Merge branch 'master' into 'master'

# Conflicts:
#   doc/RELEASE_NOTES.txt

RELEASE_NOTES.txt

@@ -8,16 +8,22 @@ Release 3.3.1 (05/06/2020)
 - 
 
 Release 3.3.0 (05/04/2020)
-=============================
-- 
+- Change log4j version from 1.2.7 to 2.13.2.  Code changes to adapt were
+   necessary.  Changed config file from log4j.properties to log4j2.xml
+- change jar file for postgresql from 9.3-1102.jdbc41 to 42.2.8.  The underlying 
+    postgresql in support changed from 9.3 to 9.6 a while ago.
 
 Release 3.2.2 (02/24/2020)
 =============================
-- 
+- Added user documentation (Getting Started guide)
 
 Release 3.2.1 (01/15/2020)
 =============================
-- 
+- DM GUI Changes:
+  - Reworked configuration options for DAQs and uploads; those now support
+    including/excluding file extensions  
+  - Fixed bug that was preventing using configuration options and additional
+    keywords at the same time
 
 Release 3.2.0 (11/05/2019)
 =============================
@@ -35,7 +41,7 @@ Release 3.1.0 (10/25/2019)
 - Enabled URL scheme for transfer plugin configuration; this allows
   multiple gridftp hosts per deployment
 - Updated support software to allow offsite installation
-- DM GUI changes
+- DM GUI changes:
   - Add settings page
     - Allow user to specify refresh rates per module. 
     - Fixed protocol parsing bug

