def Creatediagram():
desc = sadisplay.describe(globals().values())
with codecs.open('schema.plantuml', 'w', encoding='utf-8') as f:
f.write(sadisplay.plantuml(desc))
with codecs.open('schema.dot', 'w', encoding='utf-8') as f:
f.write(sadisplay.dot(desc))
def show_database_schema(
schemastem: str,
make_image: bool = False,
java: str = None,
plantuml: str = None,
height_width_limit: int = 20000,
java_memory_limit_mb: int = 2048,
) -> None:
"""
Prints the database schema to a PNG picture.
Args:
schemastem:
filename stem
make_image:
Make a PNG image? (May be impractically large!)
java:
(for ``make_image``) Java executable
plantuml:
(for ``make_image``) PlantUML Java ``.jar`` file
height_width_limit:
(for ``make_image``) maximum height and width for PNG; see
https://plantuml.com/faq
java_memory_limit_mb:
(for ``make_image``) Java virtual machine memory limit, in Mb
"""
# noinspection PyUnresolvedReferences
import camcops_server.camcops_server_core as core # delayed import; import side effects # noqa
import sadisplay # delayed import
import camcops_server.cc_modules.cc_all_models as models # delayed import
# ... a re-import to give it a name
uml_filename = f"{schemastem}.plantuml"
png_filename = f"{schemastem}.png"
log.info(f"Making schema PlantUML: {uml_filename}")
desc = sadisplay.describe([getattr(models, attr) for attr in dir(models)])
# log.debug(desc)
with open(uml_filename, "w") as f:
f.write(sadisplay.plantuml(desc))
if make_image:
import shutil # delayed import
assert shutil.which(java), f"Can't find Java executable: {java}"
assert os.path.isfile(
plantuml
), f"Can't find PlantUML JAR file: {plantuml}" # noqa
log.info(f"Making schema PNG: {png_filename}")
cmd = [
java,
f"-Xmx{java_memory_limit_mb}m",
f"-DPLANTUML_LIMIT_SIZE={height_width_limit}",
"-jar",
plantuml,
uml_filename,
]
log.info("Arguments: {}", cmd)
subprocess.check_call(cmd)
def main():
classes = [c for c in
list(chain.from_iterable([[getattr(m, a) for a in dir(m)]
for m in (terms, factset, network)]))
if type(c) is DeclarativeMeta and issubclass(c, Base)]
print(classes)
desc = sadisplay.describe(classes, show_methods=False)
open('schema.plantuml', 'w').write(sadisplay.plantuml(desc))
open('schema.dot', 'w').write(sadisplay.dot(desc))
def render(self, node):
all_names = []
for module_name in node['module']:
__import__(module_name, globals(), locals(), [], -1)
module = sys.modules[module_name]
for attr in dir(module):
try:
m = getattr(module, attr)
# !!!
# Ugly hack
repr(m) # without this statement - exception raises
# any ideas?
all_names.append(m)
except:
pass
names = []
if node['exclude']:
for i in all_names:
try:
if i.__name__ not in node['exclude']:
names.append(i)
except AttributeError:
pass
elif node['include']:
for i in all_names:
try:
if i.__name__ in node['include']:
names.append(i)
except AttributeError:
pass
else:
names = all_names
desc = sadisplay.describe(names)
render = node['render'] or self.builder.config.sadisplay_default_render
if render == 'plantuml':
content = sadisplay.plantuml(desc)
command = generate_plantuml_args(self)
elif render == 'graphviz':
content = sadisplay.dot(desc)
command = generate_graphviz_args(self)
return render_image(self, content, command)
def render(self, node):
all_names = []
for module_name in node['module']:
__import__(module_name, globals(), locals())
module = sys.modules[module_name]
for attr in dir(module):
try:
m = getattr(module, attr)
