Resolve #16

Author: nutjob4life

.dockerignore

@@ -22,3 +22,4 @@ jenkins.cfg
 parts
 support
 var
+venv

.gitignore

@@ -17,3 +17,4 @@ eggs
 parts
 var
 ops.cfg
+venv

README.md

@@ -52,14 +52,28 @@ curl --http1.1 --verbose --request POST \
 The answer will then be in the result element of the response element of the envelope element of the XML document in `/tmp/result.xml`.
 
 
+## 🔧 Developing
+
+**👉 Note:** Plone 5.2.2 (used here) is not compatible with any Python newer than 3.8. Stick with 3.8.
+
+Do the following:
+```console
+python3.8 -m venv venv
+venv/bin/pip install --upgrade pip build wheel zc.buildout setuptools==42.0.2 numpy==1.19.3
+venv/bin/buildout -c dev.cfg
+```
+
+You can then run: `bin/zope-debug fg`.
+
+
 ## 🚀 Deploying the Cancer Data Expo
 
 Here are the environment variables you'll need to set (substituting values between development and production):
 
 -   `EDRN_CANCERDATAEXPO_DATA` — set to a path to contain blobstorage, filestorage, and logs.
 -   `EDRN_CANCERDATAEXPO_PORT` — set to a free port number
--   `EDRN_CANCERDATAEXPO_VERSION` — set to a version number of `latest`
--   `EDRN_IMAGE_OWNER` — set to `nutjob4life` or leave it blank to use your local Docker containers
+-   `EDRN_CANCERDATAEXPO_VERSION` — set to a version number or `latest`
+-   `EDRN_IMAGE_OWNER` — set to `nutjob4life` or leave it blank to use your local Docker images
 
 
 ### 🧱 Building the Image
@@ -90,7 +104,7 @@ To run the CancerDataExpo for the **first time**, create empty directories to ho
             --project-name cancerdataexpo \
             up --detach
 
-The `docker-compose.yaml` assumes that `EDRN_CANCERDATAEXPO_DATA` is `usr/local/labcas/cancerdataexpo/docker-data` which is appropriate for `edrn-docker.jpl.nasa.gov` where this normally runs, and that `EDRN_CANCERDATAEXPO_PORT` is 2131, and that `EDRN_CANCERDATAEXPO_VERSION` is `latest`, so you can simply say:
+The `docker-compose.yaml` assumes that `EDRN_CANCERDATAEXPO_DATA` is `/usr/local/labcas/cancerdataexpo/docker-data` which is appropriate for `edrn-docker.jpl.nasa.gov` where this normally runs, and that `EDRN_CANCERDATAEXPO_PORT` is 2131, and that `EDRN_CANCERDATAEXPO_VERSION` is `latest`, so you can simply say:
 
     docker-compose --project-name cancerdataexpo up --detach
 

bootstrap.py

@@ -85,13 +85,11 @@
 except ImportError:
     from urllib2 import urlopen
 
-# Ez_setup is deprecated and automatically uses specific setuptools version
-# Will temporarily comment out this setup and manually install setuptools
-#ez = {}
-#if os.path.exists('ez_setup.py'):
-#    exec(open('ez_setup.py').read(), ez)
-#else:
-#    exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
+ez = {}
+if os.path.exists('ez_setup.py'):
+    exec(open('ez_setup.py').read(), ez)
+else:
+    exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
 
 if not options.allow_site_packages:
     # ez_setup imports site, which adds site packages
@@ -116,7 +114,7 @@
 if options.setuptools_to_dir is not None:
     setup_args['to_dir'] = options.setuptools_to_dir
 
-#ez['use_setuptools'](**setup_args)
+ez['use_setuptools'](**setup_args)
 import setuptools
 import pkg_resources
 

etc/versions/eggs.cfg

@@ -4,13 +4,13 @@
 # Versions of the Python components that go into the Cancer Data Expo.
 
