Todo List: SOAP

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no status	49

	(167)

Is the kegg binding broken? Compare with KEGGSOAP. That seems to be broken also.
Wrong version of the WSDL!!!!

Broken readSchema thanks to the way we now implement processSchemaTypes. Suceeds for ops.xsd, but misses the top-level schema.

Now problem in ops.wsdl with Error in setClassUnion(name, elTypes, where = where) : the member classes must be defined: not true of "exchange.publication-reference", "exchange.application-reference", "exchange.priority-claim", "publication-reference", "application-reference", "priority-claim" This is defining any-referenceType. Looks like we are getting the names from the Elements, but not from their types. This is in mapSOAPTypeToS.

For ops.wsdl, now get a " attempt to use zero-length variable name" error in getClassDef(). Trying to define priority-claimType, and that induces its base class definition and that involves a Union office-of-filingType. The repn for this has a "" in the first element. The first element of slotTypes has "" as its name. It is a ClassDefinition. The XML is

	<complexType name = "office-of-filingType">
		<choice>
			<sequence>
				<element name = "region" type = "exch:regionType"/>
				<element name = "country" type = "exch:countryType" minOccurs = "0"/>
			</sequence>
			<element name = "country" type = "exch:countryType"/>
		</choice>
	</complexType>

So we see we do have an issue with the first element - the sequence. The name should be a composition of these.

Changes now cause MassSpecAPI wsdl to infinitely recurse when resolving StringArray.
The problem is that we have two ArrayOfString elements in w@types[[1]]. Now they are both Element objects. In the older versions (0.4-0) of XMLSchema, these were SimpleSequenceType and Element. So the first one has become an element. There is no reason for this:

 <s:complexType name="ArrayOfString">
   <s:sequence>
     <s:element minOccurs="0" maxOccurs="unbounded" name="string" nillable="true" type="s:string" />
   </s:sequence>
 </s:complexType>

Are we just inserting them by name in the new processSchemaTypes and processSchemaNodes. No that's still the same. It is the fixTypeNames.

Now problem in ops.xsd (not exchange) for priority-claimType. That extends the one in exchange with the same name. When we try to define that class, we end up a with a NULL The slotType for priority-active-indicator seems to be NULL in createClassRepresentation and above that in defineClassDefinition. This happens when we resolve the baseType in defineClassDefinition for the derived class. Turns out, priority-active-indicator in w@types[[2]][["priority-active-indicator"]] is . This is an element and then a simpleType with a restriction. Problem was processSchemaElement was not handling that case and returning NULL explicitly.

4th slot in priority-claimType, i.e. priority-linkage-type. When we resolve the type slot, we end up with . The problem s that the reference to a string has the wrong nsuri. It points to exchange, not XSD.

XMLSchema:::resolve(w@types[[2]]$"priority-claimType"@slotTypes[[4]], w@types)

This goes through SOAPTypeReference first and then tries to resolve the type. But that element for priority-linkage-type has the wrong nsuri.

getElementRef wasn't matching the prefix against the names of the namespaceDefs.

Defining the class document-id from EPO/ops.wsdl causes serious infinite recursion. This is a built-in type from the XSD schema defn. So we need to define this as a built-in.

Recheck the case where we need a "" as the prototype value for slots. ?listOrganisms? and the species = ""? See r:code[@id="testProtos"

Lift nested SchemaCollection and SchemaTypes due to imports up to top-level of types. See ops.xsd and ops.wsdl.

This is broken again. But this works. Not it doesn't. CSID and token are the parameters.

 o@functions$GetExtendedCompoundInfoArray(list(CSIDs = c(23500L, 23543L)), token = token))

But

f@functions$GetExtendedCompoundInfoArray(c(23500, 23543), token)

fails in the conversion.
See createVectorCoercions in genCode.R (called from createArrayClass)
Make the coercion methods that we generate for arrays/sequences first coerce to the base type and then to the new class so that we get to include the other base types, e.g. integer, numeric, etc.

library(SSOAP)
w = processWSDL("WSDLs/MassSpecAPI.asmx?WSDL", port = "MassSpecAPIHttpPost")  
f = genSOAPClientInterface(w)
f@functions$GetExtendedCompoundInfoArray(c(23500, 23543), token)

Why do fromXML() return a list when it could simplify to a vector
Was passing the type as the second argument, not the type argument.

w = processWSDL("WSDLs/MassSpecAPI.asmx?WSDL", port = 3)
z = genSOAPClientInterface(w, verbose = TRUE)
db = z@functions$GetDatabases()

This returns a list.

Changed processRestriction to recognize result of resolving the sub-type and stripping away the SOAPComplexType.

