magna pure 96 system host interface manual, version 4

MagNA Pure 96 SystemHost Interface Manual, Version 4.0Software Version 3.0 and higher September 2014

3

Table of Content

Prologue 5

I Document Information .................................................................................................................................................5

1 Revision History ...................................................................................................................................................................52 Copyright ................................................................................................................................................................................53 Edition Notice .......................................................................................................................................................................5

II Contact Addresses .........................................................................................................................................................6

III Trademarks .........................................................................................................................................................................6

IV Preamble ..............................................................................................................................................................................6

V Abbreviations .....................................................................................................................................................................6

VI References ..........................................................................................................................................................................6

A Overview 7

1 Communication Overview ..........................................................................................................................................7

Description of HL7 Workflow .........................................................................................................................................7 Client /Server structure ....................................................................................................................................................7

2 Communication Layers ................................................................................................................................................8

B Workflow 9

1 Communication Scenarios .........................................................................................................................................9

2 Get Order ..............................................................................................................................................................................9

3 Test Result Export ......................................................................................................................................................... 10

C Message Types 12

1 Message Structure ...................................................................................................................................................... 12

Work Order Inquiry .......................................................................................................................................................... 12 Test Result Export ............................................................................................................................................................ 13

2 Work Order Inquiry Mapping ................................................................................................................................. 14

3 Order Response Mapping ....................................................................................................................................... 14

4 Test Result Export ......................................................................................................................................................... 15

4MagNA Pure 96 System Host Interface Manual, Version 4.0 – Software Version 3.0 and higher

Table of Content

D HL7 Protocol 16

1 Minimal Layer Protocol ............................................................................................................................................. 16

2 Inquiry Segments Details .........................................................................................................................................17

MSH Segment (Message Header) .............................................................................................................................17 QPD Segment (Query Parameter Definition) ..........................................................................................................17 RCP Response control Parameter ..............................................................................................................................17

3 Inquiry Response Segments Details ................................................................................................................. 18

MSH Segment (Message Header) ............................................................................................................................ 18 ORC Segment (Common Order) ................................................................................................................................ 18 OBR – Segment (Observation Request) .................................................................................................................. 19 NTE – Segment (Notes and Comments) ................................................................................................................. 19

4 Example Inquiry / Response .................................................................................................................................. 20

4.1 HL7 Record ........................................................................................................................................................................ 20

5 HL7 Result Segments Details................................................................................................................................ 21

MSH Segment (Message Header) ............................................................................................................................ 21 ORC – Segment (Common Order) ............................................................................................................................ 21 OBR – Segment (Observation Request) .................................................................................................................. 22 OBX – Segment (Observation / Result Segment) ............................................................................................... 23 NTE – Segment (Notes and Comments) ................................................................................................................. 23

6 Example Result Output .............................................................................................................................................. 24

6.1 HL7 Result Export ........................................................................................................................................................... 24

E File Sharing 26

1 Sample of XML Files .................................................................................................................................................. 26

Ordering .............................................................................................................................................................................. 26 MagNA Pure 96 Result Export (XML) ......................................................................................................................27

2 Schema Definition ....................................................................................................................................................... 28

Order Schema ................................................................................................................................................................... 28 Results Schema ................................................................................................................................................................ 29 Results Schema (continued from previous page) ............................................................................................... 30

F Sample List, LightCycler® 480 Software 31

G Communication Setup 32

1 Network Connection ................................................................................................................................................... 32

Typical Installation Scenarios: ..................................................................................................................................... 32

2 Instrument Setup .......................................................................................................................................................... 34

Host Communication ...................................................................................................................................................... 342.1 HL7 Setup ........................................................................................................................................................................... 342.2 File Transfer Setup ........................................................................................................................................................... 36 Troubleshooting: ................................................................................................................................................................37

H Known Problems / Issues / Restrictions 39

I Keywords Index 40

5Prologue

Prologue

I Document Information

1 Revision HistoryDocument Version

Software Version

Revision Date

Changes

1.0 1.0 October 2009

1.1 1.1 June 2010

2.0 2.0 January 2011 Added Section IV, Intended use.

Revised Sections VI, Conventions/ A1, Communication overview/ B3, Test result export/E, File sharing/F, Software/ G1, Network connection/G2.2, File transfer setup.

Removed Section H, HL7 Simulator

2.1 2.0 July 2011 Revised the following sections: Section IV, Intended use/V, Target Audience/ C2, Work Order Inquiry Mapping/ D3, OBR-Segment (Observation Request)/ H, Known Problems/Issues/Restrictions/ I, Keyword Index/updated screenshots in various chapters

3.0 2.0 and higher

March 2014 Revised the following sections:PrologueE, File sharingG2, HL7, Instrument SetupH, Known Problems / Issues / Restrictions

4.0 3.0 and higher

September 2014 Revised several sections regarding software 3.0

2 Copyright© Copyright 2014, Roche Diagnostics GmbH.

Information in this document is subject to change without notice. No part of this document may be reproduced or transmitted in any form or by any means, electronic or mechanical, for any purpose, without the express written permission of Roche Diagnostics Ltd.

