Re: UmlsUserApprover Error [EXTERNAL]
Hi Sean and everybody, I just wanted to confirm that I intermittently run into the same issue. I was able to fix it yesterday by removing a bunch of files from /tmp (such as conn.xml, which dictionary lookup apparently creates there under my user name). However, today, the problem returned and I haven’t found a way to fix it. Again, the same pipeline runs fine on my laptop (Mac OS) and another machine that runs Linux. Dima On Mar 13, 2018, at 14:13, Andrew Phillips mailto:aphilli...@luc.edu>> wrote: Hi Sean, I looked into changing the relevant configs to non-checking, but didn't have much success. I am back to primarily trying to troubleshoot the original error. I have tried removing files from /tmp (especially conn.xml) as they seemed to be contributing to the issue. I also tried setting up cTAKES with a freshly created account, and am still encountering this issue. Other users on the server also have varying mileage with the same task. Do you have any more ideas of anything else I can try? Thank you. *Andrew Phillips* GitHub: github.com/skeledrew<http://github.com/skeledrew> LinkedIn: www.linkedin.com/in/aphillipstech<http://www.linkedin.com/in/aphillipstech> On 27 February 2018 at 17:45, Finan, Sean mailto:sean.fi...@childrens.harvard.edu>> wrote: Hi Andrew, If you created your own dictionary then you are already bound by your own license credentials used to get the umls download. You do not need to use the ctakes license check. In your lookup configuration xml file you can change the UmlsJdbc** to the non-checking Jdbc**. There are several email threads with associated information such as http://mail-archives.apache.org/mod_mbox/ctakes-dev/ 201802.mbox/%3CCANLSW%2B%3DbGXkqDoY_fUMc%3DgvGjLbTfXfL4aq7vy-abe% 3DW6qm6Vw%40mail.gmail.com<http://40mail.gmail.com>%3E Sean -Original Message- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 5:13 PM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Re: UmlsUserApprover Error [EXTERNAL] Hi Sean, I am using a dictionary created from the 2017AA-full which I downloaded from the UTS site. Does this count as default? *Andrew Phillips* GitHub: github.com/skeledrew<http://github.com/skeledrew> LinkedIn: www.linkedin.com/in/aphillipstech<http://www.linkedin.com/in/aphillipstech> On 27 February 2018 at 15:41, Finan, Sean mailto:Sean.Finan@childrens.harvard>. edu> wrote: Hi Andrew, As far as I know there isn't an explicit timeout imposed by ctakes. There is probably a java or system timeout, but I don't know of an easy way to change it. If you use the default dictionary then you should allow the account check. Sean -Original Message- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 4:27 PM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Re: UmlsUserApprover Error [EXTERNAL] @Gandhi: I have always skipped the tests whenever I run the install command. @Sean: 2 of the 4 folders I ran on were eventually processed, and only after running the script multiple times, so it does seem to be a connection issue. However I am trying to run the commands for the last couple of folders manually and the error has been consistent. Is there any way to bypass the account check, or increase the timeout? Or can I just have a loop that continually retries until the operation succeeds? *Andrew Phillips* GitHub: github.com/skeledrew<http://github.com/skeledrew> LinkedIn: www.linkedin.com/in/aphillipstech<http://www.linkedin.com/in/aphillipstech> On 27 February 2018 at 07:18, Finan, Sean mailto:Sean.Finan@childrens.harvard>. edu> wrote: Hi Andrew, You wrote: I ran my script earlier, [...]and only the first run was successful. Are you saying that one run did succeed? If that is the case then the problem probably is your network. The umls credential check will print dots in the log as time progresses, such as the dots from your log below: 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS Account [ ... ] .. 10 ... 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov<http://uts-ws.nlm.nih.gov> It looks like the credential check took several (~15?) seconds, which might indicate a slow connection or an eventual connection refused. That does not mean that the slowdown is on your side. It could be that the nih server that handles the credential checks is rarely getting to your request. I'm not sure why that would be (No net neutrality rants, please). Anyway, if the credential check works even once then that is a good indication that the problem is outside ctakes. Sean -Original Message- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Tuesday, February 27, 2018 7:49 AM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subjec
Re: UmlsUserApprover Error [EXTERNAL]
