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Updates to some SDPHP talks and a new short overview of web services

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Jesus M. Castagnetto
2004-05-25 20:44:26 +00:00
parent 3dd22297ac
commit 98c17e7809
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sdphp_webservices.xml Normal file
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<presentation
template="php2"
titlecolor="#1111aa"
logo1="presentations/slides/sdphp/images/testsdphplogo.png"
navbarbackground="#ffffff"
navbarheight="4.1em"
>
<!-- navbarbackground="url(images/trans-ffffff.png)" -->
<topic>Web Services</topic>
<title>Overview of Web Services</title>
<subtitle>or "A Web Service by any other name... REST, XML-RPC, SOAP"</subtitle>
<!-- subtitle>Understanding the alphabet soup: REST, XML-RPC, SOAP</subtitle -->
<event>SDPHP monthly meeting</event>
<location>San Diego</location>
<url>http://www.sdphp.net/</url>
<date>May 6, 2004</date>
<speaker>Jesus M. Castagnetto</speaker>
<email>jmcastagnetto@php.net</email>
<slide>slides/sdphp/ws_title.xml</slide>
<slide>slides/sdphp/ws_toc.xml</slide>
<chapter title='Introduction'>
<slide>slides/sdphp/ws_definition.xml</slide>
<slide>slides/sdphp/ws_whyuse.xml</slide>
<slide>slides/sdphp/ws_aslibrary.xml</slide>
<slide>slides/sdphp/ws_protocols.xml</slide>
</chapter>
<chapter title="REST">
<slide>slides/sdphp/ws_rest.xml</slide>
<slide>slides/sdphp/ws_rest-xml.xml</slide>
<slide>slides/sdphp/ws_rest-example.xml</slide>
</chapter>
<chapter title="XML-RPC">
<slide>slides/sdphp/ws_xmlrpc.xml</slide>
<slide>slides/sdphp/ws_xmlrpc2.xml</slide>
<slide>slides/sdphp/ws_xmlrpc-example.xml</slide>
</chapter>
<chapter title="SOAP">
<slide>slides/sdphp/ws_soap.xml</slide>
<slide>slides/sdphp/ws_soap2.xml</slide>
<slide>slides/sdphp/ws_wsdl.xml</slide>
<slide>slides/sdphp/ws_soap-example.xml</slide>
</chapter>
<chapter title='MDB Services'>
<slide>slides/sdphp/ws_mdbasexample.xml</slide>
<slide>slides/sdphp/ws_mdballapis.xml</slide>
</chapter>
<slide>slides/sdphp/ws_glossary.xml</slide>
<slide>slides/sdphp/ws_ref-libraries.xml</slide>
<slide>slides/sdphp/ws_ref-moreinfo.xml</slide>
</presentation>

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<?xml version="1.0"?>
<!-- WSDL description of the Google Web APIs.
The Google Web APIs are in beta release. All interfaces are subject to
change as we refine and extend our APIs. Please see the terms of use
for more information. -->
<!-- Revision 2002-08-16 -->
<definitions name="GoogleSearch"
targetNamespace="urn:GoogleSearch"
xmlns:typens="urn:GoogleSearch"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/"
xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/"
xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/"
xmlns="http://schemas.xmlsoap.org/wsdl/">
<!-- Types for search - result elements, directory categories -->
<types>
<xsd:schema xmlns="http://www.w3.org/2001/XMLSchema"
targetNamespace="urn:GoogleSearch">
<xsd:complexType name="GoogleSearchResult">
<xsd:all>
<xsd:element name="documentFiltering" type="xsd:boolean"/>
<xsd:element name="searchComments" type="xsd:string"/>
<xsd:element name="estimatedTotalResultsCount" type="xsd:int"/>
<xsd:element name="estimateIsExact" type="xsd:boolean"/>
<xsd:element name="resultElements" type="typens:ResultElementArray"/>
<xsd:element name="searchQuery" type="xsd:string"/>
<xsd:element name="startIndex" type="xsd:int"/>
<xsd:element name="endIndex" type="xsd:int"/>
<xsd:element name="searchTips" type="xsd:string"/>
<xsd:element name="directoryCategories" type="typens:DirectoryCategoryArray"/>
<xsd:element name="searchTime" type="xsd:double"/>
</xsd:all>
</xsd:complexType>
<xsd:complexType name="ResultElement">
<xsd:all>
<xsd:element name="summary" type="xsd:string"/>
<xsd:element name="URL" type="xsd:string"/>
<xsd:element name="snippet" type="xsd:string"/>
<xsd:element name="title" type="xsd:string"/>
<xsd:element name="cachedSize" type="xsd:string"/>
<xsd:element name="relatedInformationPresent" type="xsd:boolean"/>
<xsd:element name="hostName" type="xsd:string"/>
<xsd:element name="directoryCategory" type="typens:DirectoryCategory"/>
<xsd:element name="directoryTitle" type="xsd:string"/>
</xsd:all>
</xsd:complexType>
<xsd:complexType name="ResultElementArray">
<xsd:complexContent>
<xsd:restriction base="soapenc:Array">
<xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:ResultElement[]"/>
</xsd:restriction>
</xsd:complexContent>
</xsd:complexType>
<xsd:complexType name="DirectoryCategoryArray">
<xsd:complexContent>
<xsd:restriction base="soapenc:Array">
<xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:DirectoryCategory[]"/>
</xsd:restriction>
</xsd:complexContent>
</xsd:complexType>
<xsd:complexType name="DirectoryCategory">
<xsd:all>
<xsd:element name="fullViewableName" type="xsd:string"/>
<xsd:element name="specialEncoding" type="xsd:string"/>
</xsd:all>
</xsd:complexType>
</xsd:schema>
</types>
<!-- Messages for Google Web APIs - cached page, search, spelling. -->
<message name="doGetCachedPage">
<part name="key" type="xsd:string"/>
<part name="url" type="xsd:string"/>
</message>
<message name="doGetCachedPageResponse">
<part name="return" type="xsd:base64Binary"/>
</message>
<message name="doSpellingSuggestion">
<part name="key" type="xsd:string"/>
<part name="phrase" type="xsd:string"/>
</message>
<message name="doSpellingSuggestionResponse">
<part name="return" type="xsd:string"/>
</message>
<!-- note, ie and oe are ignored by server; all traffic is UTF-8. -->
<message name="doGoogleSearch">
<part name="key" type="xsd:string"/>
<part name="q" type="xsd:string"/>
<part name="start" type="xsd:int"/>
<part name="maxResults" type="xsd:int"/>
<part name="filter" type="xsd:boolean"/>
<part name="restrict" type="xsd:string"/>
<part name="safeSearch" type="xsd:boolean"/>
<part name="lr" type="xsd:string"/>
<part name="ie" type="xsd:string"/>
<part name="oe" type="xsd:string"/>
</message>
<message name="doGoogleSearchResponse">
<part name="return" type="typens:GoogleSearchResult"/>
</message>
<!-- Port for Google Web APIs, "GoogleSearch" -->
<portType name="GoogleSearchPort">
<operation name="doGetCachedPage">
<input message="typens:doGetCachedPage"/>
<output message="typens:doGetCachedPageResponse"/>
</operation>
<operation name="doSpellingSuggestion">
<input message="typens:doSpellingSuggestion"/>
<output message="typens:doSpellingSuggestionResponse"/>
</operation>
<operation name="doGoogleSearch">
<input message="typens:doGoogleSearch"/>
<output message="typens:doGoogleSearchResponse"/>
</operation>
</portType>
<!-- Binding for Google Web APIs - RPC, SOAP over HTTP -->
<binding name="GoogleSearchBinding" type="typens:GoogleSearchPort">
<soap:binding style="rpc"
transport="http://schemas.xmlsoap.org/soap/http"/>
<operation name="doGetCachedPage">
<soap:operation soapAction="urn:GoogleSearchAction"/>
<input>
<soap:body use="encoded"
namespace="urn:GoogleSearch"
encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
</input>
<output>
<soap:body use="encoded"
namespace="urn:GoogleSearch"
encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
</output>
</operation>
<operation name="doSpellingSuggestion">
<soap:operation soapAction="urn:GoogleSearchAction"/>
<input>
<soap:body use="encoded"
namespace="urn:GoogleSearch"
encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
</input>
<output>
<soap:body use="encoded"
namespace="urn:GoogleSearch"
encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
</output>
</operation>
<operation name="doGoogleSearch">
<soap:operation soapAction="urn:GoogleSearchAction"/>
<input>
<soap:body use="encoded"
namespace="urn:GoogleSearch"
encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
</input>
<output>
<soap:body use="encoded"
namespace="urn:GoogleSearch"
encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
</output>
</operation>
</binding>
<!-- Endpoint for Google Web APIs -->
<service name="GoogleSearchService">
<port name="GoogleSearchPort" binding="typens:GoogleSearchBinding">
<soap:address location="http://api.google.com/search/beta2"/>
</port>
</service>
</definitions>

