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ApsComputingAndDataManagamentInfrastructure-20200210.pdf 0 → 100644
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ApsDataManagementSystem-2019.12.11.pdf 0 → 100644
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## APS DataManagement System Deployment to Beamline/Sector
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TOP = ..
SUBDIRS = sphinx user_guide
include $(TOP)/tools/make/RULES_DM
RELEASE_NOTES.txt
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Release 4.0.0 (XX/YY/2021)
=============================
- Fixed issue with non-ascii characters for daq/upload CLI tools
- Fixed issue with locations that involve host/port for SFTP observer
- Fixed issue with incorrect DAQ_DIRECTORY_MAP replacements
- Added globus_group_id to the experiment table in the DM DB, and
modified CLIs, DB and web service APIs accordingly
- Implemented API and CLI support for Globus group management:
- New commands:
* get-globus-group
* list-globus-groups
* create-globus-group
* add-globus-group-memebers
* delete-globus-group-members
* delete-globus-group
Release 3.3.2 (07/09/2020)
=============================
- Added ability to upload files from remote machines via rsync plugin and using
ssh
- Added start/end time into GUP proposal object
Release 3.3.1 (05/06/2020)
=============================
- Maintenance release
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) Release 3.2.2 (02/24/2020)
============================= =============================
- Added user documentation (Getting Started guide) - Added user documentation (Getting Started guide)
......
beamline_names.txt
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...@@ -59,6 +59,8 @@ ...@@ -59,6 +59,8 @@
"24-ID-E" "24-ID-E"
"26-ID-C" "26-ID-C"
"27-ID-B" "27-ID-B"
"28-ID-B"
"28-ID-C"
"29-ID-C,D" "29-ID-C,D"
"30-ID-B,C" "30-ID-B,C"
"31-ID-D" "31-ID-D"
......
demo/apsu-20150709/demo_notes.sv.txt deleted 100644 → 0
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# 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
demo/apsu-20150709/machine_prep_notes.sv.txt deleted 100644 → 0
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# Demo environment consists of three linux VMs:
# - data acquisition (DAQ), data storage (DS), sge cluster (HPC) nodes
# - CentOS 6.6, 64-bit
# - no shared storage
# - DS node runs PostgreSQL database server, Web Portal, DS Web Service,
# CAT Web Service, MongoDB server
# - DAQ node runs DAQ Web Service
# - HPC node runs SGE cluster
# Machine Preparation
# ===================
# install dependencies (all machines)
yum install -y gcc libgcc expect zlib-devel openssl-devel openldap-devel subversion make sed gawk autoconf automake wget readline-devel
# Download globus RPM repo and install gridftp (both machines)
# http://toolkit.globus.org/ftppub/gt6/installers/repo/globus-toolkit-repo-latest.noarch.rpm
yum install globus-gridftp
# Disable requiredtty in /etc/sudoers
# Prepare gridftp server to use sshd (dmstorage machine)
globus-gridftp-server-enable-sshftp
# create system (dm) account on both machines, configure ssh-keys and
# authorized_keys files
# create several user accounts (dmstorage machine): dmuser1, dmuser2, dmuser3
# build and install epics base and SDDS/SDDSepics extensions under
# /opt/epics (dmstorage machine)
# build SDDS python under /opt/epics/extensions/src/SDDS/python/
# copy sdds.py into /opt/DM/support/python/linux-x86_64/lib/python2.7/
# copy /opt/epics/extensions/src/SDDS/python/O.linux-x86_64/sddsdatamodule.so
# into /opt/DM/support/python/linux-x86_64/lib/python2.7/lib-dynload/
# export /opt/DM to dmhpc node
# yum install nfs-util
# edit /etc/exports and add /opt/DM 192.168.100.8(rw,sync)
# exportfs -a
# restart nfs
# install sge on hpc machine, add dmstorage as submission node,
# copy /opt/sge to dmstorage
# configure /opt/DM area for software installation
mkdir -p /opt/DM
