 +429,7 @@ 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 """
@@ -470,13 +455,7 @@ class Main(object):
else:
nb.get_nth_page(nb.page_num(self.ft_window)).hide()
# nb.get_nth_page(nb.page_num(self.period_window)).hide()
-
- if parameters['db_enable_checkbutton']:
- if db.current_db is None:
- db.start_db()
- elif not db.current_db.connected:
- db.restart_db()
-
+
comm.serial_instance.proc_pipe_p.send(self.current_exp)
# Flush data pipe
@@ -811,33 +790,6 @@ 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 6dbc720..048d1f4 100755
--- a/dstat_interface/params.py
+++ b/dstat_interface/params.py
@@ -44,8 +44,7 @@ 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):
@@ -77,6 +76,5 @@ 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 bf1f907..0aea7f5 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)
--
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