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<?php
$data = array(array('name'=>'John Q. Public', 'userID'=>'l337d00d'));
echo wddx_serialize_value($data,'results');
?>

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<results>
<timestamp>
20040506-141030PST
</timestamp>
<data>
<row>
<field>
<name>name</name>
<value>John Q. Public</name>
</field>
<field>
<name>userID</name>
<value>l337d00d</value>
</field>
</row>
</data>
</results>

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stdClass Object
(
[directoryCategories] =>
[documentFiltering] =>
[endIndex] => 10
[estimateIsExact] =>
[estimatedTotalResultsCount] => 238
[resultElements] => Array
(
[0] => stdClass Object
(
[URL] => http://metallo.scripps.edu/feedback.html
[cachedSize] => 13k
[directoryCategory] => stdClass Object
(
[fullViewableName] =>
[specialEncoding] =>
)
[directoryTitle] =>
[hostName] =>
[relatedInformationPresent] => 1
[snippet] => [MDB - TSRI]. Feedback: Thanks for taking the time to send us your feedback.<br> Make sure that you include your e-mail address and your comments. <b>...</b>
[summary] =>
[title] => MDB (Feedback) - Metalloprotein Site Database &amp; Browser
)
[1] => stdClass Object
(
[URL] => http://metallo.scripps.edu/PROMISE/CHLMAIN_REV.html
[cachedSize] => 36k
[directoryCategory] => stdClass Object
(
[fullViewableName] =>
[specialEncoding] =>
)
[directoryTitle] =>
[hostName] =>
[relatedInformationPresent] => 1
[snippet] => Created: 8 April 1998 Last modified: 19 April 1999. General references<br> on structure and function of chlorophylls and chlorophyll proteins. <b>...</b>
[summary] =>
[title] => General references on chlorophyll proteins
)
[2] => stdClass Object
(
[URL] => http://metallo.scripps.edu/sql_docs/sql_help.html
[cachedSize] => 15k
[directoryCategory] => stdClass Object
(
[fullViewableName] =>
[specialEncoding] =>
)
[directoryTitle] =>
[hostName] =>
[relatedInformationPresent] => 1
[snippet] => [MDB - TSRI]. SQL Help. <b>...</b>
[summary] =>
[title] => SQL Help Information-Metalloprotein Site Database and Browser <b>...</b>
)
[3] => stdClass Object
(
[URL] => http://www.geocities.com/dslongley/freedbs.html
[cachedSize] => 101k
[directoryCategory] => stdClass Object
(
[fullViewableName] =>
[specialEncoding] =>
)
[directoryTitle] =>
[hostName] =>
[relatedInformationPresent] => 1
[snippet] => Free Scientific and Academic Databases and Searchable Data Sets Over<br> 340 resources listed! Last updated 1/31/03. To search for databases <b>...</b>
[summary] =>
[title] => Free Scientific and Academic Databases and Searchable Data Sets
)
[4] => stdClass Object
(
[URL] => http://www.zend.com/comm_person.php?id=9
[cachedSize] => 33k
[directoryCategory] => stdClass Object
(
[fullViewableName] =>
[specialEncoding] =>
)
[directoryTitle] =>
[hostName] =>
[relatedInformationPresent] => 1
[snippet] => Who&#39;s Who - Jesus M. Castagnetto, Nominate Someone. Name, Jesus M.<br> Castagnetto, Category, Book authors. Country, United States. Email,<br> for <b>...</b>
[summary] =>
[title] => Zend - The php Company
)
[5] => stdClass Object
(
[URL] => http://directory.google.com/Top/Science/Physics/Crystallography/Databases/
[cachedSize] => 13k
[directoryCategory] => stdClass Object
(
[fullViewableName] =>
[specialEncoding] =>
)
[directoryTitle] =>
[hostName] =>
[relatedInformationPresent] => 1
[snippet] => Google, Directory Help Search only in Databases Search the Web. Databases, <b>...</b>
[summary] =>
[title] => Google Directory - Science &gt; Physics &gt; Crystallography &gt; Databases
)
[6] => stdClass Object
(
[URL] => http://www.biolinks.net.ru/Databases/more3.htm
[cachedSize] => 35k
[directoryCategory] => stdClass Object
(
[fullViewableName] =>
[specialEncoding] =>
)
[directoryTitle] =>
[hostName] =>
[relatedInformationPresent] => 1
[snippet] => Your Ad Here! Top : Databases : Page 3. Major Sequence Databases,<br> [4]. Protein Databases, [16]. Protein Domains, [5]. RNA Databases,<br> [9]. <b>...</b>
[summary] =>
[title] => Different databases
)
[7] => stdClass Object
(
[URL] => http://www.imb-jena.de/IMAGE_ABOUT.html
[cachedSize] => 39k
[directoryCategory] => stdClass Object
(
[fullViewableName] =>
[specialEncoding] =>
)
[directoryTitle] =>
[hostName] =>
[relatedInformationPresent] => 1
[snippet] => About the IMB Jena Image Library of Biological Macromolecules. Authors, <b>...</b>
[summary] =>
[title] => IMB Jena Image Library of Biological Macromolecules
)
[8] => stdClass Object
(
[URL] => http://wwwprof.uniandes.edu.co/~aviswana/bioinfo2.html
[cachedSize] => 70k
[directoryCategory] => stdClass Object
(
[fullViewableName] =>
[specialEncoding] =>
)
[directoryTitle] =>
[hostName] =>
[relatedInformationPresent] => 1
[snippet] => Bioinformatics Sites. Sequence Analysis GCG Text-based searching Pairwise<br> Alignment Multiple Sequence Alignment Sequence-based searching <b>...</b>
[summary] =>
[title] => Bioinformatics Sites
)
[9] => stdClass Object
(
[URL] => http://pecl.php.net/user/jmcastagnetto
[cachedSize] => 10k
[directoryCategory] => stdClass Object
(
[fullViewableName] =>
[specialEncoding] =>
)
[directoryTitle] =>
[hostName] =>
[relatedInformationPresent] => 1
[snippet] => PECL, Friday, April 30, 2004. <b>...</b>
[summary] =>
[title] => PECL :: Jesus M. Castagnetto
)
)
[searchComments] =>
[searchQuery] => link:metallo.scripps.edu
[searchTime] => 0.141005
[searchTips] =>
[startIndex] => 1
)

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<wddxPacket version='1.0'>
<header>
<comment>timestamp</comment>
</header>
<data>
<struct>
<var name='date'>
<string>2004-05-06</string>
</var>
<var name='time'>
<string>15:14:25</string>
</var>
</struct>
</data>
</wddxPacket>

