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  1. i2b2 Web Client
  2. WEBCLIENT-135

Some metadata terms with special characters will not run in the query tool

Details

    • Bug
    • Status: Closed
    • Major
    • Resolution: Fixed
    • 1.7.06
    • 1.7.07
    • Web Client
    • None
    • Navigate Terms, Workplace
    • Queries
    • i2b2 Web Client
    • BBP
    • All databases
    • All Web Browsers
    • Hide
      This can be reproduced in both the demo and testing environments.

      Upon further investigation I found the error occurs when there are special characters like the ampersand ('&') in the tooltip; the Web Client is not escaping the '&'.

      The Web Client is escaping the special characters when they are in the path (item_key) or the name of the item. The problem only occurs when it is in the tooltip.

      I have verified that this issue is only a problem in the Web Client. It is working correctly in the i2b2 Workbench.
      Show
      This can be reproduced in both the demo and testing environments. Upon further investigation I found the error occurs when there are special characters like the ampersand ('&') in the tooltip; the Web Client is not escaping the '&'. The Web Client is escaping the special characters when they are in the path (item_key) or the name of the item. The problem only occurs when it is in the tooltip. I have verified that this issue is only a problem in the Web Client. It is working correctly in the i2b2 Workbench.

    Description

      Ontology terms with special characters return in an error when running a query.
      It looks like this is occurs in when there is an ampersand (&) character in C_TOOLTIP.
      Steps to reproduce:
      log into https://www.i2b2.org/webclient/
      Under Navigate Terms panel, click on "Find" tab
      Search by : <space>&<space> to return Ontology term with '&' character
      "DIRECT ANTIPLATELETB&,AMP,W (LOINC:X3007-6)"
      Drag and drop the term in group panel 1 and click on run query.
      Getting"cell status message could not be understood error

      Attached screen shot of the issue

      XML Message History
      sentrcvd
      GetTermInfo
      ONT
      called by CRC:QueryTool @ T+00:00.00
      sentrcvd
      GetTermInfo
      ONT
      called by CRC:QueryTool @ T+00:00.00
      sentrcvd
      GetTermInfo
      ONT
      called by CRC:QueryTool @ T+00:00.09
      sentrcvd
      runQueryInstance_fromQueryDefinition
      CRC
      called by CRC:QueryTool @ T+00:11.79
      sentrcvd
      runQueryInstance_fromQueryDefinition
      CRC
      called by CRC:QueryTool @ T+00:17.03
      sentrcvd
      runQueryInstance_fromQueryDefinition
      CRC
      called by CRC:QueryTool @ T+01:52.19
      <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
      <ns6:request xmlns:ns4="http://www.i2b2.org/xsd/cell/crc/psm/1.1/" xmlns:ns7="http://www.i2b2.org/xsd/cell/ont/1.1/" xmlns:ns3="http://www.i2b2.org/xsd/cell/crc/pdo/1.1/" xmlns:ns5="http://www.i2b2.org/xsd/hive/plugin/" xmlns:ns2="http://www.i2b2.org/xsd/hive/pdo/1.1/" xmlns:ns6="http://www.i2b2.org/xsd/hive/msg/1.1/" xmlns:ns8="http://www.i2b2.org/xsd/cell/crc/psm/querydefinition/1.1/">
      <message_header>
      <proxy>
                  <redirect_url>http://services.i2b2.org:9090/i2b2/services/QueryToolService/request&lt;/redirect_url>
              </proxy>

      <sending_application>
      <application_name>i2b2_QueryTool</application_name>
      <application_version>1.6</application_version>
      </sending_application>
      <sending_facility>
      <facility_name>PHS</facility_name>
      </sending_facility>
      <receiving_application>
      <application_name>i2b2_DataRepositoryCell</application_name>
      <application_version>1.6</application_version>
      </receiving_application>
      <receiving_facility>
      <facility_name>PHS</facility_name>
      </receiving_facility>
      <security>
      <domain>i2b2demo</domain>
      <username>demo</username>
      <password token_ms_timeout="1800000" is_token="true">SessionKey:z413DkIHUROJ8DbeoUCx</password>
      </security>
      <message_type>
      <message_code>Q04</message_code>
      <event_type>EQQ</event_type>
      </message_type>
      <message_control_id>
      <message_num>yu2m9gGczlgPy153wxZzb</message_num>
      <instance_num>0</instance_num>
      </message_control_id>
      <processing_id>
      <processing_id>P</processing_id>
      <processing_mode>I</processing_mode>
      </processing_id>
      <accept_acknowledgement_type>messageId</accept_acknowledgement_type>
      <project_id>Demo</project_id>
      </message_header>
      <request_header>
      <result_waittime_ms>180000</result_waittime_ms>
      </request_header>
      <message_body>
      <ns4:psmheader>
      <user group="Demo" login="demo">demo</user>
      <patient_set_limit>0</patient_set_limit>
      <estimated_time>0</estimated_time>
      <query_mode>optimize_without_temp_table</query_mode>
      <request_type>CRC_QRY_runQueryInstance_fromQueryDefinition</request_type>
      </ns4:psmheader>
      <ns4:request xsi:type="ns4:query_definition_requestType" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
      <query_definition>
      <query_name>DIRECT ANTIPLAT@11:04:07</query_name>
      <query_timing>ANY</query_timing>
      <specificity_scale>0</specificity_scale>
      <panel>
      <panel_number>1</panel_number>
      <panel_accuracy_scale>100</panel_accuracy_scale>
      <invert>0</invert>
      <panel_timing>ANY</panel_timing>
      <total_item_occurrences>1</total_item_occurrences>
      <item>
      <hlevel>5</hlevel>
      <item_name>DIRECT ANTIPLATELETB&amp;AMP,AMP,W (LOINC:X3007-6)</item_name>
      <item_key>\\i2b2_LABS\i2b2\Labtests\LAB\(LLB6) Coagulation\(LLB12) Platelet Antibodies\PLTABD\LOINC:X3007-6\</item_key>
      <tooltip>Labtests \ Coagulation \ Platelet Antibodies \ PLT AB (Direct) (Group:PLTABD) \ Direct antiplateletb&amp,amp,w (LOINC:X3007-6)</tooltip>
      <class>ENC</class>
      <item_icon>LA</item_icon>
      <item_is_synonym>false</item_is_synonym>
      <constrain_by_value>
      <value_type>TEXT</value_type>
      <value_constraint>('POSITIVE')</value_constraint>
      <value_operator>IN</value_operator>
      </constrain_by_value>
      </item>
      </panel>
      </query_definition>