chown -R dm.dm /opt/DM
chmod 755 /opt/DM
# configure (or disable) firewall (both machines)
/etc/init.d/iptables stop
# DM Deployment: DS Machine
# =========================
# Log into dmstorage node and create local DM deployment directory
# in dm user home area
cd /opt/DM
ls -l
# Checkout code as release 0.2
svn co https://subversion.xray.aps.anl.gov/DataManagement/trunk dev
# Build support area
cd dev
make support
# Source setup
source setup.sh
# Create db
make db
# Configure Web Portal
# Note:
# - this needs to be done only during the first portal deployment,
# or after portal has been unconfigured explicitly
# - this step configures DB access
# - adds initial DM system user to the DB
make configure-web-portal
# Add few users
#dm-add-user --username dmuser1 --first-name Test --last-name User1
#dm-add-user --username dmuser2 --first-name Test --last-name User2
#dm-add-user --username dmuser3 --first-name Test --last-name User3
# Deploy Web Portal
# Note:
# - deploys portal war file into glassfish
# - after this step, users can access portal at
# https://dmstorage.svdev.net:8181/dm
make deploy-web-portal
# Deploy DS Web Service
# Note:
# - generates SSL certificates and configuration files
# - after this step, DS web service is accessible at port 22236
# - log files are under DM/var/log
# - configuration files are under DM/etc
# - user setup file is DM/etc/dm.setup.sh
# - service control script is under DM/dm-0.2/etc/init.d
make deploy-ds-web-service
# Check functionality. Open second terminal and log into dmstorage node
# as user sveseli
# Source setup file to get access to DM commands
source /opt/DM/etc/dm.setup.sh
# Get user list as administrator (dm) account
dm-get-users
# DM Deployment: DAQ Machine/HPC Machine
# ======================================
# Log into dmdaq node and create local DM deployment directory
# in dm user home area
cd /opt/DM
ls -l
# Checkout code as release 0.2
svn co https://subversion.xray.aps.anl.gov/DataManagement/trunk dev
# Build support area
# Note the following:
# - since demo machines are identical, we could simply copy support/dm code
# from the storage node; this is not necessarily the case in general
# - support area and DM code distribution can be shared between DAQ and DS
# nodes
# - support area on the daq node is much lighter (i.e., no need
# for glassfish, etc.)
cd dev
make support-daq
# Source setup
source setup.sh
# Deploy DAQ Web Service
# Note:
# - requires storage node to be installed
# - generates SSL certificates and configuration files
# - after this step, DAQ web service is accessible at port 33336
# - log files are under DM/var/log
# - configuration files are under DM/etc
# - user setup file is DM/etc/dm.setup.sh
make deploy-daq-web-service
demo/sdm-20150716/demo_notes.sv.txt deleted 100644 → 0
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# Need 1 terminal on DAQ node, 1 terminal on HPC node and 2 terminals on DS
# node
#####################################################################
# Prepare ahead of time
# ssh sveseli@dmstorage: add experiment e1, mm2
source /opt/DM/etc/dm.setup.sh
dm-add-experiment --name e1 --type-id 1
dm-add-experiment --name mm2 --type-id 1
# ssh dm@dmstorage: add few users
source /opt/DM/etc/dm.setup.sh