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slides/sdphp/output/test_soap_out.html Normal file
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<h2>Excercizing the sql method</h2>
[query: 'select source_id,description from protein limit 3']
<table border='1'>
<tr>
<td bgcolor='#eeeeee'>
<b>source_id</b>: 1aoo<br>
<b>description</b>: Header: [metallothionein 08-jul-97 1aoo]
Title: [ag-substituted metallothionein from saccharomyces cerevisiae, nmr, minimized average structure]
Compound: [mol_id: 1; molecule: ag-metallothionein; chain: null; synonym: ag-mt; biological_unit: monomer; other_details: ag(i) substituted]
Source: [mol_id: 1; organism_scientific: saccharomyces cerevisiae; organism_common: baker's yeast; strain: 301n]
Keywords: [copper detoxification, metal-thiolate cluster]<br>
<b>0</b>:
<br>
<b>source_id</b>: 1aqq<br>
<b>description</b>: Header: [metallothionein 31-jul-97 1aqq]
Title: [ag-substituted metallothionein from saccharomyces cerevisiae, nmr, 10 structures]
Compound: [mol_id: 1; molecule: ag-metallothionein; chain: null; synonym: ag-mt; biological_unit: monomer; other_details: ag(i) substituted]
Source: [mol_id: 1; organism_scientific: saccharomyces cerevisiae; organism_common: baker's yeast; strain: 301n]
Keywords: [copper detoxification, metal-thiolate cluster]<br>
<b>1</b>:
<br>
<b>source_id</b>: 2aw0<br>
<b>description</b>: Header: [copper transport 08-oct-97 2aw0]
Title: [fourth metal-binding domain of the menkes copper-transporting atpase, nmr, 20 structures]
Compound: [mol_id: 1; molecule: menkes copper-transporting atpase; chain: null; fragment: fourth metal-binding domain; ec: 3.6.1.36; engineered: yes; biological_unit: monomer; other_details: ag(i)-bound state]
Source: [mol_id: 1; organism_scientific: homo sapiens; organism_common: human; expression_system: escherichia coli]
Keywords: [copper-binding domain, hydrolase, copper transport]<br>
<b>2</b>:
<br>
</td>
</tr>
</table>
<hr>
<h2>Making a deliberate error using the metallopdb method</h2>
[metal: zn][mode: first][count: -3]
<br><b>OOPS we got an error</b>
<table border='1'>
<tr>
<td bgcolor='#eeeeee'>
<b>error_message_prefix</b>: PHP<br>
<b>mode</b>: 1<br>
<b>level</b>: 1024<br>
<b>code</b>: SOAP-ENV:Server<br>
<b>message</b>: Parameter count must be an integer > 0, value sent: -3<br>
<b>userinfo</b>: Errno: 256
Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php
Lineno: 46<br>
<b>file</b>: /home/server/php/lib/php/SOAP/Fault.php<br>
<b>line</b>: 49<br>
<b>function</b>: pear_error<br>
<b>class</b>: pear_error<br>
<b>type</b>: ::<br>
<b>0</b>: Parameter count must be an integer > 0, value sent: -3<br>
<b>1</b>: SOAP-ENV:Server<br>
<b>2</b>: <br>
<b>3</b>: <br>
<b>4</b>: Errno: 256
Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php
Lineno: 46<br>
<b>args</b>:
<br>
<b>0</b>:
<br>
<b>file</b>: /home/server/php/lib/php/SOAP/Base.php<br>
<b>line</b>: 320<br>
<b>function</b>: soap_fault<br>
<b>class</b>: soap_fault<br>
<b>type</b>: -><br>
<b>0</b>: Parameter count must be an integer > 0, value sent: -3<br>
<b>1</b>: SOAP-ENV:Server<br>
<b>2</b>: PHP<br>
<b>3</b>: Errno: 256
Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php
Lineno: 46<br>
<b>4</b>: <br>
<b>5</b>: <br>
<b>args</b>:
<br>
<b>1</b>:
<br>
<b>file</b>: /home/server/php/lib/php/SOAP/Client.php<br>
<b>line</b>: 508<br>
<b>function</b>: _raisesoapfault<br>
<b>class</b>: soap_client<br>
<b>type</b>: -><br>
<b>0</b>: Parameter count must be an integer > 0, value sent: -3<br>
<b>1</b>: Errno: 256
Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php
Lineno: 46<br>
<b>2</b>: PHP<br>
<b>3</b>: SOAP-ENV:Server<br>
<b>args</b>:
<br>
<b>2</b>:
<br>
<b>file</b>: /home/server/php/lib/php/SOAP/Client.php<br>
<b>line</b>: 476<br>
<b>function</b>: __decoderesponse<br>
<b>class</b>: soap_client<br>
<b>type</b>: -><br>
<b>value</b>: SOAP-ENV:Server<br>
<b>name</b>: faultcode<br>
<b>type</b>: QName<br>
<b>namespace</b>: http://schemas.xmlsoap.org/soap/envelope/<br>
<b>type_namespace</b>: http://www.w3.org/2001/XMLSchema<br>
<b>attributes</b>:
<br>
<b>arrayType</b>: <br>
<b>options</b>:
<br>
<b>name</b>: faultcode<br>
<b>ns</b>: <br>
<b>namespace</b>: http://schemas.xmlsoap.org/soap/envelope/<br>
<b>nqn</b>:
<br>
<b>name</b>: QName<br>
<b>ns</b>: <br>
<b>namespace</b>: http://www.w3.org/2001/XMLSchema<br>
<b>tqn</b>:
<br>
<b>type_prefix</b>: <br>
<b>0</b>:
<br>
<b>value</b>: Parameter count must be an integer > 0, value sent: -3<br>
<b>name</b>: faultstring<br>
<b>type</b>: string<br>
<b>namespace</b>: http://schemas.xmlsoap.org/soap/envelope/<br>
<b>type_namespace</b>: http://www.w3.org/2001/XMLSchema<br>
<b>attributes</b>:
<br>
<b>arrayType</b>: <br>
<b>options</b>:
<br>
<b>name</b>: faultstring<br>
<b>ns</b>: <br>
<b>namespace</b>: http://schemas.xmlsoap.org/soap/envelope/<br>
<b>nqn</b>:
<br>
<b>name</b>: string<br>
<b>ns</b>: <br>
<b>namespace</b>: http://www.w3.org/2001/XMLSchema<br>
<b>tqn</b>:
<br>
<b>type_prefix</b>: <br>
<b>1</b>:
<br>
<b>value</b>: PHP<br>
<b>name</b>: faultactor<br>
<b>type</b>: anyURI<br>
<b>namespace</b>: http://schemas.xmlsoap.org/soap/envelope/<br>
<b>type_namespace</b>: http://www.w3.org/2001/XMLSchema<br>
<b>attributes</b>:
<br>
<b>arrayType</b>: <br>
<b>options</b>:
<br>
<b>name</b>: faultactor<br>
<b>ns</b>: <br>
<b>namespace</b>: http://schemas.xmlsoap.org/soap/envelope/<br>
<b>nqn</b>:
<br>
<b>name</b>: anyURI<br>
<b>ns</b>: <br>
<b>namespace</b>: http://www.w3.org/2001/XMLSchema<br>
<b>tqn</b>:
<br>
<b>type_prefix</b>: <br>
<b>2</b>:
<br>
<b>value</b>: Errno: 256
Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php
Lineno: 46<br>
<b>name</b>: detail<br>
<b>type</b>: string<br>
<b>namespace</b>: http://schemas.xmlsoap.org/soap/envelope/<br>
<b>type_namespace</b>: http://www.w3.org/2001/XMLSchema<br>
<b>attributes</b>:
<br>
<b>arrayType</b>: <br>
<b>options</b>:
<br>
<b>name</b>: detail<br>
<b>ns</b>: <br>
<b>namespace</b>: http://schemas.xmlsoap.org/soap/envelope/<br>
<b>nqn</b>:
<br>
<b>name</b>: string<br>
<b>ns</b>: <br>
<b>namespace</b>: http://www.w3.org/2001/XMLSchema<br>
<b>tqn</b>:
<br>
<b>type_prefix</b>: <br>
<b>3</b>:
<br>
<b>value</b>:
<br>
<b>name</b>: Fault<br>
<b>type</b>: Struct<br>
<b>namespace</b>: http://schemas.xmlsoap.org/soap/envelope/<br>
<b>type_namespace</b>: <br>
<b>attributes</b>:
<br>
<b>arrayType</b>: <br>
<b>options</b>:
<br>
<b>name</b>: Fault<br>
<b>ns</b>: <br>
<b>namespace</b>: http://schemas.xmlsoap.org/soap/envelope/<br>
<b>nqn</b>:
<br>
<b>name</b>: Struct<br>
<b>ns</b>: <br>
<b>namespace</b>: <br>
<b>tqn</b>:
<br>
<b>type_prefix</b>: <br>
<b>0</b>:
<br>
<b>args</b>:
<br>
<b>3</b>:
<br>
<b>file</b>: /home/server/php/lib/php/SOAP/Client.php<br>
<b>line</b>: 245<br>
<b>function</b>: __parse<br>
<b>class</b>: soap_client<br>
<b>type</b>: -><br>
<b>0</b>: <?xml version="1.0" encoding="UTF-8"?>
<SOAP-ENV:Envelope xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
<SOAP-ENV:Body>
<SOAP-ENV:Fault>
<faultcode xsi:type="xsd:QName">SOAP-ENV:Server</faultcode>
<faultstring xsi:type="xsd:string">Parameter count must be an integer &gt; 0, value sent: -3</faultstring>
<faultactor xsi:type="xsd:anyURI">PHP</faultactor>
<detail xsi:type="xsd:string">Errno: 256
Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php
Lineno: 46
</detail></SOAP-ENV:Fault>
</SOAP-ENV:Body>
</SOAP-ENV:Envelope>
<br>
<b>1</b>: UTF-8<br>
<b>2</b>: <br>
<b>args</b>:
<br>
<b>4</b>:
<br>
<b>file</b>: /home/jesus/devel/php/presentations/slides/mdb/test_soap.xml<br>
<b>line</b>: 45<br>
