From Brian.Chapman at utah.edu Wed Jan 27 12:53:11 2016 From: Brian.Chapman at utah.edu (Brian E Chapman) Date: Wed, 27 Jan 2016 17:53:11 +0000 Subject: [Girder-users] Upgrading Girder and Girder Version Message-ID: Hi Everyone, I?ve got a version of Girder running in a Docker container that I built several months ago using girder:latest. MongoDB is running in a separate linked Docker container. Three questions: 1. I cannot see what version of Girder I?m running, either through the web interface or within the container (using pip freeze or importing girder and looking for the _version__ attribute. How do I determine the version of girder I?m running. 2. What is the appropriate way to upgrade girder? I don?t see anything on the admin page that indicates how to upgrade (e.g. Like in Midas). I?m tempted to create a new docker container. What data are actually stored in the docker container vs MongoDB? Just the log files? 3. I turned on the thumbnail generation plugin (version 0.1.0). When I went to generate a thumbnail, I get a PIL not installed message. When I connect to the container and try to install PIL I get a "jpeg is required unless explicitly disabled?? Has the container been tested with all the PlugIns? Curious of how much back tracking I need to do with the installation. Brian -------------- next part -------------- An HTML attachment was scrubbed... URL: From zach.mullen at kitware.com Wed Jan 27 13:14:06 2016 From: zach.mullen at kitware.com (Zach Mullen) Date: Wed, 27 Jan 2016 13:14:06 -0500 Subject: [Girder-users] Upgrading Girder and Girder Version In-Reply-To: References: Message-ID: Hi Brian, 1. The version will show up in the web UI on the front page, near the bottom of the text. For a programmatic way to query it, you can send a GET request to /api/v1/system/version, which contains the API version as well as the git sha1 hash. 2. The upgrade process, as of right now, is very simple. It sounds like you're using pip, so you can simply run `pip install -U girder` and then run `girder-install web` afterward; that should rebuild everything. The web install step requires a somewhat new version of nodejs, so you might have to update that as well if yours is too old. The log files and girder.local.cfg file will be stored within the docker container, all other system metadata lives in the mongo database. If you are using a filesystem assetstore, the files in those assetstores will also be stored locally within the container filesystem. 3. The container hasn't been tested with all the plugins; installing PIL with all the required system libraries is not done in that image. Prior to running `pip install Pillow`, you should install the following: apt-get install libjpeg-dev libfreetype6-dev zlib1g-dev libpng-dev HTH, Zach Mullen Kitware, Inc. 919-869-8858 On Wed, Jan 27, 2016 at 12:53 PM, Brian E Chapman wrote: > Hi Everyone, > > I?ve got a version of Girder running in a Docker container that I built > several months ago using girder:latest. MongoDB is running in a separate > linked Docker container. Three questions: > > > 1. I cannot see what version of Girder I?m running, either through the > web interface or within the container (using pip freeze or importing girder > and looking for the _version__ attribute. How do I determine the > version of girder I?m running. > 2. What is the appropriate way to upgrade girder? I don?t see anything > on the admin page that indicates how to upgrade (e.g. Like in Midas). I?m > tempted to create a new docker container. What data are actually stored in > the docker container vs MongoDB? Just the log files? > 3. I turned on the thumbnail generation plugin (version 0.1.0). When I > went to generate a thumbnail, I get a PIL not installed message. When I > connect to the container and try to install PIL I get a "jpeg is required > unless explicitly disabled?? Has the container been tested with all the > PlugIns? Curious of how much back tracking I need to do with the > installation. > > Brian > > > _______________________________________________ > Girder-users mailing list > Girder-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/girder-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Brian.Chapman at utah.edu Wed Jan 27 13:52:41 2016 From: Brian.Chapman at utah.edu (Brian E Chapman) Date: Wed, 27 Jan 2016 18:52:41 +0000 Subject: [Girder-users] Upgrading Girder and Girder Version In-Reply-To: References: Message-ID: Don?t know how I missed the version #. I think I was looking at the very