dm-add-user --username dmuser1 --first-name Test --last-name User1
dm-add-user --username dmuser2 --first-name Test --last-name User2
dm-add-user --username dmuser3 --first-name Test --last-name User3
#####################################################################
# Initialize demo
# 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, check SGE
cd /opt/DM/dev
source setup.sh
./etc/init.d/dm-daq-web-service start
ls -l /net/dmstorage/opt/DM
source /opt/sge/default/common/settings.sh
qstat -f
#
# Check portal: https://dmstorage.svdev.net:8181/dm
#
#####################################################################
#
# Log into portal as dm admin: https://dmstorage.svdev.net:8181/dm
#
# Show users
# Show experiments
# Add dmuser1 to experiment e1
#
# SCENARIO 2: UPLOAD + METADATA CATALOG
#
# dm@dmstorage: check directory content on the storage node, should be empty
ls -l /opt/DM/data
# dm@dmstorage: check dmuser1 user, note list of groups
id dmuser1
# ssh sveseli@dmstorage: start experiment e1
source /opt/DM/etc/dm.setup.sh
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/
# dm@dmstorage: check dmuser1 user, note user belongs to new experiment group
id dmuser1
# sveseli@dmstorage: show there are no experiment files in catalogging service
dm-get-experiment-files --experiment 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, specify few arbitrary keys
dm-upload --experiment e1 --data-directory /opt/DM/experiments/e1 ownerUser:JohnC ownerGroup:APSU memo1:ApprovedByNDA memo2:DislikedByGD
# 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/
# 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__
# 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 6: DAQ + METADATA CATALOG + SDDS PARAMETERS + HPC PROCESSING
#
# sveseli@dmstorage: add and start experiment mm2
dm-start-experiment --name mm2
# sveseli@dmstorage: get mm2 files, note no files
dm-get-experiment-files --experiment mm2
# dm@dmstorage: show no files in experiment directory
ls -l /opt/DM/data/ESAF
ls -l /opt/DM/data/ESAF/mm2
# dm@dmstorage: show processing script
more /opt/DM/processing/sge_sdds_analysis.sh
# dm@dmstorage: tail log file to observe processing
tail -f /opt/DM/var/log/dm.ds-web-service.log
# dm@dmhpc: show qstat
watch -d 'qstat -f'
# 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@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
# sveseli@dmstorage: get one mm2 .edf file, note SDDS parameters in metadata
dm-get-experiment-file --experiment mm2 --file `dm-get-experiment-files --experiment mm2 --display-keys=fileName | grep -v png | head -1 | cut -f2 -d '='` --display-keys=__all__ --display-format=dict
# sveseli@dmstorage: get mm2 .png files, note parentFile key
dm-get-experiment-files --experiment mm2 fileName:.png --display-keys=fileName,parentFile --display-format=dict
# dm@dmstorage: open one processed file
xdg-open `ls -c1 /opt/DM/data/ESAF/mm2/*.png | head -1`
# dm@dmdaq: stop DAQ for experiment mm2
dm-stop-daq --experiment mm2
demo/sdm-20150716/machine_prep_notes.sv.txt deleted 100644 → 0
View file @ fb006243
# Demo environment consists of three linux VMs:
# - data acquisition (DAQ), data storage (DS), sge cluster (HPC) nodes
# - CentOS 6.6, 64-bit
# - no shared storage
# - DS node runs PostgreSQL database server, Web Portal, DS Web Service,
# CAT Web Service, MongoDB server
# - DAQ node runs DAQ Web Service
# - HPC node runs SGE cluster
# Machine Preparation
# ===================
# install dependencies (all machines)
yum install -y gcc libgcc expect zlib-devel openssl-devel openldap-devel subversion make sed gawk autoconf automake wget readline-devel