# !!!
# Ugly hack
repr(m) # without this statement - exception raises
# any ideas?
all_names.append(m)
except:
pass
names = []
if node['exclude']:
for i in all_names:
try:
if i.__name__ not in node['exclude']:
names.append(i)
except AttributeError:
pass
elif node['include']:
for i in all_names:
try:
if i.__name__ in node['include']:
names.append(i)
except AttributeError:
pass
else:
names = all_names
desc = sadisplay.describe(names)
render = node['render'] or self.builder.config.sadisplay_default_render
if render == 'plantuml':
content = sadisplay.plantuml(desc)
command = generate_plantuml_args(self)
elif render == 'graphviz':
content = sadisplay.dot(desc)
command = generate_graphviz_args(self)
return render_image(self, content, command)
def get_ulm():
desc = sadisplay.describe(
[getattr(models, attr) for attr in dir(models)],
show_methods=True,
show_properties=True,
show_indexes=True,
)
with codecs.open('doc/database/schema.plantuml', 'w',
encoding='utf-8') as f:
f.write(sadisplay.plantuml(desc))
with codecs.open('doc/database/schema.dot', 'w', encoding='utf-8') as f:
f.write(sadisplay.dot(desc))
def render(self, node):
all_names = []
for module_name in node['module']:
__import__(module_name, globals(), locals(), [], -1)
module = sys.modules[module_name]
all_names += [getattr(module, attr) for attr in dir(module)]
names = []
if node['exclude']:
for i in all_names:
try:
if i.__name__ not in node['exclude']:
names.append(i)
except AttributeError:
pass
elif node['include']:
for i in all_names:
try:
if i.__name__ in node['include']:
names.append(i)
except AttributeError:
pass
else:
names = all_names
desc = sadisplay.describe(names)
render = node['render'] or self.builder.config.sadisplay_default_render
if render == 'plantuml':
content = sadisplay.plantuml(desc)
command = generate_plantuml_args(self)
elif render == 'graphviz':
content = sadisplay.dot(desc)
command = generate_graphviz_args(self)
return render_image(self, content, command)
def render(self, node):
all_names = []
for module_name in node["module"]:
__import__(module_name, globals(), locals(), [], -1)
module = sys.modules[module_name]
all_names += [getattr(module, attr) for attr in dir(module)]
names = []
if node["exclude"]:
for i in all_names:
try:
if i.__name__ not in node["exclude"]:
names.append(i)
except AttributeError:
pass
elif node["include"]:
for i in all_names:
try:
if i.__name__ in node["include"]:
names.append(i)
except AttributeError:
pass
else:
names = all_names
desc = sadisplay.describe(names)
render = node["render"] or self.builder.config.sadisplay_default_render
if render == "plantuml":
content = sadisplay.plantuml(desc)
command = generate_plantuml_args(self)
elif render == "graphviz":
content = sadisplay.dot(desc)
command = generate_graphviz_args(self)
return render_image(self, content, command)
Index("ix_user_title", books.c.user_id, books.c.title)
class Book(object):
pass
mapper(Book, books, {'user': relation(User, backref='books')})
# Not mapped table
notes = Table(
'notes',
BASE.metadata,
Column('id', Integer, primary_key=True),
Column('name', Unicode(200), nullable=False),
Column('user_id', Integer, ForeignKey('user_table.id')),
)
if __name__ == '__main__':
import codecs
import sadisplay
desc = sadisplay.describe(globals().values())
with codecs.open('/tmp/schema.plantuml', 'w', encoding='utf-8') as f:
f.write(sadisplay.plantuml(desc))
with codecs.open('/tmp/schema.dot', 'w', encoding='utf-8') as f:
f.write(sadisplay.dot(desc))
)
class Book(object):
pass
mapper(Book, books, {'user': relation(User, backref='books')})
# Not mapped table
notes = Table(
'notes',
BASE.metadata,
Column('id', Integer, primary_key=True),
Column('name', Unicode(200), nullable=False),
Column('user_id', Integer, ForeignKey('user_table.id')),
)
if __name__ == '__main__':
import sadisplay
desc = sadisplay.describe(globals().values())
with open('schema.plantuml', 'w') as f:
f.write(sadisplay.plantuml(desc))
with open('schema.dot', 'w') as f:
f.write(sadisplay.dot(desc))
def main() -> int:
"""
Command-line entry point.
Returns:
exit code
"""
# -------------------------------------------------------------------------
# Arguments
# -------------------------------------------------------------------------
parser = argparse.ArgumentParser(
description="whisker_serial_order v{}. Serial order task for "
"Whisker.".format(SERIAL_ORDER_VERSION))
parser.add_argument("--logfile",
default=None,
help="Filename to append log to")
parser.add_argument('--verbose',
'-v',
action='count',
default=0,
help="Be verbose. (Use twice for extra verbosity.)")
parser.add_argument('--guilog',
action="store_true",
help="Show Python log in a GUI window")
parser.add_argument('--upgrade-database',
action="store_true",
help="Upgrade database to current version.")
