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将UMLS用户名和密码添加到Ctakes

[英]Add UMLS username and password to Ctakes

I'm a new user on cTAKES. 我是cTAKES的新用户。 I followed User Install Guide and add UMLS access rights. 我遵循了《用户安装指南》,并添加了UMLS访问权限。 After I edited runctakesCPE.bat and runctakesCVD.bat, I got the following: 编辑runctakesCPE.bat和runctakesCVD.bat之后,得到以下信息:

F:\\apache-ctakes-4.0.0>set CTAKES_HOME=F:\\apache-ctakes-4.0.0 F:\\ apache-ctakes-4.0.0>设置CTAKES_HOME = F:\\ apache-ctakes-4.0.0

F:\\apache-ctakes-4.0.0>if exist "F:\\apache-ctakes-4.0.0\\bin\\runctakesCVD.bat" goto okHome F:\\ apache-ctakes-4.0.0>如果存在,则“ F:\\ apache-ctakes-4.0.0 \\ bin \\ runctakesCVD.bat”转到okHome

F:\\apache-ctakes-4.0.0>if exist "C:\\Program Files\\Java\\jdk1.8.0_65\\bin\\java.exe" set PATH=C:\\Program Files\\Java\\jdk1.8.0_65\\bin;C:\\Program Files\\Java\\jdk1.8.0_65\\bin;C:\\Program Files\\Java\\jdk1.8.0_65\\ jre\\bin;C:\\ProgramData\\Oracle\\Java\\javapath;C:\\Program Files (x86)\\Intel\\iCLS Client\\;C:\\Program Fil es\\Intel\\iCLS Client\\;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\Wi ndowsPowerShell\\v1.0\\;C:\\Program Files\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Program Fi les (x86)\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Program Files\\Intel\\Intel(R) Management Engine Components\\IPT;C:\\Program Files (x86)\\Intel\\Intel(R) Management Engine Components\\IPT;c:\\Pro gram Files (x86)\\Hewlett-Packard\\HP Performance Advisor;C:\\Program Files\\Microsoft\\Web Platform Inst aller\\;C:\\Program Files (x86)\\Microsoft ASP.NET\\ASP.NET Web Pages\\v1.0\\;C:\\Program Files (x86)\\Windo ws Kits\\8.0\\Windows Performance Toolkit\\;C:\\Program Files\\Microsoft SQL Server\\110\\Tools\\Binn F:\\ apache-ctakes-4.0.0>如果存在“ C:\\ Program Files \\ Java \\ jdk1.8.0_65 \\ bin \\ java.exe”设置PATH = C:\\ Program Files \\ Java \\ jdk1.8.0_65 \\ bin ; C:\\ Program Files \\ Java \\ jdk1.8.0_65 \\ bin; C:\\ Program Files \\ Java \\ jdk1.8.0_65 \\ jre \\ bin; C:\\ ProgramData \\ Oracle \\ Java \\ javapath; C:\\ Program Files( x86)\\ Intel \\ iCLS Client \\; C:\\ Program Fil es \\ Intel \\ iCLS Client \\; C:\\ WINDOWS \\ system32; C:\\ WINDOWS; C:\\ WINDOWS \\ System32 \\ Wbem; C:\\ WINDOWS \\ System32 \\ Wi ndowsPowerShell \\ v1.0 \\; C:\\ Program Files \\ Intel \\ Intel(R)管理引擎组件\\ DAL; C:\\ Program File(x86)\\ Intel \\ Intel(R)管理引擎组件\\ DAL; C: \\ Program Files \\ Intel \\ Intel(R)管理引擎组件\\ IPT; C:\\ Program Files(x86)\\ Intel \\ Intel(R)管理引擎组件\\ IPT; c:\\ Pro gram文件(x86)\\ Hewlett-Packard \\ HP Performance Advisor; C:\\ Program Files \\ Microsoft \\ Web Platform Iner aller \\; C:\\ Program Files(x86)\\ Microsoft ASP.NET \\ ASP.NET Web Pages \\ v1.0 \\; C:\\ Program Files( x86)\\ Windo ws Kits \\ 8.0 \\ Windows Performance Toolkit \\; C:\\ Program Files \\ Microsoft SQL Server \\ 110 \\ Tools \\ Binn \\;C:\\Pr ogram Files\\IDM Computer Solutions\\UltraEdit;C:\\Python27;C:\\Program Files (x86)\\MiKTeX 2.9\\miktex\\bi n\\;C:\\Program