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| ==CSD Links==
| | {{#externalredirect: https://wiki.ohie.org/display/SUB/CSD+Prototyping+Interface}} |
| *CSD
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| **[ftp://ftp.ihe.net/IT_Infrastructure/iheitiyr11-2013-2014/Technical_Cmte/WorkItems/CareServicesDiscovery/ IHE FTP] site
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| *XQuery Engines
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| **In browser javascript engine: [http://xqib.org/ xqib]
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| **[http://basex.org/ BaseX] XML Database
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| **[http://exist-db.org/exist/apps/homepage/index.html exist-db]
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| **[http://www.zorba.io/ Zorba]
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| ***Zorba and [https://groups.google.com/forum/?fromgroups#!topic/zorba-users/SeJNGRJA8Og large data sets]
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| ***IBM's [http://www.ibm.com/developerworks/library/x-zorba/ Zorba and PHP] article
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| ***Zorba [https://launchpad.net/zorba source code]
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| ***Zorba and PHP [http://dl.dropboxusercontent.com/u/1487285/php/php.html introductory slides]
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| **[http://luxdb.org LUX]
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| *XQuery Engine Comparison
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| **Evaluation Criteria: Programming Language, Source Code Last Updated, Source Documentation, XQuery verison, XQuery Update Facility support, Data storage, Index, Client libraries (PHP, Python, Java,etc.), Mailing List/User Forum last activity
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| ==Potential Issues for Public Comment==
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| Public comments can be submitted according to [http://wiki.ihe.net/index.php?title=Public_Comment_Process this process] at the following [http://www.ihe.net/iti/iticomments.cfm comment form]
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| *how to map hcIdentifier used in HPD to II ?
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| *no date of birth in persons
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| *do we need Org/Facility Contact to be required?
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| *orgType, orgTypeDescription, orgPrimaryName are all required but perhaps should not be. similarly for facility.
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| *minoccurs on orglanguage is not set, but is set for facilityLanguage
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| *no place to add other identifiers for facility
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| *should creation date be required?
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| *facility can be in multiple facilityorgid? how to represent one facility in multiple hierarchies that are not necc. mapped to services
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| *is a lastmodified time/create time for CSD doc needed?
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| *CareServicesDiscoveryQuery/XQueryFunction has no ability to set parameters (e.g. nid). Options would include:
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| ** for un-ordered named variables something we define such as <pre><XQueryFunction name="loopup_by_nid.xq"><value name="nid">123</value></XqueryFUnciton></pre>
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| ** [http://en.wikipedia.org/wiki/XML-RPC XML-RPC] for ordered unnamed variables
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| ** some other structured XML that knows about xquery data types (note: XQuery shares the same data types as XML Schema 1.0 , XSD).
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| *CareServicesDiscoveryQuery/XQueryResult/queryResult may not be valid XML.. Should it always be a CDATA?
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| ==Implementation Notes==
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| Source code:
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| *SVN: [http://csd.ihris.org/svn/CSD SVN]
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| *bzr mirror [https://code.launchpad.net/~his-interop/csd-prototype/CSD bzr]
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| On the test server the repo lives under /home/ubuntu/CSD with
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| *svn co http://csd.ihris.org/svn/CSD /home/ubuntu/CSD
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| ===WebDAV + Subversion===
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| Subversion is used to hold the source code and the source CSD documents. In deployment the php source code and CSD documents should not be in the same repository.
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| *installed subversion according to https://help.ubuntu.com/community/Subversion
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| *subversion installed under /home/svn/CSD with autoversioning for PUT files
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| *webdav under http://csd.ihris.org/svn/CSD
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| *to check out: svn co http://csd.ihris.org/svn/CSD CSD
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| **user: csd pass: ASK CARL FOR IT. It is also in /home/ubuntu/CSD/local/config.php
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| *webdav php client is installed with "sudo apt-get install php-sabredav"
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| Enable the web service with
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| *sudo ln -s /home/ubuntu/CSD/www /var/www/CSD
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| ===index.php, the PHP Glue===
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| *documents and queries retrieved from webdav are cached with APC is available. May need adjust [http://www.php.net/manual/en/apc.configuration.php ini.apc.shm-size] depending on size of documents.
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| *main script is "www/index.php" which should be symlinked under /var/www/where/ever/index.php
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| *configuration such as webdav server url, passwords, cache limits, etc. are stored in config.php.. You can also store in local/config.php which is ignored in the subversion repository so you can commit without storing your passwords.
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| *special doc is docs/CSD.xml which is to be considered the "published" doc. It is assumed that it is XQuery engines should track this document.
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| ===Zorba Implementation Notes===
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| **zorba does not install exactly according to the instructions found online. In particular make sure you:
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| **do "sudo apt-get install swig" before running cmake
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| **do "-D CMAKE_INSTALL_PREFIX=/usr/local .. " in the build directory
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| There is a server script to keep an instance of zorba running with the CSD loaded in memory. There are actually two, one that binds to a socket on localhost which can be started:
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| <source lang='bash'>
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| cd ~/CSD/zorba_server
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| php init_uds.php > /tmp/zorba_server.out &
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| </source>
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| and one AF_UNIX that opens a socket on /tmp/zorba_server.sock
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| <source lang='bash'>
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| cd ~/CSD/zorba_server
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| sudo -u www-data rm /tmp/zorba_server.sock
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| sudo -u www-data php init_uds.php > /tmp/zorba_server_uds.out &
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| </source>
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| ==Prototype CSD Interface==
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| ===CareServicesConsumerQuery===
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| Submit a POST request to zorba_manager.php with your document. Some sample documents are found in [http://csd.ihris.org/svn/CSD/test_csdq test_csdq]
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| You can test this with, for example:<pre> curl -X POST -d @/home/ubuntu/CSD/test_csdq/stats_named.xq.xml http://csd.ihris.org/CSD/zorba_manager.php</pre>
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| ===Searches===
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| Named/Canned Xquery searches are made available under queries/search via the web dav server. If there is a file queries/search/blah/blah.xq, you can access it as http://csd.ihris.org/CSD/zorba_manager.php/search/blah/blah.xq. The dynamic context of the search is the published CSD document at time of the zorba server initialization. For the time being, and GET variables are passed on to the query. This is wide open at the moment and we need to lock it down.