Questions or comments regarding the contents of this manual can be directed to your Roche representative.

3 Edition NoticeThe MagNA Pure 96 System Host Interface Manual is for users of the MagNA Pure 96 Software version 3.0 and higher.

Every effort has been made to ensure that all the information contained in this manual is correct at the time of publishing.

However, Roche Diagnostics GmbH reserves the right to make any changes necessary without notice as part of ongoing product development.

Document Information


II Contact AddressesManufacturer Roche Diagnostics GmbH

Sandhofer Straße 116 68305 Mannheim Germany

Made in Switzerland

Distribution Roche Diagnostics GmbH Sandhofer Straße 116 68305 Mannheim Germany

Distribution in USA Roche Diagnostics 9115 Hague Road PO Box 50457 Indianapolis, IN 46250 USA

III TrademarksCOBAS, MAGNAPURE and LIGHTCYCLER are trademarks of Roche.All other product names and trademarks are the property of their respective owners.

IV PreambleThe MagNA Pure 96 Host Interface Manual describes how to configure the MagNA Pure 96 Host Module software.The Host Module software is used to import/export data between the MagNA Pure 96 application software and the customers network.This Manual is provided to the customer on request.The intended audience for this manual is Host Interface programmers configuring and setting up the LIS connection and the Roche Field Service Engineer supporting the system.It is the customers or LIS suppliers responsibility to ensure proper configuration and operation of the LIS.

V AbbreviationsClient or TCP/IP server A network device or software initiating communication to a server application.

CU Control Unit

DB Database

LAN Local Area network

LIMS Laboratory Information Management System. Sometimes called also LIS, or HOST.

Server or TCP/IP server A network device or software application listening on a specified communication port.

UNC Uniformed Naming Convention

ACK Acknowledged

NAK/NK Not acknowledged

For more information, see the “Glossary” in the MagNA Pure 96 Operator’s Guide.

VI References[1] HL 7 Documentation Version 2.4, Health Level Seven, Ann Arbor MI, USA, www.HL7.org

Contact Addresses

7Overview

AAA Overview

1 Communication OverviewThe instrument has three modes of data exchange:

c HL7 protocol over TCP/IP (network)

c File sharing by writing and reading XML files in two defined external shared folders.These folders must reside on an external file sharing server, see File sharing, on page 26.

c Writing a specific text file in a format compatible with the sample list format of the LightCycler® 480 Soft-ware.

The internal communication is realized by XML files which are exchanged and evaluated between MagNA Pure 96 Software and Host Communication Module.

Description of HL7 Workflow

MagNA Pure 96System

Convert toHL7 XML

HL7

XML

Host Communication Module(TCP/IP Client)

LIS(TCP/IP Server)

LIS Server

Order

Result

Control Unit

Figure 1 Description of the HL7 workflow

Client /Server structureThe communication is always established by the MagNA Pure 96 Control Unit; Control unit is always the TCP/IP client and the LIS is always the TCP/IP server.

Communication Overview


AA 2 Communication LayersAs all the communication is based on network connections, this manual addresses mostly the upper layer (application) related topics.

This layer corresponds to the upper layer in the well known OSI model:

Communication Layers

9Workflow

BBB Workflow

1 Communication ScenariosThe following table shows the communication scenarios existing for the MagNA Pure 96 project.

Name Description Input Output

Get order The MagNA Pure 96 system asks the LIS to get order details for one or more Samples

The LIS send the order list

Order request

Send Results The MagNA Pure 96 system sends the LIS a list of Samples with preparation results

Note: The MagNA Pure 96 software 3.0 will send a result for every sample. MagNA Pure 96 softwares below version 3.0 will send only the complete batch status.

The host must acknowledge the results block

Preparation results list

2 Get Order

MagNA Pure 96System

IT Server(e.g. COBAS IT Server) LIS

Do the work

Import Order

Send XML Order ACK/NAK

Convert to Record format

Send HL7 Order Request

Send Hl7 Order

Convert to XML format


Send HL7 Order ACK/NAK

Send XML Order Request

Send Order to theMagNA Pure 96 System

Figure 2 Order workflow

The order request will be sent every minute.

The order will be acknowledged if accepted, or an error will be logged in the Host Module log file on page 35.

Communication Scenarios


BB3 Test Result Export

MagNA Pure 96System

IT Server(e.g. COBAS IT Server) LIS

Do the work


Send HL7 Test Results

Send HL7 Result ACK/NK

Convert to XML format

Send XML HL7 Results

Send XML Result ACK/NK

Figure 3 Test Result Export

After a test run the results become available to be exported. Once the LIS has acknowledged the results, they will be flagged as “sent” in the MagNA Pure 96 Database. However, results flags can be reset to enable automatic transmission again.

In case no answer, or a negative acknowledgement is received from the LIS, the MagNA Pure 96 Software will try to transmit results three times. Following these three attempts, the result will be flagged as “Sent” so that the system will not try to send forever. (Otherwise at the next cycle, one minute later it would retry again).

