Dear Nate, dear Peter Sorry for the delay in replying.
I can import both HTML and blastdb from a history to a data library. If I try to get the data out of the library into anothre history, I am successful for the html but not for the blastdb. The problem seems to be that the primary data file (the /path/dataset_12345.dat) is empty for the blastdb, while the html primary file has something in it. When I try to import the blastdb (from library to history) there is a message along the lines of "can't import empty file". I hypothesise (admittedly without having looked at a line of code) that there is a test for file size 0 somewhere that is either altogether unnecessary or, more likely, does not take into account that for composite datatypes it might be completely legitimate for the primary file to be empty. Or is my primary blastdb file not supposed to be empty in the first place? I can blast against it just fine. Thanks a lot for your help Ulf On 24/07/14 15:02, Peter Cock wrote: > On Thu, Jul 24, 2014 at 2:50 PM, Nate Coraor <n...@bx.psu.edu> wrote: >> On Jul 23, 2014, at 6:42 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> >>> Interesting hypothesis - you may well be right. >>> >>> Galaxy guys - who is the expert to talk to on this and/or where >>> in the code should we be looking? >>> >>> Thanks, >>> >>> Peter >> >> I think there's a bit of a mixup here - Peter, I believe you were asking >> if other composite types with an html primary dataset could be imported >> from the history to library, but Ulf, your test was the other direction >> (library->history). I'd be interested in knowing the outcome of the >> history->library test as well. > > Good catch - yes, that was what I was asking about. Ulf? > >> I am woefully ignorant about the blastdbn datatype. Is the primary >> file supposed to be html type but empty? > > The BLAST databases are 'basic' composite datatypes, of which > the most commonly used example is HTML (and some bits of > the base class code code seem to assume HTML). This means > testing if something works with HTML is a good first step. > > https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes > > Peter > ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ************************************************************************** ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