bottom, assuming a footer of sort. Thanks for the tips on updating. Brian From: Zach Mullen > Date: Wednesday, January 27, 2016 at 11:14 AM To: Brian Chapman > Cc: "girder-users at public.kitware.com" > Subject: Re: [Girder-users] Upgrading Girder and Girder Version Hi Brian, 1. The version will show up in the web UI on the front page, near the bottom of the text. For a programmatic way to query it, you can send a GET request to /api/v1/system/version, which contains the API version as well as the git sha1 hash. 2. The upgrade process, as of right now, is very simple. It sounds like you're using pip, so you can simply run `pip install -U girder` and then run `girder-install web` afterward; that should rebuild everything. The web install step requires a somewhat new version of nodejs, so you might have to update that as well if yours is too old. The log files and girder.local.cfg file will be stored within the docker container, all other system metadata lives in the mongo database. If you are using a filesystem assetstore, the files in those assetstores will also be stored locally within the container filesystem. 3. The container hasn't been tested with all the plugins; installing PIL with all the required system libraries is not done in that image. Prior to running `pip install Pillow`, you should install the following: apt-get install libjpeg-dev libfreetype6-dev zlib1g-dev libpng-dev HTH, Zach Mullen Kitware, Inc. 919-869-8858 On Wed, Jan 27, 2016 at 12:53 PM, Brian E Chapman > wrote: Hi Everyone, I?ve got a version of Girder running in a Docker container that I built several months ago using girder:latest. MongoDB is running in a separate linked Docker container. Three questions: 1. I cannot see what version of Girder I?m running, either through the web interface or within the container (using pip freeze or importing girder and looking for the _version__ attribute. How do I determine the version of girder I?m running. 2. What is the appropriate way to upgrade girder? I don?t see anything on the admin page that indicates how to upgrade (e.g. Like in Midas). I?m tempted to create a new docker container. What data are actually stored in the docker container vs MongoDB? Just the log files? 3. I turned on the thumbnail generation plugin (version 0.1.0). When I went to generate a thumbnail, I get a PIL not installed message. When I connect to the container and try to install PIL I get a "jpeg is required unless explicitly disabled?? Has the container been tested with all the PlugIns? Curious of how much back tracking I need to do with the installation. Brian _______________________________________________ Girder-users mailing list Girder-users at public.kitware.com http://public.kitware.com/mailman/listinfo/girder-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From Brian.Chapman at utah.edu Wed Jan 27 15:52:25 2016 From: Brian.Chapman at utah.edu (Brian E Chapman) Date: Wed, 27 Jan 2016 20:52:25 +0000 Subject: [Girder-users] Upgrading Girder and Girder Version In-Reply-To: References: Message-ID: Zach, As an update, your instructions worked great except I needed to install git in order for the "girder-install web? step to work. A related question, is there a process to do a batch thumbnail generation for images that are in the repository? Thanks, Brian From: Zach Mullen > Date: Wednesday, January 27, 2016 at 11:14 AM To: Brian Chapman > Cc: "girder-users at public.kitware.com" > Subject: Re: [Girder-users] Upgrading Girder and Girder Version Hi Brian, 1. The version will show up in the web UI on the front page, near the bottom of the text. For a programmatic way to query it, you can send a GET request to /api/v1/system/version, which contains the API version as well as the git sha1 hash. 2. The upgrade process, as of right now, is very simple. It sounds like you're using pip, so you can simply run `pip install -U girder` and then run `girder-install web` afterward; that should rebuild everything. The web install step requires a somewhat new version of nodejs, so you might have to update that as well if yours is too old. The log files and girder.local.cfg file will be stored within the docker container, all other system metadata lives in the mongo database. If you are using a filesystem assetstore, the files in those assetstores will also be stored locally within the container filesystem. 