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Create python package #3

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hgoerzig wants to merge 23 commits into main from createpackage

Contributor

hgoerzig commented Aug 18, 2021 •

edited

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renamed folder skript to code
separated jupyther code from python code
created a python package (nxsOnto) added requirements.txt and setup.py
removed some comments in the code and renamed file

hgoerzig added 2 commits

August 9, 2021 15:00


          setup, requirements, script -> code

b24a068


          .gitignore, git rm

0e59b28

PeterC-DLS commented Aug 18, 2021

Please edit this to provide a proper title and description

hgoerzig changed the title ~~Createpackage~~ Create python package

PeterC-DLS reviewed

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PeterC-DLS left a comment

Tree does not need to be so deep.

Remove the empty README.md.

code/nxsOnto/setup.py Outdated

+                    packages=['nxsOnto'],
+                    license='Apache 2',
+                    install_requires=[
+              		"owlready2",

PeterC-DLS Aug 18, 2021

This duplicates requirements.txt so should read that file

code/nxsOnto/setup.py Outdated

+                    version='1.1',
+                    description='Generates an ontology from nxdl files',
+                    author='Steve Collins',
+                    url="https://github.com/nexusformat/NeXusOntology/script",

PeterC-DLS Aug 18, 2021

Does not exist

Contributor

prjemian Aug 18, 2021

this URL: https://github.com/nexusformat/NeXusOntology/tree/main/script

hgoerzig added 2 commits

August 19, 2021 14:37


          removed dublicated requirements and changed url path in setup.py

eed3470


          updated readme

17130b5

PeterC-DLS commented Aug 19, 2021

The README does not explicitly say how I run this and what the outcome is.


          updated README.md

3b4d830

PeterC-DLS reviewed

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PeterC-DLS left a comment

I've add more comments from #2

Also please delete the notebook.

code/nxsOnto/nxsOnto/generator.py Outdated

@@ @@ -106,25 +106,31 @@ @@
                   The version string is the NeXus version followed by the ontology version.
               '''
+              '''
               # To avoid re-parsing NeXus files after initial run, execute this

PeterC-DLS Sep 14, 2021

All of this is commented out code! Not sure why you want it too as you run this script once.

code/nxsOnto/nxsOnto/generator.py Outdated

               g = Github(token)
               repo = g.get_repo(nexus_repo)
               with urllib.request.urlopen(repo.tags_url) as url:
                   tags = json.loads(url.read().decode())
                   tagsDict = tags[0]  # get version tags from master branch
               base_class_url = []
               for file in repo.get_contents("base_classes"):
                   if str(file).split('.')[-2] == 'nxdl':

PeterC-DLS Sep 14, 2021

What if file name does not have two '.'?

code/nxsOnto/nxsOnto/generator.py Outdated

               def addFieldToDict(classDict, field, defn_name): # make a function to be reused later
                   #defn_name is used to add application definition to field dict if the field is defined in an app deff.
                   field_name = field.getAttribute('name')
                   deprecationAttribute = field.getAttribute('deprecated')
                   if not deprecationAttribute == '':

PeterC-DLS Sep 14, 2021

Not a Pythonic way to test for an empty string

code/nxsOnto/nxsOnto/generator.py Outdated

                   deprecationAttribute = field.getAttribute('deprecated')
                   if not deprecationAttribute == '':
-                      print("=== Deprecation warning %s in %s: %s" % (field_name, className, deprecationAttribute))
+                      print("=== Deprecation warning %s in %s: %s" % (field_name, className, deprecationAttribute))

PeterC-DLS Sep 14, 2021

Where is className defined?

code/nxsOnto/nxsOnto/generator.py Outdated

		@@ -184,12 +175,12 @@ def addFieldToDict(classDict, field, defn_name): # make a function to be reused
		#print('~~~ field did not exist: %s' % long_name)
		classDict[className]['fields'][long_name] = {} # create dictionary for field if doesn't exist

PeterC-DLS Sep 14, 2021

Nicer to get the sub-dictionary classDict[className]['fields'] once rather than using the same copy and pasted expression. This applies for all dictionary access below too.

code/nxsOnto/nxsOnto/generator.py Outdated

                   class NeXusClass(AnnotationProperty):
                       pass
                   class unitCategory(NeXus):
                       comment = 'NeXus unit category. Can be considered instances of a measure. Assign data properties '             'hasValue(any), hasMinValue(any), hasMaxValue(any), hasUnits(str)'

PeterC-DLS Sep 14, 2021

Reformat this line

code/nxsOnto/nxsOnto/generator.py Outdated

               g = Github(token)
               repo = g.get_repo(nexus_repo)
               with urllib.request.urlopen(repo.tags_url) as url:
                   tags = json.loads(url.read().decode())
                   tagsDict = tags[0]  # get version tags from master branch
               base_class_url = []
               for file in repo.get_contents("base_classes"):
                   if str(file).split('.')[-2] == 'nxdl':
                       base_class_url += [file.download_url]

