Data: smp

Namespace: http://genologics.com/ri/sample
XML Schema File: sample.xsd

The data in this namespace is divided into elements and types. Types define the structure of the data. Elements define specific instances of the types, and are therefore more relevant to REST endpoints, which generally consume and/or produce elements.

The following elements are members of this namespace:

sample
samplecreation
samples

The following types are members of this namespace:

artifact
biosource
controlType
project
sample
samplebase
samplecreation
sample-link
samples
submitter

Element sample

Type: sample

The detailed representation of a sample.

Example XML

<?xml version="1.0" encoding="UTF-8"?>
<smp:sample xmlns:smp="http://genologics.com/ri/sample" limsid="..." uri="...">
  <name>
    <!--content of type 'string'-->
    ...
  </name>
  <date-received>
    <!--content of type 'string'-->
    ...
  </date-received>
  <date-completed>
    <!--content of type 'string'-->
    ...
  </date-completed>
  <project uri="..." limsid="...">
    <!--content of type 'project'-->
  </project>
  <control-type uri="..." name="...">
    <!--content of type 'controlType'-->
  </control-type>
  <submitter uri="...">
    <!--content of type 'submitter'-->
    <first-name>
      <!--content of type 'string'-->
      ...
    </first-name>
    <last-name>
      <!--content of type 'string'-->
      ...
    </last-name>
  </submitter>
  <artifact uri="..." limsid="...">
    <!--content of type 'artifact'-->
  </artifact>
  <biosource name="...">
    <!--content of type 'biosource'-->
    <description>
      <!--content of type 'string'-->
      ...
    </description>
    <udf:field xmlns:udf="http://genologics.com/ri/userdefined">...</udf:field>
    <udf:field xmlns:udf="http://genologics.com/ri/userdefined">...</udf:field>
    <!--...more "field" elements...-->
  </biosource>
  <udf:type xmlns:udf="http://genologics.com/ri/userdefined">...</udf:type>
  <udf:field xmlns:udf="http://genologics.com/ri/userdefined">...</udf:field>
  <udf:field xmlns:udf="http://genologics.com/ri/userdefined">...</udf:field>
  <!--...more "field" elements...-->
  <ri:externalid xmlns:ri="http://genologics.com/ri">...</ri:externalid>
  <ri:externalid xmlns:ri="http://genologics.com/ri">...</ri:externalid>
  <!--...more "externalid" elements...-->
  <file:file xmlns:file="http://genologics.com/ri/file">...</file:file>
  <file:file xmlns:file="http://genologics.com/ri/file">...</file:file>
  <!--...more "file" elements...-->
</smp:sample>

Element samplecreation

Type: samplecreation

Sample creation is the detailed representation required when creating a new Sample in the system.

Example XML

<?xml version="1.0" encoding="UTF-8"?>
<smp:samplecreation xmlns:smp="http://genologics.com/ri/sample" limsid="..." uri="...">
  <location>
    <!--content of type 'location'-->
    <container limsid="..." uri="...">
      <!--content of type 'container'-->
    </container>
    <value>
      <!--content of type 'string'-->
      ...
    </value>
  </location>
  <name>
    <!--content of type 'string'-->
    ...
  </name>
  <date-received>
    <!--content of type 'string'-->
    ...
  </date-received>
  <date-completed>
    <!--content of type 'string'-->
    ...
  </date-completed>
  <project uri="..." limsid="...">
    <!--content of type 'project'-->
  </project>
  <control-type uri="..." name="...">
    <!--content of type 'controlType'-->
  </control-type>
  <submitter uri="...">
    <!--content of type 'submitter'-->
    <first-name>
      <!--content of type 'string'-->
      ...
    </first-name>
    <last-name>
      <!--content of type 'string'-->
      ...
    </last-name>
  </submitter>
  <artifact uri="..." limsid="...">
    <!--content of type 'artifact'-->
  </artifact>
  <biosource name="...">
    <!--content of type 'biosource'-->
    <description>
      <!--content of type 'string'-->
      ...
    </description>
    <udf:field xmlns:udf="http://genologics.com/ri/userdefined">...</udf:field>
    <udf:field xmlns:udf="http://genologics.com/ri/userdefined">...</udf:field>
    <!--...more "field" elements...-->
  </biosource>
  <udf:type xmlns:udf="http://genologics.com/ri/userdefined">...</udf:type>
  <udf:field xmlns:udf="http://genologics.com/ri/userdefined">...</udf:field>
  <udf:field xmlns:udf="http://genologics.com/ri/userdefined">...</udf:field>
  <!--...more "field" elements...-->
  <ri:externalid xmlns:ri="http://genologics.com/ri">...</ri:externalid>
  <ri:externalid xmlns:ri="http://genologics.com/ri">...</ri:externalid>
  <!--...more "externalid" elements...-->
  <file:file xmlns:file="http://genologics.com/ri/file">...</file:file>
  <file:file xmlns:file="http://genologics.com/ri/file">...</file:file>
  <!--...more "file" elements...-->
</smp:samplecreation>

Element samples

Type: samples

The representation for a list of sample links.

