Why does query __isnull=True cause DatabaseError? - google-app-engine

When I do a filter on a ForeignKey field with __isnull=True, this exception is raised:
DatabaseError: This query is not supported by the database.
However, __isnull=False on ForeignKey works as long as there are no other inequality filters (which I would expect). And __isnull=True works for other field types.
So why does __isnull=True not work on ForeignKey? It seems that DBIndexer tries to make it work as shown here:
https://github.com/django-nonrel/django-dbindexer/blob/dbindexer-1.4/dbindexer/backends.py
But then there is an exception in djangotoolbox:
File "/Users//Documents/workspace/-gae-dev/src/django/db/models/query.py", line 107, in _result_iter
self._fill_cache()
File "/Users//Documents/workspace/-gae-dev/src/django/db/models/query.py", line 774, in _fill_cache
self._result_cache.append(self._iter.next())
File "/Users//Documents/workspace/-gae-dev/src/django/db/models/query.py", line 275, in iterator
for row in compiler.results_iter():
File "/Users//Documents/workspace/-gae-dev/src/djangotoolbox/db/basecompiler.py", line 337, in results_iter
results = self.build_query(fields).fetch(
File "/Users//Documents/workspace/-gae-dev/src/djangotoolbox/db/basecompiler.py", line 428, in build_query
self.check_query()
File "/Users//Documents/workspace/-gae-dev/src/djangotoolbox/db/basecompiler.py", line 409, in check_query
raise DatabaseError("This query is not supported by the database.")
I did come across the following commented-out test case in djangoappengine, and am wondering if is referring to the same issue?
def test_is_null(self):
self.assertEquals(FieldsWithOptionsModel.objects.filter(
floating_point__isnull=True).count(), 0)
FieldsWithOptionsModel(
integer=5.4, email='shinra.tensai#sixpaths.com',
time=datetime.datetime.now().time()).save()
self.assertEquals(FieldsWithOptionsModel.objects.filter(
floating_point__isnull=True).count(), 1)
# XXX: These filters will not work because of a Django bug.
# self.assertEquals(FieldsWithOptionsModel.objects.filter(
# foreign_key=None).count(), 1)
# (it uses left outer joins if checked against isnull)
# self.assertEquals(FieldsWithOptionsModel.objects.filter(
# foreign_key__isnull=True).count(), 1)

Alex Burgel on the NonRel project set me straight:
The NonRel/dbindexer project fixes this query (which otherwise doesn't work due to this Django bug: https://code.djangoproject.com/ticket/10790). To set up dbindexer:
of course, add it to INSTALLED_APPS
also in settings.py, set DATABASES['default]['ENGINE']= 'dbindexer'
also in settings.py, set DBINDEXER_BACKENDS to use FKNullFix. For example:
DBINDEXER_BACKENDS = (
'dbindexer.backends.BaseResolver',
'dbindexer.backends.FKNullFix',
'dbindexer.backends.InMemoryJOINResolver',
'dbindexer.backends.ConstantFieldJOINResolver',
)

Related

Why am I getting a timeout exception with flask on googles app engine when trying to append a value to a wtforms validtor?