getting_started/getting-started.md

+# Getting Started
+
+## Introduction
+
+The APS Data Management System is a system for gathering together experimental data,
+metadata about the experiment and providing users access to the data based on a users
+role.  This guide is intended to provide beamline users an introduction to the basic
+use of the Data Management System at the beamline.  This process will involve creating an 
+experiment, associating users with this experiment and then adding data, in the form of
+files, to the experiment.
+
+### Setting up the Environment
+
+On beamline Linux computers, users can set up the environment for using the Data 
+Management System by executing a setup script which is created as the Data Management
+software is installed.  This script is executed as
+
+> /home/DM\_INSTALL\_DIR/etc/dm.setup.sh
+
+where DM\_INSTALL\_DIR is the deployment directory for this beamline.  This script 
+will set up a number of environment variables which define items such
+as URLs for the various data services, the station name in the DM, the location
+of a file which defines the login to be used when running commands and adding 
+the path to DM system commands to the PATH.   
+
+## DM System Commands
+-----
+After execution of the setup script, the PATH will include the path to commands 
+for interacting with the DM System.  A list of these commands, at the time of 
+this writing is shown below.
+
+![DM commands](images/dm-system-commands.png)
+
+These commands follow some conventions, like adding a --help for convenience.  When 
+the environment variable DM\_LOGIN\_FILE is defined and points to a file that 
+contains a username/password pair (in the form 'username|password') this information
+is used for authentication when executing the commands.  In practice the account 
+defined here should have the role of station manager for the beamline.
+
+### DM Command usage examples
+
+#### Getting some data into the system
+
+As stated early, the experiment is the central object for creating entries in
+the Data Management System.  For convenience there are two commands which can 
+provide examples of creating experiments, assigning users & other attributes and 
+loading data into the system.  These commands are 
+
+> dm-STATION\_NAME-upload
+>
+> dm-STATION\_NAME-daq
+
+Where STATION\_NAME is the station name, in lower case with '-' removed.  The two
+commands here are differentiated by the two methods for moving data into the 
+system _upload_ and _daq_.  moving files using _upload_ will move all files present
+in a directory at the time the command is used while _daq_ moves will monitor
+files while active and move new files as well.  Both of these commands require 
+two parameters --experiment and --data-directory.  With only these required parameters,
+these commands will create an experiment named by --experiment and will move files
+from --data-directory.  Other parameters here will allow for specifying items such
+as a list of users, specifying the destination directory (relative to the storage 
+directory), process a workflow using the data, etc.
+
+Without the optional parameters, use of these commands would look like 
+
+> dm\-STATION_NAME\-upload --experiment=exp1 --data-directory=/home/bluser/data/2010-03
+
+This command will create an experiment with no users and move files from 
+/home/bluser/data/2010-03 to STORAGE\_DIR/STATION\_NAME/EXP\_NAME on the data storage 
+server where 
+ - STORAGE\_DIR is the base storage location on the storage sever 
+ - STATION\_NAME is the station name defined on the experiment server
+ - EXP\_NAME is the experiment name defined by --experiment, _exp1_ in this case
+
+Adding other parameters to this command can add more information to the experiment 
+such as --users to add a list of users to the system.  Other parameters such as 
+--dest-directory and --root-path allow customization of the path to the file on 
+the data storage server.  Some beamlines for instance have relied on particular 
+directory structure for legacy analysis code.  
+
+Sector 8-ID-I for instance has a file structure ROOT\_DIR/RUN/usernameYYYYMM with
+ - ROOT\_DIR base level for experiment data. In DM this is STORAGE\_ROOT/STATION\_NAME
+ - RUN is the APS Run cycle such as 2019-1 (year and cycle 1, 2 or 3)
+ - username is some form to identify the experimenter
+ - YYYY is the four digit year.
+ - MM is a 2 digit month, i.e. 02 for February
+an example of this would be STORAGE\_ROOT/8idi/2017-2/dufresne201707.  Here we 
+would use a command like
+
+> dm-8idi-upload --experiment=dufresne201707 
+>     --data-directory=/net/s8iddata/export/8-id-i/2017-2/dufresne201707
+>     --root-path=2017-2
+
+Sectors 33 & 34 use a file structure under  ROOT\_DIR/username/YYYYMMDD/EXP_NAME/.
+Here
+ - ROOT\_DIR base level for experiment data.  In DM storage server this is 
+ STORAGE\_ROOT/STATION_NAME
+ - YYYY four digit year
+ - MM 2 digit month
+ - DD 2 digit day
+ an example of this is ROOT\_DIR/jenia/20140820/FeCrbilayers.  Here we would
+ use a command like
+ 
+> dm-33bm-upload --experiment=FeCrbilayers 
+>    --data-directory=/net/s33data/export/33bm/data/jenia/20140820/FeCrbilayers
+>    --root-path=jenia/20140820
+
+#### Creating experiments based on the ESAF/Proposal
+
+For convenience, at APS, it is possible to make use of the Proposal and ESAF systems
+to create experiments based off the existing entries in these systems to populate 
+the list of users in the system.  the --proposal-id and --esaf-id options on commands
+like dm-STATION\_NAME-upload and dm-create-experiment will add a list of users which 
+are defined in the esaf or proposal to the created experiment.
+
+#### Displaying information in the system
+
+Other DM commands show useful information, and can adjust what and how the 
+information is displayed.  `dm-list-experiments` lists the experiments showing 
+info on the experiment name, experiment type, station, and start date.  adding the 
+option --display-keys can allow the user to display more or less information.
+--display-keys=name will display only the experiment name, and --display-keys=ALL
+will display all keys associated with the experiment (one experiment line is show
+as example).  
+
+```
+startDate=2019-12-09 18:35:26.738217-06:00 name=yuyin201912 description=Study of dynamics and aging in solvent segregation driven colloidal gel in a binary solvent (Proposal id: 64326) rootPath=2019-3 experimentStationId=5 id=3579 experimentTypeId=9 experimentStation={u'description': u'Sector 8 ID I', u'id': 5, u'name': u'8IDI'} experimentType={u'id': 9, u'name': u'XPCS8', u'description': u'XPCS Group (Sector 8)'} 