The system enforces a maximum number of elements when generating the list of links. When the size of the request result set is larger than the system maximum, the list represents a paged view of the overall results, and the previous-page and next-page elements provide URIs linking to the previous or next page of links in the overall results.

Example XML

<?xml version="1.0" encoding="UTF-8"?>
<smp:samples xmlns:smp="http://genologics.com/ri/sample">
  <sample limsid="..." uri="...">
    <!--content of type 'sample-link'-->
  </sample>
  <sample>
    <!--(another 'sample-link' type)-->
  </sample>
  <!--...more "sample" elements...-->
  <previous-page uri="...">
    <!--content of type 'page'-->
  </previous-page>
  <next-page uri="...">
    <!--content of type 'page'-->
  </next-page>
</smp:samples>

Type artifact

Artifact is a child element of Sample and provides a URI linking to the detailed representation of the artifact for the Sample.

Attributes

name	type	description
uri	anyURI	The URI of the artifact. Always returns with GET: Yes Creatable with POST: No Required for POST: No Updatable with PUT: No Required for PUT: No
limsid	string	The LIMS ID of the artifact. Always returns with GET: Yes Creatable with POST: No Required for POST: No Updatable with PUT: No Required for PUT: No

Type biosource

The biosource of the Sample.

A Biosource can either be preset or custom. To match a preset biosource, the name should be provided that matches the preset biosources description. If name is not provided, it is considered a custom biosource

Attributes

name	type	description
name	string	The name of the biosource. Always returns with GET: No Creatable with POST: Yes Required for POST: No Updatable with PUT: Yes Required for PUT: No

Child Elements

name (type)	min/max occurs	description
description (string)	0/1	The description of the biosource. Always returns with GET: No Creatable with POST: Yes Required for POST: No Updatable with PUT: Yes Required for PUT: No
field ()	0/unbounded	The user-defined fields of the biosource. Always returns with GET: No Creatable with POST: Yes Required for POST: No, unless the UDF has been configured as required. Updatable with PUT: Yes Required for PUT: No, unless the UDF has been configured as required. If a current UDF is not provided, existing values are deleted.

Type controlType

Control Type provides a name and a URI linking to the detailed representation of the Control Type associated with the Sample. If a Control Type is associated, the Sample will not have an associated Project.

Attributes

name	type	description
uri	anyURI	The URI of the Control Type. Always returns with GET: Yes Creatable with POST: No Required for POST: No Updatable with PUT: No Required for PUT: No
name	string	The Name of the Control Type. Always returns with GET: Yes Creatable with POST: No Required for POST: No Updatable with PUT: No Required for PUT: No

Type project

Project is a child element of Sample and provides a URI linking to the detailed representation of the Project for the Sample.

Attributes

name	type	description
uri	anyURI	The URI of the Project. Always returns with GET: Yes Creatable with POST: Yes Required for POST: Yes Updatable with PUT: No Required for PUT: No
limsid	string	The LIMS ID of the Project. Always returns with GET: Yes Creatable with POST: Yes Required for POST: Yes Updatable with PUT: No Required for PUT: No

Type sample

Extends: samplebase

The detailed representation of a sample.

Type samplebase

The base representation of a Sample, defining common elements for both Sample and Sample creation.

Attributes

name	type	description
limsid	string	The LIMS ID of the Sample. Always returns with GET: Yes Creatable with POST: No Required for POST: No Updatable with PUT: No Required for PUT: No
uri	anyURI	The URI of the Sample. Always returns with GET: Yes Creatable with POST: No Required for POST: No Updatable with PUT: No Required for PUT: No