I'm having trouble deploying a flask app to the Google app engine. It works fine when I run it locally but as soon as it's deployed to the app engine it fails. With two exceptions (I'm always getting both, I'm unsure which one comes first).
Traceback (most recent call last):
File "/opt/python3.7/lib/python3.7/logging/handlers.py", line 1008, in emit
smtp = smtplib.SMTP(self.mailhost, port, timeout=self.timeout)
File "/opt/python3.7/lib/python3.7/smtplib.py", line 251, in __init__
(code, msg) = self.connect(host, port)
File "/opt/python3.7/lib/python3.7/smtplib.py", line 338, in connect
(code, msg) = self.getreply()
File "/opt/python3.7/lib/python3.7/smtplib.py", line 391, in getreply
+ str(e))
smtplib.SMTPServerDisconnected: Connection unexpectedly closed: timed out
and
Traceback (most recent call last):
File "/opt/python3.7/lib/python3.7/smtplib.py", line 387, in getreply
line = self.file.readline(_MAXLINE + 1)
File "/opt/python3.7/lib/python3.7/socket.py", line 589, in readinto
return self._sock.recv_into(b)
socket.timeout: timed out
It consistently happens within the __init__ function of a form. And specifically in there when I try to append a validator to a validators list.
self.password.validators.append(InputRequired(message='Please enter password!'))
It is not specific to this one validator, the same thing happens with others too. I am at a complete loss as to why and how appending validators would interact with SMTP or sockets.
One thing I noticed is that I had an issue with the Email validator which also worked fine locally but required me to install the module 'email_validator' to work. When I did that it complained that it couldn't use append on a tuple when I tried to append a validator to - what was a list in my local app - but for some reason turned out to be a tuple when I ran the exact same code on the app engine. I removed the Email validator (and the import/requirements) entirely and now I'm at the problem I've described above. It may or may not be related to the Email validator issue.
Update: The error message does indeed seem to be related to the validators.append() call seeing as by setting up the validators at object creation and avoiding all further changes via validators.append() fixed the problem for me. This is the requirements.txt that goes with the application:
blinker>=1.4
Click>=7.0
Flask>=1.1.1
Flask-Login>=0.5.0
Flask-Mail>=0.9.1
Flask-SQLAlchemy>=2.4.1
Flask-WTF>=0.14.3
itsdangerous>=1.1.0
Jinja2>=2.11.1
MarkupSafe>=1.1.1
PyJWT>=1.7.1
PyMySQL>=0.9.3
python-dotenv>=0.11.0
SQLAlchemy>=1.3.13
Werkzeug>=1.0.0
WTForms>=2.2.1
Instead of a full minimal, reproducible example I can offer a minimized version of the form that was causing the issues when instanciated on the GAE:
class ExampleForm(FlaskForm):
name = StringField('Name')
original_name = HiddenField('Original Name')
def add_validators(self):
names = [a.name for a in Users.query.all()]
if self.original_name.data:
names.remove(self.original_name.data)
self.name.validators.append(InputRequired(message='Please enter name!'))
self.name.validators.append(NoneOf(names, message='Username already exists!'))
def __init__(self):
super().__init__(*args, **kwargs)
self.add_validators()
As I'm writing this it occurs to me that maybe I need to always initialize an empty validators list on creation to ensure new entries can be appended to it (like with a normal list) like this name = StringField('Name', validators=[]). I'd still be confused as to why it works locally, but if it fixes the problem that'd be what really counts for me.

