Changes between Initial Version and Version 41 of HeronAdminDev

Timestamp:

Mar 12, 2018 9:54:20 AM (3 years ago)

Author:

lpatel

Comment:

--

HeronAdminDev

@@ +1 @@
+[[PageOutline]]
+
+nearby: DevTools
+
+While we are [[Using I2B2]] for the bulk of the functionality of [[HERON]],
+[source:raven-j heron-admin] provides a regulatory enforcement web layer for [[HERON#governance]]. [[HERONTrainingMaterials]] provides end-user documentation. (''Well, it used to; see #1268)
+
+''in progress; see ticket:600#comment:11 for context''
+
+''Automated tests to match [[HERONTrainingMaterials]] sure would be nice.''
+
+== Design ==
+
+Developer documentation, including doctests, is generated from the code:
+
+  * [http://informatics.kumc.edu/devdoc/heron-admin/ heron_wsgi: Policy Enforcement Web Interface for HERON]
+
+=== Access Policy and Authority Flow ===
+
+Anyone who can login (via CAS) can review usage stats or sign a system access agreement (which is recorded in [[REDCap]]).
+
+Investigators, i.e. faculty and executives, can submit investigator requests (sponsorship, data use) to the DROC.
+
+{{{
+#!graphviz
+
+strict digraph "policy" {
+    graph [
+        rankdir = "TB",
+    ]
+
+Config -> REDCap_rd
+Config -> REDCapAPI
+Config -> LDAP_rd
+Config -> jboss_deploy
+jboss_deploy -> i2b2pm_rd
+
+login [label="CAS login"]
+
+login -> Faculty
+login -> Executive
+login -> Sign
+Sign  [color=green, label="Sign SAA"]
+REDCapAPI -> Sign
+
+
+Config -> Executive
+REDCap_rd -> DROC
+login -> DROC
+
+DROC -> Audit
+i2b2pm_rd -> Audit
+
+Audit [color=green]
+
+LDAP_rd -> Faculty
+
+Executive -> inv
+Faculty -> inv
+
+inv  [shape=invhouse, label="any"]
+
+inv -> invreq
+inv -> build_team
+
+LDAP_rd -> build_team
+build_team [color=green]
+
+invreq [color=green, label="Investigator Request"]
+
+REDCapAPI -> invreq
+
+login -> Usage
+
+i2b2pm_rd -> Usage
+Usage [ color=green]
+}
+
+}}}
+
+Investigators and sponsored users, provided their human subjects training is current and they have signed the system access agreement, can follow the "start i2b2 query tool" link; if they have an acknowledgement on file, they can use i2b2; otherwise, they can acknowledge the disclaimer.
+
+{{{
+#!graphviz
+
+strict digraph "policy" {
+    graph [
+        rankdir = "TB",
+    ]
+
+Config -> REDCap_rd
+Config -> REDCapAPI
+Config -> LDAP_rd
+Config -> jboss_deploy
+jboss_deploy -> i2b2pm_wr
+Config -> Chalk
+
+login [label="CAS login"]
+
+
+login -> Faculty
+login -> Executive
+login -> Sponsored
+login -> Training
+login -> SAA
+login -> Acknowledgement
+
+
+
+REDCap_rd -> SAA
+REDCap_rd -> Sponsored
+REDCap_rd -> Acknowledgement
+
+Config -> Executive
+
+Chalk -> Training
+
+LDAP_rd -> Faculty
+
+Faculty -> qualified
+Executive -> qualified
+Sponsored -> qualified
+
+qualified  [shape=invhouse, label="any"]
+
+qualified -> start
+Training -> start
+SAA -> start
+
+start [shape=invtriangle, label="all"]
+
+REDCap_rd -> Disclaimer
+Disclaimer -> Ack
+
+start -> Ack
+REDCapAPI -> Ack
+Ack  [color=green]
+
+start -> access
+Acknowledgement -> access
+access [shape=invtriangle, label="all"]
+
+access -> i2b2_authz
+
+i2b2_authz [color=green]
+
+i2b2pm_wr -> i2b2_authz
+
+}
+
+}}}
+
+
+=== Module Dependencies ===
+
+{{{
+#!graphviz
+
+
+# This file was generated by sfood-graph.
