running ctakes with the AggregatePlaintextProcessor - ctakes

I want to run ctakes with the AggregatePlaintextProcessor or something that doesn't require a connection for UMLS. Help!

I'm just getting started with cTAKES and had a similar question when i first installed it.
From your cTAKES home directory run this:
bin\runctakesCVD.bat desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextProcessor.xml
instead of this:
bin\runctakesCVD.bat desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml
Basically, you are just removing "FastUMLS" from the command.
More info can be found in the user install guide:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide

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Docker build fails always with error hcsshim::PrepareLayer - failed failed in Win32: Incorrect function. (0x1) Windows Containers

Steps to reproduce are very easy.
Create a Dockerfile.
My Dockerfile has many more lines, but I have trimmed them so we can focus in the source of the problem.
Said that, these two lines alone (without anything more) show the problem.
FROM microsoft/iis
SHELL ["powershell", "-Command", "$ErrorActionPreference = 'Stop'; $ProgressPreference = 'SilentlyContinue'; $VerbosePreference = 'Continue'; "]
Run docker build . and you get hcsshim::PrepareLayer - failed failed in Win32: Función incorrecta. (0x1).
Windows 10 Pro 1909 (but it happened too in 1903)
Docker version: 2.1.0.5
Engine: 19.03.5
Machine: 0.16.2
I have found the solution to the problem.
Reading all the https://github.com/docker/for-win/issues/3884 bug, some have found a simple solution: rename C:\windows\system32\driver\cbfsconnect2017.sys so it isn't loaded the next boot.
Disabling that driver enables me to do a docker build for the first time in windows containers in almost a year.
In my case Box Sync was the one using that driver.
EDIT: #GustavoTM have found that pCloud raises the same problem.
EDIT2: #VonC have noticed that some people in the issue in GitHub has solved it deleting this other file: C:\Windows\System32\drivers\cbfs6.sys. I haven't tried that, but i put it if it helps others.
The good thing is that I don't need to uninstall Box, but only rename that file.
This is still an issue (still open) with Win10.
Looks like uninstalling cloud storage providers with file system filters like Dropbox, Box, etc. as a workaround is an option for some users.
Deinstall cloud storage providers or virus scanners; if you identify which one is not working please share in https://github.com/docker/for-win/issues/3884
In my case was the problem similar but the file cbfs6.sys was placed somewhere in the rest of uninstalled application Jungle disk, somewhere in the folder c:\Program files\Jungle disk .... It's part of Callback File System signed by EldoS Corporation.
The folder could be rename only and not delete directly. So I could delete its immediately after the PC restart, before running the Docker. So it could be delete during the Docker service restart too.

How to deploy repository in Apache Geronimo 3.0.1

I am new Apache Geronimo.I read the following link for deploying repository. Even I don't know where will these concept will be useful. just i am learning.
I created sub-directory under and created .xml file according to the above link.
here, I faced the problem while deploying time. deploy(.bat) deploy <GERONIMO_HOME>/repo2/repo2.xml command is not working.
<GERONIMO_HOME>=C:\Users\Infratab Bangalore\geronimo-tomcat7-javaee6-3.0.1
I run the following command for deploying.but it's not working.
deploy(.bat) deploy C:/Users/Infratab Bangalore/geronimo-tomcat7-javaee6-3.0.1/repo2/repo2.xml
How can I fix this.
You should do following bellow steps:
1. Log in to the Administrative Console
2. Select Advanced on left bar
3. Go to Resources -> Repository