+```
+
+Adding the --display-format will change how the data is displayed.  By default 
+the output is a simple dictionary, --display-format=html will give HTML output.
+
+```
+      <tr> <td>2019-12-09 18:35:26.738217-06:00</td> <td>yuyin201912</td> <td>Study of dynamics and aging in solvent segregation driven colloidal gel in a binary solvent (Proposal id: 64326)</td> <td>2019-3</td> <td>5</td> <td>3579</td> <td>9</td> <td>{u'description': u'Sector 8 ID I', u'id': 5, u'name': u'8IDI'}</td> <td>{u'id': 9, u'name': u'XPCS8', u'description': u'XPCS Group (Sector 8)'}</td> </tr>
+```
+
+Specifying --display-format=pprint will give a nicer (prettier) output,
+breaking nicely on different lines, indenting properly where some items are objects.
+
+```
+{ u'description': u'Study of dynamics and aging in solvent segregation driven colloidal gel in a binary solvent (Proposal id: 64326)',
+  u'experimentStation': { u'description': u'Sector 8 ID I',
+                          u'id': 5,
+                          u'name': u'8IDI'},
+  u'experimentStationId': 5,
+  u'experimentType': { u'description': u'XPCS Group (Sector 8)',
+                       u'id': 9,
+                       u'name': u'XPCS8'},
+  u'experimentTypeId': 9,
+  u'id': 3579,
+  u'name': u'yuyin201912',
+  u'rootPath': u'2019-3',
+  u'startDate': u'2019-12-09 18:35:26.738217-06:00'}
+```
+
+#### Creating experiments based on the ESAF/Proposal
+
+For convenience, at APS, it is possible to make use of the Proposal and ESAF systems
+to create experiments based off the existing entries in these systems to populate 
+the list of users in the system.  the --proposal-id and --esaf-id options on commands
+like dm-STATION\_NAME-upload and dm-create-experiment will add a list of users which 
+are defined in the esaf or proposal to the created experiment.
+
+
+### dm-station-gui
+
+
+#### Overview
+One of the methods to manage processes in the APS Data Management System is the 
+application `dm-station-gui`.  This application is a PyQt application which gives 
+access to add/modify/control items such as experiments, file transfer to storage
+location ('daq' and 'uploads'), workflows and processing jobs.  An example of 
+this application is shown in the figure below.
+
+![](images/dm-station-gui-experiments.png)
+
+#### Experiments
+
+`dm-station-gui` opens showing a tab that lists experiments which have been added 
+to the DM System.  At the beamline, these experiments generally will correspond
+to an accepted proposal in the APS Proposal system.  Experiments in the DM 
+System define an entity that ties sets of managed data together.  When an 
+experiment is selected by double clicking or by clicking and then clicking the
+*Use Selected* button, the contents of the Experiment tab changes to give 
+details about that experiment.  Much of this information is pulled from the 
+proposal/ESAF databases.  This is shown in the image below.
+
+![](images/dm-station-gui-experiments-detail.png)
+
+This view of the data enable a couple of key features of the DM System.  The 
+ability to associate files with the Management system, and the ability to set 
+which users have access to the system and therefore which data they can access.
+Selecting users that will have access to experiment data is done by clicking the
+*Modify Users* button below the user list and then selecting users in the right 
+list & pressing the arrow button between the lists to add users or selecting
+users from the left list and clicking the arrow button to delete users from the
+list.  Click the _Save_ button at the bottom to accept the changes and go back 
+to the Experiment detail or click *Back* button in the upper left to exit back 
+to Experiment detail without saving.  This view is shown below.
+
+![](images/dm-station-gui-experiments-user-management.png)
+
+#### Getting Files into Data Management
+
+The overall purpose of this system is to get data into the system and providing 
+access control to that data.  This means linking the data files to the users in
+an experiment.  For each beam station there is storage location defined for that 
+station.  On the `Experiments` tab there are a couple of items relevant to 
+getting the data onto that storage location.  These items are shown in the image
+below.  Files transferred onto the storage location will go into:
+*STORAGE_LOCATION/(storage_root_path)/(experiment_name)*.  Files to go into this 
+directory are specified in the entry "Data Directory or Single File Path".  Note
+that if the data directory is specified, only the files will go into the 
+storage location, not a new sub-directory with the transferred files.  Any 
+sub-directories will be copied as will the contents.
+
+Once the the storage location and source are defined the transfer can be started
+in one of two ways:
+- A monitor can be placed on the directory and any new files/sub-directories in the directory will be transferred if you select `Start DAQ`
+- A one time copy will happen and all files/sub-directories currently in the directory will be copied if you select `Start Upload`
+
+When a transfer is started, the display will switch to either the `DAQs` or 
+`Uploads` tab.  The tab will show the status of all transfers that have been 
+started since the last restart of the system.  Status of a particular transfer is
+shown by color 
+- green: Done success
+- yellow: running
+- red: Done with an errors
+
+An example of this is shown below.
+
+![](images/dm-station-gui-uploads.png)
+
+Clicking on a particular transfer, on `DAQs` or `Uploads` will switch the 
+view to show detail of that transfer including errors.  
+
+![](images/dm-station-gui-uploads-detail.png)
+
+#### Workflows and processing data
+The tab 'Workflows' allows defining a workflows which will provide a template for processing data.  A workflow is simply a set of defined steps that will process data.  Workflows each step in the workflow executes a command on the host computer.  Commands can 
+  * be as simple as a single command such as listing a directory
+  * can transfer files between computers
+  * can launch & monitor jobs on a remote cluster
+  * can do just about anything that can be scripted on a computer.
+Workflow steps allow defining inputs that are defined at runtime and can also create outputs that can be used in following steps.
+
+The `Workflows` tab is shown below and contains a list of workflows that have been defined.
+
+![](images/dm-station-gui-workflows.png)
+
+Clicking on a workflow and then selecting the 'Inspect' button you will be able to examine and possibly modify the steps in the workflow.