      <result_output_list><result_output priority_index="11" name="patient_count_xml"/>
      </result_output_list>

      </ns4:request>

      </message_body>
      </ns6:request>
      <faultstring>com.ctc.wstx.exc.WstxUnexpectedCharException: Unexpected character ',' (code 44); expected a semi-colon after the reference for entity 'amp'
       at [row,col {unknown-source}]: [68,117]</faultstring>

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            rm302 Reeta Metta created issue -
            jmd86 Janice Donahoe made changes -
            Field Original Value New Value
            Summary Some metadata nodes with special characters will not run in the query tool Some metadata terms with special characters will not run in the query tool
            jmd86 Janice Donahoe made changes -
            Affects Database/s All databases [ 10219 ]
            Affects Web Browser/s All Web Browsers [ 10220 ]
            Fix Version/s 1.7.07 [ 10203 ]
            Reproduction Notes This can be reproduced in both the demo and testing environments.

            Upon further investigation I found the error occurs when there are special characters like the ampersand ('&') in the tooltip; the Web Client is not escaping the '&'.

            The Web Client is escaping the special characters when they are in the path (item_key) or the name of the item. The problem only occurs when it is in the tooltip.

            I have verified that this issue is only a problem in the Web Client. It is working correctly in the i2b2 Workbench.
            i2b2 Related Project/s BBP [ 10227 ]
            i2b2 Sponsored Project/s i2b2 Web Client [ 10197 ]
            Status New [ 10000 ] Open [ 1 ]
            jmd86 Janice Donahoe made changes -
            Assignee Nich [ nich ]
            nich Nich added a comment -
            The <tooltip> value in the request message was not being escaped. Therefore, any ampersands in the C_TOOLTIP would make the query fail to run.

            This is fixed in 1.7.07
            nich Nich added a comment - The <tooltip> value in the request message was not being escaped. Therefore, any ampersands in the C_TOOLTIP would make the query fail to run. This is fixed in 1.7.07
            nich Nich made changes -
            Status Open [ 1 ] In Progress [ 3 ]
            nich Nich made changes -
            Assignee Nich [ nich ] Janice Donahoe [ jmd86 ]
            Status In Progress [ 3 ] Ready to Test [ 10001 ]
            rm302 Reeta Metta made changes -
            Assignee Janice Donahoe [ jmd86 ] Nich [ nich ]
            rm302 Reeta Metta made changes -
            Assignee Nich [ nich ] Reeta Metta [ rm302 ]
            rm302 Reeta Metta made changes -
            Status Ready to Test [ 10001 ] Testing [ 10002 ]
            rm302 Reeta Metta made changes -
            Link This issue blocks WEBCLIENT-153 [ WEBCLIENT-153 ]
            rm302 Reeta Metta made changes -
            Resolution Fixed [ 1 ]
            Status Testing [ 10002 ] Resolved [ 5 ]
            rm302 Reeta Metta made changes -
            Assignee Reeta Metta [ rm302 ] Janice Donahoe [ jmd86 ]
            jmd86 Janice Donahoe added a comment - - edited
            On 01/22/2016, the 1.7.07 Release was made available at the following locations.

            https://www.i2b2.org/software/
             - zip files for release 1.7.07 are available on this site. This includes both the code and documentation.

            https://github.com/i2b2
             - source code has been tagged with v1.7.07.
            jmd86 Janice Donahoe added a comment - - edited On 01/22/2016, the 1.7.07 Release was made available at the following locations. https://www.i2b2.org/software/  - zip files for release 1.7.07 are available on this site. This includes both the code and documentation. https://github.com/i2b2  - source code has been tagged with v1.7.07.
            jmd86 Janice Donahoe made changes -
            Status Resolved [ 5 ] Closed [ 6 ]

            People

              jmd86 Janice Donahoe
              rm302 Reeta Metta
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              Dates

                Created:
                Updated:
                Resolved: