diff --git a/src/main/scripts/unix/cryo-em/cryoem-download-aterm-script-url-create b/src/main/scripts/unix/facility/facility-download-aterm-script-url-create
similarity index 99%
rename from src/main/scripts/unix/cryo-em/cryoem-download-aterm-script-url-create
rename to src/main/scripts/unix/facility/facility-download-aterm-script-url-create
index 55c6c792651a91318f69a2b8eac55e832053a596..ba172e1db9c80f2f4bea3a66ee6a0c60d363158c 100755
--- a/src/main/scripts/unix/cryo-em/cryoem-download-aterm-script-url-create
+++ b/src/main/scripts/unix/facility/facility-download-aterm-script-url-create
@@ -7,6 +7,7 @@ VERBOSE=true
NCSR=4
# root namespace for cryo-em projects
+# Set this to the correct parent when deploying
NAMESPACE_ROOT=/projects/cryo-em
# aterm.jar download url
diff --git a/src/main/scripts/unix/cryo-em/cryoem-download-shell-script-url-create b/src/main/scripts/unix/facility/facility-download-shell-script-url-create
similarity index 98%
rename from src/main/scripts/unix/cryo-em/cryoem-download-shell-script-url-create
rename to src/main/scripts/unix/facility/facility-download-shell-script-url-create
index 28216d896013f8a1bc4edb8d67b9ee235e2e485a..f15b7686f48c0909328ae7715d16909112997881 100755
--- a/src/main/scripts/unix/cryo-em/cryoem-download-shell-script-url-create
+++ b/src/main/scripts/unix/facility/facility-download-shell-script-url-create
@@ -5,7 +5,8 @@ EXPIRE_DAYS=14
OVERWRITE=false
VERBOSE=true
-# root namespace for cryo-em projects
+# root namespace for projects
+# Set this to the correct parent when deploying
NAMESPACE_ROOT=/projects/cryo-em
# aterm.jar download url
diff --git a/src/main/scripts/windows/cryo-em/cryoem-download-aterm-script-url-create.cmd b/src/main/scripts/windows/facility/facility-download-aterm-script-url-create.cmd
similarity index 88%
rename from src/main/scripts/windows/cryo-em/cryoem-download-aterm-script-url-create.cmd
rename to src/main/scripts/windows/facility/facility-download-aterm-script-url-create.cmd
index 2439557727987cb06a841832c6222d496f12db9d..2dc6c34a544eef78ba7a86885f976c332dde4574 100644
--- a/src/main/scripts/windows/cryo-em/cryoem-download-aterm-script-url-create.cmd
+++ b/src/main/scripts/windows/facility/facility-download-aterm-script-url-create.cmd
@@ -1,6 +1,12 @@
@echo off
setlocal EnableExtensions EnableDelayedExpansion
+REM This is the root namespace for projects to be located in.
+REM The caller specifies only the project ID
+REM Needs to be enhanced to allow for projects in /projects (fails if you change the root to that)
+REM When this script is deployed, you must set the root namespace correctly.
+set NAMESPACE_ROOT=/projects/cryo-em
+
REM check java
where java >nul 2>nul
IF %errorlevel% neq 0 (
@@ -49,9 +55,6 @@ set EXPIRE_DAYS=14
set OVERWRITE=false
set VERBOSE=true
-REM cryo-em project root namespace
-set NAMESPACE_ROOT=/projects/cryo-em
-
REM
set PROJECT=
set ROLE=
@@ -60,7 +63,7 @@ set EMAILS=
REM parse arguments
:loop
-if not [%~1]==[] (
+if "%~1" NEQ "" (
if "%~1"=="--ncsr" (
set NCSR=%~2
shift
@@ -84,7 +87,7 @@ if not [%~1]==[] (
goto :loop
)
if "%~1"=="--email" (
- set value=%~2
+ set "value=%~2"
set value=!value:,= !
for %%e in (!value!) do (
if "!EMAILS!"=="" ( set "EMAILS=:to %%e" ) else ( set "EMAILS=!EMAILS! :to %%e" )
@@ -121,17 +124,17 @@ if not [%~1]==[] (
exit /b 1
)
)
- if [!NAMESPACES!]==[] (
- set "NAMESPACES=:namespace !ns!"
+ if "!NAMESPACES!" EQU "" (
+ set "NAMESPACES=:namespace ^"!ns!^""
) else (
- set "NAMESPACES=!NAMESPACES! :namespace !ns!"
+ set "NAMESPACES=!NAMESPACES! :namespace ^"!ns!^""
)
shift
goto :loop
)
REM check if namespace is specified
-if "%NAMESPACES%"=="" (
+if "!NAMESPACES!"=="" (
echo Error: no namespace is specified.
call :usage
exit /b 1
diff --git a/src/main/scripts/windows/cryo-em/cryoem-download-shell-script-url-create.cmd b/src/main/scripts/windows/facility/facility-download-shell-script-url-create.cmd
similarity index 91%
rename from src/main/scripts/windows/cryo-em/cryoem-download-shell-script-url-create.cmd
rename to src/main/scripts/windows/facility/facility-download-shell-script-url-create.cmd
index 7f7093adc99f3325c598f054522851afbcdf7180..8d3e515ee2a8c56a4b2814a7ec5c3b7378ca546d 100644
--- a/src/main/scripts/windows/cryo-em/cryoem-download-shell-script-url-create.cmd
+++ b/src/main/scripts/windows/facility/facility-download-shell-script-url-create.cmd
@@ -1,191 +1,195 @@
-@echo off
-setlocal EnableExtensions EnableDelayedExpansion
-
-REM check java
-where java >nul 2>nul
-IF %errorlevel% neq 0 (
- echo error: no java is found. Install java and retry.
- exit /b 1
-)
-
-REM script file name
-set PROG=%~0
-
-REM aterm.jar download url
-set ATERM_URL=https://mediaflux.researchsoftware.unimelb.edu.au/mflux/aterm.jar
-
-REM aterm.jar location
-if [%MFLUX_ATERM%]==[] set "MFLUX_ATERM=%~dp0..\..\..\lib\aterm.jar"
-if not exist "%MFLUX_ATERM%" (
- set "MFLUX_ATERM=%USERPROFILE%\.Arcitecta\aterm.jar"
- if not exist %USERPROFILE%\.Arcitecta\NUL mkdir "%USERPROFILE%\.Arcitecta"
- call :download !ATERM_URL! !MFLUX_ATERM!
- if !errorlevel! neq 0 exit /b 1
-)
-
-REM mflux.cfg location
-if [%MFLUX_CFG%]==[] set "MFLUX_CFG=%USERPROFILE%\.Arcitecta\mflux.cfg"
-if not exist "%MFLUX_CFG%" set "MFLUX_CFG=%~dp0..\..\..\config\mflux.cfg"
-if not exist "%MFLUX_CFG%" set "MFLUX_CFG=%~dp0..\..\..\mflux.cfg"
-if not exist "%MFLUX_CFG%" set "MFLUX_CFG=%~dp0mflux.cfg"
-if not exist "%MFLUX_CFG%" (
- set "MFLUX_CFG=%USERPROFILE%\.Arcitecta\mflux.cfg"
- echo error: could not find %MFLUX_CFG%
- exit /b 1
-)
-
-REM aterm command prefix
-set "ATERM=java -jar -Dmf.cfg=%MFLUX_CFG% %MFLUX_ATERM% nogui"
-
-REM service name
-set "SERVICE=unimelb.asset.download.shell.script.url.create"
-
-REM command (prefix)
-set "COMMAND=%ATERM% %SERVICE%"
-
-REM default argument values
-set EXPIRE_DAYS=14
-set OVERWRITE=false
-set VERBOSE=true
-
-REM cryo-em project root namespace
-set NAMESPACE_ROOT=/projects/cryo-em
-
-REM
-set PROJECT=
-set ROLE=
-set NAMESPACES=
-set EMAILS=
-
-REM parse arguments
-:loop
-if not [%~1]==[] (
- if "%~1"=="--expire-days" (
- set EXPIRE_DAYS=%~2
- shift
- shift
- goto :loop
- )
- if "%~1"=="--overwrite" (
- set OVERWRITE=true
- shift
- goto :loop
- )
- if "%~1"=="--quiet" (
- set VERBOSE=false
- shift
- goto :loop
- )
- if "%~1"=="--email" (
- set value=%~2
- set value=!value:,= !
- for %%e in (!value!) do (
- if "!EMAILS!"=="" ( set "EMAILS=:to %%e" ) else ( set "EMAILS=!EMAILS! :to %%e" )
- )
- shift
- shift
- goto :loop
- )
- if "%~1"=="-h" (
- call :usage
- exit /b 0
- )
- if "%~1"=="--help" (
- call :usage %PROG%
- exit /b 0
- )
- set ns=%~1
- if "!ns:~0,18!"=="!NAMESPACE_ROOT!/" (
- for /f "delims=/" %%c in ("!ns:~18!") do (
- set "prj=%%c"
- )
- ) else (
- for /f "delims=/" %%c in ("!ns!") do (
- set "prj=%%c"
- )
- set "ns=!NAMESPACE_ROOT!/!ns!"
- )
- if [!PROJECT!]==[] (
- set PROJECT=!prj!
- set "ROLE=!prj!:participant-a"
- ) else (
- if not "!PROJECT!"=="!prj!" (
- echo error: cannot share namespaces from multiple projects.
- exit /b 1
- )
- )
- if [!NAMESPACES!]==[] (
- set "NAMESPACES=:namespace !ns!"
- ) else (
- set "NAMESPACES=!NAMESPACES! :namespace !ns!"
- )
- shift
- goto :loop
-)
-
-REM check if namespace is specified
-if "%NAMESPACES%"=="" (
- echo error: no namespace is specified.
- call :usage
- exit /b 1
-)
-
-REM compose the command
-set "COMMAND=%COMMAND% :download ^< %NAMESPACES% :token ^< :role -type role %ROLE% :to now+%EXPIRE_DAYS%day ^> :verbose %VERBOSE% :overwrite %OVERWRITE% ^> :token ^< :perm ^< :resource -type role:namespace %PROJECT%: :access ADMINISTER ^> ^>"
-
-if not "%EMAILS%"=="" (
- set "COMMAND=%COMMAND% :email ^< %EMAILS% ^>"
-)
-
-REM execute aterm command to generate the script url
-%COMMAND%
-
-if %errorlevel% neq 0 (
- exit /b 2
-)
-exit /b 0
-
-REM function to print usage
-:usage
-echo=
-echo Usage:
-echo %PROG% [-h^|--help] [--expire-days ^<number-of-days^>] [--ncsr ^<ncsr^>] [--overwrite] [--quiet] [--email ^<addresses^>] ^<namespace^>
-echo=
-echo Options:
-echo -h ^| --help prints usage
-echo --email ^<addresses^> specify the email recipient of the generated url. Can be comma-separated if there are more than one. NOTE: your need quote the comma separated values like --email "user1@domain1.org,user2@domain2.org"
-echo --expire-days ^<number-of-days^> expiry of the auth token. Defaults to ${EXPIRE_DAYS} days.
-echo --overwrite overwrite if output file exists.
-echo --quiet do not print output message.
-echo=
-echo Positional arguments:
-echo ^<namespace^> Mediaflux asset namespace to be downloaded by the scripts. Can be multiple, but must be from the same project.