Hi Sean, I looked into changing the relevant configs to non-checking, but didn't have much success. I am back to primarily trying to troubleshoot the original error. I have tried removing files from /tmp (especially conn.xml) as they seemed to be contributing to the issue. I also tried setting up cTAKES with a freshly created account, and am still encountering this issue. Other users on the server also have varying mileage with the same task. Do you have any more ideas of anything else I can try? Thank you. *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 27 February 2018 at 17:45, Finan, Sean wrote: > Hi Andrew, > > If you created your own dictionary then you are already bound by your own > license credentials used to get the umls download. You do not need to use > the ctakes license check. > > In your lookup configuration xml file you can change the UmlsJdbc** to the > non-checking Jdbc**. There are several email threads with associated > information such as http://mail-archives.apache.org/mod_mbox/ctakes-dev/ > 201802.mbox/%3CCANLSW%2B%3DbGXkqDoY_fUMc%3DgvGjLbTfXfL4aq7vy-abe% > 3DW6qm6Vw%40mail.gmail.com%3E > > Sean > > -Original Message- > From: Andrew Phillips [mailto:aphilli...@luc.edu] > Sent: Tuesday, February 27, 2018 5:13 PM > To: dev@ctakes.apache.org > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > Hi Sean, > > I am using a dictionary created from the 2017AA-full which I downloaded > from the UTS site. Does this count as default? > > *Andrew Phillips* > GitHub: github.com/skeledrew > LinkedIn: www.linkedin.com/in/aphillipstech > > On 27 February 2018 at 15:41, Finan, Sean edu> > wrote: > > > Hi Andrew, > > > > As far as I know there isn't an explicit timeout imposed by ctakes. > > There is probably a java or system timeout, but I don't know of an > > easy way to change it. > > > > If you use the default dictionary then you should allow the account > check. > > > > Sean > > > > -Original Message- > > From: Andrew Phillips [mailto:aphilli...@luc.edu] > > Sent: Tuesday, February 27, 2018 4:27 PM > > To: dev@ctakes.apache.org > > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > > > @Gandhi: I have always skipped the tests whenever I run the install > > command. > > > > @Sean: 2 of the 4 folders I ran on were eventually processed, and only > > after running the script multiple times, so it does seem to be a > > connection issue. However I am trying to run the commands for the last > > couple of folders manually and the error has been consistent. Is there > > any way to bypass the account check, or increase the timeout? Or can I > > just have a loop that continually retries until the operation succeeds? > > > > *Andrew Phillips* > > GitHub: github.com/skeledrew > > LinkedIn: www.linkedin.com/in/aphillipstech > > > > On 27 February 2018 at 07:18, Finan, Sean > edu> > > wrote: > > > > > Hi Andrew, > > > > > > You wrote: > > > > I ran my script earlier, [...]and only the first run was successful. > > > > > > Are you saying that one run did succeed? If that is the case then > > > the problem probably is your network. > > > > > > The umls credential check will print dots in the log as time > > > progresses, such as the dots from your log below: > > > > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS > > > > > Account > > > [ ... ] > > > > > .. 10 ... > > > > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov > > > > > > It looks like the credential check took several (~15?) seconds, > > > which might indicate a slow connection or an eventual connection > refused. > > > That does not mean that the slowdown is on your side. It could be > > > that the nih server that handles the credential checks is rarely > > > getting to your request. I'm not sure why that would be (No net > > neutrality rants, please). > > > > > > Anyway, if the credential check works even once then that is a good > > > indication that the problem is outside ctakes. > > > > > > Sean > > > > > > > > > > > > > > > > > > > > > -Original Message- > > > From: Gandhi Rajan Natarajan > > > [mailto:gandhi.natara...@arisglobal.com] > > > Sent: Tuesday, February 27, 2018 7:49 AM > > > To: dev@ctakes.apache.or
RE: UmlsUserApprover Error [EXTERNAL]
Hi Andrew, If you created your own dictionary then you are already bound by your own license credentials used to get the umls download. You do not need to use the ctakes license check. In your lookup configuration xml file you can change the UmlsJdbc** to the non-checking Jdbc**. There are several email threads with associated information such as http://mail-archives.apache.org/mod_mbox/ctakes-dev/201802.mbox/%3CCANLSW%2B%3DbGXkqDoY_fUMc%3DgvGjLbTfXfL4aq7vy-abe%3DW6qm6Vw%40mail.gmail.com%3E Sean -Original Message- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 5:13 PM To: dev@ctakes.apache.org Subject: Re: UmlsUserApprover Error [EXTERNAL] Hi Sean, I am using a dictionary created from the 2017AA-full which I downloaded from the UTS site. Does this count as default? *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 27 February 2018 at 15:41, Finan, Sean wrote: > Hi Andrew, > > As far as I know there isn't an explicit timeout imposed by ctakes. > There is probably a java or system timeout, but I don't know of an > easy way to change it. > > If you use the default dictionary then you should allow the account check. > > Sean > > -Original Message- > From: Andrew Phillips [mailto:aphilli...@luc.edu] > Sent: Tuesday, February 27, 2018 4:27 PM > To: dev@ctakes.apache.org > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > @Gandhi: I have always skipped the tests whenever I run the install > command. > > @Sean: 2 of the 4 folders I ran on were eventually processed, and only > after running the script multiple times, so it does seem to be a > connection issue. However I am trying to run the commands for the last > couple of folders manually and the error has been consistent. Is there > any way to bypass the account check, or increase the timeout? Or can I > just have a loop that continually retries until the operation succeeds? > > *Andrew Phillips* > GitHub: github.com/skeledrew > LinkedIn: www.linkedin.com/in/aphillipstech > > On 27 February 2018 at 07:18, Finan, Sean edu> > wrote: > > > Hi Andrew, > > > > You wrote: > > > I ran my script earlier, [...]and only the first run was successful. > > > > Are you saying that one run did succeed? If that is the case then > > the problem probably is your network. > > > > The umls credential check will print dots in the log as time > > progresses, such as the dots from your log below: > > > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS > > > > Account > > [ ... ] > > > > .. 