Sanja,
I apologize. I did not realize that another file
(process_includes.py), imported by generateDS.py, had also changed.
Actually, that new version of process_includes.py was at Bitbucket,
but there was no way for you to know that.
So, I've created a new distribution file containing this fix. You
should be able to use it as follows:
$ tar xf generateDS-2.29.7.tar.gz
$ cd generateDS-2.29.7
$ python generateDS.py -o tmp01sup.py ../test04-01.xsd
$ diff -u ../generateDS-2.29.5/tmp01sup.py tmp01sup.py
By the way, there is no need to do an install in order to run the
above from within that directory.
The last line above (diff -u ...) should produce the diff file that
I've attached (in a separate email).
The above produces the change that we have been trying to achieve, I
believe. Please let me know about that.
In a separate email, I've attached that new distribution file and
the diff file, too.
Again, I apologize for wasting your cycles.
I like to put off pushing a change to Bitbucket and pypi.python.org
until I have some confidence that we want to keep it. I need to
come up with a more reliable way to pass along a temporary change
for testing. Maybe this (producing a distribution file) is that
better way. Let me know what you think about that, too, please.
Dave
On Wed, Feb 21, 2018 at 03:47:41PM +0000, Sanja Abbott wrote:
> 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
> > > > >
> > > > > ------------------------------------------------------------------------------
> > > > > Check out the vibrant tech community on one of the world's most
> > > > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> > > > > _______________________________________________
> > > > > generateds-users mailing list
> > > > > generateds-users@lists.sourceforge.net
> > > > > https://lists.sourceforge.net/lists/listinfo/generateds-users
> > > --
> > > _____________________________________________
> > >
> > > 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
>
--
Dave Kuhlman
http://www.davekuhlman.org
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