3. The container hasn't been tested with all the plugins; installing PIL with all the required system libraries is not done in that image. Prior to running `pip install Pillow`, you should install the following: apt-get install libjpeg-dev libfreetype6-dev zlib1g-dev libpng-dev HTH, Zach Mullen Kitware, Inc. 919-869-8858 On Wed, Jan 27, 2016 at 12:53 PM, Brian E Chapman > wrote: Hi Everyone, I?ve got a version of Girder running in a Docker container that I built several months ago using girder:latest. MongoDB is running in a separate linked Docker container. Three questions: 1. I cannot see what version of Girder I?m running, either through the web interface or within the container (using pip freeze or importing girder and looking for the _version__ attribute. How do I determine the version of girder I?m running. 2. What is the appropriate way to upgrade girder? I don?t see anything on the admin page that indicates how to upgrade (e.g. Like in Midas). I?m tempted to create a new docker container. What data are actually stored in the docker container vs MongoDB? Just the log files? 3. I turned on the thumbnail generation plugin (version 0.1.0). When I went to generate a thumbnail, I get a PIL not installed message. When I connect to the container and try to install PIL I get a "jpeg is required unless explicitly disabled?? Has the container been tested with all the PlugIns? Curious of how much back tracking I need to do with the installation. Brian _______________________________________________ Girder-users mailing list Girder-users at public.kitware.com http://public.kitware.com/mailman/listinfo/girder-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zach.mullen at kitware.com Wed Jan 27 16:21:05 2016 From: zach.mullen at kitware.com (Zach Mullen) Date: Wed, 27 Jan 2016 16:21:05 -0500 Subject: [Girder-users] Upgrading Girder and Girder Version In-Reply-To: References: Message-ID: On Wed, Jan 27, 2016 at 3:52 PM, Brian E Chapman wrote: > Zach, > > As an update, your instructions worked great except I needed to install > git in order for the "girder-install web? step to work. > Thanks, good to know. > > A related question, is there a process to do a batch thumbnail generation > for images that are in the repository? > Not currently. It wouldn't be too difficult to write this in a plugin; you'd want to do a find() on the file model for anything that is an image mime type or has certain file extensions, and then run the thumbnailing on it. > Thanks, > > Brian > > > From: Zach Mullen > Date: Wednesday, January 27, 2016 at 11:14 AM > To: Brian Chapman > Cc: "girder-users at public.kitware.com" > Subject: Re: [Girder-users] Upgrading Girder and Girder Version > > Hi Brian, > > 1. The version will show up in the web UI on the front page, near the > bottom of the text. For a programmatic way to query it, you can send a GET > request to /api/v1/system/version, which contains the API version as well > as the git sha1 hash. > > 2. The upgrade process, as of right now, is very simple. It sounds like > you're using pip, so you can simply run `pip install -U girder` and then > run `girder-install web` afterward; that should rebuild everything. The web > install step requires a somewhat new version of nodejs, so you might have > to update that as well if yours is too old. The log files and > girder.local.cfg file will be stored within the docker container, all other > system metadata lives in the mongo database. If you are using a filesystem > assetstore, the files in those assetstores will also be stored locally > within the container filesystem. > > 3. The container hasn't been tested with all the plugins; installing PIL > with all the required system libraries is not done in that image. Prior to > running `pip install Pillow`, you should install the following: > > apt-get install libjpeg-dev libfreetype6-dev zlib1g-dev libpng-dev > > > HTH, > > > > Zach Mullen > Kitware, Inc. > 919-869-8858 > > On Wed, Jan 27, 2016 at 12:53 PM, Brian E Chapman > wrote: > >> Hi Everyone, >> >> I?ve got a version of Girder running in a Docker container that I built >> several months ago using girder:latest. MongoDB is running in a separate >> linked Docker container. Three questions: >> >> >> 1. I cannot see what version of Girder I?m running, either through >> the web interface or within the container (using pip freeze or importing >> girder and looking for the _version__ attribute. How do I determine >> the version of girder I?m running. >> 2. What is the appropriate way to upgrade girder? I don?t see >> anything on the admin page that indicates how to upgrade (e.g. Like in >> Midas). I?m tempted to create a new