Issuing compiling from the main branch using github
I was wondering if anybody had any advice for me on the following error, I am
trying to clean install from the head of the main branch in git.
Below are my commands; this error start with commit
d998331c1cfef48d792c78a8d3c1670498a8b925
The commands below work for the previous commit
a97258b01d455f7816994070cf64deb311b29acc
git clone https://github.com/apache/ctakes.git;
cd ctakes;
mvn clean install -ff -DskipTests=true;
error message
/root/projects/ctakes/ctakes-ytex/scripts/build-setup.xml:149: The following
error occurred while executing this line:
[ERROR] /root/projects/ctakes/ctakes-ytex/scripts/data/build.xml:148: The
following error occurred while executing this line:
[ERROR] /root/projects/ctakes/ctakes-ytex/scripts/data/build.xml:531: Warning:
Could not find file
/root/projects/ctakes/ctakes-ytex/scripts/data/${project.basedir}/conn.xml.template
to copy.
mvn -v
Apache Maven 3.6.3
Maven home: /usr/share/maven
Java version: 1.8.0_282, vendor: AdoptOpenJDK, runtime: /opt/java/openjdk/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "5.10.147+", arch: "amd64", family: "unix"
Re: Issuing compiling from the main branch using github [EXTERNAL]
Hi Scott,
Thanks for the report - especially the setup, failure message and commit
details. Would you mind copying it into the GitHub issues area?
https://github.com/apache/ctakes/issues
I think that I know what happened ...
The pom files for several modules used ${basedir} instead of the preferred
${project.basedir}. I updated them to standard. I also changed ${basedir} in
the ytex scripts and apparently, they don't have substitution for that
expression. I will have it fixed in a few minutes and try again.
Sean
From: Haag, Scott M
Sent: Friday, February 3, 2023 10:10 AM
To: dev@ctakes.apache.org
Subject: Issuing compiling from the main branch using github [EXTERNAL]
* External Email - Caution *
I was wondering if anybody had any advice for me on the following error, I am
trying to clean install from the head of the main branch in git.
Below are my commands; this error start with commit
d998331c1cfef48d792c78a8d3c1670498a8b925
The commands below work for the previous commit
a97258b01d455f7816994070cf64deb311b29acc
git clone
https://urldefense.com/v3/__https://github.com/apache/ctakes.git__;!!NZvER7FxgEiBAiR_!sNj-I6E9pJQ9g0k3JrJ_jk_1ye5PiGtLKrJi5vDzO4sZPBphb4sRIYrS9VEgT3JyiT79ME4Gnt7MZmOviJWN825Tpq417uZr$
;
cd ctakes;
mvn clean install -ff -DskipTests=true;
error message
/root/projects/ctakes/ctakes-ytex/scripts/build-setup.xml:149: The following
error occurred while executing this line:
[ERROR] /root/projects/ctakes/ctakes-ytex/scripts/data/build.xml:148: The
following error occurred while executing this line:
[ERROR] /root/projects/ctakes/ctakes-ytex/scripts/data/build.xml:531: Warning:
Could not find file
/root/projects/ctakes/ctakes-ytex/scripts/data/${project.basedir}/conn.xml.template
to copy.
mvn -v
Apache Maven 3.6.3
Maven home: /usr/share/maven
Java version: 1.8.0_282, vendor: AdoptOpenJDK, runtime: /opt/java/openjdk/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "5.10.147+", arch: "amd64", family: "unix"
Re: Issuing compiling from the main branch using github [EXTERNAL] [SUSPICIOUS]
I just checked in the revert on ctakes-ytex/scripts/data/build.xml
Packaging works on my machine, but it had also worked for all previous tests so
maybe there is still an issue.
Sean
From: Finan, Sean
Sent: Friday, February 3, 2023 11:09 AM
To: dev@ctakes.apache.org
Subject: Re: Issuing compiling from the main branch using github [EXTERNAL]
[SUSPICIOUS]
* External Email - Caution *
Hi Scott,
Thanks for the report - especially the setup, failure message and commit
details. Would you mind copying it into the GitHub issues area?
https://urldefense.com/v3/__https://github.com/apache/ctakes/issues__;!!NZvER7FxgEiBAiR_!r_NQsbbnDqD-QGMwq_ofjWAsCeeR1pGVKoB2EVnideNr2t6t24yCwJmoibSXDSf6F40_bEadTeF5AGH5NItUpOBViKAQtNUFoJM9wlumGFqmeqbv-A$
I think that I know what happened ...
