Data: stp

Namespace: http://genologics.com/ri/step
XML Schema File: step.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:

actions
placements
pools
program-status
reagents
step

The following types are members of this namespace:

actions
actions-link
action-type
container
input
next-action
output
output-placement
placements
placements-link
pooled-inputs
pools
pools-link
program-status
program-status-link
reagent-label
reagents
reagents-link
status
step
step-configuration

Element actions

Type: actions

Example XML

<?xml version="1.0" encoding="UTF-8"?>
<stp:actions xmlns:stp="http://genologics.com/ri/step" uri="...">
  <step rel="..." uri="...">
    <!--content of type 'link'-->
  </step>
  <configuration uri="...">...</configuration>
  <next-actions>
    <next-action artifact-uri="..." action="..." step-uri="...">
      <!--content of type 'next-action'-->
    </next-action>
    <next-action>
      <!--(another 'next-action' type)-->
    </next-action>
    <!--...more "next-action" elements...-->
  </next-actions>
</stp:actions>

Element placements

Type: placements

The detailed representation of a step's output artifact container placements

Example XML

<?xml version="1.0" encoding="UTF-8"?>
<stp:placements xmlns:stp="http://genologics.com/ri/step" uri="...">
  <step rel="..." uri="...">
    <!--content of type 'link'-->
  </step>
  <configuration uri="...">...</configuration>
  <selected-containers>
    <container uri="...">
      <!--content of type 'container'-->
    </container>
    <container>
      <!--(another 'container' type)-->
    </container>
    <!--...more "container" elements...-->
  </selected-containers>
  <output-placements>
    <output-placement uri="...">
      <!--content of type 'output-placement'-->
      <location>
        <!--content of type 'location'-->
        <container limsid="..." uri="...">
          <!--content of type 'container'-->
        </container>
        <value>
          <!--content of type 'string'-->
          ...
        </value>
      </location>
    </output-placement>
    <output-placement>
      <!--(another 'output-placement' type)-->
    </output-placement>
    <!--...more "output-placement" elements...-->
  </output-placements>
</stp:placements>

Element pools

Type: pools

The detailed representation of a step's pooled inputs.

Example XML

<?xml version="1.0" encoding="UTF-8"?>
<stp:pools xmlns:stp="http://genologics.com/ri/step" uri="...">
  <step rel="..." uri="...">
    <!--content of type 'link'-->
  </step>
  <configuration uri="...">...</configuration>
  <pooled-inputs>
    <pool name="..." output-uri="...">
      <!--content of type 'pooled-inputs'-->
      <input uri="...">
        <!--content of type 'input'-->
      </input>
      <input>
        <!--(another 'input' type)-->
      </input>
      <!--...more "input" elements...-->
    </pool>
    <pool>
      <!--(another 'pooled-inputs' type)-->
    </pool>
    <!--...more "pool" elements...-->
  </pooled-inputs>
  <available-inputs>
    <input uri="...">
      <!--content of type 'input'-->
    </input>
    <input>
      <!--(another 'input' type)-->
    </input>
    <!--...more "input" elements...-->
  </available-inputs>
</stp:pools>

Element program-status

Type: program-status

The current EPP status for a step (supports automatically triggered programs only).

Example XML

<?xml version="1.0" encoding="UTF-8"?>
<stp:program-status xmlns:stp="http://genologics.com/ri/step" uri="...">
  <step rel="..." uri="...">
    <!--content of type 'link'-->
  </step>
  <configuration uri="...">...</configuration>
  <status>
    <!--content of type 'status'-->
    ...
  </status>
  <message>
    <!--content of type 'string'-->
    ...
  </message>
</stp:program-status>

Element reagents

Type: reagents

The detailed representation of a step's output artifact reagents.

Example XML

<?xml version="1.0" encoding="UTF-8"?>
<stp:reagents xmlns:stp="http://genologics.com/ri/step" uri="...">
  <step rel="..." uri="...">
    <!--content of type 'link'-->
  </step>
  <configuration uri="...">...</configuration>
  <reagent-category>
    <!--content of type 'string'-->
    ...
  </reagent-category>
  <output-reagents>
    <output uri="...">
      <!--content of type 'output'-->
      <reagent-label name="...">
        <!--content of type 'reagent-label'-->
      </reagent-label>
      <reagent-label>
        <!--(another 'reagent-label' type)-->
      </reagent-label>
      <!--...more "reagent-label" elements...-->
    </output>
    <output>
      <!--(another 'output' type)-->
    </output>
    <!--...more "output" elements...-->
  </output-reagents>
</stp:reagents>

Element step

Type: step

The detailed representation of a step.