Note: There will be no error message logged if the result file can not be sent, but the message “Result with the ID ‘Resultname’ acknowledged” will not be logged in the log file of the Host Module.

The operator needs to address the situation of the LIS not taking the results and manually „unflag“ the results if they still should be transmitted automatically. See the screenshots below to remove the flags by clicking the Reset Auto Export button.

Note: The MagNA Pure 96 software 3.0 and above will send the status (passed or failed) for every sample. MagNA Pure 96 softwares below version 3.0 will send only the complete batch status.

Test Result Export

11Workflow

BB

Test Result Export


CC

C Message Types

1 Message StructureThe Message Structures are defined in the syntax also used in [1], page 6.

Work Order Inquiry

Work Order Request

MSH MESSAGE HEADER SEGMENT

{

QPD QUERY PARAMETER DEFINITION

RCP RESPONSE CONTROL PARAMETER

}

Work Order Import


{

ORC COMMON ORDER SEGMENT

{

OBR OBSERVATION REQUEST SEGMENT

NTE NOTES AND COMMENTS SEGMENT

}

}

Work Order ACK/NAK


{

MSA MESSAGE ACKNOWLEDGMENT

}

Message Structure

13Message Types

CC

Test Result Export

Test Result Export


{

ORC COMMON ORDER SEGMENT

{

OBR OBSERVATION REQUEST SEGMENT

OBX OBSERVATION/RESULT SEGMENT

NTE NOTES AND COMMENTS SEGMENT

}

}

Result ACK/NAK


{

MSA MESSAGE ACKNOWLEDGMENT

}

Test Result Export


CC

2 Work Order Inquiry Mapping

MagNA Pure 96 XML Node- or Attribute Name HL7-Mapping

OrderName ORC-2

OrderComment ORC-3

UserId ORC-10

Number OBR-1

SampleID OBR-2

SamplePlateId OBR-3-1

SamplePos OBR-3-2

KitName OBR-4-1

KitVersion OBR-4-2

TestDefinitionName OBR-15-1

TestDefinitionVersion OBR-15-2

SampleVolume OBR-18

ElutionVolume OBR-19

OutputPlateType OBR-20

InternalControlType OBR-21

Number NTE-1

Comment NTE-3

3 Order Response Mapping

MagNA Pure 96 XML Node- or Attribute Name HL7-Mapping

OrderName ORC-2

OrderComment ORC-3

UserId ORC-10

Number OBR-1

SampleID OBR-2

SamplePlateId OBR-3-1

SamplePos OBR-3-2

KitName OBR-4-1

KitVersion OBR-4-2

InputPlateFillVolume ORB-9

InputPlateType ORB-10

TestDefinitionName OBR-15-1

TestDefinitionVersion OBR-15-2

SampleVolume OBR-18


OutputPlateType OBR-20

InternalControlType OBR-21

Number NTE-1

Comment NTE-3

Work Order Inquiry Mapping

15Message Types

CC

4 Test Result Export

MagNA Pure 96 XML Node- or Attribute Name

Example HL7 Mapping

creationdate 20081122121212 MSH-7

OrderID ORC-2-1

BatchId ORC-2-2

OrderComment ORC-3

OrderEndDateTime ORC-9

Operator ORC-10

SampleID OBR-2

SamplePlateId OBR-3

KitName OBR-4

BatchStartDateTime OBR-7

BatchEndDateTime OBR-8

OutputPlateType^ICType OBR-13

PurificationProtocol OBR-15

SampleVolume OBR-18


ASSoftwareVersion OBR-20

InstrumentSerialNumber OBR-21

SamplePos OBX-3

Flags OBX-4

ICDefinitions OBX-5

ResultStatus OBX-11

RunState OBX-13

comment NTE-3

Test Result Export


DD

D HL7 Protocol

1 Minimal Layer ProtocolThe data framing uses the Minimal Lower Layer Protocol (MLLP) defined in the HL7 standard.

HL7 messages are embedded in block delimited by special (non printable) characters.

<start_block>data<end_block>[CR]

The values of the special characters are [VT] for the start block and [FS] for the end block. See table below.

<start_block> Start Block character (1 byte) ASCII [VT]

Data (variable number of bytes) The HL7 data is comprised of any displayable ASCII characters and the carriage return character, [CR].

<end_block> End Block character (1 byte) ASCII [FS].

.

[CR] Carriage Return (1 byte)

Char (ASCII) Décimal Octal Hex Name

VT 011 013 0B Vertical Tab

FS 028 034 1C File Separator

CR 013 015 0D Carriage Return

Graphical representation of data framing:

[VT] HL7 data [FS][CR]

Note that these characters will appear in the HL7 simulator displays.

Minimal Layer Protocol

17HL7 Protocol

DD

2 Inquiry Segments Details

MSH Segment (Message Header)This table is showing the field mappings between the XML file of the MagNA Pure 96 Software and the HL7 message version 2.4 message header segment.