Resolve for StringArray in port = 3. Ending up with ComplexType for the StringArray type in types[[2]][[1]] and its content is a SimpleSequenceType. Goes through processRestriction because we have

<s:complexType name="StringArray">
  <s:complexContent mixed="false">
    <s:restriction base="soapenc:Array">
      <s:sequence>
        <s:element minOccurs="0" maxOccurs="unbounded" name="String" type="s:string"/>
      </s:sequence>
    </s:restriction>
  </s:complexContent>
</s:complexType>

Then this gets resolved oddly.

ChemSpider breaks in processWSDL for port = 3

w = processWSDL("../../SOAP/WSDLs/MassSpecAPI.asmx?WSDL", port = 3)

StringArray issue. This is as a result of IsEmptyParameter being called at this stage. If we comment that out in wsdlProcess.R (#555), things are fine. Deferred until createOperationDefinition and generating code.

defining dependent classes is not working for eutils.
The warning about ItemType is legitimate as it is a self-reference to the class being defined.
Are these due to them being Element objects and do not have a corresponding class? If so, should we have mapSOAPTypeToS map an element to its actual type, (it does for Info) or should we create alias classes? The error about Info, when resolved, we have an Element with NA as its name and then a type which is an Element too and that is the .

undefined slot classes in definition of "eGqueryRequest": term(class "term"), tool(class "tool"), email(class "email")
undefined slot classes in definition of "eInfoRequest": db(class "db"), tool(class "tool"), email(class "email")
undefined slot classes in definition of "ErrorListType": PhraseNotFound(class "PhraseNotFound"), FieldNotFound(class "FieldNotFound")
undefined slot classes in definition of "TermSetType": Count(class "Count"), Explode(class "Explode")
undefined slot classes in definition of "TranslationType": From(class "From"), To(class "To")
undefined slot classes in definition of "WarningListType": PhraseIgnored(class "PhraseIgnored"), QuotedPhraseNotFound(class "QuotedPhraseNotFound"), OutputMessage(class "OutputMessage")
undefined slot classes in definition of "eSearchResult": ERROR(class "ERROR"), Count(class "Count"), RetMax(class "RetMax"), RetStart(class "RetStart"), QueryKey(class "QueryKey"), WebEnv(class "WebEnv"), QueryTranslation(class "QueryTranslation")
undefined slot classes in definition of "eSearchRequest": db(class "db"), term(class "term"), WebEnv(class "WebEnv"), QueryKey(class "QueryKey"), usehistory(class "usehistory"), tool(class "tool"), email(class "email"), field(class "field"), reldate(class "reldate"), mindate(class "mindate"), maxdate(class "maxdate"), datetype(class "datetype"), RetStart(class "RetStart"), RetMax(class "RetMax"), rettype(class "rettype"), sort(class "sort")
Class "StringEnum" is defined (with package slot ‘XMLSchema’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘.GlobalEnv’
undefined slot classes in definition of "ItemType": Item(class "ItemType")
undefined slot classes in definition of "eSummaryRequest": db(class "db"), id(class "id"), WebEnv(class "WebEnv"), query_key(class "query_key"), retstart(class "retstart"), retmax(class "retmax"), tool(class "tool"), email(class "email")
undefined slot classes in definition of "IdCheckListType": ERROR(class "ERROR")

Call wsGoBioBase method.
We can create a session using the GET interface. SearchMassC12 is not in that collection of methods, so we then have to switch over to the SOAP interface.

library(SSOAP)
z = processWSDL("WSDLs/wsGoBioSpace.asmx?WSDL", port = "wsGoBioSpaceHttpGet")
f = genSOAPClientInterface(z)
session = f@functions$CreateSession(AdductIds = c(2,3), DepositorIds = c(3,6,8))
f@functions$GetMonoisotopicWeight("H2O")
f@functions$GetMolecularWeight("H2O")

Now the SOAP interface:

library(SSOAP)
zs = processWSDL("WSDLs/wsGoBioSpace.asmx?WSDL", port = 1)
fs = genSOAPClientInterface(zs)

session = fs@functions$CreateSession(AdductIds = c(2L,3L), DepositorIds = c(3,6,8))
fs@functions$SearchMass12C(SessionID = session, mass = 579.1705, tolerance = 0.001)

[FIXED] Problem in converting the result. Had a NULL type for the adduct slot in the MassSearchHit in newSOAPClass. Explicitly determine slot if type is NULL. But is this an inherited slot and that's why we don't have the type? Yes. Perhaps when we resolve the type to put in the parameters or in the return value slot, we have to collect all the inherited slots. This can just merge the slot types. Can add an argument to resolve() to merge these, or create a new function that calls resolve and then merge.
Also, figure out how to call CreateSession with SOAP interface.

CreateSession in wsGoBioBase.
For now, let's use GET or POST

z = processWSDL("WSDLs/wsGoBioSpace.asmx?WSDL", port = "wsGoBioSpaceHttpGet")
f = genSOAPClientInterface(z)
f@functions$CreateSession(AdductIds = c(2,3), DepositorIds = c(3,6,8))

GUID should be "04729173-A960-4A1A-83A8-538B2C1E3806"
Not being converted
Not getting converted from the string returned by getForm. That was because we have an Element which is not a SOAPType. So check for GenericSchemaType.
base64 conversion.

Build converters that understand attributes, etc. [Mostly done for ClassDefinition at least].
[Fixed] Dropping the Name element on Depositor.
For wsGoBioSpace, the null arguments are elements that have a null type. Is that okay?
Also, the return from GetDepositors is wrong. We don't get the attribute and we miss the name. We need to mark the slots that are attributes as attributes and/or write a converter to get them.

z = processWSDL("WSDLs/wsGoBioSpace.asmx?WSDL")
f = genSOAPClientInterface(, z)

f@functions$GetDepositors()

eutils.wsdl. DbListType. The slot has an NA for name. But this is a curious one we can reduce. This is a choice with only one element, but that element can occur 0 or more times. We could represent this as a SimpleSequenceType with an Element DbName as the elType.
eutils.wsdl (and pmml schema [FIXED]) seem to give same problem with EnumValuesDef and NULL.
Fixed the processWSDL() for eutils. but genSOAPClientInterface() fails. Error in FUN(X[[1L]], ...) : Don't have a meaningful value for type In addition: Warning messages: 1: undefined slot classes in definition of "eGqueryRequest": term(class "term"), tool(class "tool"), email(class "email") 2: In is.na(type) : is.na() applied to non-(list or vector) of type 'S4' The type is a SimpleSequenceType of string elements. But the name is NA. This is a slot in DbListType. The name of the element should be DbName. But the name of the class could be DbListType. This need not be a slot but the actual class definition as it is zero or more elements <DbName>
[FIXED] Issue is setting the target namespace to the nsuri slot. The targetNamespace value is NULL.

"http://xml.nig.ac.jp/wsdl/ARSA.wsdl" is broken with

Error in UseMethod("xmlNamespaceDefinitions") : 
  no applicable method for 'xmlNamespaceDefinitions' applied to an object of class "NULL"

Put back the check for empty parameters in processWSDLOperation in wsdlProcess.R which induces resolving types. Turned off while debugging.
This can be deferred to the code generation stage.

Broken the following:
[FIXED - interface not tested] "http://www.massbank.jp/api/services/MassBankAPI?wsdl"
[FIXED - interface not tested] "WSDLs/webservice.php?wsdl"
"http://www.brenda-enzymes.org/soap/brenda.wsdl" - in genSOAPClientInterface() as part of mapSOAPTypeToS. Error in resolve(type, types, namespaceDefs) : can't find namespace ws.brenda of SOAPTypeReference ArrayOfIntegers in context The names on context are NULL. We should have 2 elements in the context, but we have only one. This is because we have types schema list of actual typedefs.
Need to use the names paces from each of the SchemaTypes
"WSDLs/webservice.php?wsdl" [FIXED] got the wrong URI on WSAuth SOAPTypeReference for updatePathway slot.

Do we need to store the namespace map. Compute it from the XML document with xmlNamespaceDefinitions(doc) and perhaps store it in the SOAPServerDescription and then pass it to genSOAPClientInterface() from that. But why did we not need it in the past? We must have resolved everything.
"http://www.brenda-enzymes.org/soap/brenda.wsdl" The types we end up with here is a SchemaTypes, not a SchemaCollection. Use to be fine. So something has changed. The namespaceDefs() we pass along to resolve is an empty list and is so in defineClasses.

Can process wsGoBio... but that now breaks pretty much everything but KEGG. pug_soap_csi, MassSpec and @topic="testing" doesn't give us back anything but NULL or try-error.
BIG problem is that we are repeating the element names when serializing: e.g.