10 ... > > > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov > > > > It looks like the credential check took several (~15?) seconds, > > which might indicate a slow connection or an eventual connection refused. > > That does not mean that the slowdown is on your side. It could be > > that the nih server that handles the credential checks is rarely > > getting to your request. I'm not sure why that would be (No net > neutrality rants, please). > > > > Anyway, if the credential check works even once then that is a good > > indication that the problem is outside ctakes. > > > > Sean > > > > > > > > > > > > > > -Original Message- > > From: Gandhi Rajan Natarajan > > [mailto:gandhi.natara...@arisglobal.com] > > Sent: Tuesday, February 27, 2018 7:49 AM > > To: dev@ctakes.apache.org > > Subject: RE: UmlsUserApprover Error [EXTERNAL] > > > > I guess you are running the build with test cases as I see the below > > messages in my case only while running build with test cases: > > > > >> log4j: reset attribute= "false". > > > > log4j: Threshold ="null". > > > > log4j: Retreiving an instance of org.apache.log4j.Logger. > > > > log4j: Setting [ProgressAppender] additivity to [false]. > > > > log4j: Level value for ProgressAppender is [INFO]. > > > > log4j: ProgressAppender level set to INFO > > > > > > Could you try building ' ctakes-temporal' module by skipping test > > case using the command - " mvn clean install -Dmaven.test.skip=true" ? > > > > Regards, > > Gandhi > > > > -Original Message- > > From: Andrew Phillips [mailto:aphilli...@luc.edu] > > Sent: Tuesday, February 27, 2018 7:08 AM > > To: dev@ctakes.apache.org > > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > > > Thanks fo
Re: UmlsUserApprover Error [EXTERNAL]
Hi Sean, I am using a dictionary created from the 2017AA-full which I downloaded from the UTS site. Does this count as default? *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 27 February 2018 at 15:41, Finan, Sean wrote: > Hi Andrew, > > As far as I know there isn't an explicit timeout imposed by ctakes. There > is probably a java or system timeout, but I don't know of an easy way to > change it. > > If you use the default dictionary then you should allow the account check. > > Sean > > -Original Message- > From: Andrew Phillips [mailto:aphilli...@luc.edu] > Sent: Tuesday, February 27, 2018 4:27 PM > To: dev@ctakes.apache.org > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > @Gandhi: I have always skipped the tests whenever I run the install > command. > > @Sean: 2 of the 4 folders I ran on were eventually processed, and only > after running the script multiple times, so it does seem to be a connection > issue. However I am trying to run the commands for the last couple of > folders manually and the error has been consistent. Is there any way to > bypass the account check, or increase the timeout? Or can I just have a > loop that continually retries until the operation succeeds? > > *Andrew Phillips* > GitHub: github.com/skeledrew > LinkedIn: www.linkedin.com/in/aphillipstech > > On 27 February 2018 at 07:18, Finan, Sean edu> > wrote: > > > Hi Andrew, > > > > You wrote: > > > I ran my script earlier, [...]and only the first run was successful. > > > > Are you saying that one run did succeed? If that is the case then the > > problem probably is your network. > > > > The umls credential check will print dots in the log as time > > progresses, such as the dots from your log below: > > > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS > > > > Account > > [ ... ] > > > > .. 10 > > > > ... > > > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov > > > > It looks like the credential check took several (~15?) seconds, which > > might indicate a slow connection or an eventual connection refused. > > That does not mean that the slowdown is on your side. It could be > > that the nih server that handles the credential checks is rarely > > getting to your request. I'm not sure why that would be (No net > neutrality rants, please). > > > > Anyway, if the credential check works even once then that is a good > > indication that the problem is outside ctakes. > > > > Sean > > > > > > > > > > > > > > -Original Message- > > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Tuesday, February 27, 2018 7:49 AM > > To: dev@ctakes.apache.org > > Subject: RE: UmlsUserApprover Error [EXTERNAL] > > > > I guess you are running the build with test cases as I see the below > > messages in my case only while running build with test cases: > > > > >> log4j: reset attribute= "false". > > > > log4j: Threshold ="null". > > > > log4j: Retreiving an instance of org.apache.log4j.Logger. > > > > log4j: Setting [ProgressAppender] additivity to [false]. > > > > log4j: Level value for ProgressAppender is [INFO]. > > > > log4j: ProgressAppender level set to INFO > > > > > > Could you try building ' ctakes-temporal' module by skipping test case > > using the command - " mvn clean install -Dmaven.test.skip=true" ? > > > > Regards, > > Gandhi > > > > -Original Message- > > From: Andrew Phillips [mailto:aphilli...