【发布时间】：2016-07-19 14:48:26
【问题描述】：
直到我在这里问过的上一个问题WebResponse posting a null string
当答案对问题有效时，发生了一个新问题。解析下面的xml时
<?xml version="1.0" encoding="UTF-8"?>
<hml xmlns="http://schemas.nmdp.org/spec/hml/1.0.1"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://schemas.nmdp.org/spec/hml/1.0.1 http://schemas.nmdp.org/spec/hml/1.0.1/hml-1.0.1.xsd"
version="1.0.1" >
<!--
MIRING Element 1.1 requires the inclusion of an hmlid.
hmlid can be reported in the form of an ISO Object Identifier (OID)
"root" represents a unique publically registered organization
"extension" is a unique document id managed by the reporting organization.
-->
<hmlid root="2.34.48.32" extension="HML.3245662"/>
<!--
MIRING Element 1.2 requires the inclusion of a reporting-center.
reporting-center identifies the organization sending the HML message.
"reporting-center-id" is a unique identifier of the sender.
"reporting-center-context" reports the context/naming authority of the identifier.
-->
<reporting-center reporting-center-id="567"/>
<sample id="4555-6677-8">
<typing gene-family="HLA" date="2015-01-13">
<!--
MIRING Element 3 requires the inclusion of Genotyping information.
The Genotype should include all pertinent Loci, as well as a Genotype in a standard format.
GLStrings can be included either as plain text, or as a reference to a publicly
available service, such as GL Service (gl.nmdp.org)
-->
<allele-assignment date="2015-07-28" allele-db="IMGT/HLA" allele-version="3.17.0">
<haploid locus="HLA-A" method="DNA" type="02:20:01"/>
<glstring>
HLA-A*02:20:01
</glstring>
</allele-assignment>
<typing-method>
<!--
MIRING Element 6 requires platform documentation. This could be a peer-reviewed publication,
or an identifier of a procedure on a publicly available resource, such as NCBI GTR
-->
<sbt-ngs locus="HLA-A"
test-id="HLA-A.Test.1234"
test-id-source="AcmeGenLabs">
<raw-reads uri="rawreads/read1.fastq.gz"
availability="public"
format="fastq"
paired="1"
pooled="1"
adapter-trimmed="1"
quality-trimmed="0"/>
</sbt-ngs>
</typing-method>
<consensus-sequence date="2015-01-13">
<!--
MIRING Element 2 requires the inclusion of Reference Context.
The location and identifiers of the reference sequence should be specified.
start and end attributes are 0-based, and refer to positions on the reference sequence.
-->
<reference-database availability="public" curated="true">
<reference-sequence
name="HLA-A reference"
id="Ref111"
start="945000"
end="946000"
accession="GL000123.4"
uri="http://AcmeGenReference/RefDB/GL000123.4"/>
</reference-database>
<!--
MIRING Element 4 requires the inclusion of a consensus sequence.
The start and end positions are 0-based, and refer to positions on the reference sequence (reference-sequence-id)
Multiple consensus-sequence-block elements can be included sequentially.
-->
<consensus-sequence-block reference-sequence-id="Ref111"
start="945532"
end="945832"
strand="+"
phase-set="1"
expected-copy-number="1"
continuity="true"
description="HLA-A Consensus Sequence 4.5.67">
<!--
A sequence can be reported as plain text, or as a pointer to an external reference,
or as variants from a reference sequence.
-->
<sequence>
CCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGCCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGACGAGGGTCGGGCAGGT
</sequence>
<!--
MIRING Element 5 requires the inclusion of any relevant sequence polymorphisms.
These represent variants from the reference sequence.
start and end attributes are 0-based, and refer to positions on the reference sequence.
You can see this variant at positions 10 - 15 on the sequence. (945542 - 945532 = 10)
-->
<variant id="0"
reference-bases="GTCATG"
alternate-bases="ACTCCC"
start="945542"
end="945548"
filter="pass"
quality-score="95">
<!--
The functional effects of variants can be reported using variant-effect.
They should use Sequence Ontology (SO) variant effect terms.
-->
<variant-effect term="missense_variant"/>
</variant>
</consensus-sequence-block>
</consensus-sequence>
</typing>
</sample>
<!--
Multiple samples can be included in a single message.
Each sample should have it's own reference-database(s) even if they are identical to other samples' references.