 [versions]
-setuptools =
-
-# For edrn.rdf's LabCAS feature
-# coverage = 3.6
-# Pillow = 6.2.2
-# coverage = 4.1
+# No idea why this is needed—not just the newer version (buildout issue) but paste in the first place!
+Pillow = 9.2.0
 
+# paste = 3.5.1
+# plone.recipe.zope2instance = 6.11.0
+# python-dotenv = 0.20.0
+# six = 1.16.0
 
 [plone-policies]
 backports =

etc/versions/known-good-versions.cfg

@@ -115,3 +115,111 @@ suds2 = 0.7.1
 # Required by:
 # unittest2==1.1.0
 traceback2 = 1.4.0
+
+# Added by buildout at 2022-07-06 09:13:55.535085
+biothings-client = 0.2.6
+collective.recipe.backup = 4.2.0
+isort = 5.10.1
+modernize = 0.8.0
+mr.scripty = 1.0
+unittest2 = 1.1.0
+
+# Required by:
+# unittest2==1.1.0
+argparse = 1.4.0
+
+# Required by:
+# edrn.summarizer==0.0.8
+biopython = 1.79
+
+# Required by:
+# edrn.rdf==1.3.8
+# edrn.summarizer==0.0.8
+collective.autopermission = 1.0b2
+
+# Required by:
+# modernize==0.8.0
+fissix = 21.11.13
+
+# Required by:
+# rdflib==4.2.2
+isodate = 0.6.1
+
+# Required by:
+# edrn.summarizer==0.0.8
+jsonlib-python3 = 1.6.1
+
+# Required by:
+# traceback2==1.4.0
+linecache2 = 1.0.0
+
+# Required by:
+# edrn.summarizer==0.0.8
+mygene = 3.2.2
+
+# Required by:
+# edrn.rdf==1.3.8
+pysolr = 3.9.0
+
+# Required by:
+# edrn.rdf==1.3.8
+# edrn.summarizer==0.0.8
+suds2 = 0.7.1
+
+# Required by:
+# unittest2==1.1.0
+traceback2 = 1.4.0
+
+# Added by buildout at 2022-07-06 09:46:04.546661
+biothings-client = 0.2.3
+collective.recipe.backup = 4.1.1
+isort = 5.7.0
+modernize = 0.8.0
+mr.scripty = 1.0
+unittest2 = 1.1.0
+
+# Required by:
+# unittest2==1.1.0
+argparse = 1.4.0
+
+# Required by:
+# edrn.summarizer==0.0.8
+biopython = 1.79
+
+# Required by:
+# edrn.rdf==1.3.8
+# edrn.summarizer==0.0.8
+collective.autopermission = 1.0b2
+
+# Required by:
+# modernize==0.8.0
+fissix = 20.8.0
+
+# Required by:
+# rdflib==4.2.2
+isodate = 0.6.0
+
+# Required by:
+# edrn.summarizer==0.0.8
+jsonlib-python3 = 1.6.1
+
+# Required by:
+# traceback2==1.4.0
+linecache2 = 1.0.0
+
+# Required by:
+# edrn.summarizer==0.0.8
+mygene = 3.1.0
+
+# Required by:
+# edrn.rdf==1.3.8
+pysolr = 3.9.0
+
+# Required by:
+# edrn.rdf==1.3.8
+# edrn.summarizer==0.0.8
+suds2 = 0.7.1
+
+# Required by:
+# unittest2==1.1.0
+traceback2 = 1.4.0

src/edrn.rdf/buildout.cfg

@@ -23,6 +23,8 @@
 _organPredicateURI = URIRef('urn:edrn:predicates:organ')
 _protocolPredicateURI = URIRef('urn:edrn:predicates:protocol')
 _collaborativeGroupPredicateURI = URIRef('urn:edrn:predicates:collaborativeGroup')
+_discplinePredicateURI = URIRef('urn:edrn:predicates:discipline')
+_dataCategoryPredicateURI = URIRef('urn:edrn:predicates:dataCategory')
 _cardinalityPredicateURI = URIRef('urn:edrn:predicates:cardinality')
 _ownerPrincipal = URIRef('urn:edrn:predicates:ownerPrincipal')
 _qaState = URIRef('urn:edrn:predicates:qaState')
@@ -115,6 +117,10 @@ def generateGraph(self):
                 group = _inconsistentCollaborativeGroupNaming.get(group)
                 if group is not None:
                     graph.add((subjectURI, _collaborativeGroupPredicateURI, Literal(group)))
+            for discipline in i.get('Discipline', []):
+                graph.add((subjectURI, _discplinePredicateURI, Literal(discipline)))
+            for category in i.get('DataCategory', []):
+                graph.add((subjectURI, _dataCategoryPredicateURI, Literal(category)))
             for owner in i.get('OwnerPrincipal', []):
                 # Work around https://github.com/EDRN/EDRN-metadata/issues/63
                 if owner.startswith('OwnerPrincipal='):