getting_started/gettingDataFromGlobus.md

+This guide is intended to describe the process of connecting to [Globus](https://www.globus.org) to transfer data collected at the Advanced Photon Source (APS) and stored using the APS Data Management System to a computer at a users home institution. 
+
+## Logging in
+
+The external user will need an account that allows logging into the Globus site. Some 
+institutions, which regularly use Globus, have arranged for users to log into Globus 
+using credentials from the institution's login system.  Argonne, for instance is one 
+of those sites.  When a user selects to login to Globus the first page will prompt 
+the user to select from a list of organizations.  An example of this is shown below.
+
+![globus-org-login|50%](images/globus-org-login.png)
+
+On selection of the organization you will see a login page such as the one from Argonne below.  Note this page will differ depending on the chosen organization.
+
+![globus-anl-login](images/globus-anl-login.png)
+
+## Connecting
+
+Once logged in, you will land on a File Manager page.  In the collection box on this page enter aps#data for the collection.  The first time that this is set up and then periodically after you will be asked to authenticate for access to this collection (see image below).  For this you will need the APS Data Management account which is linked to the APS Web Account. The APS Web Account is used for the APS Proposal & ESAF system. While the Data Management account and APS Web Account are different accounts, the passwords for these are synchronized by the DM system (passwords are periodically copied from APS Web to DM system).  The user name for the Web Account is the users badge number while the DM user name is the badge number prefixed by the letter 'd' (e.g. d123456).
+
+![globus-dm-authenticate](images/globus-dm-authenticate.png)
+
+Clicking __Continue__ on the page above will lead to a MyProxy login page where you will enter the DM account user name and password.  Once again, the user name is the badge prefixed with d (d123456) and the password is the same as for the proposal/ESAF system.  If you are experiencing problems logging in it is possible that the password is expired/incorrect.  Management of the password is through the APS Web portal.  See the section below on verifying accounts.  Also note that if the password in the APS Web portal has recently changed it may take about 15 minutes for this to be sync'd.  If you can log into the APS Web Portal (username = 'badge #') and cannot log into the DM system (username = 'd' + 'badge #') after considering the information above then contact your beamline contact or DM administrators ('dm-admin@aps.anl.gov').
+
+![globus-dm-authorization](images/globus-dm-authorization.png)
+
+Once logged in, the user will land on a page with a number of directories.  Files from the Data Management System will be found under the 'dm' directory.  At that level, the directories are broken down by station and then as defined by conventions on each beamline.  A user will be able to move down the directories to find their data but users will only have access to data directories associated with experiments that they are listed as an experimenter.  If you try to enter other directories, you will get a message that you are not authorized for that directory.  
+
+![](images/globus-dm-directory.png)
+
+
+![](images/globus-beamline-directory.png)
+
+
+## Verifying/updating APS Web Account
+
+All experimenters on APS Proposal or ESAF should have created an account through the [APS Web Portal](https://beam.aps.anl.gov/pls/apsweb/usercheckin.start_page).  If the user does not have a badge number, they will need to [register with the APS User Office](https://beam.aps.anl.gov/pls/apsweb/ufr_main_pkg.usr_start_page).  To verify or update the Web Password, users can try to log into the web portal above.  Like other web accounts, it is possible to update an unknown/expired password by clicking a link on the portal web page.  For this you will need to provide answers to security questions that were entered at the time the account was set up.
+
+![](images/globus-verify-account.png)
\ No newline at end of file