2007-10-04 Project-wide 3:45 BST
Attending: Alexa, Andrew, Brian, Cat, Chris, Curtis, Donald, JMarie, Josh
Agenda
- Curtis
- OME-XML Node stuff (Chris)
- need additional node types? want additional methods?
- getting parent node — e.g., get Filter for a given TransmittanceRange
- getting nodes that reference this one — e.g., get Images that reference a given Detector
- methods to add and remove children — e.g., add DetectorRefs to an Image
- Metadata revisioning (Josh)
- OME-XML/OME-TIFF timeline
- OME-XML Node stuff (Chris)
- Chris
- RE exception
- Andrew
- XML goodies
Notes
- curtis
- prototyping node types for new version of XML
- previous version only looked at STD
- now coming directly from generateDS (python)
- do you (chris) want more node types? or do you want more?
- Chris: currently generating for every element in xsd (almost compiling)
- few methods needed in OmeXmlNode
- few tricky things defined in global scope & used only once (~10)
- Curtis: Would like the hierarchy to be "true" (extensions, etc.)
- Andrew: ExperimenterType disappeared
- Curtis: great. solved that weirdness
- Curtis: test is not complete, but notes on everything
- Chris: No set Node
- Curtis: use Child(Parent) ctor
- Curtis: Should make sure "all the nodes that reference me" still works in 2007
- metadata versioning
- not so much about SVN
- repeated
- image in db
- check it out (and metadata)
- edit it
- commit back (but not delete)
- copies and deletes
- client needs to be smart
- doesn't undo globally
- want to be able to ignore others people
- tricky part is the merge
- shouldn't be too hard to add a "branch" tag to the metadata
- discuss at the next face-to-face
- Curtis will start a list of use cases
- OME-TIFF
- once the mapping work (see above) is done, things should move forward
- Curtis: cool long term solution, but the short term solution?
- Using loop back in bio-formats. Why not use that?
- Chris: matter of prioritization, how much time for what? (papers/doing it correctly)
- Curtis: quick way should only be few lines of code. Then we support OME-XML.
- Andrew: Anything to be done on XML to help this along?
- Andrew: Generating validly-wrong files!
- Curtis: keeps Andrew posted on dev. of sample data generator
- the utility for generating OME-TIFFs: https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/utils/MakeTestOmeTiff.java
- Chris: An authoritative list would be nice (for OMERO, validator, .... )
- Consistent ERROR numbers across all applications
- only have to write help for the error list once
- Andrew will start that list up on ome-xml.org trac
- Multiple file name-law
- stitching logic...
- Scan all in the same folder, and check for ids in the files?
- Something in the XML to describe the other files?
- Doesn't solve renames; changes the schema (optional)
- .ome.tiff as proper extension?
- Add to all sample datasets for parser-writers
- Official proposal (for next non-breaking release): Add optional "Path" attribute to TiffData with pointers to all other files
- Andrew: next one is breaking
- Could also allow for sub-folders
- Allow absolute paths?
- What about the later files? ... Already dealing with XML-block generation built over file and inserted at the end.
- What time for slashes? Forward-slash, good in Java. Need to qualify. Are c:\ allowed?
- prototyping node types for new version of XML
- Andrew
- Other than the above, have only added fixing PixelsType to todo list