# Download globus RPM repo and install gridftp (both machines)
# http://toolkit.globus.org/ftppub/gt6/installers/repo/globus-toolkit-repo-latest.noarch.rpm
yum install globus-gridftp
# Disable requiredtty in /etc/sudoers
# Prepare gridftp server to use sshd (dmstorage machine)
globus-gridftp-server-enable-sshftp
# create system (dm) account on both machines, configure ssh-keys and
# authorized_keys files
# create several user accounts (dmstorage machine): dmuser1, dmuser2, dmuser3
# build and install epics base and SDDS/SDDSepics extensions under
# /opt/epics (dmstorage machine)
# build SDDS python under /opt/epics/extensions/src/SDDS/python/
# copy sdds.py into /opt/DM/support/python/linux-x86_64/lib/python2.7/
# copy /opt/epics/extensions/src/SDDS/python/O.linux-x86_64/sddsdatamodule.so
# into /opt/DM/support/python/linux-x86_64/lib/python2.7/lib-dynload/
# export /opt/DM to dmhpc node
# yum install nfs-util
# edit /etc/exports and add /opt/DM 192.168.100.8(rw,sync)
# exportfs -a
# restart nfs
# install sge on hpc machine, add dmstorage as submission node,
# copy /opt/sge to dmstorage
# configure /opt/DM area for software installation
mkdir -p /opt/DM
chown -R dm.dm /opt/DM
chmod 755 /opt/DM
# configure (or disable) firewall (both machines)
/etc/init.d/iptables stop
# DM Deployment: DS Machine
# =========================
# Log into dmstorage node and create local DM deployment directory
# in dm user home area
cd /opt/DM
ls -l
# Checkout code as release 0.2
svn co https://subversion.xray.aps.anl.gov/DataManagement/trunk dev
# Build support area
cd dev
make support
# Source setup
source setup.sh
# Create db
make db
# Configure Web Portal
# Note:
# - this needs to be done only during the first portal deployment,
# or after portal has been unconfigured explicitly
# - this step configures DB access
# - adds initial DM system user to the DB
make configure-web-portal
# Add few users
#dm-add-user --username dmuser1 --first-name Test --last-name User1
#dm-add-user --username dmuser2 --first-name Test --last-name User2
#dm-add-user --username dmuser3 --first-name Test --last-name User3
# Deploy Web Portal
# Note:
# - deploys portal war file into glassfish
# - after this step, users can access portal at
# https://dmstorage.svdev.net:8181/dm
make deploy-web-portal
# Deploy DS Web Service
# Note:
# - generates SSL certificates and configuration files
# - after this step, DS web service is accessible at port 22236
# - log files are under DM/var/log
# - configuration files are under DM/etc
# - user setup file is DM/etc/dm.setup.sh
# - service control script is under DM/dm-0.2/etc/init.d
make deploy-ds-web-service
# Check functionality. Open second terminal and log into dmstorage node
# as user sveseli
# Source setup file to get access to DM commands
source /opt/DM/etc/dm.setup.sh
# Get user list as administrator (dm) account
dm-get-users
# DM Deployment: DAQ Machine/HPC Machine
# ======================================
# Log into dmdaq node and create local DM deployment directory
# in dm user home area
cd /opt/DM
ls -l
# Checkout code as release 0.2
svn co https://subversion.xray.aps.anl.gov/DataManagement/trunk dev
# Build support area
# Note the following:
# - since demo machines are identical, we could simply copy support/dm code
# from the storage node; this is not necessarily the case in general
# - support area and DM code distribution can be shared between DAQ and DS
# nodes
# - support area on the daq node is much lighter (i.e., no need
# for glassfish, etc.)
cd dev
make support-daq
# Source setup
source setup.sh
# Deploy DAQ Web Service
# Note:
# - requires storage node to be installed
# - generates SSL certificates and configuration files
# - after this step, DAQ web service is accessible at port 33336
# - log files are under DM/var/log
# - configuration files are under DM/etc
# - user setup file is DM/etc/dm.setup.sh
make deploy-daq-web-service
