doc/Makefile

+
+TOP = ..
+SUBDIRS = sphinx
+
+include $(TOP)/tools/make/RULES_DM
+

doc/RELEASE_NOTES.txt

+Release 1.1 (03/10/2017)
+=============================
+
+- Introduced integration with Beamline Scheduling System:
+  - New commands: 
+    - list-runs
+    - list-proposals
+    - get-proposal
+  - Modified add-experiment command to automatically add users associated
+    with a given beamline proposal
+- Added the following functionality for managing DAQs:
+  - Max. run time specification causes DAQ to be stopped automatically
+  - Destination directory specification causes files to be uploaded into
+    a specific directory relative to experiment root path
+  - Upload data/target directory on exit specify upload of the given
+    directory automatically after DAQ completes
+- Added the following functionality for managing uploads:
+  - Destination directory specification causes files to be uploaded into
+    a specific directory relative to experiment root path
+- Introduced framework for higher level beamline specific tools 
+  - New commands that combine adding experiment and running DAQs or
+    uploads
+- Introduced sphinx as python API documentation framework
+- Resolved possible timeout issue when starting DAQ or directory upload 
+  with a directory containing large number of files
+- Simplified data directory command line option for beamlines that use 
+  gridftp (via DM_DATA_DIRECTORY_MAP environment variable)
+
+Release 1.0 (01/31/2017)
+=============================
+
+- Introduced concept of experiment station and redesigned authorization 
+  mechanisms to allow beamline managers to manage their stations; all
+  APIs and CLIs now conform to the new authorization scheme
+- Modified get-experiments utility to allow retrieving list of experiments
+  for a given station
+- Cleaned up web portal by removing unused views, and enabled station 
+  management functionality
+- GPFS DDN (extrepid) has replaced xstor as the main APS storage
+- CLI changes:
+  - add-experiment command requires station name (can be set from env.
+    variable); experiment type can be specified using type name
+  - get-experiments command requires station name for beamline managers (can 
+    be set from env. variable)
+  - start-experiment command is now optional
+
+Release 0.15 (11/01/2016)
+=============================
+
+- Resolved issue with incorrect accounting of processing errors for DAQs
+- Improved DAQ processing algorithm to avoid resource starvation between
+  simultaneous DAQs and uploads
+- Enhanced monitoring status information for both DAQs and uploads
+
+Release 0.14 (10/14/2016)
+=============================
+
+- Introduced new framework and utilities for synchronizing users with 
+  APS DB
+- Resolved several issues with special characters in file names for
+  gridftp transfer plugin  
+
+Release 0.13 (05/27/2016)
+=============================
+
+- Added SFTP file system observer agent
+- Enhanced MongoDB plugin with file md5 sum calculation
+
+Release 0.12 (05/06/2016)
+=============================
+
+- Developed processing for HDF5 metadata in Mongo cataloging plugin
+- Modified catalog API and service interfaces to use file collections on 
+  a per-experiment basis
+
+Release 0.11 (04/29/2016)
+=============================
+
+- Resolved issue with upload command for directories containing large
+  number of files
+- Implemented enhanced upload processing algorithm to avoid resource 
+  starvation between simultaneous DAQs and uploads
+- Added new polling file system observer agent as option for monitoring 
+  directories
+- Reworked catalog API and corresponding MongoDB interfaces to use unique 
+  experiment file paths, rather than file names
+
+Release 0.10 (03/11/2016)
+=============================
+
+- Added dm-list-daqs and dm-list-uploads commands
+- Resolved issue with newly created directories treated as files for 
+  real-time data acquisitions
+
+Release 0.9 (02/25/2016)
+=============================
+
+- Developed directory processing mode for uploads; in this mode file transfer 
+  plugins transfer entire directories as opposed to individual files
+- Added dm-get-processing-plugins command
+- Resolved working directory issue that may occur with simutaneous uploads
+
+Release 0.8 (01/26/2016)
+=============================
+
+- Enhanced upload/daq performance and functionality (hidden files are not
+  processed; for uploads system can detect files that had been processed 
+  already; improved handling and reporting of processing errors)
+- Source file checksum is calculated for rsync/gridftp plugins by default
+- Added dm-stop-upload command
+- Resolved globus online user authorization delay issue 
+
+Release 0.7 (12/08/2015)
+=============================
+
+- Introduced framework and user interfaces for tracking progress of file 
+  uploads and data acquisitions in DAQ service
+- Added ability to monitor multiple directories for the same experiment 
+  simultaneously (required changes to DAQ service REST interfaces)
+- Enhanced start/stop DAQ and upload commands to use DM_FILE_SERVER_URL
+  environment variable
+- Added user interfaces and utilities that enable experiment data download
+  from machines that have SSH access to the storage host
+
+Release 0.6 (11/6/2015)
+=============================
+
+- Added file system observer agent interface for DAQ service
+- Implemented FTP file system observer for DAQ service
+- Added interfaces for deleting user experiment role in DS service
+- Introduced java REST API framework, and specific experiment DS service API 
+- Web Portal notifies DS service about experiment user modifications 
+
+Release 0.5 (10/08/2015)
+=============================
+
+- Implemented Single Sign-On solution for backend services
+- Enabled user authentication via login file
+- Added file stat (with checksum) interface in DS web service
+- After adding user role to experiment via command line, user is also
+  added to experiment group (if one exists)
+- Added rsync file transfer plugin with checksum and delete
+
+Release 0.4 (09/21/2015) 
+=============================
+
+- Number of minor modifications made in preparation for test deployment at
+  beamlines
+
+Release 0.3 (07/22/2015) 
+=============================
+
+- Developed initial version of Catalogging Web Service based on MongoDB
+- Developed sample processing plugins: file metadata catalog, SDDS processing, 
+  SGE job submission
+
+Release 0.2 (06/30/2015) 
+=============================
+
+- Implemented storage permission management and user group management
+- Developed common file processing service plugin framework
+
+Release 0.1 (04/21/2015) 
+=============================
+
+- Functional web portal (user, experiment, and policy pages)
+- Developed web service and its API/CLI frameworks
+- Developed initial version of Data Storage Web Service
+- Developed initial version of Data Acquisition Web Service;
+- DAQ service can monitor file system on a detector node and subsequently
+  transfer data to storage
+

