Activity for TIES
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Melissa Schwenk created ticket #108
Annotation form fields from earlier not displaying
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Install bug
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Query unable to save
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Control panel not displaying properly
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HL7 support for new section
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Add group section to display order
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Structured data support for incremental loads
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HL7 Validator Controller
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Duplicate entry error when loading reports
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Duplicate entry error when loading reports
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TIES Chart should count patients
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New Tags not working
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TIES Chart should count patients
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Michael Davis created ticket #95
Chart regrouping
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fixed type in dialog message
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uncommented the filter clear
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changed the priorityque to use a simple collection sorting
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Oliver Hao committed [r2451]
switched the location of age bar chart and age-gender bar chart
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minor mods to loosely support multiple document types
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HL7 validator function enhancement
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added code to handle unicode in reports and section mgt mods
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added code to handle unicode in reports and section mgt mods
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Changed the demographic chart to count the number of patients
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modified HL7 Validator to examine the validity of Section PID{MRN, Date Of Birth, SSN}, Section OBX{Observation ID}, OBR{Accession Number, Observation Date and Time, Sign out Date Time, Report status}
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removed report types selection from HL7 validator panel
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support for new section and report types; structured data loading mods
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Reber posted a comment on discussion TIES Help / Support
Did you ever resolve your issue with her-2 concept coding?
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re-created HL7 validation button on control panel
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fixed the tagging bug by changing the status of documents from idling to indexing
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fixed the tagging bug by changing the status of documents from idling to indexing
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comment out one line of code that is only for local testing purpose
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fixed search documents with criterion by adding StatsResource
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fixed resource path conflict between documents/list and documents/<id>
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Changed the return type from Response to DocumentsResource in the document service.
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Renamed mrn to patientId
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fixed uri and add a check for null; NEEDS OTHER LOGIC MODS
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Beautified code by removing blank lines and creating meaningful names.
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fix controlpanel not display content; fix for the display order for structured data
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added document search API post method: retrieve relative documents given a list of medical record numbers
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updated API by adding POST method, supporting free text search with criterion including demographics and event year
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All of a sudden we can no longer log into our TIES node. I've restarted everything including private/public tomcats and the databases. From JAVA Console: Java Web Start 11.151.2.12 x86_64 Using JRE version 1.8.0_151-b12 Java HotSpot(TM) 64-Bit Server VM User home directory = /Users/jpr101 c: clear console window f: finalize objects on finalization queue g: garbage collect h: display this help message m: print memory usage o: trigger logging p: reload proxy configuration q: hide console r: reload...
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added new api--document search by id
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changed the activity type for logging for query
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API changes to query,concept search for Exception handling, new parameters, return structure
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Fixed age < 50 query unable to save bug by removing extra </value>
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Reza Hay posted a comment on discussion TIES Help / Support
Hi Dear Noble Developers, I'm trying to use Noble in a UIMA pipeline but I get various errors. Is there a small description of how to use UIMA plugin of Noble? Thanks in advance, Reza Haydarlou VU University Amsterdam
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Sorry, none at this time
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Any update on this?
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Bug fixing for SAVE button, enabled saving for modified report
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Added notification when switching the modified annotation form
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added a save button in the annotation form ui
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added new feature to ConceptSearch --concept lookup by cui
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added concept code search to query api
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updates to the concept and query api
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Concept Search Refactor: Replace Annotation class with ConceptStringUserObject class.
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Code Refactoring:
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Added new Features
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Fixed bugs on annotation form export
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added some print statements to test
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removed wrong versions of opensaml jars and includes fix for < symbol
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enable HL7 to check and synthesize reports with Status SYNTHESIZING
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Girish Chavan committed [r2411]
Fixed bug when saving queries that contained Age <n query constraint. The < caused an xml exception when saved without a CDATA wrap. Updated the code to wrap all value domains with CDATA when saving within a query.
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Modified hasWork() in hl7 importer to check if there is any files in Synthesizing status.
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added new parameter "limit" to api query search
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fixed bugs by enabling the following feature.
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fixed bugs by enabling the following feature.
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trap error for few documents return for query
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replace tui with cui in concept search results
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added concept search api
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removed pk from payload
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fixed the patient id look up to work on non-tcga data, and changed claim (org) to name
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load index path from dir TIES/tomcatHub/webapps/api/WEB-INF/classes/config/caties.properties
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Hi Kevin, could you share the wrapper.log from when you ran 5.7 and let me know if there are any errors in there.
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New API changes
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Created this branch for bug fixes
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Created this branch for bug fixes
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Hi Kevin, could you please tell me which table/tables did you use to load the document into the database?
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Great. We will work on geting this fixed in the v5.7. Thx
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Kevin posted a comment on discussion TIES Help / Support
I followed your suggestion of downgrading to 5.65. My documents are again synthesizing. Thanks.
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ok. got it. As an interim solution (until we find the issue), for the pipelines only, you may want to downgrade to 5.65. This could possibly work by getting the old caties.jar file ((http://ties-spirit.dbmi.pitt.edu/5.65/lib/caties.jar), shuting down the pipelines and renaming the existing one in ./pipelines/common/lib/caties.jar. Then restart the pipelines.
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Our setup does not rely on files. We directly push the document fragments in to the database.
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Have any new HL7 files been added to your folder since upgrading? We noticed there have been no pending files found. Do you have any new files you can drop in the HL7 folder? This may 'jump start' the ones waiting to be processed.
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Of course I restarted... How do you explain the absence of the message "Processing documents requiring synthesis" post upgrade? k-
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i don't see any notable errors. I seems that the log time between you using version 5.65 and 5.7 was a few minutes, have you fully restarted all your piplelines after upgrading? Anything pending should then be processed
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Attached as requested. I included annotations in the log.
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Kevin, is it possible to attach or send me directly your log file from the HL7Import?
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Also, in the old logs, I used to see entries like: 2017-05-03 09:53:52,716 [Thread-2]CaTIES_HL7ImportPipeController:1061 - Processing documents requiring synthesis... I don't see this anymore.
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Hi, Ever since I upgraded to the latest version (5.7), my documents seem to get stuck in the 'SYNTHESIZING' status. I currently have 17k documents in IDENT_DOCUMENT in this status. Any ideas for troubleshooting? Thanks, k-
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I was not using the section type as we are loading the whole report into the tie.model.text column.
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Hi Reber, can you examine the input file and try to see if there is any new section types in input file not show up in the HL7ImportPipeController/classes/config/SectionHeaderConfig File? And we are publishing a validator soon which can do that task for users automatically.
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Loaded 60000 progress notes. 100 deidentified and there it's stuck. I have restarted the pipeline and server.log for the deid process stops at "Pushing section types to Public database" 2017-09-18 13:19:28,339 [WrapperSimpleAppMain]CaTIES_MGHScrubberDeIdentifier:174 - Building Known Identifiers Config... 2017-09-18 13:19:28,340 [WrapperSimpleAppMain]CaTIES_MGHScrubberDeIdentifier:193 - Loading Saved Identifiers 2017-09-18 13:19:28,575 [WrapperSimpleAppMain]CaTIES_MGHScrubberDeIdentifier:226 - Names...
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need changes to the API
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need changes to the API
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Mayur Sakthivel modified a comment on discussion TIES Help / Support
Screenshot attached.
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Screenshot.
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We are getting the error in the screenshot below when we try to launch TIES. Can you please help resolve this? Our users are unable to launch the applicaiton.
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We are in the process of geting together a document which describes how to add new reports. Stay tune. Thx
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Is there documentation available for adding new report types? Now that we have direct access to Epic's clarity database, we have several million Progress Notes, Procedures, etc that we'd like to run through TIES.