<b>function</b>: call<br>
<b>class</b>: soap_client<br>
<b>type</b>: -><br>
<b>0</b>: metallopdb<br>
<b>metal</b>: zn<br>
<b>mode</b>: first<br>
<b>count</b>: -3<br>
<b>1</b>:
<br>
<b>2</b>: urn:MDB_SOAP_Server<br>
<b>args</b>:
<br>
<b>5</b>:
<br>
<b>backtrace</b>:
<br>
<b>callback</b>: <br>
</td>
</tr>
</table>
<hr>
<h2>Using the metallopdb method correctly</h2>
[metal:zn][mode: random][count: 3]
<table border='1'>
<tr>
<td bgcolor='#eeeeee'>
<b>metal</b>: zn<br>
<b>source_id</b>: 1eb6<br>
<b>revision_date</b>: 2001/11/23<br>
<b>deposition_date</b>: 2001/07/19<br>
<b>expdata</b>: x-ray diffraction<br>
<b>r_value</b>: 0.10<br>
<b>resolution</b>: 1.00<br>
<b>authors</b>: k.e.mcauley,y.jia-xing,e.j.dodson,j.lehmbeck, p.r.ostergaard,k.s.wilson<br>
<b>description</b>: Header: [hydrolase 19-jul-01 1eb6]
Title: [deuterolysin from aspergillus oryzae]
Compound: [mol_id: 1; molecule: neutral protease ii; synonym: npii, deuterolysin; chain: a; ec: 3.4.24.39]
Source: [mol_id: 1; organism_scientific: aspergillus oryzae]
Keywords: [zinc, neutral protease ii, hydrolase]<br>
<b>0</b>:
<br>
<b>metal</b>: zn<br>
<b>source_id</b>: 1qf2<br>
<b>revision_date</b>: 2000/12/20<br>
<b>deposition_date</b>: 1999/04/06<br>
<b>expdata</b>: x-ray diffraction<br>
<b>r_value</b>: 0.16<br>
<b>resolution</b>: 2.06<br>
<b>authors</b>: j.-f.gaucher,m.selkti,g.tiraboschi,t.prange,b.p.roques, a.tomas,m.c.fournie-zaluski<br>
<b>description</b>: Header: [hydrolase 06-apr-99 1qf2]
Title: [thermolysin (e.c.3.4.24.27) complexed with (2-sulphanyl-3- phenylpropanoyl)-gly-(5-phenylproline). parameters for zn- monodentation of mercaptoacyldipeptides in metalloendopeptidase]
Compound: [mol_id: 1; molecule: thermolysin; chain: a; ec: 3.4.24.27]
Source: [mol_id: 1; organism_scientific: bacillus thermoproteolyticus]
Keywords: [zn metallopeptidase]<br>
<b>1</b>:
<br>
<b>metal</b>: zn<br>
<b>source_id</b>: 1xuf<br>
<b>revision_date</b>: 1998/12/16<br>
<b>deposition_date</b>: 1997/10/10<br>
<b>expdata</b>: x-ray diffraction<br>
<b>r_value</b>: 0.15<br>
<b>resolution</b>: 2.04<br>
<b>authors</b>: b.a.katz,j.m.clark,j.s.finer-moore,t.e.jenkins,c.r.johnson, m.j.rose,c.luong,w.r.moore,r.m.stroud<br>
<b>description</b>: Header: [serine protease 10-oct-97 1xuf]
Title: [trypsin-babim-zn+2, ph 8.2]
Compound: [mol_id: 1; molecule: trypsin; chain: null; ec: 3.4.21.4; other_details: trypsin/zn+2/small molecule ligand complex]
Source: [mol_id: 1; organism_scientific: bos taurus; organism_common: bovine]
Keywords: [trypsin-zn+2-small molecule ligand, designed small molecule ligand with nanomolar affinity]<br>
<b>2</b>:
<br>
</td>
</tr>
</table>
<hr>
<h2>Using the rssmetallopdb method</h2>
[metal: zn][mode: last][count: 3]
<table border='1'>
<tr>
<td bgcolor='#eeeeee'>
<pre>
&lt;?xml version=&quot;1.0&quot; encoding=&quot;iso-8859-1&quot;?&gt;
&lt;rdf:RDF
xmlns:rdf=&quot;http://www.w3.org/1999/02/22-rdf-syntax-ns#&quot;
xmlns=&quot;http://purl.org/rss/1.0/&quot;
xmlns:mn=&quot;http://usefulinc.com/rss/manifest/&quot;
xmlns:dc=&quot;http://purl.org/dc/elements/1.1/&quot;
&gt;
&lt;channel rdf:about=&quot;http://metallo.scripps.edu/services/soap.php&quot;&gt;
&lt;title&gt;MDB - The Metalloprotein Database and Browser&lt;/title&gt;
&lt;link&gt;http://metallo.scripps.edu&lt;/link&gt;
&lt;description&gt;Data retrieved using the MDB API&lt;/description&gt;
&lt;items&gt;
&lt;rdf:Seq&gt;
&lt;rdf:li rdf:resource=&quot;http://metallo.scripps.edu/remote/remote.php3?source_id[]=9nse&amp;amp;metal[]=zn&quot; /&gt;
&lt;rdf:li rdf:resource=&quot;http://metallo.scripps.edu/remote/remote.php3?source_id[]=9icv&amp;amp;metal[]=zn&quot; /&gt;
&lt;rdf:li rdf:resource=&quot;http://metallo.scripps.edu/remote/remote.php3?source_id[]=9ici&amp;amp;metal[]=zn&quot; /&gt;
&lt;/rdf:Seq&gt;
&lt;/items&gt;
&lt;/channel&gt;
&lt;item rdf:about=&quot;http://metallo.scripps.edu/remote/remote.php3?source_id[]=9nse&amp;amp;metal[]=zn&quot;&gt;
&lt;link&gt;http://metallo.scripps.edu/remote/remote.php3?source_id[]=9nse&amp;amp;metal[]=zn&lt;/link&gt;
&lt;title&gt;(Zn) 9nse [deposited on: 1999/01/13, revised on: 2000/10/25]&lt;/title&gt;
&lt;description&gt;Header: [oxidoreductase 13-jan-99 9nse]
Title: [bovine endothelial nitric oxide synthase, ethyl- isoselenourea complex]
Compound: [mol_id: 1; molecule: nitric oxide synthase; chain: a, b; fragment: heme domain; synonym: nos, enos; ec: 1.14.13.39; engineered: yes]
Source: [mol_id: 1; organism_scientific: bos taurus; organism_common: bovine; cell: endothelial; expression_system: escherichia coli; expression_system_common: bacteria; expression_system_strain: bl21]
Keywords: [heme protein, tetrahydrobiopterin] Authors[h.li,c.s.raman,p.martasek,v.kral,b.s.s.masters,t.l.poulos] ExpData[x-ray diffraction] R-value[0.20] Resolution[2.24]&lt;/description&gt;
&lt;/item&gt;
&lt;item rdf:about=&quot;http://metallo.scripps.edu/remote/remote.php3?source_id[]=9icv&amp;amp;metal[]=zn&quot;&gt;
&lt;link&gt;http://metallo.scripps.edu/remote/remote.php3?source_id[]=9icv&amp;amp;metal[]=zn&lt;/link&gt;
&lt;title&gt;(Zn) 9icv [deposited on: 1995/12/16, revised on: 1996/11/15]&lt;/title&gt;
&lt;description&gt;Header: [complex (nucleotidyltransferase/dna) 16-dec-95 9icv]
Title: [dna polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of dna; soaked in the presence of datp (0.1 millimolar) and zncl2 (0.2 millimolar)]
Compound: [mol_id: 1; molecule: dna polymerase beta; chain: a; ec: 2.7.7.7; engineered: yes; mol_id: 2; molecule: dna (5'-d(*cp*ap*tp*tp*ap*gp*a)-3') (dot) (5'-d(*tp*cp*tp*ap*ap*tp*g)-3'); chain: t, p; engineered: yes; other_details: soaked in the presence of datp (0.1 millimolar) and zncl2 (0.2 millimolar)]
Source: [mol_id: 1; organism_scientific: homo sapiens; organism_common: human; expression_system: escherichia coli; mol_id: 2; synthetic: yes]
Keywords: [dna replication, dna repair, nucleotidyltransferase, complex (nucleotidyltransferase/dna)] Authors[h.pelletier,m.r.sawaya] ExpData[x-ray diffraction] R-value[0.18] Resolution[2.70]&lt;/description&gt;
&lt;/item&gt;
&lt;item rdf:about=&quot;http://metallo.scripps.edu/remote/remote.php3?source_id[]=9ici&amp;amp;metal[]=zn&quot;&gt;
&lt;link&gt;http://metallo.scripps.edu/remote/remote.php3?source_id[]=9ici&amp;amp;metal[]=zn&lt;/link&gt;
&lt;title&gt;(Zn) 9ici [deposited on: 1995/12/15, revised on: 1996/11/15]&lt;/title&gt;
&lt;description&gt;Header: [complex (nucleotidyltransferase/dna) 15-dec-95 9ici]
Title: [dna polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of dna; soaked in the presence of dttp (1 millimolar) and zncl2 (1 millimolar)]
Compound: [mol_id: 1; molecule: dna polymerase beta; chain: a; ec: 2.7.7.7; engineered: yes; mol_id: 2; molecule: dna (5'-d(*cp*ap*tp*tp*ap*gp*a)-3') (dot) (5'-d(*tp*cp*tp*ap*ap*tp*g)-3'); chain: t, p; engineered: yes; other_details: soaked in the presence of dttp (1 millimolar) and zncl2 (1 millimolar)]
Source: [mol_id: 1; organism_scientific: homo sapiens; organism_common: human; expression_system: escherichia coli; mol_id: 2; synthetic: yes]
Keywords: [dna replication, dna repair, nucleotidyltransferase, complex (nucleotidyltransferase/dna)] Authors[h.pelletier,m.r.sawaya] ExpData[x-ray diffraction] R-value[0.17] Resolution[3.10]&lt;/description&gt;
&lt;/item&gt;
&lt;rdf:Description rdf:ID=&quot;manifest&quot;&gt;
&lt;mn:channels&gt;
&lt;rdf:Seq&gt;
&lt;rdf:li rdf:resource=&quot;http://metallo.scripps.edu/services/soap.php&quot; /&gt;
&lt;/rdf:Seq&gt;
&lt;/mn:channels&gt;
&lt;/rdf:Description&gt;
&lt;/rdf:RDF&gt;
</pre>
</td>
</tr>
</table>

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<wddxPacket version='1.0'>
<header>
<comment>results</comment>
</header>
<data>
<array length='1'>
<struct>
<var name='name'>
<string>John Q. Public</string>
</var>
<var name='userID'>
<string>l337d00d</string>
</var>
</struct>
</array>
</data>
</wddxPacket>

43
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<h3>Methods available at http://metallo.scripps.edu:80/services/xmlrpc.php</h3>
<hr noshade size=1><H3>method.sql</H3>
<H4>Documentation</H4><P style='font-size: 1.0em;'>General function to query the MDB database server.
Accepts a valid SQL query ("SELECT", "SHOW", or "DESCRIBE" statements only),
and returns the resulting rows as a structure.</P>
<H4>Signature</H4><P style='font-size: 1.0em;'>
<CODE style='font-size: 1.0em;'>struct method.sql(string)</CODE><BR>
</P>
<hr noshade size=1><H3>method.metallopdb</H3>
<H4>Documentation</H4><P style='font-size: 1.0em;'>Specialized function to retrieve a list of PDB structures
containing a particular metal ion, as indexed in the MDB. The retrieval
mode can be one of "first" (default) to get the first "n" PDB ids (sorted
alphabetically), "last" to get the last "n" ids, "random" to get "n"
random entries, and "new" to ge the newest "n" entries released/indexed.
The number of entries to retrieve is set using "count".
The result can be returned as XML-RPC structure, WDDX packet or RSS document</P>
<H4>Signature</H4><P style='font-size: 1.0em;'>
<CODE style='font-size: 1.0em;'>struct method.metallopdb(string, string, int, string)</CODE><BR>
</P>
<hr noshade size=1><H3>method.get</H3>
<H4>Documentation</H4><P style='font-size: 1.0em;'>Returns the requested file. It accepts 2 parameters:
the name of the file, and (optionally) the whether the base64 encoding
will be done on the "raw" (default) file, or the file after being
compressed with gzip ("gzip").</P>
<H4>Signature</H4><P style='font-size: 1.0em;'>
<CODE style='font-size: 1.0em;'>base64 method.get(string, string)</CODE><BR>
</P>
<hr noshade size=1><H3>system.listMethods</H3>
<H4>Documentation</H4><P style='font-size: 1.0em;'>This method lists all the methods that the XML-RPC server knows how to dispatch</P>
<H4>Signature</H4><P style='font-size: 1.0em;'>
<CODE style='font-size: 1.0em;'>array system.listMethods(string)</CODE><BR>
<CODE style='font-size: 1.0em;'>array system.listMethods()</CODE><BR>
</P>
<hr noshade size=1><H3>system.methodHelp</H3>
<H4>Documentation</H4><P style='font-size: 1.0em;'>Returns help text if defined for the method passed, otherwise returns an empty string</P>
<H4>Signature</H4><P style='font-size: 1.0em;'>
<CODE style='font-size: 1.0em;'>string system.methodHelp(string)</CODE><BR>
</P>
<hr noshade size=1><H3>system.methodSignature</H3>
<H4>Documentation</H4><P style='font-size: 1.0em;'>Returns an array of known signatures (an array of arrays) for the method name passed. If no signatures are known, returns a none-array (test for type != array to detect missing signature)</P>
<H4>Signature</H4><P style='font-size: 1.0em;'>
<CODE style='font-size: 1.0em;'>array system.methodSignature(string)</CODE><BR>
</P>

61
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<b>method.sql:</b>
"select source_id,expdata,rev_date,resolution,description
from protein limit 10"<br>
<table border=1>
<tr align='center'>
<th>source_id</th>
<th>expdata</th>
<th>resolution</th>
<th>description</th>
</tr>
<tr align='center'>
<td>1d8g</td>
<td>x-ray diffraction</td>
<td>0.74</td>
<td>Header: [deoxyribonucleic acid 23-oct-99 1d8g]
Title: [ultrahigh resolution crystal structure of b-dna decamer d(ccagtactgg)]
Compound: [mol_id: 1; molecule: 5'-d(*cp*cp*ap*gp*tp*ap*cp*tp*gp*gp*)-3'; chain: a; engineered: yes]
Source: [mol_id: 1; synthetic: yes]
Keywords: [calcium, alternate conformation, ultrahigh resolution, trp repressor, polyamide]</td>
</tr>
<tr align='center'>
<td>1gci</td>
<td>x-ray diffraction</td>
<td>0.78</td>
<td>Header: [serine protease 02-sep-98 1gci]
Title: [the 0.78 angstroms structure of a serine protease - bacillus lentus subtilisin]
Compound: [mol_id: 1; molecule: subtilisin; chain: null; ec: 3.4.21.62; engineered: yes; biological_unit: monomer]
Source: [mol_id: 1; organism_scientific: bacillus lentus; expression_system: bacillus subtilis]
Keywords: [bacillus lentus, hydrolase, serine protease, ultra-high resolution]</td>
</tr>
<tr align='center'>
<td>1iua</td>
<td>x-ray diffraction</td>
<td>0.80</td>
<td>Header: [electron transport 01-mar-02 1iua]
Title: [ultra-high resolution structure of hipip from thermochromatium tepidum]
Compound: [mol_id: 1; molecule: high-potential iron-sulfur protein; chain: a]
Source: [mol_id: 1; organism_scientific: thermochromatium tepidum; organism_common: bacteria]
Keywords: [ultra-high resolution, crystal structure]</td>
</tr>
<tr align='center'>
<td>1dpl</td>
<td>x-ray diffraction</td>
<td>0.83</td>
<td>Header: [deoxyribonucleic acid 27-dec-99 1dpl]
Title: [a-dna decamer gcgta(t23)tacgc with incorporated 2'-methoxy- 3'-methylenephosphate-thymidine]
Compound: [mol_id: 1; molecule: 5'-d(*gp*cp*gp*tp*ap*(t23)p*ap*cp*gp*c)-3'; chain: a, b; engineered: yes]
Source: [mol_id: 1; synthetic: yes]
Keywords: [deoxyribonucleic acid]</td>
</tr>
<tr align='center'>
<td>1m40</td>
<td>x-ray diffraction</td>
<td>0.85</td>
<td>Header: [hydrolase 01-jul-02 1m40]
Title: [ultra high resolution crystal structure of tem-1]
Compound: [mol_id: 1; molecule: beta-lactamase tem; chain: a; synonym: tem-1; ec: 3.5.2.6; engineered: yes; mutation: yes]
Source: [mol_id: 1; organism_scientific: escherichia coli; organism_common: bacteria; gene: bla; expression_system: escherichia coli; expression_system_common: bacteria; expression_system_strain: sf120; expression_system_vector_type: plasmid; expression_system_plasmid: palter ex ii - tem-1]
Keywords: [acylation mechanism, x-ray structure, ultra- high resolution]</td>
</tr>
</table>

23
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<?php
include_once 'SOAP/Client.php';
$key = 'xxxxxxxxxxxxxxxx'
$query = array(
'key' => $key,
'q' => 'link:metallo.scripps.edu',
'start' => 0,
'maxResults' => 10,
'filter' => true,
'restrict' => '',
'safeSearch' => false,
'lr' => '',
'ie' => '',
'oe' => ''
);
$wsdl = new SOAP_WSDL('GoogleSearch.wsdl');
$client = $wsdl->getProxy();
$result = $client->doGoogleSearch($query)
print_r($result);
?>

20
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<?php
$now = time();
$uptime = `uptime`;
$re='/^\s*([0-9]{1,2}:[0-9]{2}(am|pm))\s+up (.+),\s+(\d+) users,\s+load average: (.+), (.+), (.+)/';
$timestamp = gmdate('Y-m-d H:i:s', $now);
preg_match($re, $uptime, $part);
$uptime = array(
'time' => $part[1],
'duration' => $part[3],
'users' => (int)$part[4],
'load1' => (float)$part[5],
'load5' => (float)$part[6],
'load15' => (float)$part[7],
);
$packet = wddx_packet_start('uptime info');
wddx_add_vars($packet, 'timestamp', 'uptime');
$out = wddx_packet_end($packet);
echo $out;
?>

