[GeneX-dev] Curation tool bug report

[Ron O. <Ls...@wi...>]

Dear Greg D. Colello,

I am sending a bug report for the xml file as it is generated by the =
curation tool. The report is based on the minimum input request as it =
appears by the high-lighted fields. In other words, speaking I followed =
the yellow guide using the tes data provided by GeneX.
 Here is my entry path:
New Experiment set:
            Experiment set data file
            Required:=20
Array layout
Sequence feature
Array measurement
One2Many:             File information Edit
                        Required:
                                    GeneX use
                                    File name
Files default species
            Edit Experiment set
            Required:
                        Name
                        Data supplier
Treatment type
One2Many:            Hybridization and detection
                        Required
                        ArrayLayout
                        Required
                                    Name
One2Many:            ArrayMeasurments
                        Required
                                    Sample
                                    Required:
                                                Sample name
                                                Species
                                                Organism supplier
                                    Channel
                                    Type
Data File ColName
Here are XML file bugs:
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Under <external_file_list> always appears null attribute < external_file/> =
and cause
The following error:
Can't call method "getValue" on an undefined value at ./xml2db.pl line =
1548.
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After fixing this bug I got:
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Background:
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Adding a New arraylayout which required only name which I put the value =
"New".
Causing error message:
7ArrayLayout: SELECT al_pk from ArrayLayout where name =3D 'New' AND   at =
./xml2db.pl line 1650.=20
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Possible solution:
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It seemes that contact_id and technology_type are required as well.
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After fixing this bug I got:
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DBD::Pg::db do failed: ERROR:  ExecAppend: Fail to add null value in not =
null attribute biology_description at ./xml2db.pl line 1603.
7ExperimentSet: INSERT INTO ExperimentSet (release_date, treatment_type, =
submission_date, name, us_fk, is_public, group_can_update, quantity_series_=
type) VALUES ('May 31, 2000', 'developmental_stage_comparison', 'Jul 1, =
2001', 'WisExp', '0', '0', '0', '<not-applicable>')  at ./xml2db.pl line =
1603.
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Possible solution:
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<experiment_set
        id=3D"CTXML:207" owner_contact_id=3D"CTXML:69" name=3D"WisExp"
        is_public=3D"0" group_can_update=3D"0"
        treatment_type=3D"developmental_stage_comparison"
        quantity_series_type=3D"&lt;not-applicable&gt;"
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adding this line in the xml file:
        biology_description=3D"biological experiment"
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        release_date=3D"May 31, 2000"
        submission_date=3D"Jul 1, 2001">
After fixing this bug I got:
DBD::Pg::db do failed: ERROR:  ExecAppend: Fail to add null value in not =
null attribute submission_date at ./xml2db.pl line 1603.
7ArrayMeasurement: INSERT INTO ArrayMeasurement (release_date, description,=
 file_name, name, group_can_update, is_public, experiment_date, type, =
primary_es_fk, column_name, spot_measurement_units, hybridization_name, =
al_fk, channel_name, smp_fk) VALUES ('May 31, 2000', 'hjhkjhlkjh', =
'E:\Downloads\Curation Tools\ct101_usrwin\data\testdata\arraymeas.txt', =
'IH100_Rep1_Filter_1_Exp_1', '0', '0', 'May 30, 2000', 'background', '36', =
'IH100 Rep1 Filter 1 Exp 1', '<not-applicable>', 'H&DWis', '19', 'cy3', =
'50')  at ./xml2db.pl line 1603.        =20
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In the "Hybridization & Detection" screen there was no place to put =
submission date which was then not added to the ArrayMeasurement at the =
XML file. Therefore I added this:
<array_measurement
                    id=3D"CTXML:208" type=3D"background"
this line was added:
       submission_date=3D"Jul 1, 2001"
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                    name=3D"IH100_Rep1_Filter_1_Exp_1"
                    sample_id=3D"CTXML:201" channel_id=3D"CTXML:209"
                    file_name=3D"E:\Downloads\Curation Tools\ct101_usrwin\d=
ata\testdata\arraymeas.txt"
                        column_name=3D"IH100 Rep1 Filter 1 Exp 1" >
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And then I got the following message:
Your data has been successfully entered into the database.
I hope you'll find it usefull, Greg=20
and thanks for the help,
Ron
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