Files\\MATLAB\\R2015b\\runtime\\win64;C:\\Program Files\\MATLAB\\R2015b\\bin;C:\\Program Files\\ IBM\\SPSS\\Statistics\\24\\JRE\\bin;C:\\cygwin64\\bin;C:\\Program Files (x86)\\Skype\\Phone\\;C:\\Program Files (x86)\\Google\\Chrome\\Application;C:\\Program Files\\Java\\jdk1.8.0_65\\bin;C:\\Program Files\\Java\\jdk1.8.0 _65\\jre\\bin;C:\\ProgramData\\Oracle\\Java\\javapath;C:\\Program Files (x86)\\Intel\\iCLS Client\\;C:\\Program Files\\Intel\\iCLS Client\\;C:\\windows\\system32;C:\\windows;C:\\windows\\System32\\Wbem;C:\\windows\\System3 2\\WindowsPowerShell\\v1.0\\;C:\\Program Files\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Progra m Files (x86)\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Program Files\\Intel\\Intel(R) Manage ment Engine Components\\IPT;C:\\Program Files (x86)\\Intel\\Intel(R) Management Engine Components\\IPT;c: \\Program Files (x86)\\Hewlett-Packard\\HP Performance Advisor;C:\\Program Files\\Microsof \\; C:\\ Pr Graph Files文件\\ IDM Computer Solutions \\ UltraEdit; C:\\ Python27; C:\\ Program Files(x86)\\ MiKTeX 2.9 \\ miktex \\ bi n \\; C:\\ Program Files \\ MATLAB \\ R2015b \\ runtime \\ win64; C:\\ Program Files \\ MATLAB \\ R2015b \\ bin; C:\\ Program Files \\ IBM \\ SPSS \\ Statistics \\ 24 \\ JRE \\ bin; C:\\ cygwin64 \\ bin; C:\\ Program Files(x86)\\ Skype \\ Phone \\; C:\\ Program Files(x86)\\ Google \\ Chrome \\ Application; C:\\ Program Files \\ Java \\ jdk1.8.0_65 \\ bin; C:\\ Program Files \\ Java \\ jdk1.8.0 _65 \\ jre \\ bin; C:\\ ProgramData \\ Oracle \\ Java \\ javapath; C:\\ Program Files(x86)\\ Intel \\ iCLS Client \\; C:\\ Program Files \\ Intel \\ iCLS Client \\; C:\\ windows \\ system32; C:\\ windows; C:\\ windows \\ System32 \\ Wbem; C:\\ windows \\ System3 2 \\ WindowsPowerShell \\ v1.0 \\; C:\\ Program Files \\ Intel \\ Intel(R)管理引擎组件\\ DAL; C:\\ Progra m Files(x86 )\\ Intel \\ Intel(R)管理引擎组件\\ DAL; C:\\ Program Files \\ Intel \\ Intel(R)管理引擎组件\\ IPT; C:\\ Program Files(x86)\\ Intel \\ Intel(R)管理引擎组件\\ IPT; c:\\ Program Files(x86)\\ Hewlett-Packard \\ HP Performance Advisor; C:\\ Program Files \\ Microsof t\\Web Platform Installer\\;C:\\Program Files (x86)\\Microsoft ASP.NET\\ASP.NET Web Pages\\v1.0\\;C:\\Program Files (x86)\\W indows Kits\\8.0\\Windows Performance Toolkit\\;C:\\Program Files\\Microsoft SQL Server\\110\\Tools\\Binn\\;C :\\Program Files\\IDM Computer Solutions\\UltraEdit;C:\\Python27;C:\\Users\\yi chen\\AppData\\Local\\Programs \\Git\\cmd;C:\\Users\\yi chen\\AppData\\Local\\Programs\\EmEditor t \\ Web Platform Installer \\; C:\\ Program Files(x86)\\ Microsoft ASP.NET \\ ASP.NET Web Pages \\ v1.0 \\; C:\\ Program Files(x86)\\ W indows Kits \\ 8.0 \\ Windows Performance Toolkit \\; C:\\ Program Files \\ Microsoft SQL Server \\ 110 \\ Tools \\ Binn \\; C:\\ Program Files \\ IDM Computer Solutions \\ UltraEdit; C:\\ Python27; C:\\ Users \\ yi chen \\ AppData \\ Local \\ Programs \\ Git \\ cmd; C:\\ Users \\ yi chen \\ AppData \\ Local \\ Programs \\ EmEditor