Issue with pixel_array using pydicom on python 3.x

I'm using pydicom (installed with pip3, on python 3.7, using Idle) and I need to access pixel_array values.
I just copy-paste the example provided into the documentation and this leads to two errors:
first is about the get_testdata_files operation, which is not working because
Python 3.7.3 (v3.7.3:ef4ec6ed12, Mar 25 2019, 22:22:05) [MSC v.1916 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license()" for more information.
>>>
==================== RESTART: D:\OneDrive\Desktop\test.py ====================
None
Traceback (most recent call last):
File "D:\OneDrive\Desktop\test.py", line 8, in <module>
filename = get_testdata_files("bmode.dcm")[0]
IndexError: list index out of range
I have solved this not using this operation.
second is about the pixel_array and I'm not so able to decode what is wrong, but it seems like the pixel_array is not populated. However I'm able to access other fields in the dataset and the file can be displayed (using ImageJ for example).
==================== RESTART: D:\OneDrive\Desktop\test.py ====================
None
Filename.........: bmode.dcm
Storage type.....: 1.2.840.10008.5.1.4.1.1.3.1
Patient's name...: Femoral trombenarterectomy, Case Report:
Patient id.......: Case Report 1
Modality.........: US
Study Date.......: 20110824
Image size.......: 768 x 1024, 27472108 bytes
Slice location...: (missing)
Traceback (most recent call last):
File "D:\OneDrive\Desktop\test.py", line 38, in <module>
plt.imshow(dataset.pixel_array, cmap=plt.cm.bone)
File "C:\Users\marcl\AppData\Local\Programs\Python\Python37\lib\site-packages\pydicom\dataset.py", line 949, in pixel_array
self.convert_pixel_data()
File "C:\Users\marcl\AppData\Local\Programs\Python\Python37\lib\site-packages\pydicom\dataset.py", line 895, in convert_pixel_data
raise last_exception
File "C:\Users\marcl\AppData\Local\Programs\Python\Python37\lib\site-packages\pydicom\dataset.py", line 863, in convert_pixel_data
arr = handler.get_pixeldata(self)
File "C:\Users\marcl\AppData\Local\Programs\Python\Python37\lib\site-packages\pydicom\pixel_data_handlers\pillow_handler.py", line 188, in get_pixeldata
UncompressedPixelData.extend(decompressed_image.tobytes())
File "C:\Users\marcl\AppData\Local\Programs\Python\Python37\lib\site-packages\PIL\Image.py", line 746, in tobytes
self.load()
File "C:\Users\marcl\AppData\Local\Programs\Python\Python37\lib\site-packages\PIL\ImageFile.py", line 261, in load
raise_ioerror(err_code)
File "C:\Users\marcl\AppData\Local\Programs\Python\Python37\lib\site-packages\PIL\ImageFile.py", line 58, in raise_ioerror
raise IOError(message + " when reading image file")
OSError: broken data stream when reading image file
Here is my code:
import matplotlib.pyplot as plt
import sys
import pydicom
import numpy
from pydicom.data import get_testdata_files
print(__doc__)
#filename = get_testdata_files("bmode.dcm")[0]
filename = "bmode.dcm"
dataset = pydicom.dcmread(filename)
# Normal mode:
print()
print("Filename.........:", filename)
print("Storage type.....:", dataset.SOPClassUID)
print()
pat_name = dataset.PatientName
display_name = pat_name.family_name + ", " + pat_name.given_name
print("Patient's name...:", display_name)
print("Patient id.......:", dataset.PatientID)
print("Modality.........:", dataset.Modality)
print("Study Date.......:", dataset.StudyDate)
if 'PixelData' in dataset:
rows = int(dataset.Rows)
cols = int(dataset.Columns)
print("Image size.......: {rows:d} x {cols:d}, {size:d} bytes".format(
rows=rows, cols=cols, size=len(dataset.PixelData)))
if 'PixelSpacing' in dataset:
print("Pixel spacing....:", dataset.PixelSpacing)
# use .get() if not sure the item exists, and want a default value if missing
print("Slice location...:", dataset.get('SliceLocation', "(missing)"))
# plot the image using matplotlib
plt.imshow(dataset.pixel_array, cmap=plt.cm.bone)
plt.show()
Could you help me to solve these two errors and access pixel_array values?
Don't hesitate to give me some advices /remarks/...
Thanks!
Hi Marc welcome to SO!
Your first error means that the get_testdata_files returns an empty list, so your file is not found. Have a look at the pydicom source, it shows that a search is performed in [DATA_ROOT]/test_files. Is your file located in that path?
Your second error is related to PIL and that can be quite difficult to debug and fix. First try to read the pixel_array from a dataset created from one of the supplied test files. If that works, your problem is probably that PIL cannot handle the specific encoding of your image data. You want to install and use GDCM instead of PIL to see if that solves the problem. Another user has had a similar issue as you, GDCM solved the problem. It can be a bit of a headache to get working unfortunately. Or have a look at this page, it shows some other alternatives on viewing the image data.

Attribute error while exporting data from app engine using Remote APi

Use the example code from app engine will give an attribute error. The more strange thing is,
When the batch_size is 100, the first fetch will give an error while if it were set to 10, the second fetch will give the error, when the batch_size is 1, the 25th fetch will give the error. Is it due to the problem of remote API?
Python version: 2.7
App engine sdk version: 1.9.6
query = MyModel.all()
entities = query.fetch(100)
while entities:
for entity in entities:
# Do something with entity
query.with_cursor(query.cursor())
entities = query.fetch(100)
error message:
Traceback (most recent call last):
File "migrate.py", line 77, in <module>
entities = query.fetch(batch_size)
File "/home/kamel/Library/google_appengine/google/appengine/ext/db/__init__.py", line 2157, in fetch
return list(self.run(limit=limit, offset=offset, **kwargs))
File "/home/kamel/Library/google_appengine/google/appengine/ext/db/__init__.py", line 2326, in next
return self.__model_class.from_entity(self.__iterator.next())
File "/home/kamel/Library/google_appengine/google/appengine/ext/db/__init__.py", line 1435, in from_entity
entity_values = cls._load_entity_values(entity)
File "/home/kamel/Library/google_appengine/google/appengine/ext/db/__init__.py", line 1413, in _load_entity_values
value = prop.make_value_from_datastore(value)
File "/home/kamel/labola/src/model/properties.py", line 295, in make_value_from_datastore
return pickle.loads(value)
File "/usr/lib/python2.7/pickle.py", line 1382, in loads
return Unpickler(file).load()
File "/usr/lib/python2.7/pickle.py", line 858, in load
dispatch[key](self)
File "/usr/lib/python2.7/pickle.py", line 1083, in load_newobj
obj = cls.__new__(cls, *args)
AttributeError: class Reference has no attribute '__new__
I encountered the same issue when trying to unpickle python3 pickles under python2. The problem was linked to new-style classes becoming default in python3. (source)
Solution for me was to replace class AClass: by class AClass(object):

