Optional multiple file selectors,

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

Optional multiple file selectors,

Peter Cock
Hi John,

As you noticed (and posted on Twitter), I've just tweaked the NCBI
makeblastdb wrapper on GitHub to use a multiple file picker instead
of a repeat:

https://github.com/peterjc/galaxy_blast/commit/858bf541a828644ea6461b20b687c214b564d3b0

That seems to be working fine in human testing (although not on
the functional side).

I've also just tried this for the masking files - but ran into a problem.
Here the masks are optional, and I want the default to be no mask:

https://github.com/peterjc/galaxy_blast/commit/e1bcb24ac24613395a0fe327c54cd3eab343feb7

This works fine from the user interface perspective:

<param name="input_file" type="data" multiple="true" optional="false"
format="fasta" label="Input FASTA files(s)" help="One or more FASTA
files" />

This requires at least one file, although a confusing red error
message is given if none is selected:

"History does not include a dataset of the required format / build"

<param name="mask_data_file" type="data" multiple="true"
optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary"
label="Optional ASN.1 file(s) containing masking data" help="As
produced by NCBI masking applications (e.g. dustmasker, segmasker,
windowmasker)" />

This does not require a file, and defaults to selecting a new dummy
entry "Selection is Optional". This is presumably intended as a visual
cue - but it means you can do weird things like picking a read file
and the dummy entry, or no entries. Neither allows me to proceed,
instead on pressing execute I get a red error on a new page:

Error executing tool: 'NoneType' object has no attribute 'file_name'

galaxy.tools ERROR 2014-02-25 14:02:47,844 Exception caught while
attempting tool execution:
Traceback (most recent call last):
  File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line
1916, in __handle_tool_execute
    _, out_data = self.execute( trans, incoming=params,
history=history, rerun_remap_job_id=rerun_remap_job_id )
  File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line
2424, in execute
    return self.tool_action.execute( self, trans, incoming=incoming,
set_output_hid=set_output_hid, history=history, **kwargs )
  File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/actions/__init__.py",
line 287, in execute
    data.name = self.get_output_name( output, data, tool, on_text,
trans, incoming, history, wrapped_params.params, job_params )
  File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py",
line 26, in params
    self.wrap_values( self.tool.inputs, params,
skip_missing_values=not self.tool.check_values )
  File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py",
line 51, in wrap_values
    name=input.name )
  File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line
215, in __init__
    list.__init__( self, map( to_wrapper, datasets ) )
  File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line
209, in to_wrapper
    real_path = dataset.file_name
AttributeError: 'NoneType' object has no attribute 'file_name'

Any thoughts? Is zero files a little tested corner of the multiple file support?

If I have a suitable masking file in my history, and I select it,
the tool runs fine.

Thanks,

Peter
___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: Optional multiple file selectors,

John Chilton-4
Hey Peter,

Answers inline.

On Tue, Feb 25, 2014 at 8:08 AM, Peter Cock <[hidden email]> wrote:

> Hi John,
>
> As you noticed (and posted on Twitter), I've just tweaked the NCBI
> makeblastdb wrapper on GitHub to use a multiple file picker instead
> of a repeat:
>
> https://github.com/peterjc/galaxy_blast/commit/858bf541a828644ea6461b20b687c214b564d3b0
>
> That seems to be working fine in human testing (although not on
> the functional side).

Functional test support for these was added with the latest release
but only for API driven tests. Can you try adding interactor="api" to
your test cases?

https://bitbucket.org/galaxy/galaxy-central/commits/211f30207d48101a1250983d4f0f55c937f00a2e