demo/sprint-20150421/demo_notes.sv.txt deleted 100644 → 0
View file @ fb006243
# Demo environment consists of two linux VMs:
# - data acquisition (DAQ) and data storage (DS) nodes
# - CentOS 6.6, 64-bit
# - no shared storage
# - DS node runs database server, Web Portal and DS Web Service
# - DAQ node runs DAQ Web Service
# Machine Preparation
# ===================
# install dependencies (both machines)
yum install -y gcc libgcc expect zlib-devel openssl-devel openldap-devel subversion make sed gawk autoconf automake wget readline-devel
# create system (dm) account on both machines, configure ssh-keys and
# authorized_keys files
# configure /opt/DM area for software installation
mkdir -p /opt/DM
chown -R dm.dm /opt/DM
chmod 755 /opt/DM
# configure (or disable) firewall (both machines)
/etc/init.d/iptables stop
# DM Deployment: DS Machine
# =========================
# Log into dmstorage node and create local DM deployment directory
# in dm user home area
cd /opt/DM
ls -l
# Checkout code as release 0.1
svn co https://subversion.xray.aps.anl.gov/DataManagement/tags/20150421 dm-0.1
# Build support area
cd dm-0.1
make support
# Source setup
source setup.sh
# Create db
make db
# Configure Web Portal
# Note:
# - this needs to be done only during the first portal deployment,
# or after portal has been unconfigured explicitly
# - this step configures DB access
make configure-web-portal
# Deploy Web Portal
# Note:
# - deploys portal war file into glassfish
# - after this step, users can access portal at
# https://dmstorage.svdev.net:8181/dm
make deploy-web-portal
# Deploy DS Web Service
# Note:
# - generates SSL certificates and configuration files
# - after this step, DS web service is accessible at port 22236
# - log files are under DM/var/log
# - configuration files are under DM/etc
# - user setup file is DM/etc/dm.setup.sh
# - service control script is under DM/dm-0.1/etc/init.d
make deploy-ds-web-service
# Check functionality. Open second terminal and log into dmstorage node
# as user sveseli
# Source setup file to get access to DM commands
source /opt/DM/etc/dm.setup.sh
# Attempt to get list of users as user sveseli, should result
# in authorization error
# Note:
# - every command comes with common set of options
dm-get-users -h
dm-get-users --version
dm-get-users
echo $?
# Repeat command, this time us administrator (dm) account
dm-get-users
# Repeat command, note that session with DS service has been established, so no
# more password prompts until session expires
cat ~/.dm/.ds.session.cache
dm-get-users
# DM Deployment: DAQ Machine
# ==========================
# Log into dmdaq node and create local DM deployment directory
# in dm user home area
cd /opt/DM
ls -l
# Checkout code as release 0.1
svn co https://subversion.xray.aps.anl.gov/DataManagement/tags/20150421 dm-0.1
# Build support area
# Note the following:
# - since demo machines are identical, we could simply copy support/dm code
# from the storage node; this is not necessarily the case in general
# - support area and DM code distribution can be shared between DAQ and DS
# nodes
# - support area on the daq node is much lighter (i.e., no need
# for glassfish, etc.)
cd dm-0.1
make support-daq
# Source setup
source setup.sh
# Deploy DAQ Web Service
# Note:
# - requires storage node to be installed
# - generates SSL certificates and configuration files
# - after this step, DAQ web service is accessible at port 33336
# - log files are under DM/var/log
# - configuration files are under DM/etc
# - user setup file is DM/etc/dm.setup.sh
make deploy-daq-web-service
# DM Functionality: DAQ
# =====================
# add new experiment (sveseli@dmstorage)
dm-add-experiment -h
dm-add-experiment --name exp1 --type-id 1 --description test
dm-get-experiments
dm-get-experiment --name exp1
dm-get-experiment --name exp1 --display-keys=__all__
