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Merge pull request #38 from intermine/dev
1.11.1
2 parents 6663183 + eb87436 commit 646a29c

39 files changed

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‎.gitignore‎

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intermine-docs-1.00.03.zip
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build
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MANIFEST
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.idea

‎.travis.yml‎

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---
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os: linux
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language: python
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sudo: false # use container based infrastructure
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jdk: openjdk11
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dist: bionic
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services: postgresql
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addons:
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postgresql: 11
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env:
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global:
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- TESTMODEL_URL=http://localhost:8080/intermine-demo
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- TESTMODEL_PATH=intermine-demo
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before_install:
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- ./config/travis/init.sh
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script:
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- python setup.py test
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- python setup.py livetest
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global:
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- TESTMODEL_URL=http://localhost:8080/intermine-demo
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- TESTMODEL_PATH=intermine-demo
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before_script:
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- "./config/travis/init-solr.sh"
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- "./config/travis/init.sh"
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script:
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- python setup.py test
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- python setup.py livetest
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python:
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- "2.7"
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- "3.4"
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- "3.5"
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- "pypy"
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- "pypy3"
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- "3.6"
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- "3.7"
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‎README.md‎

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@@ -25,7 +25,7 @@ to perform queries. Some examples of sites that
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are powered by InterMine software, and thus offer
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a compatible webservice API, are:
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* [FlyMine](http://www.flymine.org)
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* [FlyMine](https://www.flymine.org)
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* [MouseMine](http://www.mousemine.org)
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* [YeastMine](http://yeastmine.yeastgenome.org)
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* [ZebrafishMine](http://zebrafishmine.org)
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Downloading:
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------------
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The easiest way to install is to use easy_install:
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The easiest way to install is to use pip:
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```
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sudo easy_install intermine
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pip install intermine
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```
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The client is also available via [bioconda](https://anaconda.org/bioconda/intermine).
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* Documentation on PyPi: http://packages.python.org/intermine/
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Before Making PRs:
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-------------------------------
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Please run autopep8 on your files so your code will follow the pep8 conventions. Do it as follows:
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```
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autopep8 <filenames> --in-place
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```
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For example:
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```
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autopep8 file1.py file2.py --in-place
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```
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Changes:
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0.98.14 Added status property to list objects
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0.98.13 Added query column summary support
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[badge]: https://travis-ci.org/alexkalderimis/intermine-ws-client.py.svg?branch=master
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[ci]: https://travis-ci.org/alexkalderimis/intermine-ws-client.py
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[badge]: https://travis-ci.org/intermine/intermine-ws-python.svg?branch=dev
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[ci]: https://travis-ci.org/intermine/intermine-ws-python
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Copyright and Licence
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------------------------

‎config/travis/init-solr.sh‎

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# set up solr for testmine
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# testmine's setup script populates these empty indexes
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wget http://archive.apache.org/dist/lucene/solr/8.6.2/solr-8.6.2.tgz
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tar xzf solr-8.6.2.tgz && ./solr-8.6.2/bin/solr start
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./solr-8.6.2/bin/solr create -c intermine-search
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./solr-8.6.2/bin/solr create -c intermine-autocomplete

‎config/travis/init.sh‎

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# Pull in the server code.
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git clone --single-branch --depth 1 https://github.com/intermine/intermine.git server
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export PSQL_USER=postgres
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# Set up properties
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# We will need a fully operational web-application
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echo '#---> Building and releasing web application to test against'
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(cd server/testmine && ./setup.sh)
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sleep 60 # let webapp startup
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# Travis is so slow
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sleep 90 # let webapp startup
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# Warm up the keyword search by requesting results, but ignoring the results
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$GET "$TESTMODEL_URL/service/search" > /dev/null

‎docs/make.bat‎

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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set SPHINXPROJ=Intermine
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if "%1" == "" goto help
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
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:end
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popd
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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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set SPHINXPROJ=Intermine
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if "%1" == "" goto help
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
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:end
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popd

‎docs/source/conf.py‎

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# If true, `todo` and `todoList` produce output, else they produce nothing.
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todo_include_todos = True
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\n

‎intermine.egg-info/PKG-INFO‎

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Metadata-Version: 1.1
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Name: intermine
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Version: 1.12.0
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Summary: InterMine WebService client
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Home-page: http://www.intermine.org
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Author: InterMine team
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Author-email: all@intermine.org
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License: LGPL, BSD
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Description: InterMine Webservice Client
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----------------------------
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A Python API to access bioinformatics
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data warehouses powered by the InterMine platform.
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Keywords: webservice,genomic,bioinformatics
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Platform: UNKNOWN
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Classifier: Programming Language :: Python :: 2.7
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Classifier: Programming Language :: Python :: 3
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Classifier: Development Status :: 5 - Production/Stable
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Classifier: Intended Audience :: Science/Research
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Classifier: Intended Audience :: Developers
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Classifier: License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)
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Classifier: License :: OSI Approved :: BSD License
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Classifier: Topic :: Software Development :: Libraries :: Python Modules
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Classifier: Topic :: Internet :: WWW/HTTP
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Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Classifier: Topic :: Scientific/Engineering :: Information Analysis
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Classifier: Operating System :: OS Independent
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Provides: intermine

‎intermine.egg-info/SOURCES.txt‎

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LICENSE-BSD
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LICENSE-LGPL
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MANIFEST.in
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README.md
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setup.py
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intermine/__init__.py
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intermine/bar_chart.py
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intermine/constraints.py
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intermine/decorators.py
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intermine/errors.py
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intermine/idresolution.py
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intermine/model.py
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intermine/pathfeatures.py
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intermine/query.py
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intermine/query_manager.py
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intermine/registry.py
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intermine/results.py
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intermine/util.py
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intermine/webservice.py
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intermine.egg-info/PKG-INFO
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intermine.egg-info/SOURCES.txt
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intermine.egg-info/dependency_links.txt
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intermine.egg-info/top_level.txt
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intermine/lists/__init__.py
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intermine/lists/list.py
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intermine/lists/listmanager.py

‎intermine.egg-info/dependency_links.txt‎

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