>
> I've also just tried this for the masking files - but ran into a problem.
> Here the masks are optional, and I want the default to be no mask:
>
> https://github.com/peterjc/galaxy_blast/commit/e1bcb24ac24613395a0fe327c54cd3eab343feb7
>
> This works fine from the user interface perspective:
>
> <param name="input_file" type="data" multiple="true" optional="false"
> format="fasta" label="Input FASTA files(s)" help="One or more FASTA
> files" />
>
> This requires at least one file, although a confusing red error
> message is given if none is selected:
>
> "History does not include a dataset of the required format / build"
>
> <param name="mask_data_file" type="data" multiple="true"
> optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary"
> label="Optional ASN.1 file(s) containing masking data" help="As
> produced by NCBI masking applications (e.g. dustmasker, segmasker,
> windowmasker)" />
>
> This does not require a file, and defaults to selecting a new dummy
> entry "Selection is Optional". This is presumably intended as a visual
> cue - but it means you can do weird things like picking a read file
> and the dummy entry, or no entries. Neither allows me to proceed,
> instead on pressing execute I get a red error on a new page:
>
> Error executing tool: 'NoneType' object has no attribute 'file_name'
>
> galaxy.tools ERROR 2014-02-25 14:02:47,844 Exception caught while
> attempting tool execution:
> Traceback (most recent call last):
>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line
> 1916, in __handle_tool_execute
>     _, out_data = self.execute( trans, incoming=params,
> history=history, rerun_remap_job_id=rerun_remap_job_id )
>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line
> 2424, in execute
>     return self.tool_action.execute( self, trans, incoming=incoming,
> set_output_hid=set_output_hid, history=history, **kwargs )
>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/actions/__init__.py",
> line 287, in execute
>     data.name = self.get_output_name( output, data, tool, on_text,
> trans, incoming, history, wrapped_params.params, job_params )
>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py",
> line 26, in params
>     self.wrap_values( self.tool.inputs, params,
> skip_missing_values=not self.tool.check_values )
>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py",
> line 51, in wrap_values
>     name=input.name )
>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line
> 215, in __init__
>     list.__init__( self, map( to_wrapper, datasets ) )
>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line
> 209, in to_wrapper
>     real_path = dataset.file_name
> AttributeError: 'NoneType' object has no attribute 'file_name'
>
> Any thoughts? Is zero files a little tested corner of the multiple file support?

Yes it is a corner case I personally had not tested. Are you are
running something later than the latest dist but not the latest
central? It seems like yes. Because I believe Dan has fixed the bug
that produces the particular stack trace you are seeing last week - he
has probably fixed the other problems you mentioned also? Can you
upgrade and let me know, if not let me know and I can take a look a
closer look.

>
> If I have a suitable masking file in my history, and I select it,
> the tool runs fine.
>
> Thanks,
>
> Peter
___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: Optional multiple file selectors,

Peter Cock
On Tue, Feb 25, 2014 at 2:29 PM, John Chilton <[hidden email]> wrote:

> Hey Peter,
>
> Answers inline.
>
> On Tue, Feb 25, 2014 at 8:08 AM, Peter Cock <[hidden email]> wrote:
>> Hi John,
>>
>> As you noticed (and posted on Twitter), I've just tweaked the NCBI
>> makeblastdb wrapper on GitHub to use a multiple file picker instead
>> of a repeat:
>>
>> https://github.com/peterjc/galaxy_blast/commit/858bf541a828644ea6461b20b687c214b564d3b0
>>
>> That seems to be working fine in human testing (although not on
>> the functional side).
>
> Functional test support for these was added with the latest release
> but only for API driven tests. Can you try adding interactor="api" to
> your test cases?
>
> https://bitbucket.org/galaxy/galaxy-central/commits/211f30207d48101a1250983d4f0f55c937f00a2e

Ah - examples without adding the api flag,

e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/19517715
and https://travis-ci.org/peterjc/galaxy_blast/builds/19570673

Problem where attempts to compare text log file (primary file in
the blast database composite datatype) with a fasta file (see
below).

Suspecting this was due to a change in Galaxy, not the wrapper,
I reran a previously successful TravisCI build from 5 days ago:

https://travis-ci.org/peterjc/galaxy_blast/builds/19248312

This worked - so change to the makeblastdb wrapper changes
seem to be the immediate trigger.

