OMERO and Git

[icaoberg]

I cloned omero using git

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git clone git://git.openmicroscopy.org/ome.git

There is single branch and multiple tags that reference different versions, including 4.2.1 which is the one I want to edit.

The two tags are

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v.4.2.1-insight
v.4.2.1-omero


How do I make sure that whatever commit I do only affects v.4.2.1-omero? Should I create a second branch and edit it?

The problem is that if I create a second branch and remove the top nodes until I reach the desired commit/tag, if I create a patch between the two branches the patch will add everything until 4.3.1.

[jmoore]

After you clone, you will have one branch named "master". From that point, you want to create a new branch based on our v.4.2.1-omero tag:

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git checkout -b dev_4_2_1_pslid v.4.2.1-omero


If you run "git branch" you'll see "dev_4_2_1_pslid" now. Any commits you make like:

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git commit -m "Falcon DB" lib/falcon


will be on the branch. You can see how far you've "diverged" from v.4.2.1-omero via:

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git show-branch v.4.2.1-omero dev_4_2_1_pslid


To send us your patches, use:

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git format-patch v.4.2.1-omero..dev_4_2_1_pslid


with whatever options you'd like.

Cheers,
~Josh.

[icaoberg]

We originally downloaded and installed omero.server we didn't use the git branch. Now I need to commit my changes within the branch.

We added files to

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$OMERO_HOME/lib/python

where should I add these files in the git branch?

[jmoore]

You can initially put them somewhere under OmeroPy/src, but we may want to eventually create a separate "searcher" component.

Cheers,
~Josh.

[icaoberg]

We also modified the file extensions.jar which resides in

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$OMERO_HOME/lib/server

where should this file be located within the branch?

[jmoore]

It's not a jar in the source code, but is the one location where external classes can be put by third parties. However, in your case, we want to see the code, so it's probably best to add the files elsewhere. If it's all search based, you might want to add a package under server/src, but again, eventually, we'll want to create a "searcher" component which can contain both the Java and the Python source.

Cheers,
~Josh

[icaoberg]

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/usr0/local/omepslid/ome/components/server/src
bash-3.2$ ls
ome
bash-3.2$ cd ome
bash-3.2$ ls
api  formats  logic  security  services  tools


where within this folder we add the the source?

we were basically trying to do

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cp -r $SOURCE/server/extensions.jar $DESTINATION/server/extensions.jar
git add $DESTINATION/server/extensions.jar
git commit -m 'Updated extensions.jar' $DESTINATION/server/extensions.jar


where $SOURCE was our omero.server and $DESTINATION was a clean download of omero,server. The file structure within git is different, so we need to ask about the destination of most of our code.

[jmoore]

Hi Ivan,

Have you seen OmeroBuild yet? Most importantly is the layout of source code like:

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  \components
    |
    |
    |--<component-name> ................... Each component has this same basic structure.
    |    |-- build.xml                      Main scripts
    |    |-- ivy.xml                        Jar dependencies
    |    |-- src                            Source code
    |    |-- resources                      Other files of interest
    |    |-- test                           Test source code and test resources
    |    \-- target                         Output of build (deleted on clean)


My goal would be to have all your source code (the .java files, not the .jars) either:

• in the source and resources directories of an existing component. "server" is probably ok, but if you run into any issues you can put it in "blitz".
• in a new component like "tools/OmeroSearcher"

In the long run, I think we will want all of this in its own component, but in order to get things in more quickly, I can understand if you'd prefer to wait on that.

Cheers,
~Josh

[bhcho]

Hi Josh,

we also have some python codes and a text file, which are called from both the bridge and OMERO.web page.
Thus we were assumiing those files are located in a specific folder (e.g., OMERO_HOME/lib/python/ ).

In this case, where do we need to copy those files?

best,
BK

[jmoore]

Hi BK,

as above, the python files should go into the OmeroPy/src directory. I'm not sure what your text file contains, but it will most likely need to go into one of the resources/ directories, like server/resources. What's the file ending?

~Josh.