1 of 1

Creating Notifications When Files are Added via LabLink

This topic explains how to:

Detect when files have have been uploaded.
Extract the key information that might comprise a notification.

The Files API Resource

The key resource to investigate is the files resource, which provides a listing of files within the system.

Step 1. Access the Files Resource

On a test system accessing the files resource as follows:

produces the following output:

Step 2. Filter the Files URI

Although not particularly useful in itself, the files URI becomes more interesting when we filter it to only include files uploaded after a specified date-time, and also only those files that have a published status of 'true'.

For example, the following URI:

produces this output on a test system:

This outcome is much more manageable. Because they are uploaded via the Collaborations Interface, they inherently have a published status of 'true'. We use this status to exclude regular files uploaded to the LIMS via other methods and interfaces.

Step 3. Retrieve the XML Representations of the Files

By following the URIs to retrieve the full XML representations of these files, the output is similar to the following:

and:

Step 4. Retrieve Project/Sample Information

Retrieve the associated project/sample, and extract the names and/or IDs to embed into the notification, by following the URI in the 'attached-to' elements.

In this case, the following result is produced:

and:

Proposed Solution

A script must be run periodically (hourly/daily) that queries the files resource for files that have a published status of true, and are last modified in the period of interest.

After this list of files is retrieved, the following pseudocode can be applied:

An example derived from the above XML could lead to the following notifications:

Creating Notifications When Files are Added via LabLink

This topic explains how to:

Detect when files have have been uploaded.
Extract the key information that might comprise a notification.

The Files API Resource

The key resource to investigate is the files resource, which provides a listing of files within the system.

Step 1. Access the Files Resource

On a test system accessing the files resource as follows:

produces the following output:

Step 2. Filter the Files URI

For example, the following URI:

produces this output on a test system:

Step 3. Retrieve the XML Representations of the Files

By following the URIs to retrieve the full XML representations of these files, the output is similar to the following:

and:

Step 4. Retrieve Project/Sample Information

Retrieve the associated project/sample, and extract the names and/or IDs to embed into the notification, by following the URI in the 'attached-to' elements.

In this case, the following result is produced:

and:

Proposed Solution

A script must be run periodically (hourly/daily) that queries the files resource for files that have a published status of true, and are last modified in the period of interest.

After this list of files is retrieved, the following pseudocode can be applied:

An example derived from the above XML could lead to the following notifications:

<file:files>
    <file limsid="92-932-40-16" uri="http://192.168.9.123:8080/api/v2/files/92-932-40-16"/>
    <file limsid="92-944-40-18" uri="http://192.168.9.123:8080/api/v2/files/92-944-40-18"/>
    <file limsid="92-943-40-20" uri="http://192.168.9.123:8080/api/v2/files/92-943-40-20"/>
    <file limsid="92-945-40-22" uri="http://192.168.9.123:8080/api/v2/files/92-945-40-22"/>
    <file limsid="92-942-40-24" uri="http://192.168.9.123:8080/api/v2/files/92-942-40-24"/>
    <file limsid="92-941-40-26" uri="http://192.168.9.123:8080/api/v2/files/92-941-40-26"/>
    <file limsid="ADM102A1DN3-40-28" uri="http://192.168.9.123:8080/api/v2/files/ADM102A1DN3-40-28"/>
    ...
    <file limsid="92-2587-40-459" uri="http://192.168.9.123:8080/api/v2/files/92-2587-40-459"/>
    <file limsid="92-2590-40-460" uri="http://192.168.9.123:8080/api/v2/files/92-2590-40-460"/>
    <file limsid="92-2594-40-462" uri="http://192.168.9.123:8080/api/v2/files/92-2594-40-462"/>
    <file limsid="92-2595-40-463" uri="http://192.168.9.123:8080/api/v2/files/92-2595-40-463"/>
    <file limsid="92-2596-40-465" uri="http://192.168.9.123:8080/api/v2/files/92-2596-40-465"/>
    <file limsid="92-2597-40-466" uri="http://192.168.9.123:8080/api/v2/files/92-2597-40-466"/>
    <file limsid="40-501" uri="http://192.168.9.123:8080/api/v2/files/40-501"/>
    <file limsid="40-558" uri="http://192.168.9.123:8080/api/v2/files/40-558"/>
    <file limsid="92-4555-40-609" uri="http://192.168.9.123:8080/api/v2/files/92-4555-40-609"/>
    <file limsid="92-4554-40-610" uri="http://192.168.9.123:8080/api/v2/files/92-4554-40-610"/>
    <file limsid="92-4556-40-611" uri="http://192.168.9.123:8080/api/v2/files/92-4556-40-611"/>
    <file limsid="92-4564-40-612" uri="http://192.168.9.123:8080/api/v2/files/92-4564-40-612"/>
    <file limsid="92-4563-40-613" uri="http://192.168.9.123:8080/api/v2/files/92-4563-40-613"/>
    <file limsid="92-4562-40-614" uri="http://192.168.9.123:8080/api/v2/files/92-4562-40-614"/>
    <file limsid="ACC151-40-651" uri="http://192.168.9.123:8080/api/v2/files/ACC151-40-651"/>
    <file limsid="ACC151A1-40-652" uri="http://192.168.9.123:8080/api/v2/files/ACC151A1-40-652"/>
</files>