Segment Name

Seq. ID Type Comment Values Required

MSH-1 1 String Field delimiter | Yes

MSH-2 2 String Component, Repetition, Escape and Subcomponent delimiter – exactly in this order

^ ~ \ & Yes

MSH-3 3 String Sending SYSTEM MagNA Pure 96 Yes

MSH-7 7 XML DateTime

XML DateTime of the message put by the creating system on creation of this message

YYYYMMDDhhmmss e.g. 20091123171149

Yes

MSH-9-1 9-1 String Message type code – see HL7 Doc.:

[1] Table 0076 - Message type

QBP (QBP^Q11) Yes

MSH-9-2 9-2 String Trigger event code – see HL 7 Doc.: [1] Table 0003 - Event type

Q11 (QBP^Q11) Yes

MSH-10 10 Number The name of the sending machine (PC name)

MPCZC8380G5K Yes

MSH-11 11 String Processing mode (processing priority) see HL7 Doc.:

[1] Table 0103 - Processing ID

P = Production Yes

MSH-12 12 Number Version ID – used as a version check to make sure that this message is interpreted correctly see HL7 Doc.:

[1] Table 0104 – Version ID

2.4 Yes

QPD Segment (Query Parameter Definition)

Segment

Name


QPD 1 String Message Query Name Always “QUERY_ORDER”

Yes

RCP Response control Parameter

Segment

Name


RCP 1 RCP segment is present but empty No

Inquiry Segments Details


DD

3 Inquiry Response Segments Details

MSH Segment (Message Header)

Segment

Name


MSH-1 1 String Field delimiter | Yes

MSH-2 2 String Component, Repetition, Escape and Subcomponent delimiter – exactly in this order

^ ~ \ & Yes

MSH-3 3 String Sending SYSTEM MagNA Pure 96 Yes

MSH-7 7 XML Da-teTime



Yes

MSH-9-1 9-1 String Message type code – see HL7 Doc.:

[1] Table 0076 - Message type

ORM (ORM^001) Yes

MSH-9-2 9-2 String Trigger event code – see HL 7 Doc.: [1] Table 0003 - Event type

001 (ORM^001) Yes

MSH-10 10 Number The name of the sending machine (PC name)

PC xyz No

MSH-11 11 String Processing mode (processing priority) see HL7 Doc.:

[1] Table 0103 - Processing ID

P = Production Yes

MSH-12 12 Number Version ID – [1] Table 0104 – Version ID

2.4 Yes

ORC Segment (Common Order)

Segment

Name


ORC-1 1 Number Set ID – for each order which is transmitted a own number is set starting from 1 to n

Continuous ID starting by 1

1, 2, …n

Yes

ORC-2 2 String The name of the order String:

^[A-Za-z0-9]

Yes

ORC-3 3 String A comment describing the order String:

^[A-Za-z0-9]

Yes

ORC-10 10 String The ID of the user who runs the order

String:

^[A-Za-z0-9]

Yes

Inquiry Response Segments Details

19HL7 Protocol

DD

OBR – Segment (Observation Request)

Segment

Name

Sequ. ID Type Comment Values Required

OBR-1 1 Number Set ID – for each order which is transmitted a own number is set starting from 1 to n

Continuous ID starting by 1

1, 2, …n

Yes

OBR-2 2 String Unique identifier of the sample (normaly the barcode)

String:

^[A-Za-z0-9]

Yes

OBR-3-1 3 String Unique identifier of the sample plate – usually a barcode assigned to the sample plate

String:

^[A-Za-z0-9]

Yes

OBR-3-2 3 String The position of the sample on the plate String:

^[A-Za-z0-9]

Yes

OBR-4-1 4 String Name of the reagent kit String:

^[A-Za-z0-9]

Yes

OBR-4-2 4 String Version of the kit String:

^[A-Za-z0-9]

Yes

ORB-9 9 Number The volume in the sample transfer input plate in ul.

No

ORB-10 10 String The type of the sample transfer input plate

One of the values which are defined in the Main Application

No

OBR-15-1 15 String Name of the test Definition String:

^[A-Za-z0-9]

Yes

OBR-15-2 15 String Version of the test Definition String:

^[A-Za-z0-9]

Yes

OBR-18 18 Number The volume of the sample One of the values which are stored in the corresponding Test Definition

Yes

OBR-19 19 Number The elution volume One of the values which are stored in the corresponding Test Definition

Yes

OBR-20 20 String The type of the output plate One of the values which are defined in the Main Application

Yes

OBR-21 21 String The type of the Internal Control which is used for this order

One of the values which are defined in the Main Application

No*

*Note: If there is no Internal Control defined in the order this field MUST be empty.