The pom files for several modules used ${basedir} instead of the preferred
${project.basedir}. I updated them to standard. I also changed ${basedir} in
the ytex scripts and apparently, they don't have substitution for that
expression. I will have it fixed in a few minutes and try again.
Sean
From: Haag, Scott M
Sent: Friday, February 3, 2023 10:10 AM
To: dev@ctakes.apache.org
Subject: Issuing compiling from the main branch using github [EXTERNAL]
* External Email - Caution *
I was wondering if anybody had any advice for me on the following error, I am
trying to clean install from the head of the main branch in git.
Below are my commands; this error start with commit
d998331c1cfef48d792c78a8d3c1670498a8b925
The commands below work for the previous commit
a97258b01d455f7816994070cf64deb311b29acc
git clone
https://urldefense.com/v3/__https://github.com/apache/ctakes.git__;!!NZvER7FxgEiBAiR_!sNj-I6E9pJQ9g0k3JrJ_jk_1ye5PiGtLKrJi5vDzO4sZPBphb4sRIYrS9VEgT3JyiT79ME4Gnt7MZmOviJWN825Tpq417uZr$
;
cd ctakes;
mvn clean install -ff -DskipTests=true;
error message
/root/projects/ctakes/ctakes-ytex/scripts/build-setup.xml:149: The following
error occurred while executing this line:
[ERROR] /root/projects/ctakes/ctakes-ytex/scripts/data/build.xml:148: The
following error occurred while executing this line:
[ERROR] /root/projects/ctakes/ctakes-ytex/scripts/data/build.xml:531: Warning:
Could not find file
/root/projects/ctakes/ctakes-ytex/scripts/data/${project.basedir}/conn.xml.template
to copy.
mvn -v
Apache Maven 3.6.3
Maven home: /usr/share/maven
Java version: 1.8.0_282, vendor: AdoptOpenJDK, runtime: /opt/java/openjdk/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "5.10.147+", arch: "amd64", family: "unix"
Re: Issuing compiling from the main branch using github [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
By the way, for all who are using "mvn install" and aren't interested in
creating a binary installation:
There is a new maven profile called "no-zips-build" in ctakes 5. When enabled
it will skip the creation of src and binary tar.gz and .zip files during the
package phase. This significantly speeds up build-time and sometimes you just
want the jars - such as for mvn install.
In addition, there are 2 new profiles in ctakes 5 for web war creation:
"web-rest-build" and "ytex-web-build". When enabled, these will build the
corresponding war files. By default the wars are not built. Why? Because
doing so creates 2 or 3 extra copies of ctakes. One copy of jars, one copy in
the .war, and then a 3rd in the binary .zip file. This all leads to a longer
build time and much larger disk footprint. In addition, most users do not use
the web projects, and if they do they usually want one, not both. With proper
documentation (coming soon) this should not cause any confusion.
Sean
From: Finan, Sean
Sent: Friday, February 3, 2023 11:24 AM
To: dev@ctakes.apache.org
Subject: Re: Issuing compiling from the main branch using github [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
* External Email - Caution *
I just checked in the revert on ctakes-ytex/scripts/data/build.xml
Packaging works on my machine, but it had also worked for all previous tests so
maybe there is still an issue.
Sean
From: Finan, Sean
Sent: Friday, February 3, 2023 11:09 AM
To: dev@ctakes.apache.org
Subject: Re: Issuing compiling from the main branch using github [EXTERNAL]
[SUSPICIOUS]
* External Email - Caution *
Hi Scott,
Thanks for the report - especially the setup, failure message and commit
details. Would you mind copying it into the GitHub issues area?
https://urldefense.com/v3/__https://github.com/apache/ctakes/issues__;!!NZvER7FxgEiBAiR_!r_NQsbbnDqD-QGMwq_ofjWAsCeeR1pGVKoB2EVnideNr2t6t24yCwJmoibSXDSf6F40_bEadTeF5AGH5NItUpOBViKAQtNUFoJM9wlumGFqmeqbv-A$
I think that I know what happened ...
The pom files for several modules used ${basedir} instead of the preferred
${project.basedir}. I updated them to standard. I also changed ${basedir} in
the ytex scripts and apparently, they don't have substitution for that
expression. I will have it fixed in a few minutes and try again.
Sean
From: Haag, Scott M
Sent: Friday, February 3, 2023 10:10 AM
To: dev@ctakes.apache.org
Subject: Issuing compiling from the main branch using github [EXTERNAL]
* External Email - Caution *
I was wondering if anybody had any advice for me on the following error, I am
trying to clean install from the head of the main branch in git.
Below are my commands; this error start with commit
d998331c1cfef48d792c78a8d3c1670498a8b925
The commands below work for the previous commit
a97258b01d455f7816994070cf64deb311b29acc
git clone
https://urldefense.com/v3/__https://github.com/apache/ctakes.git__;!!NZvER7FxgEiBAiR_!sNj-I6E9pJQ9g0k3JrJ_jk_1ye5PiGtLKrJi5vDzO4sZPBphb4sRIYrS9VEgT3JyiT79ME4Gnt7MZmOviJWN825Tpq417uZr$
;
cd ctakes;
mvn clean install -ff -DskipTests=true;
error message
/root/projects/ctakes/ctakes-ytex/scripts/build-setup.xml:149: The following
error occurred while executing this line:
[ERROR] /root/projects/ctakes/ctakes-ytex/scripts/data/build.xml:148: The
following error occurred while executing this line:
[ERROR] /root/projects/ctakes/ctakes-ytex/scripts/data/build.xml:531: Warning:
Could not find file
/root/projects/ctakes/ctakes-ytex/scripts/data/${project.basedir}/conn.xml.template
to copy.
mvn -v
Apache Maven 3.6.3
Maven home: /usr/share/maven
Java version: 1.8.0_282, vendor: AdoptOpenJDK, runtime: /opt/java/openjdk/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "5.10.147+", arch: "amd64", family: "unix"
[GitHub] [ctakes] Haags opened a new issue, #8: Issue clean install using maven for ctakes-ytex
Haags opened a new issue, #8:
URL: https://github.com/apache/ctakes/issues/8
I was wondering if anybody had any advice for me on the following error, I
am trying to clean install from the head of the main branch in git.
Below are my commands; this error start with commit
d998331c1cfef48d792c78a8d3c1670498a8b925
The commands below work for the previous commit
a97258b01d455f7816994070cf64deb311b29acc
steps to reproduce
git clone the ctakes repo
mvn clean install -ff -DskipTests=true;
error message
/root/projects/ctakes/ctakes-ytex/scripts/build-setup.xml:149: The following
error occurred while executing this line:
[ERROR] /root/projects/ctakes/ctakes-ytex/scripts/data/build.xml:148: The
following error occurred while executing this line:
[ERROR] /root/projects/ctakes/ctakes-ytex/scripts/data/build.xml:531:
Warning: Could not find file
/root/projects/ctakes/ctakes-ytex/scripts/data/${project.basedir}/conn.xml.template
to copy.
mvn -v
Apache Maven 3.6.3
Maven home: /usr/share/maven
Java version: 1.8.0_282, vendor: AdoptOpenJDK, runtime: /opt/java/openjdk/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "5.10.147+", arch: "amd64", family: "unix"
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[GitHub] [ctakes] seanfinan commented on issue #8: Issue clean install using maven for ctakes-ytex
seanfinan commented on issue #8:
URL: https://github.com/apache/ctakes/issues/8#issuecomment-1416323145
Hi Scott,
Thanks for the report - especially the setup, failure message and commit
details. Would you mind copying it into the GitHub issues area?
https://urldefense.com/v3/__https://github.com/apache/ctakes/issues__;!!NZvER7FxgEiBAiR_!r_NQsbbnDqD-QGMwq_ofjWAsCeeR1pGVKoB2EVnideNr2t6t24yCwJmoibSXDSf6F40_bEadTeF5AGH5NItUpOBViKAQtNUFoJM9wlumGFqmeqbv-A$
I think that I know what happened ...
