Issue 134 authorship

setup.cfg

@@ -1,28 +1,31 @@
 [metadata]
 # would we ever want to use pyproject.toml ?
+#   yes! works with setuptools and poetry
+
 name = crdch_model
-# see home_page notes
-url = https://cancerdhc.github.io/ccdhmodel
-# author metadata, license etc is totally incomplete
-# str
-# add maintainer
-author = Mark A. Miller
-author_email = [email protected]
-# summary is alias for description ?
-summary = CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH)
+# version
+
+author = Center for Cancer Data Harmonization
+# are we sure somebody reads this email?
+author_email = [email protected]
+maintainer = Gaurav Vaidya, Sujay Patil, Mark A. Miller etc. See https://github.com/cancerDHC/ccdhmodel/graphs/contributors
+
+# summary is alias for description
 description = CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH)
+
 long_description = CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH). This Python package contains the dataclasses necessary to build and operate over data objects according to the CRDC-H model.
-# is this where mkdocs artifacts gets SENT?
-# or will this be used as a base for URLs in the mkdocs artifacts?
-# should change, but be careful not to overwrite the existing ccdhmodel docs yet
-# no, this is probably just what appears on the package's PyPI page
-# see also url
-# https://setuptools.readthedocs.io/en/latest/userguide/declarative_config.html says 
-#   home-page is an alias for url
+
+
+# see also https://setuptools.readthedocs.io/en/latest/userguide/declarative_config.html 
+# which says home-page is an alias for url
 #   note hyphen vs underscore!
-home_page = https://cancerdhc.github.io/ccdhmodel
+url = https://cancerdhc.github.io/ccdhmodel
+
+# LICENSE file looks like BSD 3-clause
+# license = MIT
 license = MIT
 python_requires = >=3.7
+
 classifiers =
     Topic :: Scientific/Engineering :: Bio-Informatics
     Intended Audience :: Healthcare Industry
@@ -36,10 +39,13 @@ classifiers =
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+
+# MAM 2021-11-18 cancer research
 keywords = 
     python
     google-sheets
     linkml
+    cancer research
 
 [options]
 include_package_data = True

tests/secondary_inputs/test_AlcoholExposureObservation.json

@@ -0,0 +1,11 @@
+{
+  "id": "a1b2c3",
+  "value_integer": 6,
+  "observation_type": {
+    "text": "alcohol_drinks_per_day",
+    "coding": {
+      "code": "marksterms:dpd",
+      "system": "http://example.com/broken_uris_ok/"
+    }
+  }
+}

tests/secondary_inputs/test_ObservationSet.json

@@ -0,0 +1,21 @@
+{
+  "id": "123",
+  "category": {
+    "coding": {
+      "code": "example:123",
+      "system": "http://example.com"
+    },
+    "text": "tobacco exposure observations"
+  },
+  "observations": [
+    {
+      "observation_type": {
+        "text": "cigarettes_per_day",
+        "coding": {
+          "code": "marksterms:cpd",
+          "system": "not a real uri"
+        }
+      }
+    }
+  ]
+}

tests/secondary_inputs/test_TobaccoExposureObservation.json

@@ -0,0 +1,9 @@
+{
+  "observation_type": {
+    "text": "cigarettes_per_day",
+    "coding": {
+      "code": "marksterms:cpd",
+      "system": "not a real uri"
+    }
+  }
+}

tests/secondary_inputs/test_TobaccoExposureObservation.json.notes.txt

@@ -0,0 +1,12 @@
+# can't be a list
+#   use observation set
+# misspellings in text are tolerated, as are bogus uris in coding.system
+#   coding.system validationa s string instead of URI is a known bug
+# can enums goin any of these slots?
+#   look at values from
+# learn more about attributes vs slots
+[
+	{ "observation_type": { "text": "cigarettes_per_dayZZZ", "coding": "marksterms:cpd" }},
+	{ "observation_type": { "text": "cigarettes_per_day" }}
+]
+

tests/test_alcohol_exp_static.py

@@ -0,0 +1,35 @@
+import os
+import unittest
+
+from linkml_runtime.loaders import  json_loader, rdf_loader
+
+from crdch_model.crdch_model import AlcoholExposureObservation
+
+CWD = os.path.abspath(os.path.dirname(__file__))
+
+INPUT_DIR = os.path.join(CWD, 'secondary_inputs')
+
+
+class InputFileTestCase(unittest.TestCase):
+    def test_alcohol_file(self):
+        nyaml, njson, nttl = 0, 0, 0
+        pyaml, pjson, pttl = 0, 0, 0
+        nread, nfailures = 0, 0
+        print("AlcoholExposureObservation test")
+        alcohol_data_filename = 'test_AlcoholExposureObservation.json'
+        alcohol_data_filepath = os.path.join(INPUT_DIR, alcohol_data_filename)
+        print("Attempting to load " + alcohol_data_filepath + " as one or more AlcoholExposureObservation(s)")
+
+        try:
+            njson += 1
+            Diagnosis = json_loader.load(alcohol_data_filepath, AlcoholExposureObservation)
+            pjson += 1
+            print("Successfully parsed:")
+            print(Diagnosis)
+        except Exception as e:
+            print(e)
+            nfailures += 1
+        self.assertEqual(0, nfailures)
+
+if __name__ == '__main__':
+    unittest.main()

tests/test_tobacco_exp_static.py

@@ -0,0 +1,35 @@
+import os
+import unittest
+
+from linkml_runtime.loaders import  json_loader, rdf_loader
+
+from crdch_model.crdch_model import TobaccoExposureObservation
+
+CWD = os.path.abspath(os.path.dirname(__file__))
+
+INPUT_DIR = os.path.join(CWD, 'secondary_inputs')
+
+
+class InputFileTestCase(unittest.TestCase):
+    def test_tobacco_file(self):
+        nyaml, njson, nttl = 0, 0, 0
+        pyaml, pjson, pttl = 0, 0, 0
+        nread, nfailures = 0, 0
+        print("TobaccoExposureObservation test")
+        toboacco_data_filename = 'test_TobaccoExposureObservation.json'
+        toboacco_data_filepath = os.path.join(INPUT_DIR, toboacco_data_filename)
+        print("Attempting to load " + toboacco_data_filepath + " as one or more TobaccoExposureObservation(s)")
+
+        try:
+            njson += 1
+            Diagnosis = json_loader.load(toboacco_data_filepath, TobaccoExposureObservation)
+            pjson += 1
+            print("Successfully parsed:")
+            print(Diagnosis)
+        except Exception as e:
+            print(e)
+            nfailures += 1
+        self.assertEqual(0, nfailures)
+
+if __name__ == '__main__':
+    unittest.main()