NTE – Segment (Notes and Comments)

Segment

Name


NTE-1 1 Number Set ID – for each order which is transmitted a own number is set starting from 1 to n

Continuous ID starting by 1 1, 2, …n

Yes

NTE-3 3 String Comment for the sample String:

^[A-Za-z0-9]

No

Inquiry Response Segments Details


DD

4 Example Inquiry / Response

4.1 HL7 Record

MagNA Pure 96 System Enquiry

[VT]

MSH|^&~\|MagNA·Pure·96||||20091126081114||QBP^Q11|MPCZC8380G5K|P|2.4|[CR]

QPD|QUERY_ORDER|[CR]

RCP|[CR]

[FS][CR]

HOST Response (Order) Order: OrderID = Order790

[VT]

MSH|^~\&|||||20091126083614||ORM^O01|MPCZC8380G5K|P|2.4|[CR]

ORC|1|Order790|Order·Comment·xxx·zzz|||||||std[CR]

OBR|1|Sample·ID·1|1234567890^A1|Cellular·RNA·LV^0.2|||||||||||Cellular·RNA·LV^0.6.4|||200|50|LC·480|IC1[CR]

NTE|1||Comment·Sample·1[CR]

OBR|2|Sample·ID·2|1234567890^B1|Cellular·RNA·LV^0.2|||||||||||Cellular·RNA·LV^0.6.4|||200|50|LC·480|IC1[CR]

NTE|2||Comment·Sample·2[CR]

OBR|3|Sample·ID·3|1234567890^C1|Cellular·RNA·LV^0.2|||||||||||Cellular·RNA·LV^0.6.4|||200|50|LC·480|IC1[CR]

NTE|3||Comment·Control[CR]

OBR|4|Sample·ID·4|1234567890^F1|Cellular·RNA·LV^0.2|||||||||||Cellular·RNA·LV^0.6.4|||200|50|LC·480|IC1[CR]

NTE|4||Comment·Test[CR]

[FS][CR]

MagNA Pure 96 System Order acknowlegment

[VT]

MSH|^&~\|MagNA·Pure·96||||20091126081114||ACK|MPCZC8380G5K|P|2.4|[CR]

MSA|AA|Order790|[CR]

[FS][CR]

MagNA Pure 96 System negative acknowlegment (Example) *

[VT]

MSH|^&~\|MagNA·Pure·96||||20091126081114||ACK|MPCZC8380G5K|P|2.4|[CR]

MSA|AR|Order790|[CR]

[FS][CR]

Reasons for order not acknowledged by instrument could be found on the instrument in the Host Module log window on page 35, i.e. order already exists or user ID unknown.

Example Inquiry / Response

21HL7 Protocol

DD

5 HL7 Result Segments Details

MSH Segment (Message Header)

Segment

Name


MSH 1 String Field delimiter | Yes

MSH 2 String Component, Repetition, Escape and Subcomponent delimiter – exactly in this order

^~\& Yes

MSH 7 XML Da-teTime



Yes

MSH 9 String Message type code – see HL7 Doc.: [1] Table 0076 - Message type

OUL (OUL^R21) Yes

MSH 9-2 String Trigger event code – see HL 7 Doc.: [1] Table 0003 - Event type

R21 (OUL^R21) Yes

MSH 10 String The name of the sending machine (PC name)

1234567890 * See known problems on page 39

Yes

MSH 11 String Processing mode (processing priority) see HL7 Doc.: [1] Table 0103 - Processing ID

P = Production Yes

MSH 12 Number Version ID – used as a version check to make sure that this message is interpreted correctly. See HL7 Doc.: [1] Table 0104 – Version ID

2.4 Yes

ORC – Segment (Common Order)The Common Order Segment is used to heading the OBR segments.

Segment

Name


ORC-1 1 Number Set ID – for each order which is transmitted a own number is set starting from 1 to n

Continuous ID start-ing by 1

1, 2, …n

Yes

ORC-2-1 2 String The name of the order String:

^[A-Za-z0-9]

Yes

ORC-2-2 2-2 String The ID of the batch (Run ID) String:

^[A-Za-z0-9]

Yes

ORC-3 3 String The comment from the Order String:

^[A-Za-z0-9]

No

ORC-9 9 XML Date-Time

Timestamp when the samples have been removed from the control unit


Yes

ORC-10 10 String The name of the user which has started the processing of this sample

String:

^[A-Za-z0-9]

Yes

HL7 Result Segments Details


DD

OBR – Segment (Observation Request)This table is showing the field mappings between the XML file of the MagNA Pure 96 System and the HL7 mes-sage observation request segment.

The observation request segment is holding all information related to a sample.

Segment

Name


OBR-1 1 Number Set ID – for each order which is transmitted a own number is set starting from 1 to n

Continuous ID starting by 1 1, 2, …n

Yes

OBR-2 2 String The ID of the current Sample (Barcode)

String: ^[A-Za-z0-9]

Yes

OBR-3 3 String The ID of the Sample Plate (Barcode)


No

OBR-4 4 String The name of the reagent kit which has been used for this sample


Yes

OBR-7 7 XML Da-teTime

Timestamp when the processing has started


Yes

OBR-8 8 XML Da-teTime

Timestamp when the processing has been finished


Yes

OBR-13-1 13 String Type of the output plate String: ^[A-Za-z0-9]

Yes

OBR-13-1 14 String The IC Type String: ^[A-Za-z0-9]

Yes

OBR-15 15 String The Name of the protocol which has been used for the samples


Yes

OBR-18 18 Number Sample volume in µl Value stored in the test definition.