doc/beamline_names.txt

+"1-BM-B,C"
+"1-ID-B,C,E"
+"2-BM-A,B"
+"2-ID-D"
+"2-ID-E"
+"3-ID-B,C,D"
+"4-ID-C"
+"4-ID-D"
+"5-BM-C"
+"5-BM-D"
+"5-ID-B,C,D"
+"6-BM-A,B"
+"6-ID-B,C"
+"6-ID-D"
+"7-BM-B"
+"7-ID-B,C,D"
+"8-BM-B"
+"8-ID-E"
+"8-ID-I"
+"9-BM-B,C"
+"9-ID-B,C"
+"10-BM-A,B"
+"10-ID-B"
+"11-BM-B"
+"11-ID-B"
+"11-ID-C"
+"11-ID-D"
+"12-BM-B"
+"12-ID-B"
+"12-ID-C,D"
+"13-BM-C"
+"13-BM-D"
+"13-ID-C,D"
+"13-ID-E"
+"14-BM-C"
+"14-ID-B"
+"15-ID-B,C,D"
+"16-BM-B"
+"16-BM-D"
+"16-ID-B"
+"16-ID-D"
+"17-BM-B"
+"17-ID-B"
+"18-ID-D"
+"19-BM-D"
+"19-ID-D"
+"20-BM-B"
+"20-ID-B,C"
+"21-ID-D"
+"21-ID-E"
+"21-ID-F"
+"21-ID-G"
+"22-BM-D"
+"22-ID-D"
+"23-BM-B"
+"23-ID-B"
+"23-ID-D"
+"24-ID-C"
+"24-ID-E"
+"26-ID-C"
+"27-ID-B"
+"29-ID-C,D"
+"30-ID-B,C"
+"31-ID-D"
+"32-ID-B,C"
+"33-BM-C"
+"33-ID-D,E"
+"34-ID-C"
+"34-ID-E"
+"35-ID-B,C,D,E"