<file:file uri="http://192.168.9.123:8080/api/v2/files/ACC151A1-40-652" limsid="ACC151A1-40-652">

<attached-to>http://192.168.9.123:8080/api/v2/samples/ACC151A1</attached-to>

<content-location> sftp://192.168.9.123/home/glsftp/ACC151/ACC151A1/ACC151A1-40-652.png </content-location>

<original-location>image001.png</original-location>

<is-published>true</is-published>

</file:file>

<smp:sample uri="http://192.168.9.123:8080/api/v2/samples/ACC151A1" limsid="ACC151A1">

<name>SG-5926 -1</name>

<date-received>2013-04-18</date-received>

<project limsid="ACC151" uri="http://192.168.9.123:8080/api/v2/projects/ACC151"/ >

<submitter uri="http://192.168.9.123:8080/api/v2/researchers/1">

<first-name>System</first-name>

<last-name>Administrator</last-name>

</submitter>

<artifact limsid="ACC151A1PA1" uri="http://192.168.9.123:8080/api/v2/artifacts/ACC151A1PA1?state=451" />

<udf:field type="Boolean" name="Control?">false</udf:field>

<udf:field type="String" name="Category">treated</udf:field>

<file:file limsid="ACC151A1-40-652" uri="http://192.168.9.123:8080/api/v2/files/ACC151A1-40-652"/>

</smp:sample>

For each URI in files list:
  Retrieve the file object
    STORE the contents of the 'original-location' element
    IF the contents of the 'attached-to' element contains EITHER 'projects' OR 'samples':
      Retrieve the object pointed to by the 'attached-to' element
      STORE the contents of the 'name' element
      Compile the stored elements into a notification
Publish all notifications produced in an atomic or molecular fashion, as required

<file:files>
    <file limsid="92-932-40-16" uri="http://192.168.9.123:8080/api/v2/files/92-932-40-16"/>
    <file limsid="92-944-40-18" uri="http://192.168.9.123:8080/api/v2/files/92-944-40-18"/>
    <file limsid="92-943-40-20" uri="http://192.168.9.123:8080/api/v2/files/92-943-40-20"/>
    <file limsid="92-945-40-22" uri="http://192.168.9.123:8080/api/v2/files/92-945-40-22"/>
    <file limsid="92-942-40-24" uri="http://192.168.9.123:8080/api/v2/files/92-942-40-24"/>
    <file limsid="92-941-40-26" uri="http://192.168.9.123:8080/api/v2/files/92-941-40-26"/>
    <file limsid="ADM102A1DN3-40-28" uri="http://192.168.9.123:8080/api/v2/files/ADM102A1DN3-40-28"/>
    ...
    <file limsid="92-2587-40-459" uri="http://192.168.9.123:8080/api/v2/files/92-2587-40-459"/>
    <file limsid="92-2590-40-460" uri="http://192.168.9.123:8080/api/v2/files/92-2590-40-460"/>
    <file limsid="92-2594-40-462" uri="http://192.168.9.123:8080/api/v2/files/92-2594-40-462"/>
    <file limsid="92-2595-40-463" uri="http://192.168.9.123:8080/api/v2/files/92-2595-40-463"/>
    <file limsid="92-2596-40-465" uri="http://192.168.9.123:8080/api/v2/files/92-2596-40-465"/>
    <file limsid="92-2597-40-466" uri="http://192.168.9.123:8080/api/v2/files/92-2597-40-466"/>
    <file limsid="40-501" uri="http://192.168.9.123:8080/api/v2/files/40-501"/>
    <file limsid="40-558" uri="http://192.168.9.123:8080/api/v2/files/40-558"/>
    <file limsid="92-4555-40-609" uri="http://192.168.9.123:8080/api/v2/files/92-4555-40-609"/>
    <file limsid="92-4554-40-610" uri="http://192.168.9.123:8080/api/v2/files/92-4554-40-610"/>
    <file limsid="92-4556-40-611" uri="http://192.168.9.123:8080/api/v2/files/92-4556-40-611"/>
    <file limsid="92-4564-40-612" uri="http://192.168.9.123:8080/api/v2/files/92-4564-40-612"/>
    <file limsid="92-4563-40-613" uri="http://192.168.9.123:8080/api/v2/files/92-4563-40-613"/>
    <file limsid="92-4562-40-614" uri="http://192.168.9.123:8080/api/v2/files/92-4562-40-614"/>
    <file limsid="ACC151-40-651" uri="http://192.168.9.123:8080/api/v2/files/ACC151-40-651"/>
    <file limsid="ACC151A1-40-652" uri="http://192.168.9.123:8080/api/v2/files/ACC151A1-40-652"/>
</files>

<file:file uri="http://192.168.9.123:8080/api/v2/files/ACC151A1-40-652" limsid="ACC151A1-40-652">

<attached-to>http://192.168.9.123:8080/api/v2/samples/ACC151A1</attached-to>

<content-location> sftp://192.168.9.123/home/glsftp/ACC151/ACC151A1/ACC151A1-40-652.png </content-location>

<original-location>image001.png</original-location>

<is-published>true</is-published>

</file:file>

<smp:sample uri="http://192.168.9.123:8080/api/v2/samples/ACC151A1" limsid="ACC151A1">

<name>SG-5926 -1</name>

<date-received>2013-04-18</date-received>

<project limsid="ACC151" uri="http://192.168.9.123:8080/api/v2/projects/ACC151"/ >

<submitter uri="http://192.168.9.123:8080/api/v2/researchers/1">

<first-name>System</first-name>

<last-name>Administrator</last-name>

</submitter>

<artifact limsid="ACC151A1PA1" uri="http://192.168.9.123:8080/api/v2/artifacts/ACC151A1PA1?state=451" />

<udf:field type="Boolean" name="Control?">false</udf:field>

<udf:field type="String" name="Category">treated</udf:field>

<file:file limsid="ACC151A1-40-652" uri="http://192.168.9.123:8080/api/v2/files/ACC151A1-40-652"/>

</smp:sample>

For each URI in files list:
  Retrieve the file object
    STORE the contents of the 'original-location' element
    IF the contents of the 'attached-to' element contains EITHER 'projects' OR 'samples':
      Retrieve the object pointed to by the 'attached-to' element
      STORE the contents of the 'name' element
      Compile the stored elements into a notification
Publish all notifications produced in an atomic or molecular fashion, as required

Creating Notifications When Files are Added via LabLink

hashtagStep 1. Access the Files Resource

hashtagStep 2. Filter the Files URI

hashtagStep 3. Retrieve the XML Representations of the Files

hashtagStep 4. Retrieve Project/Sample Information

hashtagProposed Solution

Creating Notifications When Files are Added via LabLink

hashtagStep 1. Access the Files Resource

hashtagStep 2. Filter the Files URI

hashtagStep 3. Retrieve the XML Representations of the Files

hashtagStep 4. Retrieve Project/Sample Information

hashtagProposed Solution

Step 1. Access the Files Resource

Step 2. Filter the Files URI

Step 3. Retrieve the XML Representations of the Files

Step 4. Retrieve Project/Sample Information

Proposed Solution

Step 1. Access the Files Resource

Step 2. Filter the Files URI

Step 3. Retrieve the XML Representations of the Files

Step 4. Retrieve Project/Sample Information

Proposed Solution