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Instant JChem Installation and Upgrade

Instant JChem download

Installation

Instant JChem can now be installed in three different ways:

1. Traditional installer

Download the Instant JChem installer to install a new version of Instant JChem. If you are using this approach then uninstall any previously installed versions first.

Download Instant JChem

Since version 19.22.0, possibility to install Instant JChem for Windows platform from an MSI file has been added. MSI is a Windows installer package file designed to install a program (in this case IJC) to the executing system. It enables accurate control over how the installation is managed. Installation from the MSI file offers to system administrators installing IJC to cover their corporate network. The MSI package is provided without bundled Java.

Since IJC 2.4 administrator mode is needed to install IJC on Windows, to be able to register the OLE server and to avoid re-installation problems on Vista.

Once you have installed don't forget to load any updates that might be available (Tools -> Plugins).

2. Java Web Start

Since version 2.2 Instant JChem can be launched using Java Web Start (JWS). This allows you to load it directly from a web-page rather than needing to install it first. The Java Web Start version should be fine for most users, but it is slightly less flexible, for instance should you wish to install your own or a third party's extension. For more information about the Java Web Start look here or you can launch it right now:

Instant JChem Java Web Start

3. Docker image for Instant JChem

How to download the docker image in particular version:

Go to https://download.chemaxon.com/plexus-connect

Use the commands from the first section to login to Docker

It looks like this:
echo someapikeygeneratedforyou | docker login -u yousername@chemaxon.com --password-stdin hub.chemaxon.com

download the image you want with the following command:
docker pull hub.chemaxon.com/cxn-docker-release/ijc-jws-server:

wherein, for example:

  • for frequent release replace with version number of interest, etc. 22.19.0
  • accordingly, for lts release replace with etc. lts-21.15.7

How to run:

Default
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docker run -it --rm -p 8080:8080 jws-webappurl

The app will be accessible at http://localhost:8080/UrlWebApp/.

Sharing a project

Add the zip file and ijp file to a local folder (example C:\Others\docker-jws-data\shared_projects) and bind it to the container on /usr/local/ijc_shared_data . The content of the folder will be copied to the right location inside the image.

Lets assume I have myproject.zip and myproject.ijp inside
shared_projects.

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docker run -it --rm -p 8080:8080 -v C:\Others\docker-jws-data\shared_projects:/usr/local/ijc_shared_data jws-webappurl

The project can be accessed by this url:
http://localhost:8080/UrlWebApp/prj.jnlp?startJnlp

Of course, it might be helpful to also update the index.html file and add a reference to the new project. The updated index.html should also be placed in the same shared_projects folder.

Proxy to server URL: http://www.YourWeb.com:9080/urldemo/

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docker run -it --rm -p 8080:8080 -e PROXY_WEB_SERVER="http://www.YourWeb.com:9080/urldemo/"  jws-webappurl

The app will be accessible at http://localhost:8080/UrlWebApp/ but the links to projects and IJC will point to the chemaxon demo at http://www.YourWeb.com:9080/urldemo/.

Different port
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docker run -it --rm -p 8888:8080 jws-webappurl

The app will be accessible at http://localhost:8888/UrlWebApp/.

Upgrade IJC

you will need to provide a new index.html a new InstanJchem zip and a new info.properties. Put them all in a local folder, for example :\Others\docker-jws-data\shared_projects. The license file can also be put here.

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 -v C:\Others\docker-jws-data\shared_projects:/usr/local/ijc_shared_jws
Available configuration through environment vars (-e option)
  • CODEBASE
  • EXTRA_ARGUMENTS
  • LICENSE
  • PROXY_WEB_SERVER

Folders to bind:

  • /usr/local/ijc_shared_data - add here things related to application data: shared projects, html pages
  • /usr/local/ijc_shared_jws - add here things related to IJC configuration: ijc zip file, info.properties, master.jnlp

4. Autoupdate

Autoupdate allows you to pick up the latest updates for Instant JChem without needing to re-install. Autoupdate only applies to the installer based versions of IJC, not the Java Web Start versions which are updated automatically. You access it by using Tools -> Plugins. Documentation on using autoupdate can be found here .

Automatic Update Center functionality will be removed from Instant JChem after version 18.8.0. This means that version 18.8.0 will be the last version offered through Automatic Update Ceter. To update our software after version 18.8.0, you need to download the software from the web and perform reinstallation, or if desired, a clean reinstallation.

Important note for Windows Vista users

When running autoupdate, you must run IJC as an administrator to avoid problems when installing later versions.

About upgrading

When upgrading Instant JChem by any mechanism it is possible that significant changes to the JChem version and/or the organization your project information will occur. We try to make sure that these upgrades work transparently and smoothly, but if any of your projects contain important information that cannot be easily regenerated we do recommend that you backup your data prior to updating. To do this do one (or all!) of the following:

  • Export your data to a file (e.g. SD file)
  • Take a copy of the complete project. Use the file manager (e.g. Windows Explorer) to copy (or create a zip archive) of the complete directory containing your project(s). Note: this will only back up data in local databases.
  • If you are using a MySQL or Oracle database you should ensure that you have a database backup before you update. Backing up the IJC project directory will not backup the data in these databases.

Installation problems?

If you are having problems installing or running IJC then these notes might help

Userdir

IJC saves various settings and all updates it gets from the Update Center in a "userdir" which is usually found in:

  • Windows - c:\Users\\AppData\Roaming\.instantjchem\
  • Mac OS X - $HOME/Library/Application Support/instantjchem/
  • Linux - $HOME/.instantjchem/

In case of Java Web Start installation, the changes to ws_

The exact location can be found in the Help -> About Instant JChem. If you are having problems installing or running IJC then make sure no IJC instance is running and try renaming this directory and start IJC again. This will create the userdir cleanly again. You will lose your current settings and will need to re-open your projects in case of update, but you will not lose any data.

One possible scenario that could need this action is if you have downloaded some updates from the Update Center, but that these updates have become corrupted for some unknown reason. In this case you must delete your userdir to clear out these files.

Windows Vista

Windows Vista has peculiar security settings that are know to cause problems with many different software. The Windows IJC installer must be run with administrator settings to avoid these problems and to be able to register the OLE server. If you do not have administrator privileges then you will not be able to install. See here for more information about installation issues on Vista.

Other Information