doc/demo/apsu-20150709/demo_notes.sv.txt

+# Need 1 terminal on DAQ node, 1 terminal on HPC node and 2 terminals on DS
+# node
+
+#
+# SCENARIO 1: BASIC UPLOAD
+#
+
+# ssh -X dm@dmstorage: start services
+cd /opt/DM/dev
+source setup.sh
+./etc/init.d/dm-postgresql start
+./etc/init.d/dm-glassfish start
+./etc/init.d/dm-mongodb start
+./etc/init.d/dm-ds-web-service start
+./etc/init.d/dm-cat-web-service start
+
+# ssh -X dm@dmdaq: start services
+cd /opt/DM/dev
+source setup.sh
+./etc/init.d/dm-daq-web-service start
+
+# ssh -X dm@dmhpc: start services, check NFS
+cd /opt/DM/dev
+source setup.sh
+./etc/init.d/dm-daq-web-service start
+ls -l /net/dmstorage/opt/DM
+
+#####################################################################
+
+# dm@dmstorage: check directory content on the storage node
+ls -l /opt/DM/data
+
+# ssh sveseli@dmstorage: add and start experiment e1
+source /opt/DM/etc/dm.setup.sh
+dm-add-experiment --name e1 --type-id 1
+dm-start-experiment --name e1
+
+# dm@dmstorage: check directory content on the storage node 
+# note that experiment directory permissions are restricted
+ls -l /opt/DM/data/ESAF
+ls -l /opt/DM/data/ESAF/e1/
+
+# ssh dm@dmdaq: source setup file, show test data
+source /opt/DM/etc/dm.setup.sh
+ls -lR /opt/DM/experiments/e1
+cat /opt/DM/experiments/e1/file1 
+
+# dm@dmdaq: upload data for experiment e1
+dm-upload --experiment e1 --data-directory /opt/DM/experiments/e1
+
+# dm@dmstorage: check experiment storage directory content
+# note permissions, ownership
+ls -l /opt/DM/data/ESAF/e1/
+ls -l /opt/DM/data/ESAF/e1/2015/07/09/
+
+#
+# SCENARIO 2: UPLOAD + METADATA CATALOG 
+#
+
+# sveseli@dmstorage: get metadata for experiment files from catalogging service
+dm-get-experiment-files --experiment e1
+dm-get-experiment-file --experiment e1 --file file2 --display-keys=__all__
+
+# dm@dmdaq: upload data for experiment e1, this time specify extra keys
+dm-upload --experiment e1 --data-directory /opt/DM/experiments/e1 ownerUser:JohnC ownerGroup:APSU memo1:ApprovedByNDA memo2:DislikedByGD
+
+# sveseli@dmstorage: get metadata for file 2 again
+dm-get-experiment-file --experiment e1 --file file2 --display-keys=__all__
+
+# sveseli@dmstorage: show metadata updates 
+dm-update-experiment-file --experiment e1 --file file3 quality:A --display-keys=id,fileName,quality
+
+# sveseli@dmstorage: show metadata search
+dm-get-experiment-files --experiment e1 quality:A
+dm-get-experiment-files --experiment e1 storageFilePath:2015
+
+#
+# SCENARIO 3: UPLOAD + METADATA CATALOG + SDDS PARAMETERS
+#
+
+# sveseli@dmstorage: add and start experiment mm1 
+dm-add-experiment --name mm1 --type-id 1
+dm-start-experiment --name mm1
+
+# dm@dmdaq: upload data for experiment mm1, and request SDDS parameter
+# processing
+ls -lR /opt/DM/experiments/mm1
+dm-upload --experiment mm1 --data-directory /opt/DM/experiments/mm1 ownerUser:JohnC ownerGroup:APSU processSddsParameters:True
+
+# sveseli@dmstorage: get mm1 files, observe SDDS parameters 
+dm-get-experiment-files --experiment mm1 
+dm-get-experiment-files --experiment mm1 --display-keys=__all__ --display-format=dict
+
+# dm@dmstorage: compare with sddsprintout (permissions do not allow sveseli
+# account to access file)
+export PATH=$PATH:/opt/epics/extensions/bin/linux-x86_64/
+sddsprintout -parameters /opt/DM/data/ESAF/mm1/hallProbeScan-M1Proto-000000072-0009-000000.edf
+
+#
+# SCENARIO 4: UPLOAD + METADATA CATALOG + SDDS PARAMETERS + SCRIPT PROCESSING 
+#
+
+# dm@dmstorage: show processing script
+cat /opt/DM/processing/find_sdds_row_count.sh
+/opt/DM/processing/find_sdds_row_count.sh /opt/DM/data/ESAF/mm1/hallProbeScan-M1Proto-000000072-0009-000000.edf
+
+# sveseli@dmstorage: get mm1 files, note no key processingScriptOutput
+dm-get-experiment-files --experiment mm1 --display-keys=fileName,processingScriptOutput 
+
+# dm@dmdaq: upload data for experiment mm1, request SDDS parameter