-->
<sample id="4555-6677-9">
<typing gene-family="HLA" date="2015-01-13">
<allele-assignment date="2015-07-28" allele-db="IMGT/HLA" allele-version="3.17.0">
<haploid locus="HLA-A" method="DNA" type="02:20:01"/>
<glstring>
HLA-A*02:01:01:01
</glstring>
</allele-assignment>
<typing-method>
<sbt-ngs locus="HLA-A"
test-id="HLA-A.Test.1234"
test-id-source="AcmeGenLabs">
<raw-reads uri="rawreads/read2.fastq.gz"
availability="public"
format="fastq"
paired="1"
pooled="1"
adapter-trimmed="1"
quality-trimmed="0"/>
</sbt-ngs>
</typing-method>
<consensus-sequence date="2015-01-13">
<reference-database availability="public" curated="true">
<reference-sequence
name="HLA-A reference"
id="Ref112"
start="945000"
end="946000"
accession="GL000123.4"
uri="http://AcmeGenReference/RefDB/GL000123.4"/>
</reference-database>
<consensus-sequence-block
reference-sequence-id="Ref112"
start="945532"
end="945832"
strand="+"
phase-set="1"
expected-copy-number="1"
continuity="true"
description="HLA-A Consensus Sequence 4.5.89">
<sequence>
CCCAGTTCTCGTCATGATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGCCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGACGAGGGTCGGGCAGGT
</sequence>
</consensus-sequence-block>
</consensus-sequence>
</typing>
</sample>
</hml>
这是为验证器提供的示例，所以我知道它有效。但是，当我通过我宁静的 POST 代码传递它时：
@POST
@Path("/Validate")
@Produces("application/xml")
public String validate(@FormParam("xml") String xml)
{
System.out.println(xml);
try {
Client client = Client.create();
WebResource webResource = client.resource("http://miring.b12x.org/validator/ValidateMiring/");
// POST method
ClientResponse response = webResource.accept("application/xml").post(ClientResponse.class,"xml="+xml);
// check response status code
if (response.getStatus() != 200) {
throw new RuntimeException("Failed : HTTP error code : " + response.getStatus());
}
// display response
String output = response.getEntity(String.class);
System.out.println("Output from Server .... ");
System.out.println(output + "\n");
return output;
} catch (Exception e) {
e.printStackTrace();
}
return "Oops";
}
除了 Strand="+" 之外，一切都完美无缺，由于某种原因，它删除了 + 并收到错误消息 The value '' of attribute 'strand' on element 'consensus-sequence-block' is not valid with尊重它的...'
我尝试了所有的链枚举 +,-,-1,1，除了 + 之外，它们都可以工作。
使用 WEB UI (miring.b12x.org) 可以完美运行。
在使用 SAX 进行解析时，是否存在可能导致 + 被丢弃或某个枚举被丢弃的任何原因？
谢谢
编辑：这是收到的输出：
Output from Server ....
<?xml version="1.0" encoding="UTF-8"?>
<miring-report xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
timestamp="07/19/2016 15:07:31"
xsi:noNamespaceSchemaLocation="http://schemas.nmdp.org/spec/miringreport/1.0/miringreport.xsd">
<hml-compliant>reject</hml-compliant>
<miring-compliant>reject</miring-compliant>
<hmlid extension="HML.3245662" root="2.34.48.32"/>
<samples compliant-sample-count="4"
noncompliant-sample-count="0"
sample-count="2">
<sample hml-compliant="true" id="4555-6677-8" miring-compliant="true"/>
<sample hml-compliant="true" id="4555-6677-9" miring-compliant="true"/>
</samples>
<fatal-validation-errors>
<miring-result miring-rule-id="reject" severity="fatal">
<description>[cvc-attribute.3:, The, value, ', ', of, attribute, 'strand', on, element, 'consensus-sequence-block', is, not, valid, with, respect, to, its, type,, 'null'.]</description>
<solution>Verify that your HML file is well formed, and conforms to http://schemas.nmdp.org/spec/hml/1.0.1/hml-1.0.1.xsd</solution>
</miring-result>
<miring-result miring-rule-id="reject" severity="fatal">
<description>[cvc-attribute.3:, The, value, ', ', of, attribute, 'strand', on, element, 'consensus-sequence-block', is, not, valid, with, respect, to, its, type,, 'null'.]</description>
<solution>Verify that your HML file is well formed, and conforms to http://schemas.nmdp.org/spec/hml/1.0.1/hml-1.0.1.xsd</solution>
</miring-result>
<miring-result miring-rule-id="reject" severity="fatal">
<description>[cvc-enumeration-valid:, Value, ', ', is, not, facet-valid, with, respect, to, enumeration, '[-1,, 1,, +,, -]'., It, must, be, a, value, from, the, enumeration.]</description>
<solution>Verify that your HML file is well formed, and conforms to http://schemas.nmdp.org/spec/hml/1.0.1/hml-1.0.1.xsd</solution>
</miring-result>
<miring-result miring-rule-id="reject" severity="fatal">
<description>[cvc-enumeration-valid:, Value, ', ', is, not, facet-valid, with, respect, to, enumeration, '[-1,, 1,, +,, -]'., It, must, be, a, value, from, the, enumeration.]</description>
<solution>Verify that your HML file is well formed, and conforms to http://schemas.nmdp.org/spec/hml/1.0.1/hml-1.0.1.xsd</solution>
</miring-result>
</fatal-validation-errors>
<validation-warnings>
<miring-result miring-rule-id="1.2.b" severity="warning">
<description>The node reporting-center is missing a reporting-center-context attribute.</description>
<solution>Please add a reporting-center-context attribute to the reporting-center node. You can use reporting-center-context to specify the naming authority of the reporting center identifier. Reporting-center-context is not explicitly required.</solution>
<xpath>/hml[1]/reporting-center[1]</xpath>
</miring-result>
</validation-warnings>
</miring-report>
【问题讨论】：
-
请将完整的堆栈跟踪添加到您的问题中。
-
添加了验证器的输出。
-
你没有设置你的WebResource的type，我不知道请求的默认Content-Type是什么，但我怀疑它是application/x-www-form -urlencoded，这意味着
+被视为一个空格。如果是这种情况，将“xml="+xml 更改为"xml=" + URLEncoder.encode(xml, "UTF-8")可能会解决问题。 -
就是这样！如果可能的话，您能否将您的答案改写为非评论，以便我可以接受它作为正确答案？此外，如果您能解释 URLEncoder.encode 的全部功能，那就太好了。