The pom files for several modules used ${basedir} instead of the preferred
${project.basedir}. I updated them to standard. I also changed ${basedir} in
the ytex scripts and apparently, they don't have substitution for that
expression. I will have it fixed in a few minutes and try again.
Sean
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: dev-unsubscr...@ctakes.apache.org
For queries about this service, please contact Infrastructure at:
us...@infra.apache.org
[GitHub] [ctakes] seanfinan commented on issue #8: Issue clean install using maven for ctakes-ytex
seanfinan commented on issue #8: URL: https://github.com/apache/ctakes/issues/8#issuecomment-1416323915 I just checked in the revert on ctakes-ytex/scripts/data/build.xml Packaging works on my machine, but it had also worked for all previous tests so reopen if this is still an issue. Sean -- This is an automated message from the Apache Git Service. To respond to the message, please log on to GitHub and use the URL above to go to the specific comment. To unsubscribe, e-mail: dev-unsubscr...@ctakes.apache.org For queries about this service, please contact Infrastructure at: us...@infra.apache.org
[GitHub] [ctakes] seanfinan closed issue #8: Issue clean install using maven for ctakes-ytex
seanfinan closed issue #8: Issue clean install using maven for ctakes-ytex URL: https://github.com/apache/ctakes/issues/8 -- This is an automated message from the Apache Git Service. To respond to the message, please log on to GitHub and use the URL above to go to the specific comment. To unsubscribe, e-mail: dev-unsubscr...@ctakes.apache.org For queries about this service, please contact Infrastructure at: us...@infra.apache.org
Crash course in cTakes
Hello everyone, Can anyone point me to an exhaustive set of documentation regarding cTakes? The main site feels like it was written by a marketing major, lots of flash and catchiness, but little in the way of detailed documentation. Even the User Install Guide and the Developer Install guide read like what they are, install guides. For example: Is cTakes the whole package, or just the front end? If it's just the front end, what's the back end? It mentions using my UMLS credentials, can you use a local copy of the relevant UMLS data? If so how? Are the requirements listed, 1GB drive space, Oracle Java 1.8 the minimum or the recommended? What about RAM or CPU? Is non-Oracle Java acceptable? What about 1.17, the current LTS version? So, does anyone know where I can find out this information? Thanks. rik.
Re: Crash course in cTakes [EXTERNAL]
Hi Rick, Thank you for the questions and for reminding us that the documentation is sparse, outdated and not very detailed. Everybody needs a prod now and then to get things done. I hope that we can get a solid README and Wiki going on GitHub, as well as an update to the primary website. It will take a lot of work and some cooperation by committers and users alike. I have tried to address your questions inline below. Sean From: Rick Coleman Sent: Friday, February 3, 2023 3:14 PM To: dev@ctakes.apache.org Subject: Crash course in cTakes [EXTERNAL] * External Email - Caution * Hello everyone, Can anyone point me to an exhaustive set of documentation regarding cTakes? * Not really. The wiki that you found is the most that there is. * Most information is scattered across emails written on the dev and user lists. You can search them here: https://apache.markmail.org/ The main site feels like it was written by a marketing major, lots of flash and catchiness, but little in the way of detailed documentation. Even the User Install Guide and the Developer Install guide read like what they are, install guides. For example: Is cTakes the whole package, or just the front end? * ctakes is a clinical nlp platform (vague enough?). I would say "whole package", but extendable. * It is built on Apache UIMA and allows users to create pipelines of various nlp and i/o components. * It comes with many components that have been built for clinical nlp. * It is extendable; UIMA components from other sources can be placed in the pipelines. * There are front-ends for some tasks, such as running a pipeline or creating a custom dictionary. If it's just the front end, what's the back end? * I would say that each UIMA component is a bit of back-end, as is the controller that actually runs the pipeline. * As mentioned above, you can extend it with non-ctakes back-end components . It mentions using my UMLS credentials, can you use a local copy of the relevant UMLS data? If so how? * If you are compiling and running the source then ctakes will automatically download a default dictionary. * If you are running a packaged binary then you'll need to manually pull down a dictionary. * Previous to ctakes 5 downlaoding, unzipping and copying the dictionary was a manual process. * If you are using v5 then you can run bin/getUmlsDictionary and a simple gui will do it for you. * You can also create your own custom dictionary. * The wiki has a page on the dictionary creator gui. * There are instructions on youtube that start with first steps. Are the requirements listed, 1GB drive space, Oracle Java 1.8 the minimum or the recommended? What about RAM or CPU? Is non-Oracle Java acceptable? What about 1.17, the current LTS version? > 1GB disk == Java 1.8 > 2GB RAM (>= 4 recommended) >= 64bit CPU OpenJDK seems to be fine. Every java release past 8 is bad for ctakes. ctakes has a lot of dependencies, many of which are old and rely on a java 8 feature here and there. ctakes itself probably requires a java 8 special here and there, but I honestly don't know. Unfortunately, ctakes needs to have a serious update effort - maybe for v6. Part of the problem is actually its capabilities and versatility - the availability of multiple available components and workflows. A 'minor' change can require a dozen end-to-end tests in dev and user environments on multiple platforms. Unit tests do not suffice. So, does anyone know where I can find out this information? Thanks. rik.
