Open Microscopy Environment

Hm...this is a critical problem.

What we are planning is...A user (1) will create/save a h5 OMERO table for image content repository with a name of xxx_0000001.h5. Then that user (1) also save the most recent repository file name somewhere (such as tag, annotation)

After that, another user (2) will retrieve the file name of the most recent repository. then it will retrieve the file by querying the file name. Moreover, this user (2) will add another rows to the existing file and save it as xxx_0000002.h5. Of course the tag or annotation that contains the most recent file name should be updated.

And this keeps going.

Could you give me some advice to implement this? I mean, is there any detour method to do this?

Best,
BK

bhcho wrote:Could you give me some advice to implement this? I mean, is there any detour method to do this?

At the moment, my best suggestion would be to have a single group which everyone is a member of. That may take some work on your part. For example, your bridge could notice any newly created users and add them to the group.

Longer-term, we are certainly thinking about public-read and public-write permissions, but it will be some time until they get implemented. Feel free to get involved in those tickets, though.

Cheers,
~Josh.

my best suggestion would be to have a single group which everyone is a member of. That may take some work on your part. For example, your bridge could notice any newly created users and add them to the group.

1. if there are two accounts which are members of the same group, then does this mean that they can read/write the same annotation/tag?

2. why my bridge needs to recognize any newly created users and add them to the group?

BK

bhcho wrote:1. if there are two accounts which are members of the same group, then does this mean that they can read/write the same annotation/tag?

As long as the group is collaborative (rwrw).

2. why my bridge needs to recognize any newly created users and add them to the group?

Just a suggestion for one way of keeping all new users in the same group. You may (or may not) need some mechanism to do so.

~Josh.

As long as the group is collaborative (rwrw).

Sounds great. Then could you tell me how to create/modify an annotation(or tag, or whatever a user can save a string), WITHOUT attaching to anything?

Always thanks.
BK

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tag = session.getUpdateService().saveAndReturnObject(omero.model.TagAnnotationI())


would suffice, but you'll want to set the values on the tag first.

~Josh

Thanks Josh,

I was able to set/get the text using the 'tag' by

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In [16]: tag.setTextValue('hahaha')
In [17]: tag.getTextValue()
Out[17]: 'hahaha'
In [18]: tag.setNs('Recent_File')
In [19]: tag.getNs()
Out[19]: 'Recent_File'

But could you tell me how can I access to this 'tag' using other accounts? Using Ns?

This is just creating a tag, right?

Code: Select all

tag = session.getUpdateService().saveAndReturnObject(omero.model.TagAnnotationI())

BK

There are a couple of ways you could do it:

• By some unique NS: iQuery.findByQuery("select ta from TagAnnotation where ta.ns = '348952983475298347520983745'", None), but you will need to share this value between all users.
• Assume that the newest (oldest?) annotation in the special group is the one you're looking for: iQuery.findByQuery("select ta from TagAnnotation ta order by ta.id desc", omero.sys.ParametersI().page(0, 1))
• Attach the annotation to the group itself: iQuery.findAllByQuery("select ann from ExperimenterGroupAnnotationLink link join link.annotation an where link.parent.id = 5 and an.ns = 'Recent_File'", None). In this case, there could possibly be more than one which you would have to handle somehow.

Cheers,
~Josh

Hi Josh,

It seems like I can directly search the newest OMERO.table among the ones with the same file name, right?
if so, that would be the easiest way (without using tag annotations).

BK

Another followup question. (Hopefully final one on this thread )

I'd like to make a function that retrieves a table A, create a new table B with copying data from the table A, then save it with a different name. (Of course, the new table file name will be updated in the tagAnnotation, which is shared by everyone in the same group)

The reason why I'm doing this is to let every account update the table (actually creating a new one) by adding each one's new data (I think this is the only way to have a pseudo-"world-writable" OMERO.tables)

So, I want to know how to copy the table and create a new one?

I can retrieve a table by

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table = conn.getSharedResources().openTable( omero.model.OriginalFileI( fid, False ) ) # fid is the file id of the table

Then If I'm not the owner of the table, I don't think I can directly update the table by

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        num_data = table.getNumberOfRows()
        columns = []
        columns.append(omero.grid.LongColumn( 'INDEX', 'Data Index', [] ))
        columns.append(omero.grid.LongColumn( 'iid', 'Image ID', [] ))
        columns.append(omero.grid.LongColumn( 'pixels', 'Pixel Index', [] ))
        columns.append(omero.grid.LongColumn( 'channel', 'Channel Index', [] ))
        columns.append(omero.grid.LongColumn( 'zslice', 'zSlice Index', [] ))
        columns.append(omero.grid.LongColumn( 'timepoint', 'Time Point Index', [] ))

        IND = num_data + 1
        columns[0].values.append( long(IND) )   #INDEX
        columns[1].values.append( long(iid) )   
        columns[2].values.append( long(pixels) )
        columns[3].values.append( long(channel) )
        columns[4].values.append( long(zslice) ) 
        columns[5].values.append( long(timepoint) )
        table.addData(columns)
        table.close()


I guess before I update the table, I think I should copy this table to a newly created table first.
Could you please help me here?

Best,
BK