+# processing, specify processing script
+dm-upload --experiment mm1 --data-directory /opt/DM/experiments/mm1 processSddsParameters:True processingScript:/opt/DM/processing/find_sdds_row_count.sh
+
+# sveseli@dmstorage: get mm1 files, note present key processingScriptOutput
+dm-get-experiment-files --experiment mm1 --display-keys=fileName,processingScriptOutput 
+
+#
+# SCENARIO 5: UPLOAD + METADATA CATALOG + SDDS PARAMETERS + HPC PROCESSING 
+#
+
+# dm@dmstorage: show processing script
+more /opt/DM/processing/sge_sdds_analysis.sh
+
+# dm@dmstorage: show no png files in experiment directory
+ls -l /opt/DM/data/ESAF/mm1/*.png
+
+# dm@dmhpc: show empty home directory
+cd
+ls -l
+
+# dm@dmhpc: show qstat
+source /opt/sge/default/common/settings.sh
+qstat -f
+watch -d 'qstat -f'
+
+# sveseli@dmstorage: get mm1 files, note only 1 file
+dm-get-experiment-files --experiment mm1 
+
+# dm@dmdaq: upload data for experiment mm1, request SDDS parameter
+# processing, specify SGE processing script
+dm-upload --experiment mm1 --data-directory /opt/DM/experiments/mm1 processSddsParameters:True sgeJobScript:/opt/DM/processing/sge_sdds_analysis.sh
+
+# sveseli@dmstorage: get mm1 files, note 2 files
+dm-get-experiment-files --experiment mm1 
+
+# sveseli@dmstorage: get mm1 .png files, note parentFile key
+dm-get-experiment-files --experiment mm1 fileName:.png --display-keys=__all__
+
+# dm@dmhpc: show SGE output in home directory
+ls -l
+
+# dm@dmstorage: open processed file
+xdg-open /opt/DM/data/ESAF/mm1/hallProbeScan-M1Proto-000000072-0009-000000.edf.png
+
+#
+# SCENARIO 6: DAQ + METADATA CATALOG + SDDS PARAMETERS + HPC PROCESSING 
+#
+
+# sveseli@dmstorage: add and start experiment mm2 
+dm-add-experiment --name mm2 --type-id 1
+dm-start-experiment --name mm2
+
+# sveseli@dmstorage: get mm2 files, note no files
+dm-get-experiment-files --experiment mm2 
+
+# dm@dmstorage: show no png files in experiment directory
+ls -l /opt/DM/data/ESAF/mm2/*.png
+
+# dm@dmstorage: tail log file to observe processing
+tail -f /opt/DM/var/log/dm.ds-web-service.log
+
+# dm@dmdaq: start DAQ for experiment mm2, request SDDS parameter
+# processing, specify SGE processing script
+rm -rf /tmp/data/mm2
+mkdir -p /tmp/data/mm2
+dm-start-daq --experiment mm2 --data-directory /tmp/data/mm2 processSddsParameters:True sgeJobScript:/opt/DM/processing/sge_sdds_analysis.sh
+
+# dm@dmhpc: show qstat
+watch -d 'qstat -f'
+
+# dm@dmdaq: copy experiment mm2 files into observed directory, watch qstat
+ls -l /opt/DM/experiments/mm2/
+cp /opt/DM/experiments/mm2/* /tmp/data/mm2/ && sleep 5 && touch /tmp/data/mm2/* &
+tail -f /opt/DM/var/log/dm.daq-web-service.log
+
+
+# sveseli@dmstorage: get mm2 files, note original + processed files
+dm-get-experiment-files --experiment mm2 
+
+# dm@dmstorage: show png files in experiment directory
+ls -l /opt/DM/data/ESAF/mm2/*.png
+
+# dm@dmdaq: stop DAQ for experiment mm2
+dm-stop-daq --experiment mm2 
+
+#
+# SCENARIO 7: DATASET DEFINITION
+#
+
+# sveseli@dmstorage: add metadata for couple of experiment e2 files 
+# with different keys
+dm-add-experiment-file --experiment e2 --file x1 status:good
+dm-add-experiment-file --experiment e2 --file y1 status:bad
+dm-get-experiment-files --experiment e2 --display-keys=fileName,status
+
+# sveseli@dmstorage: add dataset metadata 
+dm-add-experiment-dataset --experiment e2 --dataset d1 status:g.*
+
+# sveseli@dmstorage: get dataset files, note only one file matches
+dm-get-experiment-dataset-files --experiment e2 --dataset d1
+
+# sveseli@dmstorage: add metadata for anothare e2 file that 
+# should match dataset constraint
+dm-add-experiment-file --experiment e2 --file x2 status:great
+dm-get-experiment-files --experiment e2 --display-keys=fileName,status
+
+# sveseli@dmstorage: get dataset files, note two files match
+dm-get-experiment-dataset-files --experiment e2 --dataset d1
+