+# and then the boring stuff was edited out
+
+strict digraph "dependencies" {
+    graph [
+        rankdir = "LR",
+        overlap = "scale",
+        size = "8,10",
+        ratio = "fill",
+        fontsize = "16",
+        fontname = "Helvetica",
+        clusterrank = "local"
+        ]
+
+       node [
+           fontsize=7
+           shape=ellipse
+//           style=filled
+//           shape=box
+       ];
+
+//     node [
+//         fontsize=7
+//       style=ellipse
+//     ];
+
+"heron_wsgi/admin_lib/checklist.py"  [style=filled];
+"heron_wsgi/admin_lib/checklist.py" -> "heron_wsgi/admin_lib/heron_policy.py";
+"heron_wsgi/admin_lib/checklist.py" -> "heron_wsgi/admin_lib/medcenter.py";
+"heron_wsgi/admin_lib/disclaimer.py"  [style=filled];
+"heron_wsgi/admin_lib/disclaimer.py" -> "heron_wsgi/admin_lib/redcap_connect.py";
+"heron_wsgi/admin_lib/disclaimer.py" -> "heron_wsgi/admin_lib/redcapdb.py";
+"heron_wsgi/admin_lib/heron_policy.py"  [style=filled];
+"heron_wsgi/admin_lib/heron_policy.py" -> "heron_wsgi/admin_lib/disclaimer.py";
+"heron_wsgi/admin_lib/heron_policy.py" -> "heron_wsgi/admin_lib/i2b2pm.py";
+"heron_wsgi/admin_lib/heron_policy.py" -> "heron_wsgi/admin_lib/medcenter.py";
+"heron_wsgi/admin_lib/heron_policy.py" -> "heron_wsgi/admin_lib/noticelog.py";
+"heron_wsgi/admin_lib/heron_policy.py" -> "heron_wsgi/admin_lib/redcap_connect.py";
+"heron_wsgi/admin_lib/heron_policy.py" -> "heron_wsgi/admin_lib/redcapdb.py";
+"heron_wsgi/admin_lib/i2b2pm.py"  [style=filled];
+"heron_wsgi/admin_lib/medcenter.py"  [style=filled];
+"heron_wsgi/admin_lib/noticelog.py"  [style=filled];
+"heron_wsgi/admin_lib/noticelog.py" -> "heron_wsgi/admin_lib/redcapdb.py";
+"heron_wsgi/admin_lib/redcap_connect.py"  [style=filled];
+"heron_wsgi/admin_lib/redcapdb.py"  [style=filled];
+"heron_wsgi/cas_auth.py"  [style=filled];
+"heron_wsgi/drocnotice.py"  [style=filled];
+"heron_wsgi/drocnotice.py" -> "heron_wsgi/admin_lib/heron_policy.py";
+"heron_wsgi/drocnotice.py" -> "heron_wsgi/admin_lib/noticelog.py";
+"heron_wsgi/drocnotice.py" -> "heron_wsgi/admin_lib/redcapdb.py";
+"heron_wsgi/drocnotice.py" -> "heron_wsgi/genshi_render.py";
+"heron_wsgi/genshi_render.py"  [style=filled];
+"heron_wsgi/heron_srv.py"  [style=filled];
+"heron_wsgi/heron_srv.py" -> "heron_wsgi/admin_lib/checklist.py";
+"heron_wsgi/heron_srv.py" -> "heron_wsgi/admin_lib/disclaimer.py";
+"heron_wsgi/heron_srv.py" -> "heron_wsgi/admin_lib/heron_policy.py";
+"heron_wsgi/heron_srv.py" -> "heron_wsgi/admin_lib/medcenter.py";
+"heron_wsgi/heron_srv.py" -> "heron_wsgi/admin_lib/redcap_connect.py";
+"heron_wsgi/heron_srv.py" -> "heron_wsgi/admin_lib/redcapdb.py";
+"heron_wsgi/heron_srv.py" -> "heron_wsgi/cas_auth.py";
+"heron_wsgi/heron_srv.py" -> "heron_wsgi/drocnotice.py";
+"heron_wsgi/heron_srv.py" -> "heron_wsgi/genshi_render.py";
+"heron_wsgi/heron_srv.py" -> "heron_wsgi/stats.py";
+"heron_wsgi/stats.py"  [style=filled];
+"heron_wsgi/stats.py" -> "heron_wsgi/admin_lib/heron_policy.py";
+
+
+}
+
+
+}}}
+
+== Development process  #dev-process
+
+[http://genshi.edgewall.org/wiki/Documentation/xml-templates.html genshi template language] @@...
+
+see source:raven-j/heron_wsgi/Makefile and 
+source:raven-j/README.rst
+
+
+=== Clone Repository
+