F:\\apache-ctakes-4.0.0>cd F:\\apache-ctakes-4.0.0 F:\\ apache-ctakes-4.0.0> cd F:\\ apache-ctakes-4.0.0

F:\\apache-ctakes-4.0.0>IF "" == "" GOTO NoParam F:\\ apache-ctakes-4.0.0> IF“” ==“”转到NoParam

F:\\apache-ctakes-4.0.0>echo Use the GUI to select the AE to load Use the GUI to select the AE to load F:\\ apache-ctakes-4.0.0> echo使用GUI选择要加载的AE使用GUI选择要加载的AE

F:\\apache-ctakes-4.0.0>java -Dctakes.umlsuser= "F:\\apache-ctakes-4.0.0\\desc\\;F:\\apache-ctakes-4.0.0\\ resources\\;F:\\apache-ctakes-4.0.0\\lib*" -Dlog4j.configuration=file:\\F:\\apache-ctakes-4.0.0\\config\\l og4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD 0-cp The system cannot find the file specified. F:\\ apache-ctakes-4.0.0> java -Dctakes.umlsuser =“” F:\\ apache-ctakes-4.0.0 \\ desc \\; F:\\ apache-ctakes-4.0.0 \\ resources \\; F:\\ apache -ctakes-4.0.0 \\ lib *“ -Dlog4j.configuration = file:\\ F:\\ apache-ctakes-4.0.0 \\ config \\ l og4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD 0-cp系统找不到指定的文件。

F:\\apache-ctakes-4.0.0>GOTO ChangeBack F:\\ apache-ctakes-4.0.0>转到更改返回

Can anyone help to figure it? 有人可以帮忙弄清楚吗? I really need your help. 我真的需要你的帮助。 Thanks! 谢谢!

Answering this question for sake of people who get this issue in future. 为将来获得此问题的人们回答这个问题。

@jhshi : The changes you made in runCVD.bat do not seem correct. @jhshi:您在runCVD.bat中所做的更改似乎不正确。

The documentation requires you to add your UMLS account username and password in every bat file (or sh file for dearest Linux users). 该文档要求您在每个bat文件(或对于最亲爱的Linux用户为sh文件)中添加UMLS帐户用户名和密码。 Which means every cTAKES user has to create a UMLS account here . 这意味着每个cTAKES用户都必须在此处创建UMLS帐户。

This is done using the java cmd line arguments "-Dctakes.umlsuser" & " -Dctakes.umlspw". 使用java cmd行参数“ -Dctakes.umlsuser”和“ -Dctakes.umlspw”完成此操作。 Look at my java invocation line from the runCVD.bat file below. 在下面的runCVD.bat文件中查看我的Java调用行。

java -Dctakes.umlsuser="gprakhar" -Dctakes.umlspw="XXXXXXX" -cp "%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*" -Dlog4j.configuration=file:\%CTAKES_HOME%\config\log4j.xml -Xms512M -Xmx2g org.apache.uima.tools.cvd.CVD

What you did was to pass the value of some PATH like variable to the umlsuser cmd line argument. 您所做的是将一些PATH之类的值传递给umlsuser cmd行参数。

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