Peter


Snippet from failing test,

AssertionError: History item 1 different than expected, difference (using diff):
( /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test-data/four_human_proteins_taxid.fasta.log
v. /tmp/tmpNDhPnX/tmpj7U79F/new_files_path_LGtc1w/tmpdBuU0jfour_human_proteins_taxid.fasta.log
)
--- local_file
+++ history_data
@@ -1,10 +1,61 @@
-
-
-Building a new DB, current time: 02/10/2014 18:40:09
-New DB name:   four_human_proteins_taxid.fasta
-New DB title:  Just 4 human proteins
-Sequence type: Protein
-Keep Linkouts: T
-Keep MBits: T
-Maximum file size: 1000000000B
-Adding sequences from FASTA; added 4 sequences in 0.00230002 seconds.
+>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
OS=Homo sapiens GN=ERP44 PE=1 SV=1
+MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF
+SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK
+REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER
+VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK
+CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD
+CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF
+HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL
+>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
GN=BMP2K PE=1 SV=2
+MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEG
+GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS
+DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD
********
*SNIP *
********
+TVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETL
+EIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE
+RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQ
+NVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFS
+DERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWE
+RQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL
+KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAF
+PNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYV
+SARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCV
+SRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG
+PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSR
+EKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKG
+FTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMA
+AEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV
+RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDN
+CPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEME
+FEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSN
+PS
+>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
+MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
+VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
+GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP
+EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
+ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
+YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA

P.S. The extra space in "*SNIP *" got lost in my emailed patch,
https://bitbucket.org/galaxy/galaxy-central/diff/test/base/twilltestcase.py?diff2=15fc8675064e&at=default
___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: Optional multiple file selectors,

Peter Cock
In reply to this post by John Chilton-4
On Tue, Feb 25, 2014 at 2:29 PM, John Chilton <[hidden email]> wrote:

> On Tue, Feb 25, 2014 at 8:08 AM, Peter Cock <[hidden email]> wrote:
>>
>> I've also just tried this for the masking files - but ran into a problem.
>> Here the masks are optional, and I want the default to be no mask:
>>
>> https://github.com/peterjc/galaxy_blast/commit/e1bcb24ac24613395a0fe327c54cd3eab343feb7
>>
>> This works fine from the user interface perspective:
>>
>> <param name="input_file" type="data" multiple="true" optional="false"
>> format="fasta" label="Input FASTA files(s)" help="One or more FASTA
>> files" />
>>
>> This requires at least one file, although a confusing red error
>> message is given if none is selected:
>>
>> "History does not include a dataset of the required format / build"
>>
>> <param name="mask_data_file" type="data" multiple="true"
>> optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary"
>> label="Optional ASN.1 file(s) containing masking data" help="As
>> produced by NCBI masking applications (e.g. dustmasker, segmasker,
>> windowmasker)" />
>>
>> This does not require a file, and defaults to selecting a new dummy
>> entry "Selection is Optional". This is presumably intended as a visual
>> cue - but it means you can do weird things like picking a read file
>> and the dummy entry, or no entries. Neither allows me to proceed,
>> instead on pressing execute I get a red error on a new page:
>>
>> Error executing tool: 'NoneType' object has no attribute 'file_name'
>>
>> galaxy.tools ERROR 2014-02-25 14:02:47,844 Exception caught while
>> attempting tool execution:
>> Traceback (most recent call last):
>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line
>> 1916, in __handle_tool_execute
>>     _, out_data = self.execute( trans, incoming=params,
>> history=history, rerun_remap_job_id=rerun_remap_job_id )
>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line
>> 2424, in execute
>>     return self.tool_action.execute( self, trans, incoming=incoming,
>> set_output_hid=set_output_hid, history=history, **kwargs )
>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/actions/__init__.py",
>> line 287, in execute
>>     data.name = self.get_output_name( output, data, tool, on_text,
>> trans, incoming, history, wrapped_params.params, job_params )
>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py",
>> line 26, in params
>>     self.wrap_values( self.tool.inputs, params,
>> skip_missing_values=not self.tool.check_values )
>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py",
>> line 51, in wrap_values
>>     name=input.name )
>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line
>> 215, in __init__
>>     list.__init__( self, map( to_wrapper, datasets ) )
>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line
>> 209, in to_wrapper
>>     real_path = dataset.file_name
>> AttributeError: 'NoneType' object has no attribute 'file_name'
>>
>> Any thoughts? Is zero files a little tested corner of the multiple file support?
>
> Yes it is a corner case I personally had not tested. Are you are
> running something later than the latest dist but not the latest
> central? It seems like yes. Because I believe Dan has fixed the bug
> that produces the particular stack trace you are seeing last week - he
> has probably fixed the other problems you mentioned also? Can you
> upgrade and let me know, if not let me know and I can take a look a
> closer look.