doc/mongo_express_notes.txt

+ cd /local/DmSystem/dm
+ source setup.sh 
+ make deploy-cat-web-service
+
+ cd /local/DmSystem/support
+ ./bin/install_node.sh 
+ cd /local/DmSystem/support/node/linux-x86_64/bin/node_modules/mongo-express/
+ cp config.default.js config.js 
+ vi config.js 
+ export PATH=/local/DmSystem/support/node/linux-x86_64/bin:$PATH
+ ../forever/bin/forever start app.js
+ ../forever/bin/forever list

doc/rhel7_package_list.txt

+RHEL7 Packages
+===============
+
+make
+autoconf
+expect
+gcc
+g++
+subversion
+zlib-devel
+openssl-devel
+libffi-devel
+openldap-devel
+readline-devel
+ncurses-devel
+qt-x11
+qt-postgresql
+qt-devel
+gtk2-devel
+
+Globus Packages
+===============
+
+globus-openssl-module
+globus-ftp-client
+globus-gsi-proxy
+globus-gsi-openssl
+globus-ftp-control
+globus-gass-copy
+globus-common-16.8
+globus-gass-transfer
+globus-io-11.8
+globus-gss-assist
+globus-gsi-cert
+globus-xio-popen
+globus-xio-gsi
+globus-gsi-credential
+globus-callout-3.15
+globus-gsi-sysconfig
+globus-gsi-callback
+globus-xio-5.14
+globus-gssapi-gsi
+globus-gass-copy
+globus-gsi-proxy
+globus-gssapi-error
+

doc/sphinx/.svnignore

+build
+