Child Elements

name (type)	min/max occurs	description
name (string)	0/1	The name of the Sample. Always returns with GET: Yes Creatable with POST: Yes Required for POST: Yes Updatable with PUT: Yes Required for PUT: Yes
date-received (string)	0/1	The date the Sample was received. Always returns with GET: No Creatable with POST: Yes Required for POST: No Updatable with PUT: Yes Required for PUT: No, but if not provided, any previous value is removed.
date-completed (string)	0/1	The date the Sample was completed. Always returns with GET: No Creatable with POST: Yes Required for POST: No Updatable with PUT: Yes Required for PUT: No, but if not provided, any previous value is removed.
project (project)	0/1	Project provides a URI linking to the detailed representation of the Project for the Sample. Always returns with GET: No Creatable with POST: Yes Required for POST: Yes Updatable with PUT: No Required for PUT: No
control-type (controlType)	0/1	Control Type provides a name and a URI linking to the detailed representation of the Control Type associated with the Sample. If a Control Type is associated, the Sample will not have an associated Project. Always returns with GET: No Creatable with POST: No Required for POST: No Updatable with PUT: No Required for PUT: No
submitter (submitter)	0/1	Submitter provides a URI linking to the detailed representation of the submitter for the Sample. Always returns with GET: Yes Creatable with POST: Yes Required for POST: No, but submitter must have valid credentials and if no value is provided, any previous value is removed. Updatable with PUT: Yes Required for PUT: No, but submitter must have valid credentials and if no value is provided, any previous value is removed.
artifact (artifact)	0/1	Artifact provides a URI linking to the detailed representation of the Artifact for the Sample. Always returns with GET: Yes Creatable with POST: No Required for POST: No Updatable with PUT: No Required for PUT: No
biosource (biosource)	0/1	The biosource of the Sample. Always returns with GET: No Creatable with POST: Yes Required for POST: No Updatable with PUT: Yes Required for PUT: No, but if not provided, any existing biosource information is maintained, which is contrary to normal REST behaviour whereby data is deleted if not provided in a PUT.
type ()	0/1	The user-defined type of the Sample. Always returns with GET: No Creatable with POST: Yes Required for POST: No, unless the UDT has been configured as required. Updatable with PUT: Yes Required for PUT: No, unless the UDT has been configured as required. If a current UDT is not provided, existing values are deleted.
field ()	0/unbounded	The user-defined fields of the Sample. Always returns with GET: No Creatable with POST: Yes Required for POST: No, unless the UDF has been configured as required. Updatable with PUT: Yes Required for PUT: No, unless the UDF has been configured as required. If a current UDF is not provided, existing values are deleted.
externalid ()	0/unbounded	Each external id is an identifier that allows looking up related information about the Sample from an external system. Always returns with GET: No Creatable with POST: Yes Required for POST: No Updatable with PUT: Yes Required for PUT: No
file ()	0/unbounded	Each file provides a URI linking to the detailed representation of a file associated with the Sample. Always returns with GET: No Creatable with POST: Yes Required for POST: No Updatable with PUT: Yes Required for PUT: No, but files cannot be removed in this manner, only added. A file must be HTTP DELETED, or PUT to a new Sample to remove it from the old Sample.

Type samplecreation

Extends: samplebase

Sample creation is the detailed representation required when creating a new Sample in the system.

Child Elements

name (type)	min/max occurs	description
location (location)	0/1	The location of the Sample's artifact within a container. Always returns with GET: No Creatable with POST: Yes Required for POST: Yes

Type sample-link

Sample-link is a child element type of samples and provides a URI linking to the detailed representation of a sample.

Attributes

name	type	description
limsid	string	The LIMSID of the sample.
uri	anyURI	The URI of the sample.

Type samples

The representation for a list of sample links.

The system enforces a maximum number of elements when generating the list of links. When the size of the request result set is larger than the system maximum, the list represents a paged view of the overall results, and the previous-page and next-page elements provide URIs linking to the previous or next page of links in the overall results.

Child Elements

name (type)	min/max occurs	description
sample (sample-link)	0/unbounded	Sample provides a URI linking to the detailed representation of a sample.
previous-page (page)	0/1	When working with large lists of samples, the previous-page element provides a URI that links to the previous page of samples.
next-page (page)	0/1	When working with large lists of samples, the next-page element provides a URI that links to the next page of samples.

Type submitter

Submitter is a child element of Sample and provides a URI linking to the detailed representation of the submitter for the Sample.

Attributes

name	type	description
uri	anyURI	The URI of the submitter. Always returns with GET: Yes Creatable with POST: Yes Required for POST: No, but if present submitter must be a valid technician. Updatable with PUT: Yes, but uri of submitter must be a valid technician. Required for PUT: No

Child Elements

name (type)	min/max occurs	description
first-name (string)	0/1	The first name of the submitter. Always returns with GET: Yes Creatable with POST: No Required for POST: No Updatable with PUT: No Required for PUT: No
last-name (string)	0/1	The last name of the submitter. Always returns with GET: Yes Creatable with POST: No Required for POST: No Updatable with PUT: No Required for PUT: No

REST API

Data: smp

Element sample

Example XML

Element samplecreation

Example XML

Element samples

Example XML

Type artifact

Attributes

Type biosource

Attributes

Child Elements

Type controlType

Attributes

Type project

Attributes

Type sample

Type samplebase

Attributes

Child Elements

Type samplecreation

Child Elements

Type sample-link

Attributes

Type samples

Child Elements

Type submitter

Attributes

Child Elements

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