Yes

OBR-19 19 Number Elution volume in µl Value stored in the test definition.

Yes

OBR-20 20 String The version of the Application Software

String:

^[A-Za-z0-9]

Yes

OBR-21 21 String The serial number of the instrument String:

^[A-Za-z0-9]

Yes


23HL7 Protocol

DD

OBX – Segment (Observation / Result Segment)

Segment

Name


OBX-1 1 Number Sequence No. Continuous ID starting by 1 1, 2, …n

Yes

OBX-3 3 String The position of the sample on the sample plate e.g. A1

String: ^[A-H0-9] Yes

OBX-4 4 String The Processing Flags String: ^[A-Za-z0-9] No

OBX-5-1 5 String The definitions of the used Internal Control:

- IC Volume

String:^[A-Za-z0-9] No

OBX-5-2 6 String - Barcode String:^[A-Za-z0-9] No

OBX-5-3 7 String - Expiration date String:^[A-Za-z0-9] No

OBX-5-4 8 String - Production lot String:^[A-Za-z0-9] No

OBX-11 11 String Result status P = Passed F = Failed

Yes

OBX-13 13 String The state of the whole run (Passed/Failed)

String: ^[A-Za-z0-9] Yes

NTE – Segment (Notes and Comments)

Segment

Name


NTE-1 1 Number Sequence No. Continuous ID starting by 1 1, 2, …n

Yes

NTE-3 3 String Comment for the sample String: ^[A-Za-z0-9]

No



DD

6 Example Result Output

6.1 HL7 Result Export

MagNA Pure 96 result output

MSH|^&~\|||||20091126141120||OUL^R21|1234567890|P|2.4|[CR] ORC|1|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|1|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|1||A1||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|1||Comment for the Sample X|[CR] ORC|2|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|2|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|2||B1||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|2||Comment for the Sample X|[CR] ORC|3|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|3|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|3||C1||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|3||Comment for the Sample X|[CR] ORC|4|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|4|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|4||D1||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|4||Comment for the Sample X|[CR] ORC|5|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|5|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|5||E1||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|5||Comment for the Sample X|[CR] ORC|6|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|6|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|6||F1||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|6||Comment for the Sample X|[CR] ORC|7|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|7|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|7||G1||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|7||Comment for the Sample X|[CR] ORC|8|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|8|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|8||H1||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|8||Comment for the Sample X|[CR] ORC|9|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|9|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|9||A2||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|9||Comment for the Sample X|[CR] ORC|10|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

Example Result Output

25HL7 Protocol

DD

OBR|10|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|10||B2||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|10||Comment for the Sample X|[CR] ORC|11|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|11|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|11||C2||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|11||Comment for the Sample X|[CR] ORC|12|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|12|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|12||D2||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|12||Comment for the Sample X|[CR] ORC|13|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|13|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|13||E2||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|13||Comment for the Sample X|[CR] ORC|14|243^506_200908281313|Comment to Order 243||||||20090828130858|std|[CR]

OBR|14|zxc|0405090000004225|RNA_LV·1.0|||20090828130828|20090828130851|||||<none>^sad ||SW_Test_MP96_RNA_LV_IC_Handling·1.1|||450|200|1.0.0|506|[CR] OBX|14||F2||20^0012123456780240^20090829000800^||||||P||Passed|[CR] NTE|14||Comment for the Sample X|[CR] [FS][CR]

Host acknowledge ACK: OrderID = 243

[VT] MSH|^~\&|||||20091126142926||ACK|20091126142925|P|2.4[CR] MSA|AA|243[CR] [FS][CR]

Character indicates the actual HL7 data continues next line without a break.

Example Result Output


EE

E File Sharing

Due to security concerns, the file sharing configuration has limitations.

There are only 2 scenarios where the file sharing option can be utilized.

1. Direct connection: The MagNA Pure 96 may be directly connected to the LightCycler® 480 as part of an isolated, island network or as part of a Roche protected network behind a Roche Firewall.

2. Customer PC or server: The MagNA Pure 96 may be connected to a customer PC or server via an IP Address based UNC share through the mandatory Roche Firewall. The customer machine must be outside the firewall. Under this scenario, the MagNA Pure 96 is the client and initiates all contact as the connection through the firewall is outbound only. The file sharing service looks on the customers Import share for the specific XML files. In addition, the MagNA Pure 96 can export result files to the customer’s Export share.

See also the example networks on page 32.