-echo=
-echo Examples:
-echo %PROG% --email user1@unimelb.edu.au --expire-days 10 proj-abc-1128.4.999/RAW_DATA proj-abc-1128.4.999/PROCESSED_DATA
-echo=
-exit /b 0
-
-REM function to download from url
-:download
-setlocal
-set url=%~1
-set out=%~2
-if not exist %out% (
- where powershell >nul 2>nul
- if %errorlevel% equ 0 (
- echo downloading %out%
- powershell -command "(New-Object Net.WebClient).DownloadFile('%url%', '%out%')" >nul 2>nul
- if %errorlevel% neq 0 (
- echo error: failed to download %url%
- exit /b 1
- )
- if not exist "%out%" (
- echo error: failed to download %url% to %out%
- exit /b 1
- )
- ) else (
- echo error: cannot download %out%. No powershell found.
- exit /b 1
- )
-)
+@echo off
+setlocal EnableExtensions EnableDelayedExpansion
+
+REM This is the root namespace for projects to be located in.
+REM The caller specifies only the project ID
+REM Needs to be enhanced to allow for projects in /projects (fails if you change the root to that)
+REM When this script is deployed, you must set the root namespace correctly.
+set NAMESPACE_ROOT=/projects/cryo-em
+
+REM check java
+where java >nul 2>nul
+IF %errorlevel% neq 0 (
+ echo error: no java is found. Install java and retry.
+ exit /b 1
+)
+
+REM script file name
+set PROG=%~0
+
+REM aterm.jar download url
+set ATERM_URL=https://mediaflux.researchsoftware.unimelb.edu.au/mflux/aterm.jar
+
+REM aterm.jar location
+if [%MFLUX_ATERM%]==[] set "MFLUX_ATERM=%~dp0..\..\..\lib\aterm.jar"
+if not exist "%MFLUX_ATERM%" (
+ set "MFLUX_ATERM=%USERPROFILE%\.Arcitecta\aterm.jar"
+ if not exist %USERPROFILE%\.Arcitecta\NUL mkdir "%USERPROFILE%\.Arcitecta"
+ call :download !ATERM_URL! !MFLUX_ATERM!
+ if !errorlevel! neq 0 exit /b 1
+)
+
+REM mflux.cfg location
+if [%MFLUX_CFG%]==[] set "MFLUX_CFG=%USERPROFILE%\.Arcitecta\mflux.cfg"
+if not exist "%MFLUX_CFG%" set "MFLUX_CFG=%~dp0..\..\..\config\mflux.cfg"
+if not exist "%MFLUX_CFG%" set "MFLUX_CFG=%~dp0..\..\..\mflux.cfg"
+if not exist "%MFLUX_CFG%" set "MFLUX_CFG=%~dp0mflux.cfg"
+if not exist "%MFLUX_CFG%" (
+ set "MFLUX_CFG=%USERPROFILE%\.Arcitecta\mflux.cfg"
+ echo error: could not find %MFLUX_CFG%
+ exit /b 1
+)
+
+REM aterm command prefix
+set "ATERM=java -jar -Dmf.cfg=%MFLUX_CFG% %MFLUX_ATERM% nogui"
+
+REM service name
+set "SERVICE=unimelb.asset.download.shell.script.url.create"
+
+REM command (prefix)
+set "COMMAND=%ATERM% %SERVICE%"
+
+REM default argument values
+set EXPIRE_DAYS=14
+set OVERWRITE=false
+set VERBOSE=true
+
+REM
+set PROJECT=
+set ROLE=
+set NAMESPACES=
+set EMAILS=
+
+REM parse arguments
+:loop
+if "%~1" NEQ "" (
+ if "%~1"=="--expire-days" (
+ set EXPIRE_DAYS=%~2
+ shift
+ shift
+ goto :loop
+ )
+ if "%~1"=="--overwrite" (
+ set OVERWRITE=true
+ shift
+ goto :loop
+ )
+ if "%~1"=="--quiet" (
+ set VERBOSE=false
+ shift
+ goto :loop
+ )
+ if "%~1"=="--email" (
+ set "value=%~2"
+ set value=!value:,= !