@luc.edu] > > Sent: Tuesday, February 27, 2018 7:08 AM > > To: dev@ctakes.apache.org > > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > > > Thanks for the ideas. > > > > There hasn't been any such changes, and network connectivity shouldn't > > be an issue. I ran my script earlier, which automatically runs the > > same pipeline on several different folders, and only the first run was > > successful. The others failed with the same error. My latest attempt > > is to remove the .m2 directory and recompile and reinstall, and it is > > currently processing the first directory, so I don't know if it will > > fail on the next as yet. > > > > My primary interface is over SSH to a remote server, and this is the > > script: > > UmlsLP () { mvn exec:java > > -Dexec.mainClass
RE: UmlsUserApprover Error [EXTERNAL]
Hi Andrew, As far as I know there isn't an explicit timeout imposed by ctakes. There is probably a java or system timeout, but I don't know of an easy way to change it. If you use the default dictionary then you should allow the account check. Sean -Original Message- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 4:27 PM To: dev@ctakes.apache.org Subject: Re: UmlsUserApprover Error [EXTERNAL] @Gandhi: I have always skipped the tests whenever I run the install command. @Sean: 2 of the 4 folders I ran on were eventually processed, and only after running the script multiple times, so it does seem to be a connection issue. However I am trying to run the commands for the last couple of folders manually and the error has been consistent. Is there any way to bypass the account check, or increase the timeout? Or can I just have a loop that continually retries until the operation succeeds? *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 27 February 2018 at 07:18, Finan, Sean wrote: > Hi Andrew, > > You wrote: > > I ran my script earlier, [...]and only the first run was successful. > > Are you saying that one run did succeed? If that is the case then the > problem probably is your network. > > The umls credential check will print dots in the log as time > progresses, such as the dots from your log below: > > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS > > > Account > [ ... ] > > > .. 10 > > > ... > > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov > > It looks like the credential check took several (~15?) seconds, which > might indicate a slow connection or an eventual connection refused. > That does not mean that the slowdown is on your side. It could be > that the nih server that handles the credential checks is rarely > getting to your request. I'm not sure why that would be (No net neutrality > rants, please). > > Anyway, if the credential check works even once then that is a good > indication that the problem is outside ctakes. > > Sean > > > > > > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > Sent: Tuesday, February 27, 2018 7:49 AM > To: dev@ctakes.apache.org > Subject: RE: UmlsUserApprover Error [EXTERNAL] > > I guess you are running the build with test cases as I see the below > messages in my case only while running build with test cases: > > >> log4j: reset attribute= "false". > > > log4j: Threshold ="null". > > > log4j: Retreiving an instance of org.apache.log4j.Logger. > > > log4j: Setting [ProgressAppender] additivity to [false]. > > > log4j: Level value for ProgressAppender is [INFO]. > > > log4j: ProgressAppender level set to INFO > > > Could you try building ' ctakes-temporal' module by skipping test case > using the command - " mvn clean install -Dmaven.test.skip=true" ? > > Regards, > Gandhi > > -Original Message- > From: Andrew Phillips [mailto:aphilli...@luc.edu] > Sent: Tuesday, February 27, 2018 7:08 AM > To: dev@ctakes.apache.org > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > Thanks for the ideas. > > There hasn't been any such changes, and network connectivity shouldn't > be an issue. I ran my script earlier, which automatically runs the > same pipeline on several different folders, and only the first run was > successful. The others failed with the same error. My latest attempt > is to remove the .m2 directory and recompile and reinstall, and it is > currently processing the first directory, so I don't know if it will > fail on the next as yet. > > My primary interface is over SSH to a remote server, and this is the > script: > UmlsLP () { mvn exec:java > -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" > -Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/" > -Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn > exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" > -Dexec.args="--input-dir $1/no/ --output-dir $2/no/" > -Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo > Finished UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;} > > Thank you. > > > *Andrew Phillips* > GitHub: github.com/skeledrew > LinkedIn: www.linkedin.com/in/aphillipstech > > On 26 February 2018 at 13:00, Miller, Timothy < Timothy.Miller@childrens. > harvard.edu> wrote: > > > Is it possible there is som
Re: UmlsUserApprover Error [EXTERNAL]
