Events:August2008XNATDesktop - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:07:28Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Karchie: /* TO-DO items for XND side */

2008-08-29T22:09:27Z

TO-DO items for XND side

Pieper: /* TO-DO items for XND side */

2008-08-22T22:18:12Z

TO-DO items for XND side

Pieper: /* Plan for supporting initial use case */

2008-08-22T22:11:29Z

Plan for supporting initial use case

Karchie: /* TO-DO items for XND side */

2008-08-22T21:29:29Z

TO-DO items for XND side

Karchie: /* Plan for supporting initial use case */

2008-08-22T21:08:47Z

Plan for supporting initial use case

Karchie: /* Plan for supporting initial use case */

2008-08-22T21:08:02Z

Plan for supporting initial use case

Karchie: /* Plan for supporting initial use case */

2008-08-22T21:02:57Z

Plan for supporting initial use case

Karchie: /* TO-DO items for XND side */

2008-08-22T20:29:29Z

TO-DO items for XND side

Pieper: /* Other Topics */

2008-08-22T20:22:16Z

@@ Line 141: / Line 141: @@
 == Use scenario 3: saving MRML files to hosted repository ==
-[http://www.slicer.org/slicerWiki/index.php/Slicer3:XCEDE_use_cases#Slicer_use-case_.230:_Demo_we_would_like_to_show_for_BIRN described here] (similar to above).
+[https://www.slicer.org/wiki/Slicer3:XCEDE_use_cases#Slicer_use-case_.230:_Demo_we_would_like_to_show_for_BIRN described here] (similar to above).
 === notes ===
@@ Line 151: / Line 151: @@
 * what if a MRML scene contains data from multiple subjects, or multiple experiments, or multiple projects? How to upload this?
-(Link to XNAT Desktop [http://www.slicer.org/slicerWiki/index.php/Slicer3:XND tutorial] for Slicer.)
+(Link to XNAT Desktop [https://www.slicer.org/wiki/Slicer3:XND tutorial] for Slicer.)
 = some design & usability stuff: =

@@ Line 94: / Line 94: @@
 * command-line server style version of file server repository
-Available here:  http://nrg.wustl.edu/projects/XND/engine-demo.tar.gz
+Available here:  http://nrg.wustl.edu/projects/XND
-Unpack the archive and read the README for server setup instructions.  And see [[image:XNAT-FileServer-HOWTO.txt |this file for usage examples]].
 * command-line script for using XND rules for importing data in XND database?

@@ Line 95: / Line 95: @@
 Available here:  http://nrg.wustl.edu/projects/XND/engine-demo.tar.gz
-Unpack the archive and read the README for server setup instructions.
+Unpack the archive and read the README for server setup instructions.  And see [[image:XNAT-FileServer-HOWTO.txt |this file for usage examples]].
 * command-line script for using XND rules for importing data in XND database?

← Older revision		Revision as of 22:11, 22 August 2008
Line 67:		Line 67:

	Clinician cuts network link to remote repository (all files are locally cached so OR system is self sufficient).		Clinician cuts network link to remote repository (all files are locally cached so OR system is self sufficient).
		+
		+	''Demo install at SPL''
		+
		+	* code is in /projects/birn/pieper/xnat
		+	* server is running on bobby on port 8000
		+	* example commands:
		+	curl http://bobby:8000/search

	== TO-DO items for XND side==		== TO-DO items for XND side==

@@ Line 79: / Line 79: @@
 HTML description of services available here:
 src/site/methods.html
 * Add credentialing on XND before a server is set up in a public place (consistent with XNAT E)
@@ Line 87: / Line 86: @@
 * command-line server style version of file server repository
 * command-line script for using XND rules for importing data in XND database?
 * turn on multiple remote repositories in the client interface, and more convenient/automated upload/download with XND client

@@ Line 54: / Line 54: @@
   '''response:''' URI of posted file (as message body, also in Location: HTTP header)
   '''send:''' curl -T $filepath $url
-  '''response:''' (empty)
+  '''response:''' none
 '''Step5.''' In IGT, download scene for patient (subject) into slicer.
 Query for a subject and query for available scene files...
-  '''send:''' curl -T GET $srv/search?subject=$subj&fileType=MRML
+  '''send:''' curl $srv/search?subject=$subj&fileType=MRML
   '''response:''' xml containing URIs of all MRML files

