[WEBCLIENT-135] Some metadata terms with special characters will not run in the query tool Created: 02/Sep/15 Updated: 25/Jan/16 Resolved: 07/Dec/15 |
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| Status: | Closed |
| Project: | i2b2 Web Client |
| Component/s: | Web Client |
| Affects Version/s: | 1.7.06 |
| Fix Version/s: | 1.7.07 |
| Type: | Bug | Priority: | Major |
| Reporter: | Reeta Metta | Assignee: | Janice Donahoe |
| Resolution: | Fixed | Votes: | 0 |
| Labels: | None | ||
| Remaining Estimate: | Not Specified | ||
| Time Spent: | Not Specified | ||
| Original Estimate: | Not Specified | ||
| Issue Links: |
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| Affects View/s: |
Navigate Terms, Workplace
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| i2b2 Feature/s: |
Queries
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| i2b2 Sponsored Project/s: |
i2b2 Web Client
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| i2b2 Related Project/s: |
BBP
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| Affects Database/s: |
All databases
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| Affects Web Browser/s: |
All Web Browsers
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| 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. |
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| Participant/s: | |||||||||
| Description |
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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</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,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,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> |
| Comments |
| Comment by Nich [ 03/Dec/15 ] |
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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 |
| Comment by Janice Donahoe [ 25/Jan/16 ] |
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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. |