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<?php
// Sample REST server - returns uptime information
// Jesus M. Castagnetto
//$host = 'www.example.com';
//$port = 80;
//$serverPath = '/xmlrpc/server.php'
$host = 'jmc.sdsc.edu';
$port = 6666;
$serverPath = '/misc/ws_rest_sample_server.php';
$packet = file_get_contents("http://{$host}:{$port}{$serverPath}");
$tmp = wddx_deserialize($packet);
extract($tmp);
$sep = str_repeat('*',50);
echo <<< _END
$sep
Uptime for : $host
Timestamp (UTC) : $timestamp
Local time at host : {$uptime['time']}
Host has run for : {$uptime['duration']}
Number of current users : {$uptime['users']}
Average number of jobs in queue
1 minute : {$uptime['load1']}
5 minutes : {$uptime['load5']}
15 minutes : {$uptime['load15']}
$sep
_END;
?>

25
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<?php
// Sample REST server - returns uptime information
// Jesus M. Castagnetto
$re = '/^\s*([0-9]{1,2}:[0-9]{2}(am|pm))\s+up (.+),';
$re .= '\s+(\d+) users,\s+load average: (.+), (.+), (.+)/';
$now = time();
$uptime = `uptime`;
preg_match($re, $uptime, $part);
$timestamp = gmdate('Y-m-d H:i:s', $now);
$uptime = array(
'time' => $part[1],
'duration' => $part[3],
'users' => (int)$part[4],
'load1' => (float)$part[5],
'load5' => (float)$part[6],
'load15' => (float)$part[7],
);
$packet = wddx_packet_start('uptime info');
wddx_add_vars($packet, 'timestamp', 'uptime');
$out = wddx_packet_end($packet);
echo $out;
?>

20
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<?php
function getUptime() {
$now = time();
$uptime = `uptime`;
$re = '/^\s*([0-9]{1,2}:[0-9]{2}(am|pm))\s+up (.+),';
$re .= '\s+(\d+) users,\s+load average: (.+), (.+), (.+)/';
$timestamp = gmdate('Y-m-d H:i:s', $now);
preg_match($re, $uptime, $part);
$uptime = array(
'time' => $part[1],
'duration' => $part[3],
'users' => (int)$part[4],
'load1' => (float)$part[5],
'load5' => (float)$part[6],
'load15' => (float)$part[7],
);
return array($timestamp, $uptime);
}
?>

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<?php
require_once 'XML/RPC.php';
//$host = 'www.example.com';
//$port = 80;
//$serverPath = /rest/uptime.php';
$host = 'jmc.sdsc.edu';
$port = 6666;
$serverPath = '/misc/ws_xmlrpc_sample_server.php';
$message = new XML_RPC_Message('method.serverUptime');
$client = new XML_RPC_Client($serverPath, $host, $port);
$resp = $client->send($message);
$value = $resp->value();
$uptime = $value->getval();
$sep = str_repeat('~',56);
echo <<< _END
$sep
Uptime for : $host
Timestamp (UTC) : {$uptime['timestampUTC']}
Local time at host : {$uptime['timestampLocal']}
Host has run for : {$uptime['duration']}
Number of current users : {$uptime['users']}
Average number of jobs in queue
1 minute : {$uptime['load1']}
5 minutes : {$uptime['load5']}
15 minutes : {$uptime['load15']}
$sep
_END;
?>

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<?php
require_once 'XML/RPC/Server.php';
function hostUptime() {
$now = time();
$uptime = `uptime`;
$re = '/^\s*([0-9]{1,2}:[0-9]{2}(am|pm))\s+up (.+),';
$re .= '\s+(\d+) users,\s+load average: (.+), (.+), (.+)/';
preg_match($re, $uptime, $part);
// create the XML-RPC values
$timestamp = new XML_RPC_Value(gmdate('Ymd\TH:i:s', $now), 'dateTime.iso8601');
$host_ts = new XML_RPC_Value(date('Ymd\TH:i:s', $now), 'dateTime.iso8601');
$host_uptime = new XML_RPC_Value($part[3], 'string');
$host_users = new XML_RPC_Value($part[4], 'int');
$host_load1 = new XML_RPC_Value($part[5], 'double');
$host_load5 = new XML_RPC_Value($part[6], 'double');
$host_load15 = new XML_RPC_Value($part[7], 'double');
$hostInfo = array(
'timestampUTC' => $timestamp,
'timestampLocal' => $host_ts,
'duration' => $host_uptime,
'users' => $host_users,
'load1' => $host_load1,
'load5' => $host_load5,
'load15' => $host_load15
);
$uptime = new XML_RPC_Value($hostInfo, 'struct');
return new XML_RPC_Response($uptime);
}
// method metainfo
$hostUptime_sig = array(array($XML_RPC_Struct));
$hostUptime_doc = 'Returns the uptime information of the host,'
.' and a timestamp (UTC timezone) when the'
.' measure was made.';
// dispatch map
$map = array (
'method.serverUptime' => array (
'function' => 'hostUptime',
'signature' => $hostUptime_sig,
'docstring' => $hostUptime_doc
)
);
// start server
$server = new XML_RPC_Server($map);
$server->service();
?>

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<slide title='WS as library'>
<image align='center'
filename='images/local_extrnl_libs.png'/>
</slide>

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<slide title='What &amp; How'>
<break lines='2'/>
<blurb title='What is a web service?'>
Basically, a *web service* is an application with which other
applications can communicate over via a network, often using
XML to encapsulate data and context, and HTTP as the transport layer.
</blurb>
<break lines='2'/>
<blurb title='How do we expose a Web Service?'>
There are several ways (protocols) we can expose our web services
to the rest of the world, from a the minimalistic approach of the
"RESTafarians", to using XML-RPC, to SOAP and all its accompanying
specifications (UDDI, WSDL, WS-Security, WS-Context, etc.)
</blurb>
</slide>

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<slide title='Glossary'>
<list>
<bullet>*REST*: REpresentational State Transfer (the architecture
style of the Net)</bullet>
<bullet>*XML-RPC*: XML Remote Procedure Call</bullet>
<bullet>*SOAP*: Simple Object Access Protocol</bullet>
<bullet>*WSDL*: Web Services Description Language</bullet>
<bullet>*HTTP*: HyperText Transfer Protocol</bullet>
<bullet>*UDDI*: Universal Description, Discovery, and Integration</bullet>
<bullet>*CORBA*: Common Object Request Broker Architecture</bullet>
<bullet>*IDL*: (CORBA's) Interface Description Language</bullet>
<bullet>*RMI*: (Java's) Remote Method Invocation</bullet>
<bullet>*JINI*: Sun's Java-based system to network devices and applications
(includes Javaspaces, JINI Extensible Remote Incovation, etc.)</bullet>
<bullet>*SOA*: Services Oriented Architecture</bullet>
</list>
</slide>

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<slide title='MDB services'>
<list title='REST' fontsize='2.5em'>
<bullet>
URL: *http://metallo.scripps.edu/services/rest.php*
</bullet>
<bullet>
Functions: *sql* and *metallopdb*
</bullet>
<bullet>
Example:
http://metallo.scripps.edu/services/rest.php?func=metallopdb
&amp;metal=zn&amp;mode=new&amp;count=5&amp;format=rss
</bullet>
<!-- bullet>
*sql* Parameters: _query_ = urlencoded SQL query;
[_format_] = csv (default), wddx, serialized, table.
Example:
http://metallo.scripps.edu/services/rest.php?function=sql&amp;query=select
+source_id+from+protein+limit+10&amp;format=wddx
</bullet -->
<!-- bullet>
*metallopdb* Parameters: _metal_ = atomic symbol for the metal;
[_mode_]: one of: first (default), last, random, new;
[_count_]: how many PDB entries to retrieve (default = 5);
[_format_]: csv (default), wddx, rss, serialized
</bullet -->
</list>
<list title='XML-RPC' fontsize='2.5em'>
<bullet>
URL: *http://metallo.scripps.edu/services/xmlrpc.php*
</bullet>
<bullet>
struct *method.sql*(string query)
<!--
General function to query the MDB database server. Accepts a valid SQL
query ("SELECT", "SHOW", or "DESCRIBE" statements only), and returns the
resulting rows as a structure.
-->
</bullet>
<bullet>
struct *method.metallopdb*(string metal, string mode, int count, string format)
<!--
Specialized function to retrieve a list of PDB structures containing a
particular metal ion, as indexed in the MDB. The retrieval mode can be one
of "first" (default) to get the first "n" PDB ids (sorted alphabetically),
"last" to get the last "n" ids, "random" to get "n" random entries, and
"new" to ge the newest "n" entries released/indexed. The number of entries
to retrieve is set using "count". The result can be returned as XML-RPC
structure, WDDX packet or RSS document
-->
</bullet>
</list>
<list title='SOAP' fontsize='2.5em'>
<bullet>
URL: *http://metallo.scripps.edu/services/soap.php*
</bullet>
<bullet>
Methods: *sql*, *metallopdb*, *rssmetallopdb*
</bullet>
<!-- bullet>
*sql* : allows for SELECT, SHOW, DESCRIBE SQL queries
</bullet>
<bullet>
*metallopdb* : information about metal containing proteins given a
metal, a mode, and a count
</bullet>
<bullet>
*rssmetallopdb* : similar to the _metallopdb_ with an RSS document as
output.
</bullet -->
</list>
</slide>