@@ Line 46: / Line 46: @@
 Slicer parses XML and presents list of URIs, researcher2 requests to download uris of interest...
   '''send:''' curl $uri
-  '''response:
+  '''response: file contents
 '''Step4.''' Completed neurosurgical planning analysis and upload results.
@@ Line 52: / Line 52: @@
 Create metadatadocument (XML) for individual data file, or for scene + selected data. First, post each dataset, and assemble MRML file using returned uris. Then, post or put mrml file.
   '''send:''' curl -X POST -H "Content-Type: application/x-xnat-metadata+xml" -H "Content-Disposition: x-xnat-metadata; filename=\"$filename\"" -d @$metadata.xml $srv/data
-  ""response:"" URI of posted file (as message body, also in Location: HTTP header)
+  '''response:''' URI of posted file (as message body, also in Location: HTTP header)
   '''send:''' curl -T $filepath $url
   '''response:''' (empty)

@@ Line 33: / Line 33: @@
 Query for all subjects on system...
-  '''send:''' curl -T GET $srv/search??subject
+  '''send:''' curl $srv/search??subject
   '''response:''' xml for all subjects in xnd.bwh.harvard.edu
 Choose a subject, query for available data...
-  '''send:''' curl -T GET $srv/search?subject=$subj
+  '''send:''' curl $srv/search?subject=$subj
   '''response:''' xml containing URIs of all resources for the individual subject $subj
 Slicer parses XML and presents list of all resources; researcher2 queries for for only DICOM data for a particular subject...
-  '''send:''' curl -T GET $srv/search?subject=$subj&fileType=DICOM
+  '''send:''' curl $srv/search?subject=$subj&file_type=DICOM
   '''response:''' xml containing URIs of all DICOM resources for subject $subj
 Slicer parses XML and presents list of URIs, researcher2 requests to download uris of interest...
-  '''send:''' curl -T GET $uri
+  '''send:''' curl $uri
   '''response:
@@ Line 51: / Line 51: @@
 Create metadatadocument (XML) for individual data file, or for scene + selected data. First, post each dataset, and assemble MRML file using returned uris. Then, post or put mrml file.
-  '''send:''' curl -T POST contentType= .... (please flesh this out!)
+  '''send:''' curl -X POST -H "Content-Type: application/x-xnat-metadata+xml" -H "Content-Disposition: x-xnat-metadata; filename=\"$filename\"" -d @$metadata.xml $srv/data
-  '''response:''' uri of posted file (xml or just uri?)
+  ""response:"" URI of posted file (as message body, also in Location: HTTP header)
-  '''send:''' curl -T PUT with filename?
+  '''send:''' curl -T $filepath $url
-  '''response:''' (?)
+  '''response:''' (empty)
 '''Step5.''' In IGT, download scene for patient (subject) into slicer.
@@ Line 63: / Line 63: @@
 Slicer parses XML and presents list of MRML files, and clinican selects one with $uri.
-  '''send:''' curl -T GET $uri
+  '''send:''' curl -T $local_file $uri
-  '''response:''' (?)
+  '''response:''' none
 Clinician cuts network link to remote repository (all files are locally cached so OR system is self sufficient).

@@ Line 71: / Line 71: @@
 * Send example metadata XML file (and script that writes it?) to Slicer dev.
 * Provide some info on webservices API as it develops
 * Add credentialing on XND before a server is set up in a public place (consistent with XNAT E)
 * Establish public (read-only?) access to source code of XND web services and visual client, in version control system;
 * command-line server style version of file server repository
 * command-line script for using XND rules for importing data in XND database?

@@ Line 97: / Line 97: @@
 === Other Topics ===
-Misha to meet with Bernhard about deidentification algorithms for full body CT scans.
+Misha to meet with Bernhard about deidentification algorithms for full body CT scans.  ''Done - Misha to coordinate with Dan''
 =Use-case scenarios=