Installable and importable as 'transmart'

.gitignore

@@ -1,2 +1,9 @@
 .ipynb_checkpoints
 *.pyc
+.idea/
+*.ipynb
+__pycache__/
+build/
+dist/
+transmart.egg-info/
+transmart/__pycache__/

README.md

@@ -1,3 +1,5 @@
 The tranSMART API Training given on [2015 tranSMART Foundation Annual Meeting in Amsterdam](http://transmartfoundation.org/2015-annual-meeting/)
 
-The Python part of this training is in this branch meant to work with Python 3.x.
+The python client created for that project has now been recovered to work with version 2 of the tranSMART API. 
+
+This is meant to work with Python 3.x only.

requirements.txt

@@ -0,0 +1,2 @@
+protobuf
+

setup.py

@@ -0,0 +1,52 @@
+import setuptools
+import os
+import re
+
+
+VERSIONFILE=os.path.join('transmart', '__init__.py')
+verstrline = open(VERSIONFILE, "rt").read()
+VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
+mo = re.search(VSRE, verstrline, re.M)
+if mo:
+    version_string = mo.group(1)
+else:
+    raise RuntimeError("Unable to find version string in {}.".format(VERSIONFILE,))
+
+with open("requirements.txt", 'r') as f:
+    required_packages = f.read().splitlines()
+
+if os.environ.get('READTHEDOCS') == 'True':
+    for dependency in ['pandas']:
+        for package in required_packages:
+            if package.startswith(dependency):
+                required_packages.remove(package)
+
+
+setuptools.setup(
+    name="transmart",
+    version=version_string,
+    url="https://www.github.com/thehyve/transmart-api-client-py/",
+
+    maintainer="[email protected]",
+    maintainer_email="[email protected]",
+
+    description="An python client for communicating with the transmart rest api.",
+    long_description=open('README.md').read(),
+
+    packages=setuptools.find_packages(exclude=['tests', 'tests.*']),
+    include_package_data=True,
+
+    keywords=['transmart', 'rest', 'api', 'data', 'science'],
+
+    download_url='https://github.com/thehyve/transmart-api-client-py/tarball/{}/'.format(version_string),
+
+    install_requires=required_packages,
+
+    classifiers=[
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+    ],
+)

transmart/__init__.py

@@ -0,0 +1,8 @@
+"""tmtk - A toolkit for ETL curation for the tranSMART data warehouse."""
+
+from .transmart_api import TransmartApi
+from . import utils
+
+__version__ = "0.1.0"
+__author__ = 'The Hyve'
+__all__ = []

transmart/highdim.proto

@@ -0,0 +1,71 @@
+// Copyright 2014 Janssen Research & Development, LLC.
+//
+// This file is part of REST API: transMART's plugin exposing tranSMART's
+// data via an HTTP-accessible RESTful API.
+//
+// This program is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by the
+// Free Software Foundation, either version 3 of the License, or (at your
+// option) any later version, along with the following terms:
+//
+//   1. You may convey a work based on this program in accordance with
+//      section 5, provided that you retain the above notices.
+//   2. You may convey verbatim copies of this program code as you receive
+//      it, in any medium, provided that you retain the above notices.
+//
+// This program is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+// Public License for more details.
+//
+// You should have received a copy of the GNU General Public License along
+// with this program. If not, see <http://www.gnu.org/licenses/>.
+
+
+package highdim;
+
+option java_package = "org.transmartproject.rest.protobuf";
+option java_outer_classname = "HighDimProtos";
+
+//command to compile this file, from the transmart-rest-api base folder:
+//protoc --java_out=src/java src/protobuf/highdim/highdim.proto
+message HighDimHeader {
+
+    repeated Assay assay = 1;
+    repeated ColumnSpec columnSpec = 2;
+}
+
+message ColumnSpec {
+    enum ColumnType { DOUBLE = 1; STRING = 2; }
+
+    required string name = 1;
+    required ColumnType type = 2;
+}
+
+message Assay {
+    required int64 assayId = 1;
+    required string patientId = 2;
+    optional string sampleTypeName = 3;
+    optional string timepointName = 4;
+    optional string tissueTypeName = 5;
+    optional string platform = 6;
+    optional string sampleCode = 7;
+}
+
+// One Row per bioMarker/label
+message Row {
+    required string label = 1;
+    optional string bioMarker = 2;
+    // A ColumnValue per column (as given by the used projection).
+    // For single-column projections such as zscore/default_real/etc this has only one entry.
+    // Each ColumnValue has a corresponding ColumnSpec entry in the header.
+    repeated ColumnValue value = 3;
+}
+
+message ColumnValue {
+    // Only ONE of these should be set!
+    // The type that is set must correspond to that indicated in the corresponding ColumnType for this column in the header.
+    // Every value corresponds to one assay (matching the order in the header), there are as many values as there are assays
+    repeated double doubleValue = 1 [packed=true];
+    repeated string stringValue = 2;
+}