Add in more documentation from trying to get this running more

completely.  Being able to add users, experiments, etc.

Installation/APSDeveloperInstallation.md

@@ -58,12 +58,26 @@ An example of setting up the Data Management system for a developer is described
               - __dmadmin__ BSS login password.  This is a password to allow the Data Management system access to the APS Beamline Scheduling system.  This is a password to an external system and and is therefore a pre-existing password that developers will need to get from the Data Management system administrator.
               - __dmadmin__ ESAF DB password.  This is a password to allow the Data Management system access to the ESAF system.  This is a password to an external system and and is therefore a pre-existing password that developers will need to get from the Data Management system administrator.
          - Scripts in the Data Management system need a location for the data storage directory.  Files will be moved to/from this directory.            
-    
+
+For initial test purposes, it is necessary to shortcut some parts of the service, such as using LDAP and Linux services to manage permissions and access control lists on the files.  To do this edit the following files in the top level etc directory:
+ * dm.aps-db-web-service.conf 
+    - Comment out the entry for principalAuthenticator2 which uses the LDAP authenticator
+ * dm.cat-web-service.conf
+    - Comment out the entry for principalAuthenticator2 which uses the LDAP authenticator
+ * dm.daq-web-service.conf
+    - Comment out the entry for principalAuthenticator2 which uses the LDAP authenticator
+ * dm.daq-web-service.conf
+    - Comment out the entry for principalAuthenticator2 which uses the LDAP authenticator
+	- comment out the two lines for platformUtility which use LinuxUtility and LdapLinuxPlatformUtility
+	- Add a new platformUtility line in place of the other two
+	   * platformUtility=dm.common.utility.noopPlatformUtility.NoopPlatformUtility()
+	   
+
 ### Removing Test system
 Often in the development of Data Management system components it will be necessary to remove/reload components of the system.  The script _dm/_remove/_test/_test/_system.sh_ in the sbin directory of the 'dm' repository (/local/DataManagement/dev/sbin from the directory describe above) issues commands to clear out database & configurations to allow creating a clean installation of the system.
 
-### Testing the Installed System
-The installed development system has a few tools for managing the system.  
+### Overview of the sytem & tools
+The installed development system has a few tools for managing the system.  This section describes some of the available tools and process ideas for the system.  The next section will describe some steps to walk through final setup and use.
  - A web portal which should now be up and running at the URL https://localhost:8181/dm.  This portal is powered by a Payara application server which has its own setup page at https://localhost:4848 (once configured above, you may not need to do much with the Payara config page).  
  - A PyQt app installed dm-station-gui which can be used to setup/monitor experiment definition, file trasfers and data workflows.  
  - A set of command-line scripts for manipulating the system.  THese commands are made accessible by sourcing the file DM_INSTALL_DIR/etc/dm.setup.sh (Note there are some definitions that are blank in the default version of this file). 
@@ -73,7 +87,7 @@ The installed development system has a few tools for managing the system.
 
 To start with the Data Management (DM) System is configured with one user __dm__ which is a management account, the third account listed above.  One of the first items to handle is to create accounts that will be associated with managing the beamline setup and some (possibly the same accounts) that will be associated with experiments.  In practice, the DM system is loosely linked to the list of users in the APS Proposal/ESAF system.  Accounts on the ESAF system are coordinated with a list of users on the DM system.  This is done by using the dm-update-users-from-aps-db.  This will require a configuration file (find a good place to put the file).   One other possibility is to create users manually from the supplied web portal. Note that, in the ESAF system, the user name is the badge number of the individual, while in the DM system a 'd' is prepended to the badge number for the user name.
 
-Once users have benn added to the system, the DM web portal can be used to associate users with a beamline or with experiments that are created.  The __dm__ user can be used to log into the web portal and from the _Experiment Stations_ tab new stations can be added or existing stations, such as the test station, can be edited and station managers can be added.  To create experiments, station managers can log into the system and add/manage experiments for that station.  From the test installation the user can manually create experiments & add users to the experiment.  In practice, at the APS, when a user adds an experiment they are provided with a list of experiments from the proposal system and the list of users is populated from the (Proposal/ESAF ??) info.  Note that it is also possible to add/modify experiments either through the dm-station-gui or through the command line interface with commands such as dm-add-experiment or dm-update-experiment.
+Once users have been added to the system, the DM web portal can be used to associate users with a beamline or with experiments that are created.  The __dm__ user can be used to log into the web portal and from the _Experiment Stations_ tab new stations can be added or existing stations, such as the test station, can be edited and station managers can be added.  To create experiments, station managers can log into the system and add/manage experiments for that station.  From the test installation the user can manually create experiments & add users to the experiment.  In practice, at the APS, when a user adds an experiment they are provided with a list of experiments from the proposal system and the list of users is populated from the (Proposal/ESAF ??) info.  Note that it is also possible to add/modify experiments either through the dm-station-gui or through the command line interface with commands such as dm-add-experiment or dm-update-experiment.
 
 After defining an experiment, it is possible to then manage tasks such as file transfers (daq or upload) or workflows & processing jobs.  These tasks can be done using either the dm-station-gui or by the command line interface.  
 
@@ -87,3 +101,33 @@ DM workflows define a sequence of commands that would operate on data sets to:
  - Add results to files that are tracked by Data Management
 
 Each step in a workflow can define inputs and outputs which can then be used in subsequent steps. 
+
+### Restarting the test system
+If needed the test system can be restarted running a couple of startup commands.  Change directory the DM install directory and then
+
+ * dm/etc/init.d/dm-test-services restart
+ * dm/etc/init.d/dm-ds-services restart
+ 
+This may be necessary if, for instance, the system has been rebooted.  These commands restart several services in the install directory.  If you have modified something in only one of these services you may be able to restart that service.  For instance if only the data storage web service needs to be rebooted then you can run
+
+ * dm/etc/init.d/dm-ds-webservice restart
+
+### Testing the sytem
+
+As mentioned earlier, after the inital install we have one user __dm__ which is intended to be for the overall system.  We now need to set up a user for administration of a beamline and start some steps to use the sytem.
+
+You should at this point have a directory installed which has both the _Data Manangement_ and _support_ software installed.  After doing the installs described above there should be a number of other directories as well such as etc, log and var.  We are now going to walk through changes needed in the etc directory which will allow us to interact with the system.
+ 1.  source the file _etc/dm.setup.sh_.  This defines a number of environment variables and modifies the path to include, in particular, a number of commands beginning with __dm-__ which interact with the underlying system to add/modify users, experiments, upload and daq (both to move files) and workflows and processes (to define & monitor processing of the collected data).
+      - source etc/dm.setup.sh
+ 2. add a user __dmtest__ to the system which will assume the role of manage what is going on in the system.  
+     - dm-add-user --username dmtest --first-name DM --last-name Test --password dmtest
+ 3. add a system role to the created user __dmtest__ to make this a manager of the station TEST which is already defined in the system.
+      - dm-add-user-system-role --role Manager --station TEST --username dmtest
+ 4. create a file, _etc/.dmtest.system.login_, in the same directory as the dm.setup.sh). This will contain the username & password.
+      - dmtest|dmtest      (example contents)
+ 5. Edit the  file _etc/dm.setup.sh_, the one from step 1, to modify the line DM\_LOGIN\_FILE to point at the file created in step 4.
+      - DM\_LOGIN\_FILE=/home/dmadmin/etc/.dmtest.system.login   (modified in file)
+ 6. Re-source the setup file from step 1.
+      - source etc/dm.setup.sh
+
+At this point we will are more in a position to start using the sytem.  The users
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