# parser.add_argument('--debug-qt-signals', action="store_true",
# help="Debug QT signals.")
parser.add_argument(
"--dburl",
default=None,
help="Database URL (if not specified, task will look in {} "
"environment variable).".format(DB_URL_ENV_VAR))
parser.add_argument('--dbecho',
action="store_true",
help="Echo SQL to log.")
parser.add_argument(
"--outdir",
default=None,
help="Directory for output file (if not specified, task will look in "
"{} environment variable, or if none, working directory).".format(
OUTPUT_DIR_ENV_VAR))
parser.add_argument('--gui',
'-g',
action="store_true",
help="GUI mode only")
parser.add_argument('--schema',
action="store_true",
help="Generate schema picture and stop")
parser.add_argument(
"--java",
default='java',
help="Java executable (for schema diagrams); default is 'java'")
parser.add_argument(
"--plantuml",
default='plantuml.jar',
help="PlantUML Java .jar file (for schema diagrams); default "
"is 'plantuml.jar'")
parser.add_argument(
"--schemastem",
default='schema',
help="Stem for output filenames (for schema diagrams); default is "
"'schema'; '.plantuml' and '.png' are appended")
parser.add_argument(
"--testtrialplan",
action="store_true",
help="Print a test trial plan of the specified sequence length "
"+/- restrictions")
parser.add_argument("--seqlen",
metavar='SEQUENCE_LEN',
type=int,
default=None,
help="Sequence length for --testtrialplan")
parser.add_argument(
"--choice_hole_restriction",
metavar='CHOICE_HOLE_GROUPS',
type=ChoiceHoleRestriction,
help="Optional choice hole restrictions for --testtrialplan; use "
"e.g. '--choice_hole_restriction \"1,2;3,4\"' to restrict the "
"choice phase to holes 1 v 2 and 3 v 4")
parser.add_argument(
"--serial_pos_restriction",
metavar='SERIAL_ORDER_POS_GROUPS',
type=SerialPosRestriction,
help="Optional choice serial order position restrictions for "
"--testtrialplan; use e.g. '--serial_pos_restriction "
"\"1,2;1,3\"' to restrict the choice phase to serial positions "
"1 v 2 and 1 v 3")
parser.add_argument(
"--side_dwor_multiplier",
metavar="SIDE_DWOR_MULTIPLIER",
type=int,
default=1,
help="Draw-without-replacement (DWOR) multiplier for shuffling on the "
"basis of whether the left or right side is correct; see docs.")
# We could allow extra Qt arguments:
# args, unparsed_args = parser.parse_known_args()
# Or not:
args = parser.parse_args()
unparsed_args = []
qt_args = sys.argv[:1] + unparsed_args
# -------------------------------------------------------------------------
# Modify settings if we're in a PyInstaller bundle
# -------------------------------------------------------------------------
in_bundle = getattr(sys, 'frozen', False)
if in_bundle:
args.gui = True
if not args.gui:
args.guilog = False
# -------------------------------------------------------------------------
# Create QApplication before we create any windows (or Qt will crash)
# -------------------------------------------------------------------------
qt_app = QApplication(qt_args)
# -------------------------------------------------------------------------
# Logging
# -------------------------------------------------------------------------
loglevel = logging.DEBUG if args.verbose >= 1 else logging.INFO
main_only_quicksetup_rootlogger(loglevel)
logging.getLogger('whisker').setLevel(
logging.DEBUG if args.verbose >= 2 else logging.INFO)
if args.logfile:
copy_root_log_to_file(args.logfile)
if args.guilog:
rootlogger = logging.getLogger()
log_window = LogWindow(level=loglevel,
window_title=WINDOW_TITLE + " Python log",
logger=rootlogger)
log_window.show()
# If any exceptions happen up to this point, we're a bit stuffed.
# But from now on, we can trap anything and see it in the GUI log, if
# enabled, even if we have no console.
# noinspection PyBroadException,PyPep8
try:
# ---------------------------------------------------------------------
# Info
# ---------------------------------------------------------------------
log.info("whisker_serial_order v{}: Serial order task for Whisker, "
"by Rudolf Cardinal ([email protected])".format(
SERIAL_ORDER_VERSION))
log.debug("args: {}".format(args))
log.debug("qt_args: {}".format(qt_args))
log.debug("PyQt version: {}".format(PYQT_VERSION_STR))
log.debug("QtCore version: {}".format(QT_VERSION_STR))
log.debug("Whisker client version: {}".format(whisker.version.VERSION))
if in_bundle:
log.debug("Running inside a PyInstaller bundle")
if args.gui:
log.debug("Running in GUI-only mode")