PeterC-DLS Sep 14, 2021

Use append

code/nxsOnto/nxsOnto/generator.py

                   deprecationAttribute = field.getAttribute('deprecated')
                   if not deprecationAttribute == '':
-                      print("=== Deprecation warning %s in %s: %s" % (field_name, className, deprecationAttribute))
+                      print("=== Deprecation warning %s in %s: %s" % (field_name, className, deprecationAttribute))
                   long_name = className + join_string + field_name

PeterC-DLS Sep 14, 2021

Use .join

code/nxsOnto/nxsOnto/generator.py Outdated

+              import json
+              import xml.dom.minidom
+              import pickle
+              from owlready2 import *

PeterC-DLS Sep 14, 2021

Do not use wildcard imports

code/nxsOnto/nxsOnto/generator.py Outdated

		# create individuals - these are just for testing


		with onto:

PeterC-DLS Sep 14, 2021

Test code should be in a separate function

hgoerzig and others added 15 commits

October 1, 2021 07:05


          Remove commented code line 109. Comment #3 (comment)

2e3bab7


          Remove commented code: Parameter configuration

#token = '' # insert your github token
#out_path = 'ontology'
#tmp_file_path = 'tmp'


           str(file.path).endswith('nxdl.xml') if not deprecationAttribute == ''

Comment: #3 (comment)


           created : classname_fields from classDict[className]['fields']

c53afac

Comment: #3 (comment)


          removed extra lines and comments

d6de196


          line break

8552a5b

Comment: #3 (comment)


          use append

e013280

Comment: #3 (comment)


          use join

04d17ce

Comment: htthttps://github.com//pull/3#discussion_r708150087


          Do not use wildcard imports

1a058be

Comment: #3 (comment)


          Create functions


          Organise globals

ad6fadf


          FIX #1 add conda environment

f33f21e


          DOC #3 describe conda usage, apply md formatting

9355dff


          MNT #1 typo

9ca1d68


          MNT #3 git should ignore some things

2ccdd90

Contributor

prjemian commented Dec 15, 2021

Following the instructions in the README, I setup the conda environments and ran this code as instructed. Worked for me. Output text file was readable:

(NeXusOntology) prjemian@zap:~/.../code/nxsOnto$ ll /tmp/onto/
total 904K
-rw-rw-r-- 1 prjemian prjemian 904K Dec 15 09:30 NeXusOntology.owl

Aside from this PR: Must add the font size of the Protege software running on Windows with a 4k monitor is much too small. Even setting the preference for larger font, still there is tiny text in the window corners that is unreadable. Not an issue for this PR to resolve.

Contributor

prjemian commented Dec 15, 2021

example:

(NeXusOntology) prjemian@zap:/tmp/onto$ python -m nxsOnto.generator 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 /tmp/onto /tmp
Deprecation warning definition_local in NXentry: see same field in :ref:`NXsubentry` for preferred use
Deprecation warning average_value_error in NXlog: see: https://github.com/nexusformat/definitions/issues/639
Deprecation warning wavelength_error in NXmonochromator: see https://github.com/nexusformat/definitions/issues/820
Deprecation warning energy_error in NXmonochromator: see https://github.com/nexusformat/definitions/issues/820
Deprecation warning radiation in NXsource: Use either (or both) ``probe`` or ``type`` fields from ``NXsource`` (issue #765)
Deprecation warning incident_wavelength_weight in NXbeam: use incident_wavelength_weights, see https://github.com/nexusformat/definitions/issues/837

Contributor

prjemian commented Dec 15, 2021

I would like to see these commands:

NeXusOntology/code/nxsOnto/nxsOnto/generator.py

Lines 449 to 454 in 2ccdd90

    
           dictionary_from_types() 
        
           dictionary_from_base_class_files() 
        
           parse_base_classes() 
        
           parse_application_definitions() 
        
           write_ontology() 
        
           create_test_individuals()

wrapped into a function such as:

def main():
    dictionary_from_types()
    dictionary_from_base_class_files()
    parse_base_classes()
    parse_application_definitions()
    write_ontology()
    create_test_individuals()

then add this code at the end of the file:

if __name__ == "__main__":
    main()

These changes enable setup.py to describe an entry point so the code (as installed) can be started more easily, such as:

nexusontology [token] [output_dir] [temporary_dir]

With the changes above, here is my suggested revised setup.py:

#!/usr/bin/env python
#
# To use this file type:
#
#        python setup.py install

from setuptools import setup

__entry_points__ = {
    "console_scripts": [
        "nexusontology = nxsOnto.generator:main",
    ],
    # 'gui_scripts': [],
}

setup(name='NeXusOntologyGenerator',
      version='1.1',
      description='Generates an ontology from nxdl files',
      author='Steve Collins',
      url="https://github.com/nexusformat/NeXusOntology/code/nxsOnto",
      packages=['nxsOnto'],
      license='Apache 2',
      entry_points=__entry_points__,
      )

prjemian mentioned this pull request

29 generate contributed defs nexusformat/exampledata#30

Draft


          Functions called by main now

1159d44

hgoerzig added 2 commits

January 12, 2022 17:06


          Added entry point for console script

33139c0


          Merge branch 'createpackage' of https://github.com/nexusformat/NeXusO…

8862cf2

…ntology into createpackage

Contributor Author

hgoerzig commented Feb 23, 2022

Can the branches be merged? Or are there some objections?

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