Re: Crash course in cTakes [EXTERNAL]
Sean, Thanks for getting back to me in this. I was afraid that was what the answer was going to be. I appreciate you taking the time to fill in some of the gaps. If it's so dependent on Java 1.8, someone should probably remove the "or higher" on the download page. I look forward to getting this application up and running. Until then, rik. On 2/3/23 15:57, Finan, Sean wrote: Hi Rick, Thank you for the questions and for reminding us that the documentation is sparse, outdated and not very detailed. Everybody needs a prod now and then to get things done. I hope that we can get a solid README and Wiki going on GitHub, as well as an update to the primary website. It will take a lot of work and some cooperation by committers and users alike. I have tried to address your questions inline below. Sean From: Rick Coleman Sent: Friday, February 3, 2023 3:14 PM To: dev@ctakes.apache.org Subject: Crash course in cTakes [EXTERNAL] * External Email - Caution * Hello everyone, Can anyone point me to an exhaustive set of documentation regarding cTakes? * Not really. The wiki that you found is the most that there is. * Most information is scattered across emails written on the dev and user lists. You can search them here: https://apache.markmail.org/ The main site feels like it was written by a marketing major, lots of flash and catchiness, but little in the way of detailed documentation. Even the User Install Guide and the Developer Install guide read like what they are, install guides. For example: Is cTakes the whole package, or just the front end? * ctakes is a clinical nlp platform (vague enough?). I would say "whole package", but extendable. * It is built on Apache UIMA and allows users to create pipelines of various nlp and i/o components. * It comes with many components that have been built for clinical nlp. * It is extendable; UIMA components from other sources can be placed in the pipelines. * There are front-ends for some tasks, such as running a pipeline or creating a custom dictionary. If it's just the front end, what's the back end? * I would say that each UIMA component is a bit of back-end, as is the controller that actually runs the pipeline. * As mentioned above, you can extend it with non-ctakes back-end components . It mentions using my UMLS credentials, can you use a local copy of the relevant UMLS data? If so how? * If you are compiling and running the source then ctakes will automatically download a default dictionary. * If you are running a packaged binary then you'll need to manually pull down a dictionary. * Previous to ctakes 5 downlaoding, unzipping and copying the dictionary was a manual process. * If you are using v5 then you can run bin/getUmlsDictionary and a simple gui will do it for you. * You can also create your own custom dictionary. * The wiki has a page on the dictionary creator gui. * There are instructions on youtube that start with first steps. Are the requirements listed, 1GB drive space, Oracle Java 1.8 the minimum or the recommended? What about RAM or CPU? Is non-Oracle Java acceptable? What about 1.17, the current LTS version? 1GB disk == Java 1.8 2GB RAM (>= 4 recommended) = 64bit CPU OpenJDK seems to be fine. Every java release past 8 is bad for ctakes. ctakes has a lot of dependencies, many of which are old and rely on a java 8 feature here and there. ctakes itself probably requires a java 8 special here and there, but I honestly don't know. Unfortunately, ctakes needs to have a serious update effort - maybe for v6. Part of the problem is actually its capabilities and versatility - the availability of multiple available components and workflows. A 'minor' change can require a dozen end-to-end tests in dev and user environments on multiple platforms. Unit tests do not suffice. So, does anyone know where I can find out this information? Thanks. rik.