@Gandhi: I have always skipped the tests whenever I run the install command. @Sean: 2 of the 4 folders I ran on were eventually processed, and only after running the script multiple times, so it does seem to be a connection issue. However I am trying to run the commands for the last couple of folders manually and the error has been consistent. Is there any way to bypass the account check, or increase the timeout? Or can I just have a loop that continually retries until the operation succeeds? *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 27 February 2018 at 07:18, Finan, Sean wrote: > Hi Andrew, > > You wrote: > > I ran my script earlier, [...]and only the first run was successful. > > Are you saying that one run did succeed? If that is the case then the > problem probably is your network. > > The umls credential check will print dots in the log as time progresses, > such as the dots from your log below: > > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS Account > [ ... ] > > > .. 10 > > > ... > > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov > > It looks like the credential check took several (~15?) seconds, which > might indicate a slow connection or an eventual connection refused. That > does not mean that the slowdown is on your side. It could be that the nih > server that handles the credential checks is rarely getting to your > request. I'm not sure why that would be (No net neutrality rants, please). > > Anyway, if the credential check works even once then that is a good > indication that the problem is outside ctakes. > > Sean > > > > > > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > Sent: Tuesday, February 27, 2018 7:49 AM > To: dev@ctakes.apache.org > Subject: RE: UmlsUserApprover Error [EXTERNAL] > > I guess you are running the build with test cases as I see the below > messages in my case only while running build with test cases: > > >> log4j: reset attribute= "false". > > > log4j: Threshold ="null". > > > log4j: Retreiving an instance of org.apache.log4j.Logger. > > > log4j: Setting [ProgressAppender] additivity to [false]. > > > log4j: Level value for ProgressAppender is [INFO]. > > > log4j: ProgressAppender level set to INFO > > > Could you try building ' ctakes-temporal' module by skipping test case > using the command - " mvn clean install -Dmaven.test.skip=true" ? > > Regards, > Gandhi > > -Original Message- > From: Andrew Phillips [mailto:aphilli...@luc.edu] > Sent: Tuesday, February 27, 2018 7:08 AM > To: dev@ctakes.apache.org > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > Thanks for the ideas. > > There hasn't been any such changes, and network connectivity shouldn't be > an issue. I ran my script earlier, which automatically runs the same > pipeline on several different folders, and only the first run was > successful. The others failed with the same error. My latest attempt is to > remove the .m2 directory and recompile and reinstall, and it is currently > processing the first directory, so I don't know if it will fail on the next > as yet. > > My primary interface is over SSH to a remote server, and this is the > script: > UmlsLP () { mvn exec:java > -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" > -Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/" > -Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn exec:java > -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" > -Dexec.args="--input-dir $1/no/ --output-dir $2/no/" > -Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo Finished > UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;} > > Thank you. > > > *Andrew Phillips* > GitHub: github.com/skeledrew > LinkedIn: www.linkedin.com/in/aphillipstech > > On 26 February 2018 at 13:00, Miller, Timothy < Timothy.Miller@childrens. > harvard.edu> wrote: > > > Is it possible there is some network issue preventing connectivity? > > New institutional firewall maybe? > > > > Otherwise, it looks like somehow your credentials are not getting into > > the right place. Possible a configuration file had them before and > > it's been changed out from under you? > > > > One thing you can try, if you are using an IDE, you can directly put > > your credentials into the VM options for your run configuration with: > > -Dctakes.umlsuser=
RE: UmlsUserApprover Error [EXTERNAL]
Hi Andrew, You wrote: > I ran my script earlier, [...]and only the first run was successful. Are you saying that one run did succeed? If that is the case then the problem probably is your network. The umls credential check will print dots in the log as time progresses, such as the dots from your log below: > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS Account [ ... ] > > .. 10 > > ... > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov It looks like the credential check took several (~15?) seconds, which might indicate a slow connection or an eventual connection refused. That does not mean that the slowdown is on your side. It could be that the nih server that handles the credential checks is rarely getting to your request. I'm not sure why that would be (No net neutrality rants, please). Anyway, if the credential check works even once then that is a good indication that the problem is outside ctakes. Sean -Original Message- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Tuesday, February 27, 2018 7:49 AM To: dev@ctakes.apache.org Subject: RE: UmlsUserApprover Error [EXTERNAL] I guess you are running the build with test cases as I see the below messages in my case only while running build with test cases: >> log4j: reset attribute= "false". > > log4j: Threshold ="null". > > log4j: Retreiving an instance of org.apache.log4j.Logger. > > log4j: Setting [ProgressAppender] additivity to [false]. > > log4j: Level value for ProgressAppender is [INFO]. > > log4j: ProgressAppender level set to INFO Could you try building ' ctakes-temporal' module by skipping test case using the command - " mvn clean install -Dmaven.test.skip=true" ? Regards, Gandhi -Original Message- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 7:08 AM To: dev@ctakes.apache.org Subject: Re: UmlsUserApprover Error [EXTERNAL] Thanks for the ideas. There hasn't been any such changes, and network connectivity shouldn't be an issue. I ran my script earlier, which automatically runs the same pipeline on several different folders, and only the first run was successful. The others failed with the same error. My latest attempt is to remove the .m2 directory and recompile and reinstall, and it is currently processing the first directory, so I don't know if it will fail on the next as yet. My primary interface is over SSH to a remote server, and this is the script: UmlsLP () { mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" -Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/" -Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" -Dexec.args="--input-dir $1/no/ --output-dir $2/no/" -Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo Finished UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;} Thank you. *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 26 February 2018 at 13:00, Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > Is it possible there is some network issue preventing connectivity? > New institutional firewall maybe? > > Otherwise, it looks like somehow your credentials are not getting into > the right place. Possible a configuration file had them before and > it's been changed out from under you? > > One thing you can try, if you are using an IDE, you can directly put > your credentials into the VM options for your run configuration with: > -Dctakes.umlsuser= -Dctakes.umlspw > > and see if you still get the issue. > > Tim > > > On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote: > > Hello, > > > > I am getting an error after recompiling a script in my pipeline. My > > setup was working fine the last time I did a compile several months > > ago, and I have logged into my UMLS account to ensure it isn't an > > issue with my credentials, as well as done a complete reinstall from > > the GitHub repo and checked out the 4.0.0 release. The minor change > > I made in the script was just uncommenting something that I've used > > before, so I know there are no errors in it. Any insights as to what > > the issue may be? I've included the complete output below. Thank > > you. > > > > > > [INFO] Scanning for projects... > > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is > > missing, no dependency information available [WARNING] Failed to > > retrieve plugin descriptor for > >
RE: UmlsUserApprover Error [EXTERNAL]
I guess you are running the build with test cases as I see the below messages in my case only while running build with test cases: >> log4j: reset attribute= "false". > > log4j: Threshold ="null". > > log4j: Retreiving an instance of org.apache.log4j.Logger. > > log4j: Setting [ProgressAppender] additivity to [false]. > > log4j: Level value for ProgressAppender is [INFO]. > > log4j: ProgressAppender level set to INFO Could you try building ' ctakes-temporal' module by skipping test case using the command - " mvn clean install -Dmaven.test.skip=true" ? Regards, Gandhi -Original Message- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 7:08 AM To: dev@ctakes.apache.org Subject: Re: UmlsUserApprover Error [EXTERNAL] Thanks for the ideas. There hasn't been any such changes, and network connectivity shouldn't be an issue. I ran my script earlier, which automatically runs the same pipeline on several different folders, and only the first run was successful. The others failed with the same error. My latest attempt is to remove the .m2 directory and recompile and reinstall, and it is currently processing the first directory, so I don't know if it will fail on the next as yet. My primary interface is over SSH to a remote server, and this is the script: UmlsLP () { mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" -Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/" -Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" -Dexec.args="--input-dir $1/no/ --output-dir $2/no/" -Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo Finished UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;} Thank you. *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 26 February 2018 at 13:00, Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > Is it possible there is some network issue preventing connectivity? > New institutional firewall maybe? > > Otherwise, it looks like somehow your credentials are not getting into > the right place. Possible a configuration file had them before and > it's been changed out from under you? > > One thing you can try, if you are using an IDE, you can directly put > your credentials into the VM options for your run configuration with: > -Dctakes.umlsuser= -Dctakes.umlspw > > and see if you still get the issue. > > Tim > > > On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote: > > Hello, > > > > I am getting an error after recompiling a script in my pipeline. My > > setup