The local psql command could not be located

I'm following the instructions found here.
When I try to run $ heroku pg:psql or $ heroku pg:psql HEROKU POSTGRESQL_BROWN I recieve the following error message:
! The local psql command could not be located ! For help
installing psql, see local-postgresql
I can't find anything useful on the link it gives me (it just links to the instructions I was already using, but further down the page) nor can I find this error anywhere else.
If I've missed anything you need to know to answer this, just let me know. I'm rather new to all this and teaching myself as I go.
I had same error even after installing Postgres locally.
But after seeing this
I saw that "pqsl" was not in the PATH so I then did
PATH=%PATH%;C:\Program Files\PostgreSQL\9.2\bin
which worked for me
I have since solved this myself. When I ran heroku pg:info it says the version number is 9.1.8, I was locally running 9.2
installing 9.1.8 and ensuring Path pointed to the appropriate folder solved the problem.
After you change the path, make sure to restart the terminal!
Set the PATH. To find out the PATH of your psql script (on mac) open the sql shell script from your finder in Applications/Postgres installation. This will give you a hint as to where it is installed. That opened a window which told me it is located here: /Library/PostgreSQL/8.4/scripts/runpsql.sh
Then, I set the PATH variable from the terminal window by typing:
$ PATH="/Library/PostgreSQL/8.4/bin:$PATH"
(depends on the location of your PostgreSQL installation, find your bin path first, another exp: /usr/local/Cellar/postgresql#9.6/9.6.8/bin)
OR.....
You can also connect to the shell by opening the shell directly from your postgres installation folder. Then enter the credentials. If you don't know the credentials, here is how to find them out:
$ heroku pg:info
=== HEROKU_POSTGRESQL_RED_URL (DATABASE_URL)
$ heroku pg:credentials HEROKU_POSTGRESQL_RED_URL
Top answer wouldn't work for me oddly, my system would not add the Path via cmd with administrator access (Not sure why).
So check this > Windows key > environment variables > system variables
And add the last line (your version may differ in the path)
Make sure you've installed the toolbelt as psql is installed by default.
However you also need to ensure you've installed a local copy of PostgreSQL; if you don't the toolbelt will be unable to find the native psql client.
Assuming you have installed a local copy of PostgreSQL, make sure you can execute psql from the command line directly (i.e make sure you PATH is set correctly ). If the command does not execute, check your PATH, if it does execute see if you can connect via the PSQL connection string provided in the Heroku control panel. If you can connect reinstall the toolbelt, if you are unable to connect provision another dev database and try again.
If there are still issues, I would suggest contacting Heroku support for assistance after verifying no API issues are listed on the status page located here.
I got rid if this annoying message on Windows by adding a path element without the spaces, i.e.
C:\Progra~1\PostgreSQL\9.4\data
instead of
“C:\Program Files\PostgreSQL\9.4\data”
I followed the instructions here: http://www.computerhope.com/issues/ch000549.htm, which worked for me if you prefer to go the point-and-click configuration of the PATH variable.
This type of error usually appears in the Windows environment, because if you do not update the PATH after installing Postgresql, heroku pg:psql command does not work.
So you need to update your PATH environment variable to add the bin directory of your Postgres installation. The directory will look like this:
C:\Program Files\PostgreSQL\<VERSION>\bin.
For more information, go to the Heroku in Local setup website:
heroku-postgresql: Local setup
I had the same problem and discovered that Heroku doesn't seem to provision the latest version of PostgreSQL by default. Where the Heroku Getting Started instructions said
heroku addons:create heroku-postgresql:hobby-dev
That provisioned a v10 database for some reason (which you can check by clicking on Heroku Postgres in the Add-ons tab of your dashboard). I deleted that database and provisioned a new database using the --version flag:
heroku addons:create heroku-postgresql:hobby-dev --version 11
As of now, at least, you can find the latest version of Postgres supported by Heroku at this link: https://devcenter.heroku.com/articles/heroku-postgresql#version-support-and-legacy-infrastructure
I'm writing this in early 2019, but according to the PostgreSQL website the next version (12) is "tentatively scheduled" for third quarter of 2019 so if you're reading this in late 2019 potentially the same problem will come up for v12 instead
On Mac you can use the following:
export PATH="/Library/PostgreSQL/12/bin/:$PATH"
The only solution that I found on Windows:
go to advanced system settings
go to environment variables
select Path variable and click Edit
add a new line and enter your bin directory path (C:\Program Files\PostgreSQL<version>\bin) and click ok
restart your terminal
enter your psql command (heroku pg:psql)

ERROR installing apache archiva on my sytem

Can anyone help regarding this... i'm stuck :(
Goto the folder apache-archiva-1.3.3 and the following:
.\bin\archiva.bat install
As khmarbaise says above, you probably need to log in with administrative rights.
Another alternative is to run:
archiva console
This will start it within that console - however you'll then need to keep it open and restart manually after a reboot, where a service can run in the background and start automatically.

Apache and Sqlite3 issue

I'm using ports only on this server. After restarting apache I got "segment fault (core dumped)" message. But apache is started at least... httpd-error.log shows this:
profiling:/usr/ports/databases/sqlite3/work/sqlite-3.7.3/.libs/sqlite3.gcda:Cannot open
profiling:/usr/ports/databases/sqlite3/work/sqlite-3.7.3/.libs/sqlite3.gcda:Cannot open
profiling:/usr/ports/databases/sqlite3/work/sqlite-3.7.3/.libs/sqlite3.gcda:Cannot open
profiling:/usr/ports/databases/sqlite3/work/sqlite-3.7.3/.libs/sqlite3.gcda:Cannot open
Listing of that dir:
baccy# ls /usr/ports/databases/sqlite3/work/sqlite-3.7.3/.libs/
libsqlite3.a libsqlite3.la libsqlite3.lai libsqlite3.so libsqlite3.so.8 sqlite3 sqlite3.gcno sqlite3.o
On this system I've got redmine installed, that's why sqlite is included in here.. now I installed django and I need sqlite3 so much..
It would be nice to know, WHY this error appears, and HOW to handle this =)
Just found an answer
it's GCONV param fault... just go to /usr/ports/databases/sqlite3 and then make config, and remove GCONV param.