Hi Dave,
Thank you for sending me generateDS.py (version 2.29.7), a schema for
testing the fixed attributes (test04-01.xsd) and the output file
(tmp07sup.py) you get by running this script.
I have tried to replicate your results but I get this error:
sanja-ml:generateDS-2.29.5 sanja$ python generateDS.py -o "test.py"
../../Desktop/test04-01.xsd
Traceback (most recent call last):
File "generateDS.py", line 7438, in <module>
main()
File "generateDS.py", line 7426, in main
superModule=superModule)
File "generateDS.py", line 6904, in parseAndGenerate
no_redefine_groups=noRedefineGroups,
TypeError: 'lxml.etree._ElementTree' object is not iterable
To explain how I got there. I've downloaded your latest available package
generateDS-2.29.5.tar.gz. Ran the following commands:
tar xzvf generateDS-2.29.5.tar.gz
cd generateDS-2.29.5
python setup.py build
python setup.py install
Then I renamed generateDS.py to generateDS_original.py and copied
generateDS.py version '2.29.7' into the generateDS-2.29.5 folder. You can
see that the two generateDS scripts are in the same directory and they are
different:
sanja-ml:generateDS-2.29.5 sanja$ diff generateDS.py generateDS_original.py
232c232
< VERSION = '2.29.7'
---
VERSION = '2.29.5'
264d263
< SchemaNamespaceDict = {}
1434,1435c1433
< default=None,
< fixed=None):
---
default=None):
1440,1442d1437
< # treat `fixed` the same as `default`.
< if fixed is not None:
< self.default = fixed
1702,1705d1696
< if 'fixed' in attrs:
< fixed = attrs['fixed']
< else:
< fixed = None
1708,1709c1699
< attribute = XschemaAttribute(
< name, data_type, use, default, fixed)
---
attribute = XschemaAttribute(name, data_type, use,
default)
1713,1714c1703
< attribute = XschemaAttribute(
< name, data_type, use, default, fixed)
---
attribute = XschemaAttribute(name, data_type, use,
default)
2824,2829d2812
< ns_prefix = SchemaNamespaceDict.get(name)
< if ns_prefix is not None and ns_prefix[0] is not None:
< namespace = ns_prefix[0] + ':'
< ns_def = 'xmlns:{}'.format(ns_prefix[0])
< if ns_def not in nameSpacesDef:
< nameSpacesDef += ' {}="{}"'.format(ns_def, ns_prefix[1])
4365c4348
< pats2 = [u'^{}$'.format(replaceVbars(p1)) for p1 in pats1]
---
pats2 = ['^{}$'.format(replaceVbars(p1)) for p1 in pats1]
4561,4562d4543
< # Check special case: simpletype that restricts xs:simpletype.
< # Prevent infinite recursion.
6870,6871c6851
< SchemaLxmlTree, ModuleSuffix, UseSourceFileAsModuleName, \
< SchemaNamespaceDict
---
SchemaLxmlTree, ModuleSuffix, UseSourceFileAsModuleName
6898c6878
< doc, SchemaNamespaceDict =
process_includes.process_include_files(
---
doc = process_includes.process_include_files(
6935c6915
< doc, SchemaNamespaceDict =
process_includes.process_include_files(
---
doc = process_includes.process_include_files(
If I ran generateDS_original.py on your schema (test04-01.xsd) and compare
the result with the tmp07sup.py file you've provided I get:
sanja-ml:generateDS-2.29.5 sanja$ python generateDS_original.py -o "test.py"
../../Desktop/test04-01.xsd
sanja-ml:generateDS-2.29.5 sanja$ diff test.py ../../Desktop/tmp07sup.py
5,6c5,6
< # Generated Wed Feb 21 15:32:42 2018 by generateDS.py version 2.29.5.
< # Python 2.7.11 (v2.7.11:6d1b6a68f775, Dec 5 2015, 12:54:16) [GCC 4.2.1
(Apple Inc. build 5666) (dot 3)]
---
# Generated Mon Feb 19 14:13:30 2018 by generateDS.py version 2.29.7.
# Python 3.6.3 (default, Oct 3 2017, 21:45:48) [GCC 7.2.0]
9c9,14
< # ('-o', 'test.py')
---
# ('-f', '')
# ('-o', 'tmp07sup.py')
# ('-s', 'tmp07sub.py')
# ('--super', 'tmp07sup')
# ('--member-specs', 'dict')
# ('--export', 'write')
12c17
< # ../../Desktop/test04-01.xsd
---
# test04-01.xsd
15c20
< # generateDS_original.py -o "test.py" ../../Desktop/test04-01.xsd
---
# ./generateDS.py -f -o "tmp07sup.py" -s "tmp07sub.py"
--super="tmp07sup" --member-specs="dict" --export="write" test04-01.xsd
18c23
< # generateDS-2.29.5
---
# Test01
448c453
< ExternalEncoding = 'ascii'
---
ExternalEncoding = 'utf-8'
718a724,728
member_data_items_ = {
'garden_name': MemberSpec_('garden_name', 'xs:string', 0, 0,
{'use': 'required'}),
'version': MemberSpec_('version', 'xs:token', 0, 0, {'use':
'required'}),
'vegetable': MemberSpec_('vegetable', 'xs:string', 1, 1, {'name':
'vegetable', 'type': 'xs:string', 'minOccurs': '0', 'maxOccurs':
'unbounded'}, None),
}
721c731
< def __init__(self, garden_name=None, version=None, vegetable=None):
---
def __init__(self, garden_name='dave\'s backyard', version='3.0.0.0',
vegetable=None):
778c788
< if self.garden_name is not None and 'garden_name' not in
already_processed:
---
if self.garden_name != "dave's backyard" and 'garden_name' not in
already_processed:
781c791
< if self.version is not None and 'version' not in
already_processed:
---
if self.version != "3.0.0.0" and 'version' not in
already_processed:
924,925c934,935
< sys.stdout.write('#from test import *\n\n')
< sys.stdout.write('import test as model_\n\n')
---
sys.stdout.write('#from tmp07sup import *\n\n')
sys.stdout.write('import tmp07sup as model_\n\n')
As expected, my test.py was created with the original generateDS script and
it's different to yours, mine used version '2.29.5', yours the intended
version '2.29.7'.
However, if I repeat the same with your new generateDS.py version '2.29.7'
script I get the following:
sanja-ml:generateDS-2.29.5 sanja$ python generateDS.py -o "test.py"
../../Desktop/test04-01.xsd
Traceback (most recent call last):
File "generateDS.py", line 7438, in <module>
main()
File "generateDS.py", line 7426, in main
superModule=superModule)
File "generateDS.py", line 6904, in parseAndGenerate
no_redefine_groups=noRedefineGroups,
TypeError: 'lxml.etree._ElementTree' object is not iterable
I'm not sure what I could do next. I would be very grateful if you could
suggest what that might be.
Thank you,
Sanja
On 19/02/2018 22:36, Dave Kuhlman wrote:
Sanja,
If I understand you correctly, we are getting different results.
I have the following in my test XML schema:
<xs:attribute name="garden_name" type="xs:string"
fixed="dave's backyard" use="required" />
<xs:attribute name="version" type="xs:token" use="required"
fixed="3.0.0.0"/>
And, the constructor that is generated by generateDS.py is the
following:
def __init__(self, garden_name='dave\'s backyard', version='3.0.0.0',
vegetable=None):
Am I right that this is what you want generated?
If so, and if you are not getting that result, is it possible that
another version of generateDS.py on your machine is being used by
mistake.
Or, maybe there is something that I don't understand correctly?
I'll send the complete files (schema, generated module, and
generateDS.py) in a separate email so as not to put too much bulk in
the generateds-users email list.
Let me know if there is something else I need to test.
About, the generateds-users email list -- Yes, it would be good to
reply to or CC that list. For one thing, that gives me an archive
of comments, requests, fixes, etc. And, also, there may be other
users who are interested, have suggestions, etc.
Thanks for help with this.
Dave
On Mon, Feb 19, 2018 at 12:30:20PM +0000, Sanja Abbott wrote:
Dear Dave,
thank you for sending me the fix for the issue of 'fixed values for
attributes'. I've tested your solution and it seems it's not producing the
result I expected.
I'd like to have this attribute:
<xs:attribute name="version" type="xs:token" use="required"
fixed="3.0.0.0"/>
For my purpose it's essential that the attribute is 'required'. If I remove
use="required" and set default="3.0.0.0" (default can't be required):
<xs:attribute name="version" type="xs:token" default="3.0.0.0"/>
I get exactly what I need in the python script using generateDS.py:
def __init__(self, emdb_id=None, version='3.0.0.0', admin=None,
crossreferences=None, sample=None, ...
However, the attribute I require creates:
def __init__(self, emdb_id=None, version=None, admin=None,
crossreferences=None, sample=None, ...
Is there anything that can be done so that I can use the intended format for
my attribute.
Since it's my first time contacting you I wasn't sure if I should cc
generateds-users as well. Please let me know.
Thank you for your help,
Sanja
On 15/02/2018 21:20, Dave Kuhlman wrote:
Sanja,
I've been thinking about this issue a bit more.
From what I can learn, an attribute with a `fixed` value is the same
as one with a `default` value except that a validating parser should
enforce the `fixed` restriction. That means that if the value of
that attribute is different from the value specified by `fixed` in
the schema, then the parser should report that the XML document does
not validate.
Here is a bit of information, if you are interested:
- https://www.w3schools.com/xml/el_attribute.asp
- https://msdn.microsoft.com/en-us/library/ms256143(v=vs.110).aspx
The parsers generated by generateDS.py are *not* validating parsers.
So, I believe that we're good by treating `fixed` attributes in the
same way as `default` attributes.
With this change, you will be able to get that fixed value even
when the XML instance document omits it.
If the user (you, for example) wants to validate an XML instance
document and wants to enforce the `fixed` restriction, then s/he can
run `xmllint` (or some other XML validation program) against the XML
document and the schema.
I've attached a modified version of generateDS.py containing this
fix to a separate email.
Let me know what you think and whether this solves the problem for
you.
And, thank you for suggesting this enhancement.
Dave
On Fri, Feb 09, 2018 at 11:42:22AM +0000, Sanja Abbott wrote:
Hi,
I wonder if you could implement 'fixed' values for attributes in your
generateDS. My schema has an attribute called 'version':
However, the python script that generateDS creates has no means to use this
fixed value.
Thank you,
Sanja Abbott
--
_____________________________________________
Sanja Abbott, PhD
Bioinformatician and Software Infrastructure Manager
Cellular Structures and 3D Bioimaging
European Bioinformatics Institute
Welcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK
http://www.ebi.ac.uk
Tel: 01223 49 4300
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--
_____________________________________________
Sanja Abbott, PhD
Bioinformatician and Software Infrastructure Manager
Cellular Structures and 3D Bioimaging
European Bioinformatics Institute
Welcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK
http://www.ebi.ac.uk
Tel: 01223 49 4300
--
_____________________________________________
Sanja Abbott, PhD
Bioinformatician and Software Infrastructure Manager
Cellular Structures and 3D Bioimaging
European Bioinformatics Institute
Welcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK
http://www.ebi.ac.uk
Tel: 01223 49 4300