1 Sample of XML Files

Ordering

<?xml version=”1.0” encoding=”UTF-8” standalone=”yes”?><OrderTemplate> <OrderParameter KitName=”Cellular RNA LV” KitVersion=”2.0” TestDefinitionName=”Cellular RNA LV” TestDefinitionVersion=”2.0” SampleVolume=”200” ElutionVolume=”50” OrderName=”TestOrder” Sample-PlateId=”0412100000001234” InputPlateFillVolume=”0” InputPlateType=”<none>” OutputPlateType=”MP96 Output Plate” InternalControlType=”<none>”/> <SampleData> <Number>1</Number> <SampleID>test </SampleID> <Comment/> <SamplePos>A1</SamplePos> </SampleData> <SampleData> <Number>2</Number> <SampleID>test </SampleID> <Comment/> <SamplePos>B1</SamplePos> </SampleData> | (continuous numbering of samples up to 96 ) | <SampleData> <Number>96</Number> <SampleID>test </SampleID> <Comment/> <SamplePos>H12</SamplePos> </SampleData></OrderTemplate>

Note: For clarity, the table has been cut and sample data from 3 to 95 had been removed. The text in bold red characters is not part of XML data. See also order schema definition on page 28.

Sample of XML Files

27File Sharing

EE

MagNA Pure 96 Result Export (XML)

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>

<BatchResultDataSet> <BatchInformation> <Operator>Developer</Operator> <BatchStartDateTime>2009-05-05T09:00:50.025+02:00</BatchStartDateTime> <BatchEndDateTime>2009-05-05T09:02:22.62+02:00</BatchEndDateTime> <RunState>-</RunState> <ASSoftwareVersion>0.5.0</ASSoftwareVersion> <ISSoftwareVersion>unknown ApplicationVersion</ISSoftwareVersion> <InstrumentSerialNumber>1234</ InstrumentSerialNumber > <BatchId>_200905050900</BatchId> <SamplePlateId>4711</SamplePlateId > <OrderComment>Test Run</OrderComment> <OutputPlateType>LC 480</OutputPlateType> <ICType>IC1</ICType> <OrderID>TestOrder</OrderID> <OrderEndDateTime>2009-05-05T09:02:39.541+02:00</OrderEndDateTime> </BatchInformation> <BatchTestparameter> <KitName>DNA/tNA PW 3</KitName> <PurificationProtocol>SW_Test_alpha4_DNA 2.0</PurificationProtocol> <SampleVolume>50</SampleVolume> <ElutionVolume>50</ElutionVolume> </BatchTestparameter> <SampleData> <Number>1</Number> <SampleID>Sample 1</SampleID> <Comment>Comment Sample 1</Comment> <SamplePos>A1</SamplePos> <Flags /> <ResultStatus>Passed</ResultStatus> </SampleData> <SampleData> <Number>2</Number> <SampleID>Sample 2</SampleID> <Comment>Comment Sample 2</Comment> <SamplePos>B1</SamplePos> <Flags /> <ResultStatus>Passed</ResultStatus> </SampleData> </BatchResultDataSet>

Sample of XML Files


EE

2 Schema Definition

Order Schema

Picture for documentation purpose only

Schema Definition

29File Sharing

EE

Results Schema


continued on next page

Schema Definition


EE

Results Schema (continued from previous page)


Schema Definition

31 Sample List, LightCycler® 480 Software

FF

F Sample List, LightCycler® 480 Software

Detailed instructions for this workflow are out of scope of this manual. For instructions to transfer sample lists to the LightCycler® 480 Instruments via shared folders, some extra installation steps and instructions are required on the MagNA Pure 96 Instrument as well as on the LightCycler® 480 System. Please ask the local Roche Field Service Engineer.

Note: The lines within the exported textfile may appear unsorted.


GG

G Communication Setup

1 Network ConnectionThe MagNA Pure 96 may be directly connected to the LightCycler® 480 as part of an isolated, island network (plugged directly into the LightCycler® 480 or through a separate network switch that has NO other network resources connected) or as part of a Roche protected network behind the mandatory Roche Firewall.

Typical Installation Scenarios:

Network Diagrams

Figure 4 Simple network diagram with LightCycler® 480 System

Network Connection

33Communication Setup

GG

Figure 5 Network diagram with database (DB) server

Network Connection


GG

2 Instrument Setup

Host CommunicationThis installation has to be performed by qualified Roche service personnel.

Once the software for host interface has been installed, some parameters can be changed to match the requirements of the LIS system.

2.1 HL7 Setup

Host Module Setup for HL7

The HL7 communication parameters are set in the file hosts and in the file services in c:\Windows\System_32\drivers\etc

IP address

LIS IP address is setup during Host Module installation. It can be changed later on without redoing the installation. It can be found in the file 'Hosts' under the name: MPHTCServer

HL/ communication port

The default HL7 port setting is 13588 in file 'Services' under the name: MPHTCService

Start the Host Module Setup screen by double clicking the Host Module icon on the system desktop

and log on. Then go the the File Transfer TAB

To use HL7 transmission of orders and results, the option file transfer must NOT be enabled.

This option is needed for the transfer that may be used to exchange through file sharing.

If enabled it will compete with the HL7 transfer and only one mode may be enabled at a time.

Instrument Setup


GG

Select the checkbox to enable HL7 transfer. This will start the automatic query of orders and results. Once every minute the MagNA Pure 96 Software will request pending orders from the LIS. Incoming orders will be processed whether they come after a request or not.