docker container. What data are >> actually stored in the docker container vs MongoDB? Just the log files? >> 3. I turned on the thumbnail generation plugin (version 0.1.0). When >> I went to generate a thumbnail, I get a PIL not installed message. When I >> connect to the container and try to install PIL I get a "jpeg is required >> unless explicitly disabled?? Has the container been tested with all the >> PlugIns? Curious of how much back tracking I need to do with the >> installation. >> >> Brian >> >> >> _______________________________________________ >> Girder-users mailing list >> Girder-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/girder-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Brian.Chapman at utah.edu Wed Jan 27 16:22:42 2016 From: Brian.Chapman at utah.edu (Brian E Chapman) Date: Wed, 27 Jan 2016 21:22:42 +0000 Subject: [Girder-users] Upgrading Girder and Girder Version In-Reply-To: References: Message-ID: Good reason for me to dive into the API! From: Zach Mullen > Date: Wednesday, January 27, 2016 at 2:21 PM To: Brian Chapman > Cc: "girder-users at public.kitware.com" > Subject: Re: [Girder-users] Upgrading Girder and Girder Version On Wed, Jan 27, 2016 at 3:52 PM, Brian E Chapman > wrote: Zach, As an update, your instructions worked great except I needed to install git in order for the "girder-install web? step to work. Thanks, good to know. A related question, is there a process to do a batch thumbnail generation for images that are in the repository? Not currently. It wouldn't be too difficult to write this in a plugin; you'd want to do a find() on the file model for anything that is an image mime type or has certain file extensions, and then run the thumbnailing on it. Thanks, Brian From: Zach Mullen > Date: Wednesday, January 27, 2016 at 11:14 AM To: Brian Chapman > Cc: "girder-users at public.kitware.com" > Subject: Re: [Girder-users] Upgrading Girder and Girder Version Hi Brian, 1. The version will show up in the web UI on the front page, near the bottom of the text. For a programmatic way to query it, you can send a GET request to /api/v1/system/version, which contains the API version as well as the git sha1 hash. 2. The upgrade process, as of right now, is very simple. It sounds like you're using pip, so you can simply run `pip install -U girder` and then run `girder-install web` afterward; that should rebuild everything. The web install step requires a somewhat new version of nodejs, so you might have to update that as well if yours is too old. The log files and girder.local.cfg file will be stored within the docker container, all other system metadata lives in the mongo database. If you are using a filesystem assetstore, the files in those assetstores will also be stored locally within the container filesystem. 3. The container hasn't been tested with all the plugins; installing PIL with all the required system libraries is not done in that image. Prior to running `pip install Pillow`, you should install the following: apt-get install libjpeg-dev libfreetype6-dev zlib1g-dev libpng-dev HTH, Zach Mullen Kitware, Inc. 919-869-8858 On Wed, Jan 27, 2016 at 12:53 PM, Brian E Chapman > wrote: Hi Everyone, I?ve got a version of Girder running in a Docker container that I built several months ago using girder:latest. MongoDB is running in a separate linked Docker container. Three questions: 1. I cannot see what version of Girder I?m running, either through the web interface or within the container (using pip freeze or importing girder and looking for the _version__ attribute. How do I determine the version of girder I?m running. 2. What is the appropriate way to upgrade girder? I don?t see anything on the admin page that indicates how to upgrade (e.g. Like in Midas). I?m tempted to create a new docker container. What data are actually stored in the docker container vs MongoDB? Just the log files? 3. I turned on the thumbnail generation plugin (version 0.1.0). When I went to generate a thumbnail, I get a PIL not installed message. When I connect to the container and try to install PIL I get a "jpeg is required unless explicitly disabled?? Has the container been tested with all the PlugIns? Curious of how much back tracking I need to do with the installation. Brian _______________________________________________ Girder-users mailing list Girder-users at public.kitware.com http://public.kitware.com/mailman/listinfo/girder-users -------------- next part -------------- An HTML attachment was scrubbed... URL: