[ome-devel] API call can crash server 5.1.4

[Aleksandra Tarkowska (Staff)]

I forgot to mention, if regular select is too slow, you can either use limit and offset or IQuery projection. Query will look like:

“””
select new map(img.id as id,
               img.name as name,
               pix.sizeX as sizeX,
               orf.path as path
            )
from Image img
         left outer join img.pixels pix
         left outer join img.fileset as fs
         left outer join fs.usedFiles as uf
         left outer join uf.originalFile orf
where img.details.owner.id = :id and
         not exists (
             select obl from DatasetImageLink as obl
             where obl.child=img.id)
         and not exists (
             select ws from WellSample as ws where ws.image=img.id )
        order by lower(img.name), img.id
"""

Ola
Software Engineer
Open Microscopy Environment
University of Dundee

On 12 Feb 2016, at 22:07, Aleksandra Tarkowska (Staff) <A.Tarkowska at dundee.ac.uk<mailto:A.Tarkowska at dundee.ac.uk>> wrote:

Hi Damir

Thanks for reporting having an issue with query.

Inorder to load orphaned images your query should be:

sql = """select img from Image img
    join fetch img.fileset as fs
    join fetch fs.usedFiles as uf
    join fetch uf.originalFile as of
    join fetch img.pixels as pxl
    join fetch pxl.pixelsType as pxt
    where
        not exists (
            select obl from DatasetImageLink as obl
            where obl.child=img.id)
        and not exists (
            select ws from WellSample as ws where ws.image=img.id )
    order by lower(img.name), img.id
“""

You have to check if DatasetImageLink exist rather then dataset id is null
Please remember that image can be in Plate.

Let us know if that works better

Ola
Software Engineer
Open Microscopy Environment
University of Dundee

On 12 Feb 2016, at 19:56, Damir Sudar <dsudar at lbl.gov<mailto:dsudar at lbl.gov>> wrote:

Hi all,

We're using the API to query the OMERO server (currently running 5.1.4) and have run into a situation where this can crash the server or at least get the server into a state where it becomes unresponsive. A hopefully useful chunk from the OMEROweb.log is enclosed. I did not see anything in the other logs that appeared related to the activity that caused the crash or the crash itself. An excerpt of the code that causes the crash is here:

const std::string orphanedImagesQueryString =
    "select img from Image as img "
    "left outer join fetch img.datasetLinks as idl "
    "left outer join fetch idl.parent as dst "
    "left outer join fetch img.fileset as fs "
    "join fetch fs.usedFiles as uf "
    "join fetch uf.originalFile as of "
    "join fetch img.pixels as pxl "
    "join fetch pxl.pixelsType as pxt ";
//  "where dst.id<http://dst.id/> is null";

omero::sys::ParametersIPtr dsParams = new omero::sys::ParametersI();
dsParams->addLong("id", omero::rtypes::rlong(803));
auto imageObjects = query->findAllByQuery(orphanedImagesQueryString, dsParams);
for (auto image : omero::cast<omero::model::ImagePtr>(imageObjects)) {
    std::cout << "i: "  << image->getId()->getValue() << " " << image->getName()->getValue() << "\n";
}

I'm not sure, but as I understand, the crash occured when I commented "where dst.id<http://dst.id/> is null" condition. The query with "where dst.id<http://dst.id/> is null" didn't return result and I tried to remove the  "is null" condition - to see what would happen. And the server crashed.

It appears that the server crashed when we tried to query images without parent dataset ("orphaned images”). I.e. something related to handling a situation where a parent pointer is NULL.

- Damir

--
Damir Sudar - Staff Scientist
Lawrence Berkeley National Laboratory
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov<mailto:DSudar at lbl.gov>

Visiting Scientist, Oregon Health and Science University
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