All genomes from genome group not showing up in Protein Family Sorter

[ARWattam]

Am I cursed? I created a group first with Streptococcus pneumoniae D39 and saved to to my workspace. Then I added Streptococcus pyogenes MGAS315 to the same group. When I check in my workspace, all appears normal: However, when I deploy the protein family sorter , select that group, and put in something simple, like DnaA, this is what returns, showing that there is only one genome in the group

And yes, both genomes have dnaA.

[hyoo]

I cannot reproduce this problem. Rebecca, can you test again? Here is what I did.

1. Go to genome finder http://www.alpha.patricbrc.org/portal/portal/patric/GenomeFinder?cType=taxon&cId=131567&dm=
2. change keyword to genome name (in 2. Enter keyword) and add Streptococcus pneumoniae D39 Streptococcus pyogenes MGAS315 and click search (Yes, this is new functionality I just added!)
3. create a genome group with two genomes found.
4. go to PFS and select the group I created.
5. put dnaA in "Filter by one or more keyword" textarea.
6. click filter

this is what I have

[hyoo]

This is a problem of workspace api. If you create a group with selection, it will work fine. If you create a group and add next item to the existing group, the group content is corrupted.

case 1. two genomes were added when the group is created.

{
    "error": null,
    "id": "1",
    "result": [
        [
            [
                [
                    "pfs test",
                    "genome_group",
                    "/harry@patricbrc.org/home/Genome Groups/",
                    "2015-04-17T19:14:10",
                    "ED584910-E535-11E4-808A-EFF3682E0674",
                    "harry@patricbrc.org",
                    68,
                    {},
                    {
                        "item_count": 2
                    },
                    "o",
                    "n",
                    ""
                ],
                "{\"id_list\":{\"genome_id\":[\"373153.27\",\"198466.3\"]},\"name\":\"pfs test\"}"
            ]
        ]
    ]
}

case 2. second genome added into the existing group

{
    "error": null,
    "id": "1",
    "result": [
        [
            [
                [
                    "pfs test2",
                    "genome_group",
                    "/harry@patricbrc.org/home/Genome Groups/",
                    "2015-04-17T20:33:40",
                    "084C1FAC-E541-11E4-8234-4BF5682E0674",
                    "harry@patricbrc.org",
                    86,
                    {},
                    {
                        "item_count": 2
                    },
                    "o",
                    "n",
                    ""
                ],
                "{\"id_list\":{\"genome_id\":[\"198466.3\"],\"genome_group\":[\"373153.27\"]},\"name\":\"pfs test2\"}"
            ]
        ]
    ]
}

However, in both cases, workspace UI displays two genomes without any problem.

[hyoo]

The bug related adding items to existing group is fixed. However, you many need to delete the old group and create another to make it work

[mshukla1]

Tested on beta. working as expected.

[rwill1]

what about external users with existing groups?�� Do we have a way
to let them know this information?� Was� it just groups created in a
small interim - or all existing groups or ??� (that is, how bad is
our exposure w/ external users?)

On 4/17/15 6:52 PM, Harry Yoo wrote:

  The bug related adding items to existing group is fixed.
    However, you many need to delete the old group and create
    another to make it work
  �
    Reply to this email directly or view
      it on GitHub.

[dmachi]

It is isolated to when users added to an existing group (regardless of when it was created) from UI components defined on the jboss side of the application.

On Apr 20, 2015, at 3:06 PM, rwill1 wrote:

what about external users with existing groups?�� Do we have a way to let them know this information?� Was� it just groups created in a small interim - or all existing groups or ??� (that is, how bad is our exposure w/ external users?)

On 4/17/15 6:52 PM, Harry Yoo wrote:

The bug related adding items to existing group is fixed. However, you many need to delete the old group and create another to make it work � Reply to this email directly or view it on GitHub. — Reply to this email directly or view it on GitHub.