Appengine datastore is corrupted, how to reset

I am using Go + Google AppEngine, and it seems like I have caused my datastore to become corrupted. I ran a query with Filter("ContentId !=", val), and apparently that is not a supported operation. Moreover, it corrupted my database! When I go to localhost:8000/datastore, I get a long stack trace that ends with:
File "/Users/me/go_appengine/google/appengine/api/yaml_listener.py", line 177, in _HandleEvents
raise yaml_errors.EventError(e, event_object)
EventError: could not determine a constructor for the tag '!ContentId'
in "<string>", line 15, column 11:
- name: !ContentId
^
in "<string>", line 15, column 11:
- name: !ContentId
It looks like it made a tag labeled !ContentId.
My question is, how do I reset the datastore to remove this corrupted dev_appserver.py --clear_datastore=yes myapp, but that does not fix it.
To remove the tag edit your index.yaml file in your project root and deploy it again.
!= is not in the list of supported property filters for golang.
If you'd provide your full query and some context we may come up with a good workaround.

Getting error "ImportError: Could not find 'input_readers' on path 'map reduce'" trying to start mapReduce job

I'm getting this error... "ImportError: Could not find 'input_readers' on path 'map reduce'" when trying to Run my map reduce job via the http://localhost:8080/mapreduce launcher page.
It looks like my problem is similar to this post, AppEngine mapper API import error. Unfortunately, no definitive answers were given.
I've simplified it down to this tiny testmapreduce.py:
from google.appengine.ext import db
class TestEntity(db.Model):
value = db.StringProperty()
def mapperhandler(test):
print test.value
return
And my mapreduce.yaml:
mapreduce:
- name: Simplest MapReduce
mapper:
handler: testmapreduce.mapperhandler
input_reader: mapreduce.input_readers.DatastoreInputReader
params:
- name: entity_kind
default: testmapreduce.TestEntity
One possible clue is the presence of __init__.py has no effect (whether in the project root, the mapreduce directory, or both). I'm sure I'm making a beginner mistake, but over the last couple of days I have read every bit of documentation, and all the examples I can find. Thanks.
UPDATE:
I get the same error trying to invoke it via...
control.start_map(
"Give awards",
"testmapreduce.mapperhandler",
"mapreduce.input_readers.DatastoreInputReader",
{"entity_kind": "testmapreduce.TestEntity"},
shard_count=10)
UPDATE:
As requested, the stack trace -- let me know what else would be helpful...
ERROR 2011-10-16 17:09:27,216 _webapp25.py:464] Could not find 'input_readers' on path 'mapreduce'
Traceback (most recent call last):
File "/Develop/GoogleAppEngineLauncher.app/Contents/Resources/GoogleAppEngine-default.bundle/Contents/Resources/google_appengine/google/appengine/ext/webapp/_webapp25.py", line 701, in __call__
handler.get(*groups)
File "/Users/lc/PycharmProjects/mrtest/testmapreduce.py", line 22, in get
shard_count=10) # handle web form test interface
File "/Users/lc/PycharmProjects/mrtest/mapreduce/control.py", line 94, in start_map
transactional=transactional)
File "/Users/lc/PycharmProjects/mrtest/mapreduce/handlers.py", line 811, in _start_map
mapper_input_reader_class = mapper_spec.input_reader_class()
File "/Users/lc/PycharmProjects/mrtest/mapreduce/model.py", line 393, in input_reader_class
return util.for_name(self.input_reader_spec)
File "/Users/lc/PycharmProjects/mrtest/mapreduce/util.py", line 94, in for_name
module = for_name(module_name, recursive=True)
File "/Users/lc/PycharmProjects/mrtest/mapreduce/util.py", line 102, in for_name
short_name, module_name))
ImportError: Could not find 'input_readers' on path 'mapreduce'
INFO 2011-10-16 22:09:27,253 dev_appserver.py:4247] "GET /giveawards HTTP/1.1" 500 -
This problem turned out to be that I was using the 2.7 version of the Python Interpreter in my local environment. When I switched to 2.5, it works fine.

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