+UsingVersionControl: Clone the [https://bmi-work.kumc.edu/changes/raven-j raven-j] (a.k.a Heron Admin) repository from using your preferred method (e.g. TortoiseHg, Hg command-line, etc.).
+
+=== 2. Setup Virtualenv ===
+
+If you want use anaconda as virtualenv, please use the following pattern.
+Please push requirements.sh and requirements.txt to a git repo.
+
+{{{
+cat requirements.sh
+############################################################################################
+# Part-1 How did you create the environment (this helps in future if you need to recreate it)
+############################################################################################
+
+# conda create -n lav_test_env python=2.7
+# source activate lav_test_env
+
+# Now installing pip inside virtul-env
+# conda install pip
+
+# I will manually install the latest version of pandas, during this installation, I will
+# find out what is the version(by pip freeze), and then I 'll put it in requiremnts.txt.
+# pip install pandas
+
+# if you know the exact version, skip the above step and write the exact version in requirements.txt
+# Please always write versions for each libary in requiremnts.txt
+# pip install -r requiremnts.txt
+
+# if you can't install the certain library with pip, then install with conda
+# conda install cx_Oracle
+
+############################################################################################
+# Part-2 activate env
+############################################################################################
+
+source activate lav_test_env
+
+############################################################################################
+# Part-3 Print dependencies as well as child dependencies
+############################################################################################
+
+which python
+python --version
+pip freeze
+conda env export
+
+############################################################################################
+# Part-4 Run Code
+############################################################################################
+
+python test.py
+
+############################################################################################
+# Part-5 deactivate env
+############################################################################################
+
+source deactivate
+}}}
+
+dependencies... mysql, cx_Oracle, etc. ... PythonVirtualEnvironment, PythonOnWindows
+
+2.1. Create an associated Python virtualenv (optimally separated from the code).
+{{{
+$ virtualenv <venv-path>
+}}}
+2.2. Activate your virtualenv.
+{{{
+$ source <venv-path>/bin/activate
+}}}
+2.3. Use PIP to install necessary Python
+{{{
+$ cd <raven-j-path>
+$ pip install -r requirements.txt
+}}}
+... and (introduced in #653 `ldap_cert_653`; TODO: merge requirements files) ...
+{{{
+$ cd <raven-j-path>/traincheck/
+$ pip install -r requirements.txt
+}}}
+
+''see also PythonVirtualEnvironment, PythonOnWindows, WritingQualityCode#pypy)''
+
+Unit test can be run with:
+{{{
+$ python -m doctest <file>
+}}}
+
+== CLI Integration Testing ==
+
+see GroupOnly/HeronAdmin
+
+
+== History ==
+
+
+oops... heron-admin is now ambiguous: support email address and software package.
+
+
+  * milestone:RavenBeta, milestone:heron-system-access for development history