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<slide title='Multi-WS'>
<blurb title='The MDB case'>
A set of simple modular functions that can be wrapped
in each of the services.
</blurb>
<image align='center'
filename='images/mdbapi_impl.png'/>
</slide>

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<slide title='Protocols'>
<break lines='4'/>
<blurb title='The Good, The Bad, and The Ugly'>
There are at least 3 ways to expose a web service. Two are what we
understand as communication/transport protocols (XML-RPC and SOAP),
and the other is more a "way of doing things" (REST).
</blurb>
<blurb>
You decide which is which %:-)%
</blurb>
</slide>

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<slide title='Libraries'>
<list title='REST' fontsize='2.5em'>
<bullet>PEAR::XML_Wddx, http://pear.php.net/package/XML_Wddx</bullet>
<bullet>PHP's wddx extension (--enable-wddx)</bullet>
</list>
<list title='XML-RPC' fontsize='2.5em'>
<bullet>PEAR::XML_RPC, http://pear.php.net/package/XML_RPC</bullet>
<bullet>Useful Inc's XML-RPC, http://xmlrpc.usefulinc.com/php.html </bullet>
<bullet>PHP's xmlrpc extension (--with-xmlrpc)</bullet>
<bullet>More implementations: http://www.xmlrpc.com/directory/1568/implementations</bullet>
</list>
<list title='SOAP' fontsize='2.5em'>
<bullet>PEAR::SOAP, http://pear.php.net/package/SOAP</bullet>
<bullet>NuSOAP, http://dietrich.ganx4.com/nusoap/</bullet>
<bullet>PHP5's SOAP extension (--enable-soap)</bullet>
</list>
</slide>

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<slide title='More refs'>
<list fontsize='2.5em' title='Basic specs to know'>
<bullet>*XML*: http://www.w3.org/XML</bullet>
<bullet>*XML Namespaces*: http://www.w3.org/TR/REC-xml-names</bullet>
<bullet>*XML Schemas*: http://www.w3.org/XML/Schema</bullet>
<bullet>*WDDX*: http://www.openwddx.org/</bullet>
<bullet>*REST*: http://internet.conveyor.com/RESTwiki/moin.cgi/FrontPage</bullet>
<bullet>*XML-RPC*: http://www.xmlrpc.com/</bullet>
<bullet>*SOAP*: http://www.w3.org/TR/soap</bullet>
<bullet>*WSDL*: http://www.w3.org/TR/wsdl</bullet>
<bullet>*Web Services Activity*: http://www.w3.org/2002/ws/</bullet>
</list>
<list fontsize='2.5em' title='Sites, talks, articles, etc.'>
<bullet>*W3C*: http://www.w3.org/</bullet>
<bullet>*OASIS committees*: BR/
http://www.oasis-open.org/committees/committees.php</bullet>
<bullet>*Cover Pages*: http://xml.coverpages.org/</bullet>
<bullet>*WebServices.org*: http://webservices.org/</bullet>
<bullet>Web Services section at http://talks.php.net/</bullet>
<bullet>Papers at http://webservices.org/</bullet>
<bullet>XML-RPC tutorials at
http://www.xmlrpc.com/directory/1568/tutorialspress</bullet>
</list>
</slide>

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<slide title='More information'>
<list fontsize='2.5em' title='Basic specs to know' type='none'>
<bullet>*XML*: http://www.w3.org/XML</bullet>
<bullet>*XML Namespaces*: http://www.w3.org/TR/REC-xml-names</bullet>
<bullet>*XML Schemas*: http://www.w3.org/XML/Schema</bullet>
<bullet>*WDDX*: http://www.openwddx.org/</bullet>
<bullet>*REST*: http://internet.conveyor.com/RESTwiki/moin.cgi/FrontPage</bullet>
<bullet>*XML-RPC*: http://www.xmlrpc.com/</bullet>
<bullet>*SOAP*: http://www.w3.org/TR/soap</bullet>
<bullet>*WSDL*: http://www.w3.org/TR/wsdl</bullet>
<bullet>*Web Services Activity*: http://www.w3.org/2002/ws/</bullet>
</list>
<list fontsize='2.5em' title='Sites, talks, articles, etc.' type='none'>
<bullet>*W3C*: http://www.w3.org/</bullet>
<bullet>*OASIS committees*: BR/
http://www.oasis-open.org/committees/committees.php</bullet>
<bullet>*Cover Pages*: http://xml.coverpages.org/</bullet>
<bullet>*WebServices.org*: http://webservices.org/</bullet>
<bullet>Web Services section at http://talks.php.net/</bullet>
<bullet>Papers at http://webservices.org/</bullet>
<bullet>XML-RPC tutorials at
http://www.xmlrpc.com/directory/1568/tutorialspress</bullet>
</list>
</slide>

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<slide title='Articles, etc.'>
<list>
<bullet>Web Services section at http://talks.php.net/</bullet>
<bullet>Papers at http://webservices.org/</bullet>
<bullet>XML-RPC tutorials at
http://www.xmlrpc.com/directory/1568/tutorialspress</bullet>
</list>
</slide>

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<slide title='References'>
<list title='Presentations and articles'>
<bullet>*SOAP*: Simple Object Access Protocol</bullet>
<bullet>The RESTful way</bullet>
<bullet>XML-RPC: remote calls made easy</bullet>
<bullet>SOAP: flexible, extendable, and not so "simple"</bullet>
<bullet>WSDL, WS-SIG and other SOAP buddies</bullet>
<bullet>References</bullet>
</list>
<list title='Packages and libraries'>
<bullet>PEAR::SOAP http://pear.php.net/SOAP</bullet>
<bullet>The RESTful way</bullet>
<bullet>XML-RPC: remote calls made easy</bullet>
<bullet>SOAP: flexible, extendable, and not so "simple"</bullet>
<bullet>WSDL, WS-SIG and other SOAP buddies</bullet>
<bullet>References</bullet>
</list>
<list title='Specifications'>
<bullet>*SOAP*: Simple Object Access Protocol</bullet>
<bullet>The RESTful way</bullet>
<bullet>XML-RPC: remote calls made easy</bullet>
<bullet>SOAP: flexible, extendable, and not so "simple"</bullet>
<bullet>WSDL, WS-SIG and other SOAP buddies</bullet>
<bullet>References</bullet>
</list>
</slide>

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<?xml version="1.0" encoding="ISO-8859-1"?>
<slide title="REST service">
<example type='php' filename='scripts/rest-example.php'
output='0'/>
<example type='xml' filename='output/rest-example.out'/>
</slide>

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<?xml version="1.0" encoding="ISO-8859-1"?>
<slide title="REST &amp; XML">
<example title='Assume we have the array' type='php'>
<![CDATA[$data = array(
array(
'name'=>'John Q. Public',
'userID'=>'l337d00d'
));]]>
</example>
<blurb title='WDDX'>
Simple data enconding format, handles scalars, arrays/structures,
date and time.
</blurb>
<example type='xml' fontsize='2em' filename='output/wddx_example.xml'/>
<example title='... or use my own XML format' type='xml'
fontsize='2em' filename='output/myown.xml'/>
</slide>

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<?xml version="1.0" encoding="ISO-8859-1"?>
<slide title="Being RESTful">
<blurb>
*REST* is the acronym for *RE*presentational *S*tate *T*ransfer, and is a
term coined by Roy Fielding [1] in a dissertation attempting to describe
formally the Web architectural style.
</blurb>
<blurb>
The argument is that the HTTP methods (GET, POST, etc.) define a limited set
of *verbs* that can be applied to an (in principle) infinite number of
*nouns* (URIs).
</blurb>
<blurb>
This design has some beneficial effects:
</blurb>
<list type="alpha" fontsize="2.5em" marginright="1em">
<bullet>
It allows simpler interoperation between otherwise uncoordinated agents
(web clients, servers, spiders, etc.)
</bullet>
<bullet>
The HTTP semantics constitutes a coordination language general enough to
be of use in any desired communication pattern. Its methods make it akin
to message passing or function calling protocols.
</bullet>
<bullet>
Offering a service is a simple as publishing a URL.
</bullet>
</list>
<blurb fontsize="1.5em">
[1] Roy Fielding's Ph.D. dissertation
"_Architectural Styles and the Design of Network-based Software Architectures_"
</blurb>
</slide>

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<?xml version="1.0" encoding="ISO-8859-1"?>
<slide title="SOAP client">
<example title='A simple Google search client'
fontsize='2em'
output='0' type='php' filename='scripts/ex_php_google.php'/>
<example title='... and the result of running it'
fontsize='1.5em'
filename='output/php_google.out'/>
</slide>