Example XML

<?xml version="1.0" encoding="UTF-8"?>
<stp:step xmlns:stp="http://genologics.com/ri/step" uri="..." limsid="...">
  <configuration uri="...">...</configuration>
  <actions uri="...">
    <!--content of type 'actions-link'-->
  </actions>
  <reagents uri="...">
    <!--content of type 'reagents-link'-->
  </reagents>
  <pools uri="...">
    <!--content of type 'pools-link'-->
  </pools>
  <placements uri="...">
    <!--content of type 'placements-link'-->
  </placements>
  <program-status uri="...">
    <!--content of type 'program-status-link'-->
  </program-status>
</stp:step>

Type actions

Attributes

name	type	description
uri	anyURI	(no documentation provided)

Child Elements

name (type)	min/max occurs	description
step (link)	0/1	The step (process). Always returns with GET: Yes Updatable with PUT: No Required for PUT: No
configuration (step-configuration)	0/1	The protocol step configuration. Always returns with GET: Yes Updatable with PUT: No Required for PUT: No
next-actions/next-action (next-action)	0/unbounded	All samples belong to one step; these samples can move forward for another configured step work or need special handling, such as remove from the workflow they are in, leave in their existing queue for rework, or require view by a manager, etc...

Type actions-link

Identifies the resource that represents the actions applied or to be applied by the step.

Attributes

name	type	description
uri	anyURI	The URI of corresponding step actions resource.

Type action-type

Special actions for samples.

Possible Values

value	description
leave	Leave the sample in the QC protocol.
repeat	Repeat this step.
remove	Remove from workflow.
review	Request manager review.
complete	Mark protocol as complete.
store	Store for later.
nextstep	Continue to the next step.
rework	Rework from an earlier step. Note - this action is read only.
unknown	The action is unknown.

Type container

Provides a URI linking to a selected container to be used for placement.

Attributes

name	type	description
uri	anyURI	The URI of the container. Always returns with GET: Yes Creatable with POST: No Required for POST: Yes

Type input

Provides input URI links.

Attributes

name	type	description
uri	anyURI	The URI of the artifact. Always returns with GET: Yes Updatable with PUT: No Required for PUT: Yes

Type next-action

Sample next action or step.

Attributes

name	type	description
artifact-uri	anyURI	The URI of the artifact. Always returns with GET: Yes Updatable with PUT: no Required for PUT: yes
action	action-type	The next action for the sample. Always returns with GET: no; the sample may not have a next action. Updatable with PUT: yes Required for PUT. If the action is not present during an update, the existing action for the sample will be removed if there is one.
step-uri	anyURI	The next protocol step for the sample. Always returns with GET: no; the sample may not have a next step. Updatable with PUT: yes Required for PUT. If the step is not present during an update, the existing step for the sample will be removed if there is one.

Type output

Provides a URI linking to the output artifact and reagent label.

Attributes

name	type	description
uri	anyURI	The URI of the artifact. Always returns with GET: Yes Creatable with POST: No Required for POST: Yes

Child Elements

name (type)	min/max occurs	description
reagent-label (reagent-label)	0/unbounded	The reagent labels for the artifact. Always returns with GET: No; the artifact may not have reagent labels. Creatable with POST: Yes Required for POST: No; If specified, an existing reagent label will be replaced with the new label. If not specified, existing labels will be removed.

Type output-placement

Provides a URI linking to the output artifact and container placement.

Attributes

name	type	description
uri	anyURI	The URI of the artifact. Always returns with GET: Yes Creatable with POST: No Required for POST: Yes

Child Elements

name (type)	min/max occurs	description
location (location)	0/1	The container placement for the artifact. Always returns with GET: No; the artifact may not have a placement. Creatable with POST: Yes Required for POST: No; If specified, any existing placement will be replaced with the new placement. If not specified, any existing placement will be removed.

Type placements

The detailed representation of a step's output artifact container placements

Attributes

name	type	description
uri	anyURI	The URI of the StepPlacements. Always returns with GET: Yes Creatable with POST: No Required for POST: No

Child Elements

name (type)	min/max occurs	description
step (link)	0/1	The protocol step of the StepPlacements. Always returns with GET: Yes Creatable with POST: No Required for POST: No
configuration (step-configuration)	0/1	The protocol step configuration. Always returns with GET: Yes Creatable with POST: No Required for POST: No
selected-containers/container (container)	0/unbounded	The selected containers for step placement. Always returns with GET: Yes Creatable with POST: Yes Required for POST: No
output-placements/output-placement (output-placement)	0/unbounded	The output artifacts for this step with placement if they have one. Always returns with GET: Yes Creatable with POST: Yes Required for POST: No

Type placements-link

Identifies the resource that represents the output placements for the step.