    <SearchByMass2 xmlns="http://www.chemspider.com/">
      <mass>
        <mass xmlns="http://www.chemspider.com/">89.04767</mass>
      </mass>
      <range>
        <range xmlns="http://www.chemspider.com/">0.01</range>
      </range>
    </SearchByMass2>

pmml again.

library(XMLSchema)
tt = readSchema("/Users/duncan/Rpackages/XMLSchema/samples/pmml-4-0.xsd")

pmml schema. Problem with the group element. There is no name. Need to merge the group into the slot types list. processSequence. We do process the group (with processGroup) and that resolves the elements but not necessarily correctly. It also returns them as a single object (in this case SOAPComplexType). But shouldn't this really be a group and we know that we should merge the elements.

tt = readSchema("/Users/duncan/Rpackages/XMLSchema/samples/pmml-4-0.xsd")

<xs:sequence>
  <xs:element ref="Extension" minOccurs="0" maxOccurs="unbounded"/>
  <xs:group ref="PREDICATE"/>
  <xs:choice>
    <xs:sequence>
      <xs:element ref="Partition" minOccurs="0"/>
      <xs:element ref="ScoreDistribution" minOccurs="0" maxOccurs="unbounded"/>
      <xs:element ref="Node" minOccurs="0" maxOccurs="unbounded"/>
    </xs:sequence>
    <xs:group ref="EmbeddedModel"/>
  </xs:choice>
</xs:sequence>

When creating a class that extends string, create a coercion method for it.

Make certain the counts are on the different elements/types so that we know if they are option. See GetIDList
getElementRef() computes them.

pug_soap broken again now that we have fixed up some of the schema stuff in processSchemaType (with groups, gluing together additional attributes, etc.) Also MassSpec. computeName with NULL.
Issue for pug_soap is in resolve of GetOperationStatus - AGAIN!!! The ns is wrong in the SOAPTypeReference. It is AnyKeyType which is the value of the type.

Make certain we can handle base64Binary as a PrimitiveSOAPType

w = processWSDL("WSDLs/wikipathways.wsdl")
wk = genSOAPClientInterface(, w)
x = wk@functions$getPathwayAs(list(fileType = "svg", pwId = "WP1984"))

And now when we convert this to raw

z = as(x@data, "character")
substring(z, 1, 1000)

x = wk@functions$getPathwayAs(list(fileType = "png", pwId = "WP1984"))
z = as(x@data, "raw")
writeBin(z, "/tmp/foo.png")  # or use rasterImage to draw it.

pug = processWSDL("http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl")
pugi = genSOAPClientInterface(, pug)

i.e. that we have the R classes already defined
Or use wikipathways and getPathwayAs.

wsGoBioSpace fails. Now because of a zero-length name of a slot in MassSearchHit.
[FIXED] Currently because of short and unsignedByte.

w = processWSDL("WSDLs/wsGoBioSpace.asmx?WSDL")
f = genSOAPClientInterface(, w)

GET and POST support
Now that we can generate the interface, we have to deal with HttpGet methods. Done, but need to handle arrays. (See http://www.chemspider.com/MassSpecAPI.asmx?op=GetExtendedCompoundInfoArray)

z = getForm("http://www.chemspider.com/MassSpecAPI.asmx/SearchByMass2", 
               mass = 89.0476, range = 0.01, .opts = list(httpheader = c("Content-Type" = "application/soap+xml")))
z = getURLContent("http://www.chemspider.com/MassSpecAPI.asmx/GetDatabases", .opts = list(httpheader = c("Content-Type" = "application/soap+xml")))

z = getForm("http://www.chemspider.com/MassSpecAPI.asmx/SearchByFormula2", formula = "H2O", .opts = list(httpheader = c("Content-Type" = "application/soap+xml")))

z = getForm("http://www.chemspider.com/MassSpecAPI.asmx/GetExtendedCompoundInfo", csid = "23543", token = token,
              .opts = list(httpheader = c("Content-Type" = "application/soap+xml")))

chemSpi = function(op, ..., token = getOption("ChemSpiderToken", NA), server = "http://www.chemspider.com/MassSpecAPI.asmx/") { u = sprintf("%s%s", server, op) args = list(...) if(!is.na(token)) args$token = token z = getForm(u, .params = args, .opts = list(httpheader = c("Content-Type" = "application/soap+xml")))<xml:attr></xml:attr> z } makeFun = function(op, params, type, location = "http://www.chemspider.com/MassSpecAPI.asmx/") { u = sprintf("%s%s", location, op) } So it looks like if we had a .SOAPHttpGet function, this would just change the way we package the arguments and then convert the result in the same way as .SOAP
[FIXED] ChemSpider breaks in processWSDL for port = 3

library(SSOAP)
trace(XMLSchema:::resolve, quote({print(c(class(obj), class(context))); print(obj)}))
cs = processWSDL("http://www.chemspider.com/MassSpecAPI.asmx?WSDL", port = 3)
o = genSOAPClientInterface(, cs)

The names for the complex type seem to have disappeared in eutils.wsdl, e.g.

w = processWSDL("WSDLs/eutils.wsdl")
names(w@types[[4]])

Caused by the new code to handle additional attributes.

KEGG now gets into infinite recursion for resolve() because of a SOAPTypeReference with name ArrayOfSubtype in the XSD namespace.
[FIXED] So does ChemSpider!!! Because of "GetExtendedCompoundInfoResponse"

WORKS - but calls don't Broke chemspider. Problem with recursively finding string. Looks like we may be making a mistake on the ns slot (s rather than the XSD ns). But I don't think we use this.

o = XMLSchema:::resolve(cs@types[[1]]$GetRecordMol, cs@types)

???Need to recognize that the string is in XSD???. No, it is the local one that then extends the XSD string.

ChemSpider. After removing new("SOAPTypeReference") in getElementRef and using SOAPType(), get Warning message: undefined slot classes in definition of "GetCompressedRecordsSdf": eComp(class "ECompression")
The name of the element is being used as the name of the class ECompression.
The slotTypes in GetCompressedRecordsSdf are LocalElement objects and the first two are primitives so they are okay. But the third is a simple SOAPType which just refers to ECompression. Shouldn't it be a SOAPTypeReference. Yes. That fixes it.

Fix the undefined slots now arising in MassSpecAPI. All are ArrayOfString. Broken when we we did not collapse the Element to a SimpleSequenceType. These appear to be pending for some reason.
Fixed now by stripping away the Elements and LocaElements down to the actual types.

ChemSpider doesn't work now. Problem is with a LocalElement.

cs = processWSDL("http://www.chemspider.com/MassSpecAPI.asmx?WSDL")
o = genSOAPClientInterface(, cs)
o@functions$SearchByMass2(list(mass = 89.04767, range = 0.01)) 
o@functions$SearchByMass2(mass = 89.04767, range = 0.01) # also works 
o@functions$GetExtendedCompoundInfo(list(CSID=23078572L, token = "717cf9b9-9721-4e8b-825a-b6a65e106c1e"))
o@functions$GetExtendedCompoundInfo(CSID=23078572L, token = "717cf9b9-9721-4e8b-825a-b6a65e106c1e") # works too.

Is it the LocalElement? Should we get rid of this? (in getElementRef.) If we do, then genSOAPClientInterface() fails! Our ArrayOfString class is a SimpleSequenceType, but its element type has also become a SimpleSequenceType! If we leave it there, the WSDL method fails. So we leave it in.
Now we fail converting the result. The return value name is SearchByMass2Response. This is the name of the element for the response. The next node is SearchByMass2Result and then we have a collection of strings.

Problem with referencing enum types in setClass() which we don't define an actual class for. The name is the anonymous name @LNG. 11: undefined slot classes in definition of "IconUrlType": attribute(class "@LNG.Enum") undefined slot classes in definition of "IdType": attribute(class "@HasLinkOut.Enum")
We now have a method for defClass for EnumValuesDef. There is a chance that the name may be wrong if the type is not defined in an attribute definition (AttributeDef) but that is easy to fix.

When defining IdUrlSetType, we don't have the union type yet defined. undefined slot classes in definition of "IdUrlSetType": NA(class "ListOfObjUrlType.character")
Still got an issue with the IdUrlSetType. undefined slot classes in definition of "IdUrlSetType": NA(class "list.Info")
eutils.wsdl Problem in IdUrlListType. The slot types in the choice refer to the @name of the element, not they @type.
In eutils.wsdl and IdUrlSetType. What do we call the UnionDefinition when we need to refer to it in the representation. We can use any name as long is it is consistent.

Similarly, ERROR is not getting defined and all the other classes that give rise to warnings.
For eGqueryRequest, the term, tool and email classes are not yet defined. These are now resolved.

Get rid of the namespace prefixes on the slot names, e.g. eGquerResult and tns:term, tns:tool, etc..
Is getElementName() the only place where this happens? It is now (check).

readSchema doesn't work for pmml.

library(XMLSchema)
pm = readSchema("../XMLSchema/inst/samples/pmml-4-0.xsd")

The issue is the attribute named "type". We try to create an AttributeDef object and set its type slot with a RestrictedStringDefinition rather than the expected AttributeType. The RestrictedStringDefinition has potentially more information (e.g. the converter), but the AttributeType is just the EnumValues or a string. Do we really want the type slot of AttributeDef to be AttributeType or something richer. Or instead of EnumValuesDef, allow a RestrictedStringType which would include a RestrictedStringPatternDefinition

We end up with undefined slot classes in definition of setClass and these are warnings. Some are not defined. Others are defined later(?).

w = processWSDL("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl")
iface = genSOAPClientInterface(, w)

Info is not defined by the time we use it in a ClassUnion. eutils.wsdl.
In defUnionClass, resolving the second slot leads to a SOAPTypeReference, and not the PrimitiveSOAPType we expect.
Recursively resolve the SOAPTypeReference in the Element, list method for resolve. We may need to include more types.