# check directory content on the storage node (dm@dmstorage)
ls -l /opt/DM/data
# start experiment (sveseli@dmstorage)
dm-start-experiment --name exp1
# check directory content on the storage node (dm@dmstorage)
ls -l /opt/DM/data
ls -l /opt/DM/data/ESAF
ls -l /opt/DM/data/ESAF/exp1/
# at this point we can log into the portal to see experiment that was created
# observe that start time is entered correctly
# in the first terminal on the daq node, tail log file (dm@dmdaq)
tail -f /opt/DM/var/log/dm.daq-web-service.log
# open second terminal for daq node, login as system (dm) user
# source setup file (dm@dmdaq)
cat /opt/DM/etc/dm.setup.sh
source /opt/DM/etc/dm.setup.sh
# prepare DAQ directory for this experiment (dm@dmdaq)
mkdir -p /tmp/data/exp1
# start DAQ (dm@dmdaq)
dm-start-daq -h
dm-start-daq --experiment exp1 --data-directory /tmp/data/exp1
# create test file in the DAQ directory (daq node)
# observe log file entries, point out file transfer
touch /tmp/data/exp1/file1
echo "Hello there, data management is here" > /tmp/data/exp1/file1
# check directory content on the storage node (dm@dmstorage)
# file1 should be transferred
ls -l /opt/DM/data/ESAF/exp1/
# stop DAQ (dm@dmdaq)
dm-stop-daq -h
dm-stop-daq --experiment exp1
# DM Functionality: Upload
# ========================
# prepare data directory we want to upload (dm@dmdaq)
mkdir -p /tmp/data/exp1/2015/04/21
echo "this is file 2" > /tmp/data/exp1/2015/04/21/file2
echo "this is file 3" > /tmp/data/exp1/2015/04/21/file3
# check directory content on the storage node (dm@dmstorage)
ls -l /opt/DM/data/ESAF/exp1/
# upload data (dm@dmdaq)
dm-upload -h
dm-upload --experiment exp1 --data-directory /tmp/data/exp1
# check directory content on the storage node (dm@dmstorage)
ls -l /opt/DM/data/ESAF/exp1/
ls -l /opt/DM/data/ESAF/exp1/2015/04/21/
cat /opt/DM/data/ESAF/exp1/2015/04/21/file3
# stop experiment (sveseli@dmstorage)
dm-stop-experiment --name exp1
# at this point we can log into the portal to see modified experiment
# observe that end time is entered correctly
demo/sprint-20150630/demo_notes.sv.txt deleted 100644 → 0
View file @ fb006243
# Demo environment consists of two linux VMs:
# - data acquisition (DAQ) and data storage (DS) nodes
# - CentOS 6.6, 64-bit
# - no shared storage
# - DS node runs database server, Web Portal and DS Web Service
# - DAQ node runs DAQ Web Service
# Machine Preparation
# ===================
# install dependencies (both machines)
yum install -y gcc libgcc expect zlib-devel openssl-devel openldap-devel subversion make sed gawk autoconf automake wget readline-devel
# Download globus RPM repo and install gridftp (both machines)
# http://toolkit.globus.org/ftppub/gt6/installers/repo/globus-toolkit-repo-latest.noarch.rpm
yum install globus-gridftp
# Disable requiredtty in /etc/sudoers
# Prepare gridftp server to use sshd (dmstorage machine)
globus-gridftp-server-enable-sshftp
# create system (dm) account on both machines, configure ssh-keys and
# authorized_keys files
# create several user accounts (dmstorage machine): dmuser1, dmuser2, dmuser3
# build and install epics base and SDDS/SDDSepics extensions under
# /opt/epics (dmstorage machine)
# configure /opt/DM area for software installation
mkdir -p /opt/DM
chown -R dm.dm /opt/DM
chmod 755 /opt/DM
# configure (or disable) firewall (both machines)
/etc/init.d/iptables stop
# DM Deployment: DS Machine
# =========================
# Log into dmstorage node and create local DM deployment directory
# in dm user home area
cd /opt/DM
ls -l
# Checkout code as release 0.2
svn co https://subversion.xray.aps.anl.gov/DataManagement/tags/20150630 dm-0.2
# Build support area
cd dm-0.2
make support
# Source setup
source setup.sh
# Create db
make db
# Configure Web Portal
# Note:
# - this needs to be done only during the first portal deployment,
# or after portal has been unconfigured explicitly
# - this step configures DB access
# - adds initial DM system user to the DB
make configure-web-portal