Attributes

name	type	description
uri	anyURI	The URI of corresponding step placements resource.

Type pooled-inputs

Provides pooled input groups.

Attributes

name	type	description
name	string	The pool name. Always returns with GET: Yes Updatable with PUT: Yes Required for PUT: Yes
output-uri	anyURI	The URI of the pooled output artifact. Always returns with GET: Yes Updatable with PUT: No Required for PUT: No

Child Elements

name (type)	min/max occurs	description
input (input)	0/unbounded	The pooled input artifacts for this pool. Always returns with GET: Yes Updatable with PUT: Yes Required for PUT: Yes

Type pools

The detailed representation of a step's pooled inputs.

Attributes

name	type	description
uri	anyURI	The URI of the StepPools. Always returns with GET: Yes Updatable with PUT: No Required for PUT: No

Child Elements

name (type)	min/max occurs	description
step (link)	0/1	The step (process). Always returns with GET: Yes Updatable with PUT: No Required for PUT: No
configuration (step-configuration)	0/1	The protocol step configuration. Always returns with GET: Yes Updatable with PUT: No Required for PUT: No
pooled-inputs/pool (pooled-inputs)	0/unbounded	The pooled input artifacts for this step. Always returns with GET: Yes Updatable with PUT: Yes Required for PUT: No
available-inputs/input (input)	0/unbounded	The available input artifacts for this step. Always returns with GET: Yes

Type pools-link

Identifies the resource that represents the pools added by the step.

Attributes

name	type	description
uri	anyURI	The URI of corresponding step pools resource.

Type program-status

The current EPP status for a step (supports automatically triggered programs only).

Attributes

name	type	description
uri	anyURI	The URI to this status.

Child Elements

name (type)	min/max occurs	description
step (link)	0/1	The step (process). Always returns with GET: Yes Updatable with PUT: No Required for PUT: No
configuration (step-configuration)	0/1	The protocol step configuration. Always returns with GET: Yes Updatable with PUT: No Required for PUT: No
status (status)	0/1	The nature of the status.
message (string)	0/1	The user-facing message for this status.

Type program-status-link

Identifies the resource that represents the program status for the step.

Attributes

name	type	description
uri	anyURI	The URI of corresponding step program status resource.

Type reagent-label

Reagent-label is a child element of ExtStepReagentListElement and provides the name of a label or reagent that has been added to the Artifact.

Attributes

name	type	description
name	string	The reagent label name for the artifact. Always returns with GET: No; the artifact may not have a reagent label. Creatable with POST: Yes Required for POST: No; If specified, an existing reagent label will be replaced with the new label. If not specified, existing labels will be removed.

Type reagents

The detailed representation of a step's output artifact reagents.

Attributes

name	type	description
uri	anyURI	The URI of the StepReagents. Always returns with GET: Yes Creatable with POST: No Required for POST: No

Child Elements

name (type)	min/max occurs	description
step (link)	0/1	The step (process). Always returns with GET: Yes Creatable with POST: No Required for POST: No
configuration (step-configuration)	0/1	The protocol step configuration. Always returns with GET: Yes Creatable with POST: No Required for POST: No
reagent-category (string)	0/1	The permitted reagent category of the step. Reagent labels used in the POST must be from this reagent category. Always returns with GET: Yes Creatable with POST: No Required for POST: No
output-reagents/output (output)	0/unbounded	The output artifacts for this step. Always returns with GET: Yes

Type reagents-link

Identifies the resource that represents the reagents added by the step.

Attributes

name	type	description
uri	anyURI	The URI of corresponding step reagents resource.

Type status

Describes the different natures of status for an external program.

Possible Values

value	description
OK	The program finished successfully.
ERROR	The program failed to run or failed when executing.
WARNING	The program finished successfully but generated a warning message.
RUNNING	A program is currently in progress. This status cannot be set, only read.

Type step

The detailed representation of a step.

Attributes

name	type	description
uri	anyURI	(no documentation provided)
limsid	string	The LIMS ID of the Step/Process.

Child Elements

name (type)	min/max occurs	description
configuration (step-configuration)	0/1	The configuration information for the step run.
actions (actions-link)	0/1	The corresponding step actions.
reagents (reagents-link)	0/1	The corresponding step reagents.
pools (pools-link)	0/1	The corresponding step pools.
placements (placements-link)	0/1	The corresponding step placements.
program-status (program-status-link)	0/1	The corresponding step program status, if one exists.

Type step-configuration

Identifies the configuration information for the step run.

Attributes

name	type	description
uri	anyURI	The URI of the protocol step.

Value

Type: string

(no documentation provided)

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Data: stp

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