Why isn't the Info element a LocalElement ? It isn't anymore.

Activate the code in processSchemaType, line 350.
It appears we are ignoring attributes on complex types, e.g. ItemType in eutils.wsdl. Fix processSchemaType. We just call processSequence

if (xmlName(type) == "complexType" && ((xmlSize(type) == 1 &&   names(type) == "sequence") || ("sequence" %in% names(type) && 
    all(names(type) %in% c("attribute", "annotation", "sequence")))))

IdUrlSetType in eutils.wsdl broken again.

st = w@types[[5]]$IdUrlSetType

class(st@slotTypes[[2]]) # UnionDefinition
st@slotTypes[[2]]@slotTypes[[1]]  # LocalElement. Could turn this into a SimpleSequence at this point
i.e. when we transform from Element to Type in elementToType. That's where we have the count.

Entrez (NCBI) WSDL.

library(SSOAP)
w = processWSDL("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl")
iface = genSOAPClientInterface(, w)

[Fixed] Now we are having issues with a class definition - IconUrlType - trying to define dependent/referenced classes that are enumerations! The class has an AttributeDef whose type slot is an EnumValuesDef. So we should just be mapping this to the R type corresponding to the name of the Enum type. If there is no name, let's make one up from the name of the outer class and the slot name (LNG). At present, the name is coming from combining the enum names.
The class IconUrlType should be an Extension class
This IdUrlSetType object also has a slot that is a choice of two elements so we need an intermediate ClassUnion for this.
SpelledQuery is similar. Also getting the wrong type here. It should be a sequence of 0 or more entries of the UnionDefinition, not just a single instance. (We could use the names of the element for the names of the elements. These are also both strings so we could use a character rather than a list here.) We also don't need to define a class here but just map the element straight to the type - a character.
[Done] Problem in classes for setClassUnion - string. TranslationStackType. The element OP needs to be converted to an XSD string. Done

Implemented with computeUniqueTypeNames and passed as a function to fixTypeNames(). Should also be in processSchemaTypes.
We can improve fixTypeNames so that we don't a) cause problems with types in the same prefix b) process Elements which won't lead to types.
The following is fixed in fixTypeNames.
In EPO, application-referenceType is in http://www.epo.org/exchange and http://ops.eop.org target namespaces and the latter extends the former. So we need the names to be different. We also need to ensure the base class is defined
In eutils.wsdl, classes with the same name there are two LinkType complexType nodes and we have to be careful to refer to the correct one in all cases and not define a single global class with name.
Write a function to identify conflicts in a SchemaCollection across the SchemaTypes elements.

tests/wikiPathways.R . Dealing with empty inputs.

w = processWSDL("WSDLs/wikipathways.wsdl")
wk = genSOAPClientInterface(, w)
wk@functions$listOrganisms()  # Works again.
wk@functions$listOrganisms(new("listOrganisms"))   # no longer works. Nowit does agai and 
wk@functions$findPathwaysByText(list(query = "apoptosis")) # okay, but wk@functions$findPathwaysByText(query = "apoptosis") is not.

wk@functions$findPathwaysByXref(list(ids = 'P45985', codes=""))  # need the codes. Would like to have prototype create that.
wk@functions$findPathwaysByXref(list(ids = 'P45985'))  # Done

wk@functions$findPathwaysByText(list(query = "apoptosis", species = "")) 
wk@functions$findPathwaysByText(list(query = "apoptosis"))

Problem with listOrganisms input being an empty sequence???
We probably want to deal with the name "parameters" as being an element and strip that away and allow the elements to be specified as separate arguments
See checkIsEmptyParameter.

Return from listOrganisms() (above) is coming out as NULL as the getReturnNode() yields NULL.

putFunctions = TRUE puts the functions into where. Can specify an environment for putFunctions.
In wsdlProcess.R in SSOAP code.

wk = genSOAPClientInterface(, w, putFunctions = TRUE)
e = new.env()
wk = genSOAPClientInterface(, w, putFunctions = e)

Honor the binding to use POST in the MassSpec. Or HTTPGet, etc.

Explore the return value of o@functions$GetExtendedCompoundInfo:

cs = processWSDL("http://www.chemspider.com/MassSpecAPI.asmx?WSDL")
o = genSOAPClientInterface(, cs)
o@functions$GetExtendedCompoundInfo(new("GetExtendedCompoundInfo", CSID=23078572L, token = "717cf9b9-9721-4e8b-825a-b6a65e106c1e"))
o@functions$GetExtendedCompoundInfo(list(CSID=23078572L, token = "717cf9b9-9721-4e8b-825a-b6a65e106c1e")) # works too.

See GetExtendedCompoundInfo_result.xml for a sample result.
We were having trouble with that data type when processing the schema.

Warnings in

pug = processWSDL("http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl")
pugi = genSOAPClientInterface(, pug)

about defClass() and no code to handle PrimitiveSOAPType...
All but one of these relates to int or string.

Use GetListItemsCount instead. In pugi_soap_cgi, GetEntrezUrl is an element but not a complex type. So we don't define an R class for it. But the corresponding function (GetEntrezUrl) expects an object of that class. So we cannot coerce anything to that since there is not such class.

pug = processWSDL("http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl")
pugi = genSOAPClientInterface(, pug, putFunctions = TRUE)

strKey = pugi@functions$InputStructure(structure = "c1ccccc1", format = "eFormat_SMILES")
std = pugi@functions$Standardize(list(strKey))

listKey = pugi@functions$IdentitySearch(StrKey = strKey, idOptions = list(eIdentity = "eIdentity_SameConnectivity"))

pugi@functions$GetListItemsCount(listKey)
pugi@functions$GetListItemsCount(list(ListKey = listKey))  # works too.

pugi@functions$GetIDList(list(ListKey = listKey))


ekey = pugi@functions$GetEntrezKey(list(ListKey = listKey))
u = pugi@functions$GetEntrezUrl(ekey)


xx = pugi@functions$Download(list(ListKey = listKey, eFormat = "eFormat_XML", eCompress = "eCompress_GZip"))
xx@DownloadKey

  # nothing in the DataBlob
 slotNames(xx@DataBlob)
 xx@DataBlob@BlobFormat
 v = as(xx@DataBlob@Data, "raw")

  # Get the URL of the file
u = pugi@functions$GetDownloadUrl(xx@DownloadKey)

library(RCurl)
v = getURLContent(u, binary = TRUE, isHTTP = FALSE)
library(Rcompression)
val = gunzip(v)

pugi@functions$GetEntrezUrl('')

We want to recognize that this is an element and so want parameters that correspond to its elements.

Resolving type

pug = processWSDL("http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl")
pugi = genSOAPClientInterface(, pug)

Why do we end up with NULL in defClass for "GetOperationStatus" Failed to resolve GetOperationStatus. This is an element in the WSDL but not in the pug@types. We get end up using another name <s:element name="GetOperationStatus" type="tns:AnyKeyType" /> Also lots of warnings in genSOAPClientInterface.
We end up with the SOAPTypeReference but the name is the name of the type to which we refer, not the name of the element. So we need to have either the correct name or two names. So now we create an Element and put the SOAPTypeReference as the type slot.
Put the namespace on the Element

This fails in a resolve()

w = processWSDL("http://stats.oecd.org/SDMXWS/sdmx.asmx?WSDL")

Added method to resolve AnySOAPType.

In the MassSpec WSDL, we are getting a recursive problem resolving the return type. This refers to a string in the chemspider.com namespace (line 223 of the WSDL). It is the return value type in GetRecordMol.

cs = processWSDL("http://www.chemspider.com/MassSpecAPI.asmx?WSDL")
library(XMLSchema)
resolve(cs@operations[[1]]$GetRecordMol@returnValue, cs@types)

Why is cs@types[[1]]$string a SOAPTypeReference with no nsuri. Explore processSchemaType and why it does this.
cs@operations[[1]]$GetRecordMol@returnValue

An object of class "SOAPType"
Slot "count":
numeric(0)

Slot "abstract":
logical(0)

Slot "name":
[1] "string"

Slot "ns":
[1] "tns"

Slot "nsuri":
[1] "http://www.chemspider.com/"

Slot "documentation":
character(0)

In defUnionClass(), need to ensure that referenced classes are already defined. So find those objects in the Schema and define those.

Not able to resolve references to element definitions in genSOAPClientInterface().

Problem in converting result. Expect an ArrayOfString, but get a character vector back, as we would expect. See modis.R

library(SSOAP)
w = processWSDL("http://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb_subset/MODIS_webservice.wsdl")
def = genSOAPClientInterface(, w)
d = def@functions$getdates(40,-110, "MOD13Q1")
d = d[c(length(d)-1, length(d))]
o = def@functions$getsubset(40, -110, "MOD13Q1", "250m_16_days_NDVI", d[1], d[2], 10,  10)

Retain the name of the node containing the result from the name attribute of the response message of the operation, e.g. MODIS_webservice.wsdl Currently, if this is not return, we use the first child node and things work fine. But we have this information, so should use it for completeness and thoroughness.
Done via returnNodeName in WSDLMethod and set in createOperationDefinition.