# The above step used two new utilities that go directly to the db:
dm-add-user -h
dm-add-user-system-role -h
# Add few users
dm-add-user --username dmuser1 --first-name Test --last-name User1
dm-add-user --username dmuser2 --first-name Test --last-name User2
dm-add-user --username dmuser3 --first-name Test --last-name User3
# Deploy Web Portal
# Note:
# - deploys portal war file into glassfish
# - after this step, users can access portal at
# https://dmstorage.svdev.net:8181/dm
make deploy-web-portal
# Show no sudo functionality for DM account
sudo -l
# Deploy DS Web Service
# Note:
# - generates SSL certificates and configuration files
# - after this step, DS web service is accessible at port 22236
# - log files are under DM/var/log
# - configuration files are under DM/etc
# - user setup file is DM/etc/dm.setup.sh
# - service control script is under DM/dm-0.2/etc/init.d
make deploy-ds-web-service
# Show sudo functionality for DM account that enables group/permission
# management
sudo -l
# Check functionality. Open second terminal and log into dmstorage node
# as user sveseli
# Source setup file to get access to DM commands
source /opt/DM/etc/dm.setup.sh
# Get user list as administrator (dm) account
dm-get-users
# DM Deployment: DAQ Machine
# ==========================
# Log into dmdaq node and create local DM deployment directory
# in dm user home area
cd /opt/DM
ls -l
# Checkout code as release 0.2
svn co https://subversion.xray.aps.anl.gov/DataManagement/tags/20150630 dm-0.2
# Build support area
# Note the following:
# - since demo machines are identical, we could simply copy support/dm code
# from the storage node; this is not necessarily the case in general
# - support area and DM code distribution can be shared between DAQ and DS
# nodes
# - support area on the daq node is much lighter (i.e., no need
# for glassfish, etc.)
cd dm-0.2
make support-daq
# Source setup
source setup.sh
# Deploy DAQ Web Service
# Note:
# - requires storage node to be installed
# - generates SSL certificates and configuration files
# - after this step, DAQ web service is accessible at port 33336
# - log files are under DM/var/log
# - configuration files are under DM/etc
# - user setup file is DM/etc/dm.setup.sh
make deploy-daq-web-service
# DM Functionality: DAQ
# =====================
# add new experiment and couple of users (sveseli@dmstorage)
dm-add-experiment --name exp1 --type-id 1 --description test
dm-add-user-experiment-role --username dmuser1 --experiment exp1 --role=User
dm-add-user-experiment-role --username dmuser2 --experiment exp1 --role=User
# Note that dmuser1 and 2 are on the list of experiment users
dm-get-experiments
dm-get-experiment --name exp1 --display-keys=__all__
# check directory content on the storage node (dm@dmstorage)
ls -l /opt/DM/data
# Show that unix account corresponding to dmuser1 has no special groups
# associated with it
id dmuser1
# Show there is no exp1 unix group
grep exp1 /etc/group
# start experiment (sveseli@dmstorage)
dm-start-experiment --name exp1
# Show there is now exp1 unix group
grep exp1 /etc/group
# check directory content on the storage node (dm@dmstorage)
# note that experiment directory permissions are restricted
ls -l /opt/DM/data/ESAF
ls -l /opt/DM/data/ESAF/exp1/
# Check experiment user groups: only 1 and 2 should have new group assigned
# to them
id dmuser1
id dmuser2
id dmuser3
# in the first terminal on the storage node, tail log file (dm@dmdstorage)
tail -f /opt/DM/var/log/dm.ds-web-service.log
# in the first terminal on the daq node, tail log file (dm@dmdaq)
tail -f /opt/DM/var/log/dm.daq-web-service.log
# open second terminal for daq node, login as system (dm) user
# source setup file (dm@dmdaq)
source /opt/DM/etc/dm.setup.sh