+ for %%e in (!value!) do (
+ if "!EMAILS!"=="" ( set "EMAILS=:to %%e" ) else ( set "EMAILS=!EMAILS! :to %%e" )
+ )
+ shift
+ shift
+ goto :loop
+ )
+ if "%~1"=="-h" (
+ call :usage
+ exit /b 0
+ )
+ if "%~1"=="--help" (
+ call :usage %PROG%
+ exit /b 0
+ )
+
+
+ set ns=%~1
+ if "!ns:~0,18!"=="!NAMESPACE_ROOT!/" (
+ for /f "delims=/" %%c in ("!ns:~18!") do (
+ set "prj=%%c"
+ )
+ ) else (
+ for /f "delims=/" %%c in ("!ns!") do (
+ set "prj=%%c"
+ )
+ set "ns=!NAMESPACE_ROOT!/!ns!"
+ )
+
+ if [!PROJECT!]==[] (
+ set PROJECT=!prj!
+ set "ROLE=!prj!:participant-a"
+ ) else (
+ if not "!PROJECT!"=="!prj!" (
+ echo error: cannot share namespaces from multiple projects.
+ exit /b 1
+ )
+ )
+ if "!NAMESPACES!" EQU "" (
+ set "NAMESPACES=:namespace ^"!ns!^""
+ ) else (
+ set "NAMESPACES=!NAMESPACES! :namespace ^"!ns!^""
+ )
+ shift
+ goto :loop
+)
+
+REM check if namespace is specified
+if "!NAMESPACES!"=="" (
+ echo error: no namespace is specified.
+ call :usage
+ exit /b 1
+)
+REM compose the command
+set "COMMAND=%COMMAND% :download ^< %NAMESPACES% :token ^< :role -type role %ROLE% :to now+%EXPIRE_DAYS%day ^> :verbose %VERBOSE% :overwrite %OVERWRITE% ^> :token ^< :perm ^< :resource -type role:namespace %PROJECT%: :access ADMINISTER ^> ^>"
+if not "%EMAILS%"=="" (
+ set "COMMAND=%COMMAND% :email ^< %EMAILS% ^>"
+)
+
+REM execute aterm command to generate the script url
+%COMMAND%
+
+if %errorlevel% neq 0 (
+ exit /b 2
+)
+exit /b 0
+
+REM function to print usage
+:usage
+echo=
+echo Usage:
+echo %PROG% [-h^|--help] [--expire-days ^<number-of-days^>] [--ncsr ^<ncsr^>] [--overwrite] [--quiet] [--email ^<addresses^>] ^<namespace^>
+echo=
+echo Options:
+echo -h ^| --help prints usage
+echo --email ^<addresses^> specify the email recipient of the generated url. Can be comma-separated if there are more than one. NOTE: your need quote the comma separated values like --email "user1@domain1.org,user2@domain2.org"
+echo --expire-days ^<number-of-days^> expiry of the auth token. Defaults to ${EXPIRE_DAYS} days.
+echo --overwrite overwrite if output file exists.
+echo --quiet do not print output message.
+echo=
+echo Positional arguments:
+echo ^<namespace^> Mediaflux asset namespace to be downloaded by the scripts. Can be multiple, but must be from the same project.
+echo=
+echo Examples:
+echo %PROG% --email user1@unimelb.edu.au --expire-days 10 proj-abc-1128.4.999/RAW_DATA proj-abc-1128.4.999/PROCESSED_DATA
+echo=
+exit /b 0
+
+REM function to download from url
+:download
+setlocal
+set url=%~1
+set out=%~2
+if not exist %out% (
+ where powershell >nul 2>nul
+ if %errorlevel% equ 0 (
+ echo downloading %out%
+ powershell -command "(New-Object Net.WebClient).DownloadFile('%url%', '%out%')" >nul 2>nul
+ if %errorlevel% neq 0 (
+ echo error: failed to download %url%
+ exit /b 1
+ )
+ if not exist "%out%" (
+ echo error: failed to download %url% to %out%
+ exit /b 1
+ )
+ ) else (
+ echo error: cannot download %out%. No powershell found.
+ exit /b 1
+ )
+)