Once the parameters are set, go to the Host Modul Control tab, then press the Stop button and afterwards the Start button to activate the changes.

Data exchange is logged in this window and can be used for troubleshooting purposes.

Instrument Setup


GG

2.2 File Transfer Setup

Host Module Setup for XML File Transfer

c Start the Host Module and Log in.

c On the File Transfer tab fill the appropriate fields for the order import and result export locations as shown above (The locations must be different). You can prepare a Network Share with two different sub-directories, i.e. the share is named “test” with directories IN and OUT.

c Fill in the necessary user name and password to obtain access to the network share.

c The URL must be defined with an IP Address and not a hostname. Note: The URL must not contain any space character, else the import/export will not work.

c The Domain can either be the Domain of the sharing server or the sharing server’s name, however the field CANNOT be empty.

Important: Even if you are not using a domain, the field cannot be empty. If the field is left empty, the test will always produce a failed status. A minus sign is enough to avoid this problem.

c Tick the Enabled boxes as shown (1,2 and 3).

c Click the two Test buttons to make sure that the URL are accessible. In case of a successful test, the Status becomes “Passed”. If it display “failed”, see the troubleshooting section on page 37.

Periodically, the system will look for files with XML extensions, as defined in File sharing on page 26 (ordering).

The Host Module will try to interpret the data in the XML structure and if everything is correctly defined, it will add a corresponding order to the database. If it fails to accept the order, a log entry on page 37 will be created to explain the first error encountered. If the XML structure have several errors, only the first error will be reported. All errors will have to be corrected in an iterative process before the order can be accepted.

Note: The HL7 Transfer must not be activated simultaneously, as this task will compete with the result export for the intermediate XML files.

Instrument Setup


GG

Troubleshooting:If problems occur and the Status always displays Failed, check the following:

c The service runs (Host Module Control tab, see example below (1)).

c The System where the Directories are setup runs and

c The Network connection is up and running.

c If a firewall is used, the IP address is that of the files server and not of the firewall.

c The Directories are shared properly and sufficient access is granted.

c The name used in the URL field is the effective share name, and not the name of the directory. (i.e. in the example above it is test).

The directory and share name are usually the same, but not necessarily.

When the system runs properly, the import and export operations will be displayed in the Log window.(2)

If an order import fails, the reason will be displayed in the log (3). An error log file [Name.import.log] will be placed in the directory and the order file will be renamed as [Name.xml.error].

Instrument Setup


GG

The error log file contains an indication similar to the entry in the Host Module log window.

Example, the file order.Import.log contains:

3/3/2010 14:46:24 : Order ‘\\10.10.1.100\test\OUT\Order.XML’ not imported because the referenced test definition is not present

Instrument Setup

39 Known Problems / Issues / Restrictions

HH

H Known Problems / Issues / Restrictions

c The HL7, file sharing and LightCycler® 480 Software output should not be activated in parallel. The intended use is that only one mode is active at one time.

If more than one transmission mode is active, one of the tasks will get hold of the results and remove them from the output list.

Therefore the others will fail to produce data.

c MSH 10 field does not display intended value but 1234567890 instead. Workaround: Ignore this value in result output headers.

c OBR segment in Order response from LIS:

If failed samples are present, they must be transmitted and eventually flagged as such.

Workaround: The number of transmitted samples must always match the samples physically present in the plate. Failure to comply will result in an error message: “Order not imported: Reason: Not all sample data is

defined”.

c The order name shall NOT contain forward slash (/) or backslash (\). The HL7 protocol can not handle this. The order will not be imported/exported and the HL7 communication will be corrupted.

c The URL used for file sharing shall NOT contain any space character. If a space character is used, the connection test using the Test button will results in neither passed nor failed

status, but remains blank.

Import of files using the Host Module:

Error message: “The referenced kit definition is not present”.

Cause: Control unit not restarted after installation of Host Module.

Solution: Restart Control Unit.


II

I Keywords Index

A

Automatic query ........................................................34

C

Client .................................................................................6Client/Server structure ...............................................7Communication layer ..................................................8Communication port ................................................34

D

DNA...................................................................................6

E

Elution ...............................................................................6

F

File Hosts ......................................................................34Firewall .......................................................................... 32

H

HL7 port ........................................................................34Host module ................................................................34

I

Installation scenarios ............................................... 32IP address ....................................................................34

L

Layer ..................................................................................8LightCycler® 480 Instrument .................................31

N

Network Diagrams .................................................... 32

O

OSI model .......................................................................8

P

Port setting ..................................................................34

S

Schema ......................................................................... 28Server ................................................................................6Shared folders ............................................................31

T

TCP/IP client ..................................................................7TCP/IP server ............................................................6, 7

For the intended use of the MagNA Pure 96 System refer to the Operators Guide.

Published byRoche Diagnostics GmbH Sandhofer Straße 11668305 MannheimGermany

© 2014 Roche Diagnostics GmbH.

COBAS, MAGNA PURE and LIGHTCYCLER are trademarks of Roche.

www.lifescience.roche.com

magna pure 96 system host interface manual, version 4

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