# if args.debug_qt_signals:
# enable_signal_debugging_simply()
# ---------------------------------------------------------------------
# Schema diagram generation only?
# ---------------------------------------------------------------------
if args.schema:
umlfilename = args.schemastem + '.plantuml'
log.info("Making schema PlantUML: {}".format(umlfilename))
desc = sadisplay.describe(
[getattr(models, attr) for attr in dir(models)])
log.debug(desc)
with open(umlfilename, 'w') as f:
f.write(sadisplay.plantuml(desc))
log.info("Making schema PNG: {}".format(args.schemastem + '.png'))
cmd = [args.java, '-jar', args.plantuml, umlfilename]
log.debug(cmd)
subprocess.check_call(cmd)
sys.exit(0)
# ---------------------------------------------------------------------
# Demo trial plan only?
# ---------------------------------------------------------------------
if args.testtrialplan:
seqlen = args.seqlen
if seqlen is None or seqlen < MIN_SEQUENCE_LENGTH:
raise ValueError("--seqlen must be an integer >= {}".format(
MIN_SEQUENCE_LENGTH))
tplist = SerialOrderTask.create_trial_plans(
seqlen=seqlen,
choice_hole_restriction=args.choice_hole_restriction,
serial_pos_restriction=args.serial_pos_restriction,
side_dwor_multiplier=args.side_dwor_multiplier)
print("""
Explanation:
- there are 5 holes, numbered 1-5
- sequence: the sequence of hole numbers presented in the trial
e.g. for a sequence length of 3, you might have sequence=(3, 1, 4),
meaning that the subject will be shown hole 3, then hole 1, then hole 4,
in the first phase
- hole_choice: the two holes presented during the choice phase
e.g. hole_choice=[3,4]
- serial_order_choice: the serial order, in the first phase, of the two holes
offered in the second (choice) phase -- in this example, you would get
serial_order_choice=[1,3], because hole 3 was offered in the choice phase
and was in position 1 in the sequence, and hole 4 was offered in the
choice phase and was in position 3 in the sequence.
Hint: use grep to check the output.
Choice hole restrictions: {chr}
Serial position restrictions: {spr}
""".format(
chr=args.choice_hole_restriction,
spr=args.serial_pos_restriction,
))
for i, tp in enumerate(tplist, start=1):
print("{}. {}".format(i, tp))
sys.exit(0)
# ---------------------------------------------------------------------
# File output
# ---------------------------------------------------------------------
if args.outdir:
set_output_directory(args.outdir)
log.info("Using output directory: {}".format(get_output_directory()))
if not os.access(get_output_directory(), os.W_OK):
raise ValueError("Cannot write to output directory")
# ---------------------------------------------------------------------
# Database
# ---------------------------------------------------------------------
# Get URL, or complain
if args.dburl:
set_database_url(args.dburl)
if args.dbecho:
set_database_echo(args.dbecho)
if not dbsettings['url']:
if args.gui:
win = NoDatabaseSpecifiedWindow()
if args.guilog:
# noinspection PyUnboundLocalVariable
win.exit_kill_log.connect(log_window.exit)
return run_gui(qt_app, win)
raise ValueError(MSG_DB_ENV_VAR_NOT_SPECIFIED)
log.debug("Using database URL: {}".format(dbsettings['url']))
if database_is_sqlite(dbsettings):
log.critical(
"Avoid SQLite: not safe for concurrent use in this context")
sys.exit(1)
# Has the user requested a command-line database upgrade?
if args.upgrade_database:
sys.exit(
upgrade_database(ALEMBIC_CONFIG_FILENAME, ALEMBIC_BASE_DIR))
# Is the database at the correct version?
(current_revision, head_revision) = get_current_and_head_revision(
dbsettings['url'], ALEMBIC_CONFIG_FILENAME, ALEMBIC_BASE_DIR)
if current_revision != head_revision:
if args.gui:
win = WrongDatabaseVersionWindow(current_revision,
head_revision)
if args.guilog:
# noinspection PyUnboundLocalVariable
win.exit_kill_log.connect(log_window.exit)
return run_gui(qt_app, win)
raise ValueError(
WRONG_DATABASE_VERSION_STUB.format(
head_revision=head_revision,
current_revision=current_revision))
# ---------------------------------------------------------------------
# Run app
# ---------------------------------------------------------------------
log.debug("Seeding random number generator")
random.seed()
win = MainWindow(dbsettings)
if args.guilog:
# noinspection PyUnboundLocalVariable
win.exit_kill_log.connect(log_window.exit)
return run_gui(qt_app, win)
except:
if args.guilog:
log.critical(traceback.format_exc())
log_window.set_may_close(True)
return qt_app.exec_()
else:
raise