# prepare DAQ directory for this experiment (dm@dmdaq)
mkdir -p /tmp/data/exp1
# create test file in the DAQ directory (daq node)
# observe log file entries, point out file transfer
echo "Hello there, data management is here" > /tmp/data/exp1/file1
# check directory content on the storage node (dm@dmstorage)
# file1 should be transferred
ls -l /opt/DM/data/ESAF/exp1/
# upload data (dm@dmdaq)
dm-upload --experiment exp1 --data-directory /tmp/data/exp1
# check directory content on the storage node (dm@dmstorage)
# file1 should be transferred
# note permissions
ls -l /opt/DM/data/ESAF/exp1/
# as root@dmstorage, su into dmuser1 account and try to read data
# should work
cat /opt/DM/data/ESAF/exp1/file1
# as root@dmstorage, su into dmuser3 account and try to read data
# should fail
cat /opt/DM/data/ESAF/exp1/file1
# Demonstrate retries: show config file
vi /opt/DM/etc/dm.daq-web-service.conf
# As root@dmdaq, temporarily move rsync
mv /usr/bin/rsync /usr/bin/rsync.orig
# upload new data (dm@dmdaq), observe how transfer fails
echo "Hello there, data management is here again" > /tmp/data/exp1/file1
dm-upload --experiment exp1 --data-directory /tmp/data/exp1
# As root@dmdaq, restore rsync, observe how transfer succeeds
mv /usr/bin/rsync.orig /usr/bin/rsync
# check directory content on the storage node (dm@dmstorage)
# file1 should be transferred
ls -l /opt/DM/data/ESAF/exp1/
# Demonstrate gridftp plugin
# Edit config file as dm@dmdaq, comment out rsync plugin, uncomment gridftp
# plugin; restart service
vi /opt/DM/etc/dm.daq-web-service.conf
./etc/init.d/dm-daq-web-service restart
tail -f /opt/DM/var/log/dm.daq-web-service.log
# upload new data (dm@dmdaq), observe how transfer succeeds
echo "Hello there, data management is here yet again" > /tmp/data/exp1/file1
dm-upload --experiment exp1 --data-directory /tmp/data/exp1
# stop experiment (sveseli@dmstorage)
dm-stop-experiment --name exp1
dm_test_system_deployment_notes.txt deleted 100644 → 0
View file @ fb006243
Prerequisites:
======================
- required OS packages are listed here:
https://confluence.aps.anl.gov/display/DMGT/DM+Station+System+Requirements
- make sure that user ssh login keys are setup and work for both 127.0.0.1
interface, as well as for the short/full installation machine name
- installing DM support software and deploying test system should not
require elevated privileges
- instructions below assume that user's git ssh keys have been setup
Installing DM Support
======================
1) mkdir -p DM_INSTALL_DIR && cd DM_INSTALL_DIR
2) git clone git@git.aps.anl.gov:DM/dm-support support
3) cd support
4) ./sbin/install_support_all.sh
- you will need to enter two passwords of your choice for glassfish
(master and admin password)
- each password needs to be entered only once, as expect scripts handle
repeated requests
Deploying Test System
======================
1) cd DM_INSTALL_DIR
2) git clone git@git.aps.anl.gov:DM/dm
3) cd dm
4) ./sbin/dm_deploy_test_system.sh
- passwords needed:
* postgres admin password (your choice)
* dm db management password (manages database itself; your choice)
* dm system account (DM user with admin privileges; your choice)
* dmadmin LDAP password (existing)
* dmadmin BSS login password (existing)
* dmadmin ESAF DB password (existing)
- scripts also require entry for the data storage directory
(e.g, DM_INSTALL_DIR/data), etc
- for most of the required entries the defaults, if given, are fine
Removing Test System
======================
1) DM_INSTALL_DIR/dev/sbin/dm_remove_test_system.sh
getting_started/getting-started.md
View file @ ae1437b1
# Getting Started Document can now be found [here](https://git.aps.anl.gov/DM/dm-docs/-/wikis/DM/HowTos/Getting-Started) on the [DM Wiki](https://git.aps.anl.gov/DM/dm-docs/-/wikis/home).
## 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.
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