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| *Basic Stats defined in [http://csd.ihris.org/svn/CSD/queries/search/stats.xq queries/search/stats.xq] [http://csd.ihris.org/CSD/zorba_manager.php/search/stats.xq Example]
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| *Search By NID [http://csd.ihris.org/svn/CSD/queries/search/search_by_nid.xq queries/search/search_by_nid.xq] [http://csd.ihris.org/CSD/zorba_manager.php/search/search_by_nid.xq?nid=1197580084757020 Example]
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| *Get all provider records with NIDs [http://csd.ihris.org/svn/CSD/queries/search/search_by_nid.xq queries/search/all_nids.xq] [http://csd.ihris.org/CSD/zorba_manager.php/search/all_nids.xq Example]
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| *Get a list of all active facilities sorted alphapbetically [http://csd.ihris.org/svn/CSD/queries/search/active_facilities.xq queries/search/active_facilities.xq] [http://csd.ihris.org/CSD/zorba_manager.php/search/active_facilities.xq Example]
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| ===Publishing===
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| Named/Canned Xquery use to publish CSD documents are made available under queries/publish via the web dav server. If there is a file queries/publish/blah/blah.xq, you can access it as http://csd.ihris.org/CSD/zorba_manager.php/publish/blah/blah.xq. Each document under docs, with the exclusion of CSD.xml, is available to the xquery. If the resulting document passes validation via the .xsd it is published to the web dav server.
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| Currently there is one publishing script [http://csd.ihris.org/svn/CSD/queries/publish/simple_merge.xq queries/publish/simple_merge.xq].
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| Currently, there is no way to tell the zorba server to reload/refresh the CSD source document after publication. You need to login to the server and restart the "zorba_server/init.php" process manually.
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| ===Updating===
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| Named/Canned Xquery use to publish CSD documents are made available under queries/publish via the web dav server. If there is a file queries/publish/blah/blah.xq, you can access it as http://csd.ihris.org/CSD/zorba_manager.php/update/blah/blah.xq. Each document under docs is available to the xquery and "CSD.xml" is set to be the default context. If the resulting document passes validation via the .xsd it is published to the web dav server.
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| There are no update scripts as of yet. The intention is that scripts here are used to update the currently published CSD.xml, for example with an update of facilities. How this update occurs is defined by the update script. An example workflow would be:
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| *XML data exported from FRED-API compliant FR with updates since a given time.
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| *This data is posted to webdav server under the docs/ directory as, for example, "fr_updates.xml"
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| *There is an xquery script, for example "fr_update.xq", under "queries/update/" that would:
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| **scan fr_updates.xml for any new facilities and add them to the CSD.xml, which is the default context
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| **scan fr_updates.xml for any existing facilities and either delete/replace the entire <facility> node, or overwrite any values contained within it as necessary.
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| ==Profiling==
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| Currently there are no indices are the zorba server's data store.
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| *It can process about 95 NID look-ups per second through the web interface on localhost.
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| *Actually executing the query on zroba takes, for example, 0.0078308582305908 seconds so there is not too much overhead in the php script
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| *Loading the CSD.xml document in zorba's memory store required 2.5mb.
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| *Results on m1.large Amazon EC2 instance
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| <pre>
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| $ httperf --hog --server localhost --uri /CSD/index.php/search/search_by_nid.xq?nid=1197580084757020 --num-conn 500
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| httperf --hog --client=0/1 --server=localhost --port=80 --uri=/CSD/index.php/search/search_by_nid.xq?nid=1197580084757020 --send-buffer=4096 --recv-buffer=16384 --num-conns=500 --num-calls=1
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| httperf: warning: open file limit > FD_SETSIZE; limiting max. # of open files to FD_SETSIZE
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| Maximum connect burst length: 1
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| Total: connections 500 requests 500 replies 500 test-duration 5.260 s
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| Connection rate: 95.1 conn/s (10.5 ms/conn, <=1 concurrent connections)
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| Connection time [ms]: min 5.1 avg 10.5 max 16.9 median 10.5 stddev 1.0
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| Connection time [ms]: connect 0.2
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| Connection length [replies/conn]: 1.000
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| Request rate: 95.1 req/s (10.5 ms/req)
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| Request size [B]: 120.0
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| Reply rate [replies/s]: min 95.0 avg 95.0 max 95.0 stddev 0.0 (1 samples)
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| Reply time [ms]: response 10.3 transfer 0.0
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| Reply size [B]: header 193.0 content 281.0 footer 0.0 (total 474.0)
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| Reply status: 1xx=0 2xx=500 3xx=0 4xx=0 5xx=0
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| CPU time [s]: user 0.98 system 3.38 (user 18.6% system 64.3% total 82.9%)
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| Net I/O: 55.1 KB/s (0.5*10^6 bps)
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| Errors: total 0 client-timo 0 socket-timo 0 connrefused 0 connreset 0
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| Errors: fd-unavail 0 addrunavail 0 ftab-full 0 other 0
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| </pre>
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