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<?xml version="1.0" encoding="ISO-8859-1"?>
<slide title="SOAP">
<blurb title="Simple Object Access Protocol">
It is a "lightweight protocol
for exchange of information in a decentralized,
distributed environment" [1]
</blurb>
<list type="arrow" title="SOAP provides">
<bullet>XML based messaging</bullet>
<bullet>Support for message routing</bullet>
<bullet>Encoding rules for expressing data types (XML Schema)</bullet>
<bullet>Conventions for using SOAP for RPC</bullet>
<bullet>Transport Independence</bullet>
</list>
<blurb title="Related specs and standards">
WSDL, UDDI, MIME and DIME attachements,
SOAP Authentication, ebXML, XML Security, etc.
</blurb>
<blurb fontsize="1.5em">
[1] from the SOAP specs, http://www.w3.org/TR/SOAP/
</blurb>
</slide>

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<?xml version="1.0" encoding="ISO-8859-1"?>
<slide title='MDB SOAP'>
<list title='Methods'>
<bullet>_sql_ : allows for SELECT, SHOW, DESCRIBE SQL queries</bullet>
<bullet>_metallopdb_ : information about metal containing proteins given a
metal, a mode, and a count</bullet>
<bullet>_rssmetallopdb_ : similar to the _metallopdb_ with the output
formated as an RSS document</bullet>
</list>
<example title='Using the methods sql, metallopdb and rssmetallopdb'
type='html' align='center' examplebackground='#ffffdd'
result='0' fontsize='1.5em' filename='output/test_soap_out.html'/>
</slide>

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<?xml version="1.0" encoding="ISO-8859-1"?>
<slide template="titlepage" fontsize='3.5em'>
<title>Welcome!</title>
</slide>

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<slide title='Contents'>
<break lines='2'/>
<list fontsize='4em' type='darrow' effect='hide'>
<bullet>What is a web service?</bullet>
<bullet>The RESTful way</bullet>
<bullet>XML-RPC: remote calls made easy</bullet>
<bullet>SOAP: flexible, extendable, and not so "simple"</bullet>
<bullet>WSDL and an example (Google Search)</bullet>
<bullet>Glossary, libraries, and references</bullet>
</list>
</slide>

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<?xml version="1.0" encoding="ISO-8859-1"?>
<slide title="Using XML">
<blurb title='WDDX'>
Simple data enconding format, handles scalars, arrays/structures,
date and time.
[http://www.openwddx.org/]
</blurb>
<blurb title='CML'>
A very complete format specification for chemical data:
structural information (coordinates, sequence, etc.) and properties (charges,
spectroscopical data, etc.). One of the first XML applications designed.
[http://www.xml-cml.org/]
</blurb>
<blurb title='RSS'>
Widely used for news syndication (e.g. Slashdot, Freshmeat,
PHPBuilder).
[http://groups.yahoo.com/group/rss-dev/files/namespace.html]
</blurb>
</slide>

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<slide title='Why use WS?'>
<list title='A WS gives you'>
<bullet>Language, Operating System, and Implementation independence</bullet>
<bullet>Loose coupling between components/applications</bullet>
<bullet>Abstract way of exposing what each service offers</bullet>
</list>
<blurb>
When we have components that are loosely coupled, can be composed easily,
and are independent, we have a system designed using a "Services Oriented
Architecture" (SOA).
</blurb>
<blurb>
In the past, SOAs were built from CORBA/IDL components, JINI/RMI, or other
similar approaches, none of which combined the characteristics provided by
Web Services.
</blurb>
<blurb>
*But*, at the present time, Web Services do support some of the more
interesting parts of SOAs: orchestration and dynamic composition of
services, reliable aysnchronous communication, etc. Although there are
specs in the works for all of these aspects.
</blurb>
</slide>

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<?xml version="1.0" encoding="ISO-8859-1"?>
<slide title="WSDL">
<blurb>
The Web Services Description Language, describes the API a
web service exposes to the world. It is usually generated from
an interface, rarely written from scratch (unless the programmer
likes pain, a lot)
</blurb>
<blurb>
A WSDL document usually has 4 major sections: type definition,
message definition (which refers to the types), port description
(what input and output message are associated),
and a binding definitions (how the ports map into the services
methods).
</blurb>
<example title='The Google Search WSDL' type='xml'
fontsize='1em' filename='misc/GoogleSearch.wsdl'/>
</slide>

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<slide title='method.sql'>
<example title='Using method.sql from the XML-RPC service' result='0'
fontsize='1.2em' rfontsize='1em' outputbackground='#ffffdd'>
<![CDATA[<?php
require_once "XML/RPC.php";
require_once "slides/mdb/scripts/xmlrpc_util.php";
require_once "slides/mdb/scripts/mdb_tests.cfg";
?>
<b>method.sql:</b>
<small>"select source_id,expdata,rev_date,resolution,description
from protein limit 10"</small><br>
<?php
$method = "method.sql";
$query = "select source_id,expdata,resolution,description ";
$query .= "from protein where expdata like '%x-ray%' and ";
$query .= "resolution >= 0.7 order by resolution limit 5";
$q = new XML_RPC_Value($query, $GLOBALS['XML_RPC_String']);
$msg = new XML_RPC_Message($method,array($q));
$c=new XML_RPC_Client(XMLRPC_URI, MDB_SERVER_NAME, MDB_SERVER_PORT);
$r = $c->send($msg);
if (!$r->faultCode()) {
echo toTable(XML_RPC_decode($r->value()));
} else {
echo "<pre>\n";
echo "ERROR: ".$r->faultCode()." -- ".$r->faultString();
echo "</pre>\n";
}
?>
]]>
</example>
<example title='Output' type='html' filename='output/xmlrpc_method_sql_out.html'
fontsize='1.5em' examplebackground='#ffffdd'/>
</slide>

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<?xml version="1.0" encoding="ISO-8859-1"?>
<slide title="XML-RPC">
<blurb>
"It's a spec and a set of implementations that allow software running on
disparate operating systems, running in different environments to make
procedure calls over the Internet." [1]
</blurb>
<blurb>
"It's remote procedure calling using HTTP as the transport and XML as the
encoding. XML-RPC is designed to be as simple as possible, while allowing
complex data structures to be transmitted, processed and returned." [1]
</blurb>
<blurb>
It supports server introspection. Making it easy for a client application to
interrogate and discover the available methods and their paramaters.
</blurb>
<blurb>
XML-RPC also supports "box-carring" of requests, i.e. sending a series
of RPC calls at one time. Uses the *system.multicall* method.
</blurb>
<blurb>
It does not support message passing/redirection, or complex data type
definitions. But it does support mappings to simple and structured data
types to/from many languages.
</blurb>
<blurb fontsize="1.5em">
[1] from http://www.xmlrpc.org/
</blurb>
</slide>

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<slide title='XML-RPC (2)'>
<example type='php' result='0' fontsize='1.0em' rfontsize='1.0em'
outputbackground='#ffffdd'>
<![CDATA[
<?php
require_once "XML/RPC.php";
require_once "xmlrpc_util.php";
require_once "myconfig.cfg";
$c=new XML_RPC_Client(XMLRPC_URI, MDB_SERVER_NAME, MDB_SERVER_PORT);
$f=new XML_RPC_Message('system.listMethods');
$v=rpc_call($c, $f);
print "<h2>Methods available at http://" . $c->server . ":" .
$c->port . $c->path . "</h2>\n";
if ($v) {
for($i=0; $i<$v->arraysize(); $i++) {
$mname=$v->arraymem($i);
print "<hr noshade size=1><H3>" . $mname->scalarval() . "</H3>\n";
$f=new XML_RPC_Message('system.methodHelp');
$f->addParam(new XML_RPC_Value($mname->scalarval(), "string"));
$w=rpc_call($c, $f);
if ($w) {
$txt=$w->scalarval();
if ($txt!="") {
print "<H4>Documentation</H4><P style='font-size: 1.0em;'>${txt}</P>\n";
} else {
print "<P>No documentation available.</P>\n";
}
}
$f=new XML_RPC_Message('system.methodSignature');
$f->addParam(new XML_RPC_Value($mname->scalarval(), "string"));
$w=rpc_call($c, $f);
if ($w) {
print "<H4>Signature</H4><P style='font-size: 1.0em;'>\n";
if ($w->kindOf()=="array") {
for($j=0; $j<$w->arraysize(); $j++) {
$x=$w->arraymem($j);
$ret=$x->arraymem(0);
print "<CODE style='font-size: 1.0em;'>" . $ret->scalarval() . " " .
$mname->scalarval() ."(";
if ($x->arraysize()>1) {
for($k=1; $k<$x->arraysize(); $k++) {
$y=$x->arraymem($k);
print $y->scalarval();
if ($k<$x->arraysize()-1) {
print ", ";
}
}
}
print ")</CODE><BR>\n";
}
} else {
print "Signature unknown\n";
}
print "</P>\n";
}
}
}
?>
]]>
</example>
<example title='Output' type='html' filename='output/xmlrpc_api_out.html'
fontsize='1em' examplebackground='#ffffdd'/>
</slide>