[biomart-users] Error when searching across tables v0.9

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[biomart-users] Error when searching across tables v0.9

Jayson Harshbarger
Hello Arek/Others,

I've been trying to migrate to Biomart v0.9 from v0.7, but I am having trouble with some types of searches.  I am uncertain if this is an issue with my setup or a bug.  In my DB I have two tables joined by a common field (one to one).  Nearly the same setup as v0.7.  I can filter and browse the results fine except for instances where the filter is on a field in one table, but the requested attributes are on the other.

For example, the attached image shows a query that is failing.  "Cage peaks" and "Annotation" are two separate tables joined by a `name_key`. If I don't try to filter on any "Annotation" field the query returns results.  If I include any "Annotation" attribute in the query I get results.  However, if I filter on an "Annotation" field but don't include an "Annotation" attribute BioMart shows "Error has occurred".  For some reason the reverse, filter on the "CAGE Peak" field but don't include a "CAGE Peak" attribute, works fine.

The SQL log shows the following query is being run when the error occurs.

SELECT f5_phase2_hg19.hg19_phase2_peaks__robust__main.name_key, f5_phase2_hg19.hg19_phase2_peaks__robust__main.name_key FROM f5_phase2_hg19.hg19_phase2_peaks__robust__main WHERE (hg19_phase2_peaks__robust__main.

The query appears incomplete.

Any hints?  One option could be to "materialize" these tables into one in the DB...  a step I would like to avoid if possible.

Thank you,

Jayson Harshbarger

Genome Information Analysis Team

RIKEN Center for Life Science Technologies

Yokohama, JAPAN









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Re: [biomart-users] Error when searching across tables v0.9

Arek Kasprzyk
Hi Jason,

The 'difficulty' that you are describing i.e filtering on one table and getting attributes from another should not be an issue. It is difficult for me to advise you any more on this without looking at your database schema.
One thing however that jumps at me looking at your incomplete query is that you are asking for the same attribute twice?

Anyway, i am happy to have a closer look if you send me the your schema dump


a.









On 16 September 2015 at 06:37, Jayson Harshbarger <[hidden email]> wrote:
Hello Arek/Others,

I've been trying to migrate to Biomart v0.9 from v0.7, but I am having trouble with some types of searches.  I am uncertain if this is an issue with my setup or a bug.  In my DB I have two tables joined by a common field (one to one).  Nearly the same setup as v0.7.  I can filter and browse the results fine except for instances where the filter is on a field in one table, but the requested attributes are on the other.

For example, the attached image shows a query that is failing.  "Cage peaks" and "Annotation" are two separate tables joined by a `name_key`. If I don't try to filter on any "Annotation" field the query returns results.  If I include any "Annotation" attribute in the query I get results.  However, if I filter on an "Annotation" field but don't include an "Annotation" attribute BioMart shows "Error has occurred".  For some reason the reverse, filter on the "CAGE Peak" field but don't include a "CAGE Peak" attribute, works fine.

The SQL log shows the following query is being run when the error occurs.

SELECT f5_phase2_hg19.hg19_phase2_peaks__robust__main.name_key, f5_phase2_hg19.hg19_phase2_peaks__robust__main.name_key FROM f5_phase2_hg19.hg19_phase2_peaks__robust__main WHERE (hg19_phase2_peaks__robust__main.

The query appears incomplete.

Any hints?  One option could be to "materialize" these tables into one in the DB...  a step I would like to avoid if possible.

Thank you,

Jayson Harshbarger

Genome Information Analysis Team

RIKEN Center for Life Science Technologies

Yokohama, JAPAN









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