Why doesn't the weather example in Examples/Examples.xml parse the result rather than hand it back as a string containing XML. Are the converters not built or is this something with the weather.gov WSDL?

f@functions$NDFDgenByDay(38.9936, -77.0224, Sys.time() + 60*24*60, 5, "12 hourly")

The .convert value is a PrimitiveSOAPType of type string. Sure enough, the WSDL says the response types are xsd:string.

Converter for Sequence may need to create the class definition if it doesn't appear in the schema. e.g. in the operation listMethods, the return type is a sequence:

trace(SSOAP:::processWSDLOperation, quote(if(xmlGetAttr(node, "name") == "listMethods") browser()))
w = processWSDL("http://www.fedora.info/definitions/api/Fedora-API-A-LITE.wsdl")
f = genSOAPClientInterface(,w)

The problem seems to be that the listMethodsResponse element is complexType/sequence with a type attribute and so we could infer is an R list of ObjectMethodsDef. But the listMethodsResponse message element has <message name="listMethodsResponse"> <part name="response" type="fedora-types:ArrayOfObjectMethodsDef"> <documentation>A set of method definitions that represent all possible disseminations that can be run on the object. </documentation> </part> </message> Note the fedora-types prefix on the value of the type attribute. <operation name="listMethods"> <input message="fedora-api:listMethodsRequest"/> <output message="fedora-api:listMethodsResponse"/> </operation> In resolve for SOAPType, if we fail to find a definition, we can look at the name of the type and see if it starts with ArrayOf. If so, we can create an ArrayType

Infinite recursion in resolve:

w = processWSDL("http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl")
iface = genSOAPClientInterface(, w)

infinite recursion
The following is fixed: method for resolve() for UnionDefinition.

w = processWSDL("http://soap.bind.ca/wsdl/bind.wsdl")
mol = genSOAPClientInterface(, w)
Now get infinite recursion.
Same with 


Error in stop("No method for this type ", class(obj)) : 
  No method for this type UnionDefinition
In addition: Warning message:
Ambiguous method selection for "resolve", target "UnionDefinition#SchemaCollection" (the first of the signatures shown will be used)
    BasicSOAPType#list
    SOAPType#SchemaCollection

Similarly for Element.

w = processWSDL("http://pubmlst.org/api/mlst.wsdl")
f = genSOAPClientInterface(, w)

Need to make the signature more explicit. Was dispatching to BasicSOAPType, list rather than Element when we just had the signature as "Element" and not "SchemaCollection"

Allow a date to be given as a string and then just pass it on.

Keep the documentation for operations from the WSDL.
For eBay, the documentation is in the schema types!
This is in the .operation object (@documentation) of the generated functions.

For arrays where there is an explicit class, e.g. in KEGG ArrayOfstring, get the namespace right for this.

Ambiguous method selection for "toSOAP", target "character#textConnection#ArrayType" (the first of the signatures shown will be used)

obj_list = c('eco:b0514', 'eco:b2913')
fg_list  = c('#ff0000', '#00ff00')
bg_list  = c('#ffff00', 'yellow')
kegg.iface@functions$color_pathway_by_objects('path:eco00260',
                                               obj_list, fg_list, bg_list)

Generate the XML for the request with internal nodes, not strings.

For arrays of primitive types, map class to extend basic R type, e.g. ArrayOfstring and character.
Or make a class union or an alias as we don't necessarily want to create a more specific class. So perhaps just leave as "character" or whatever type it is.

When generating class definitions, create setAs(XMLNode, "type") methods that set the slots directly or some similar method e.g. fromSOAPStruct.
Also leave the generic version that uses slot(obj, dynFieldName).
Also, enforce the optional and required fields in these methods.

Switch to internal nodes and XPath for parsing the WSDL.

Generate converter function to be used in auto generated code.

In WSDL code generation, need the name of the S class of the return type.
See examples/KEGGArray.R

Resolving URIs in import calls.
Use code in XML package?
getRelativeURL()

Write an XML Schema parser in R and use that here.
i.e. separate the schema parsing and the WSDL parsing.
Done some work on using libxml for this. Will proceed via the RSWIG bindings.
See XMLSchema package.

testing

Rcompression (or RCurl)

SDMX

XMLSchema

ERROR