was working fine the last time I did a compile several months > > ago, and I have logged into my UMLS account to ensure it isn't an > > issue with my credentials, as well as done a complete reinstall from > > the GitHub repo and checked out the 4.0.0 release. The minor change > > I made in the script was just uncommenting something that I've used > > before, so I know there are no errors in it. Any insights as to what > > the issue may be? I've included the complete output below. Thank > > you. > > > > > > [INFO] Scanning for projects... > > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is > > missing, no dependency information available [WARNING] Failed to > > retrieve plugin descriptor for > > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin > > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies > > could not be resolved: Failure to find > > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in > > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apac > > h > > e.org_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU& > > r > > =Heup-IbsIg9Q1TPOylpP9FE4GTK- > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- > > Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh- > > PSEuxpA&e= was cached in the local repository, resolution will not > > be reattempted until the update interval of central has elapsed or > > updates are forced [INFO] [INFO] > > --- > > - > > [INFO] Building Apache cTAKES Temporal Information Extraction 4.0.1- > > SNAPSHOT [INFO] > > --- > > - > > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is > > missing, no dependency information available [WARNING] Failed to > > retrieve
Re: UmlsUserApprover Error [EXTERNAL]
Thanks for the ideas. There hasn't been any such changes, and network connectivity shouldn't be an issue. I ran my script earlier, which automatically runs the same pipeline on several different folders, and only the first run was successful. The others failed with the same error. My latest attempt is to remove the .m2 directory and recompile and reinstall, and it is currently processing the first directory, so I don't know if it will fail on the next as yet. My primary interface is over SSH to a remote server, and this is the script: UmlsLP () { mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" -Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/" -Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" -Dexec.args="--input-dir $1/no/ --output-dir $2/no/" -Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo Finished UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;} Thank you. *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 26 February 2018 at 13:00, Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > Is it possible there is some network issue preventing connectivity? New > institutional firewall maybe? > > Otherwise, it looks like somehow your credentials are not getting into > the right place. Possible a configuration file had them before and it's > been changed out from under you? > > One thing you can try, if you are using an IDE, you can directly put > your credentials into the VM options for your run configuration with: > -Dctakes.umlsuser= -Dctakes.umlspw > > and see if you still get the issue. > > Tim > > > On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote: > > Hello, > > > > I am getting an error after recompiling a script in my pipeline. My > > setup > > was working fine the last time I did a compile several months ago, > > and I > > have logged into my UMLS account to ensure it isn't an issue with my > > credentials, as well as done a complete reinstall from the GitHub > > repo and > > checked out the 4.0.0 release. The minor change I made in the script > > was > > just uncommenting something that I've used before, so I know there > > are no > > errors in it. Any insights as to what the issue may be? I've included > > the > > complete output below. Thank you. > > > > > > [INFO] Scanning for projects... > > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is > > missing, no dependency information available > > [WARNING] Failed to retrieve plugin descriptor for > > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin > > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies > > could > > not be resolved: Failure to find > > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in > > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach > > e.org_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r > > =Heup-IbsIg9Q1TPOylpP9FE4GTK- > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- > > Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh- > > PSEuxpA&e= was cached in the local repository, > > resolution will not be reattempted until the update interval of > > central has > > elapsed or updates are forced > > [INFO] > > [INFO] > > --- > > - > > [INFO] Building Apache cTAKES Temporal Information Extraction 4.0.1- > > SNAPSHOT > > [INFO] > > --- > > - > > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is > > missing, no dependency information available > > [WARNING] Failed to retrieve plugin descriptor for > > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin > > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies > > could > > not be resolved: Failure to find > > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in > > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach > > e.org_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r > > =Heup-IbsIg9Q1TPOylpP9FE4GTK- > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- > > Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh- > > PSEuxpA&e= was cached in the local repository, > > resolution will not be reattempted until the update interval of > > central has > > elapsed or updates are forced > > [INFO] > > [INFO] >>> exec-maven-plugin:1.2.1:java (default-cli) > validate @ > > ctakes-misc >>> > > [INFO] > > [INFO] <<< exec-maven-plugin:1.2.1:java (default-cli) < validate @ > > ctakes-misc <<< > > [INFO] > > [INFO] > > [INFO] --- exec-maven-plugin:1.2.1:java (default-cli) @ ctakes-misc > > --- > > log4j: reset attribute= "false". > > log4j: Threshold ="null". > > log4j: Retreiving an instance of org.apache.log4j.Logger. > > log4j: Setting [ProgressAppender] additivity to [false]. > > log4j: Level value for
Re: UmlsUserApprover Error [EXTERNAL]
Is it possible there is some network issue preventing connectivity? New institutional firewall maybe? Otherwise, it looks like somehow your credentials are not getting into the right place. Possible a configuration file had them before and it's been changed out from under you? One thing you can try, if you are using an IDE, you can directly put your credentials into the VM options for your run configuration with: -Dctakes.umlsuser= -Dctakes.umlspw and see if you still get the issue. Tim On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote: > Hello, > > I am getting an error after recompiling a script in my pipeline. My > setup > was working fine the last time I did a compile several months ago, > and I > have logged into my UMLS account to ensure it isn't an issue with my > credentials, as well as done a complete reinstall from the GitHub > repo and > checked out the 4.0.0 release. The minor change I made in the script > was > just uncommenting something that I've used before, so I know there > are no > errors in it. Any insights as to what the issue may be? I've included > the > complete output below. Thank you. > > > [INFO] Scanning for projects... > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is > missing, no dependency information available > [WARNING] Failed to retrieve plugin descriptor for > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies > could > not be resolved: Failure to find > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach > e.org_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r > =Heup-IbsIg9Q1TPOylpP9FE4GTK- > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- > Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh- > PSEuxpA&e= was cached in the local repository, > resolution will not be reattempted until the update interval of > central has > elapsed or updates are forced > [INFO] > [INFO] > --- > - > [INFO] Building Apache cTAKES Temporal Information Extraction 4.0.1- > SNAPSHOT > [INFO] > --- > - > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is > missing, no dependency information available > [WARNING] Failed to retrieve plugin descriptor for > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies > could > not be resolved: Failure to find > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach > e.org_maven2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r > =Heup-IbsIg9Q1TPOylpP9FE4GTK- > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=NHws3pftXkncEWsu- > Y6fCtMKfY3WWkYQmDYrA4AVcvU&s=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh- > PSEuxpA&e= was cached in the local repository, > resolution will not be reattempted until the update interval of > central has > elapsed or updates are forced > [INFO] > [INFO] >>> exec-maven-plugin:1.2.1:java (default-cli) > validate @ > ctakes-misc >>> > [INFO] > [INFO] <<< exec-maven-plugin:1.2.1:java (default-cli) < validate @ > ctakes-misc <<< > [INFO] > [INFO] > [INFO] --- exec-maven-plugin:1.2.1:java (default-cli) @ ctakes-misc > --- > log4j: reset attribute= "false". > log4j: Threshold ="null". > log4j: Retreiving an instance of org.apache.log4j.Logger. > log4j: Setting [ProgressAppender] additivity to [false]. > log4j: Level value for ProgressAppender is [INFO]. > log4j: ProgressAppender level set to INFO > log4j: Class name: [org.apache.log4j.ConsoleAppender] > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" > log4j: Setting property [conversionPattern] to [%m]. > log4j: Adding appender named [noEolAppender] to category > [ProgressAppender]. > log4j: Retreiving an instance of org.apache.log4j.Logger. > log4j: Setting [ProgressDone] additivity to [false]. > log4j: Level value for ProgressDone is [INFO]. > log4j: ProgressDone level set to INFO > log4j: Class name: [org.apache.log4j.ConsoleAppender] > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" > log4j: Setting property [conversionPattern] to [%m%n]. > log4j: Adding appender named [eolAppender] to category > [ProgressDone]. > log4j: Level value for root is [INFO]. > log4j: root level set to INFO > log4j: Class name: [org.apache.log4j.ConsoleAppender] > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" > log4j: Setting property [conversionPattern] to [%d{dd MMM > HH:mm:ss} > %5p %c{1} - %m%n]. > log4j: Adding appender named [consoleAppender] to category [root]. > 24 Feb 2018 18:22:23 INFO LvgAnnotator - URL for lvg.properties > =/home/aphillips5/ctakes/ctakes- > misc/target/classes/org/apache/ctakes/lvg/data/config/lvg.properties > 24 Feb 2018 18:22:23 INFO SentenceD