This one on TravisCI (which looks like the latest galaxy-central)
fails with:

Fatal error: Matched on Error:
Error: Ignoring mask file 'None' as it does not exist.

https://travis-ci.org/peterjc/galaxy_blast/builds/19577818

Perhaps I can workaround this in the Cheetah template, but
ideally the no-files case would be handled nicely in the framework.

Peter
___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: Optional multiple file selectors,

John Chilton-4
Okay, known issue I guess. No inputs evaluates as a list with just
"None" in it. This is less than ideal and there is an open Trello card
on this (see top item of TODO list) https://trello.com/c/lp5YmA1O.

I think vanilla (non-data) select tools work the same - but maybe not.

-John

On Tue, Feb 25, 2014 at 8:44 AM, Peter Cock <[hidden email]> wrote:

> On Tue, Feb 25, 2014 at 2:29 PM, John Chilton <[hidden email]> wrote:
>> On Tue, Feb 25, 2014 at 8:08 AM, Peter Cock <[hidden email]> wrote:
>>>
>>> I've also just tried this for the masking files - but ran into a problem.
>>> Here the masks are optional, and I want the default to be no mask:
>>>
>>> https://github.com/peterjc/galaxy_blast/commit/e1bcb24ac24613395a0fe327c54cd3eab343feb7
>>>
>>> This works fine from the user interface perspective:
>>>
>>> <param name="input_file" type="data" multiple="true" optional="false"
>>> format="fasta" label="Input FASTA files(s)" help="One or more FASTA
>>> files" />
>>>
>>> This requires at least one file, although a confusing red error
>>> message is given if none is selected:
>>>
>>> "History does not include a dataset of the required format / build"
>>>
>>> <param name="mask_data_file" type="data" multiple="true"
>>> optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary"
>>> label="Optional ASN.1 file(s) containing masking data" help="As
>>> produced by NCBI masking applications (e.g. dustmasker, segmasker,
>>> windowmasker)" />
>>>
>>> This does not require a file, and defaults to selecting a new dummy
>>> entry "Selection is Optional". This is presumably intended as a visual
>>> cue - but it means you can do weird things like picking a read file
>>> and the dummy entry, or no entries. Neither allows me to proceed,
>>> instead on pressing execute I get a red error on a new page:
>>>
>>> Error executing tool: 'NoneType' object has no attribute 'file_name'
>>>
>>> galaxy.tools ERROR 2014-02-25 14:02:47,844 Exception caught while
>>> attempting tool execution:
>>> Traceback (most recent call last):
>>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line
>>> 1916, in __handle_tool_execute
>>>     _, out_data = self.execute( trans, incoming=params,
>>> history=history, rerun_remap_job_id=rerun_remap_job_id )
>>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line
>>> 2424, in execute
>>>     return self.tool_action.execute( self, trans, incoming=incoming,
>>> set_output_hid=set_output_hid, history=history, **kwargs )
>>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/actions/__init__.py",
>>> line 287, in execute
>>>     data.name = self.get_output_name( output, data, tool, on_text,
>>> trans, incoming, history, wrapped_params.params, job_params )
>>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py",
>>> line 26, in params
>>>     self.wrap_values( self.tool.inputs, params,
>>> skip_missing_values=not self.tool.check_values )
>>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py",
>>> line 51, in wrap_values
>>>     name=input.name )
>>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line
>>> 215, in __init__
>>>     list.__init__( self, map( to_wrapper, datasets ) )
>>>   File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line
>>> 209, in to_wrapper
>>>     real_path = dataset.file_name
>>> AttributeError: 'NoneType' object has no attribute 'file_name'
>>>
>>> Any thoughts? Is zero files a little tested corner of the multiple file support?
>>
>> Yes it is a corner case I personally had not tested. Are you are
>> running something later than the latest dist but not the latest
>> central? It seems like yes. Because I believe Dan has fixed the bug
>> that produces the particular stack trace you are seeing last week - he
>> has probably fixed the other problems you mentioned also? Can you
>> upgrade and let me know, if not let me know and I can take a look a
>> closer look.
>
> This one on TravisCI (which looks like the latest galaxy-central)
> fails with:
>
> Fatal error: Matched on Error:
> Error: Ignoring mask file 'None' as it does not exist.
>
> https://travis-ci.org/peterjc/galaxy_blast/builds/19577818
>
> Perhaps I can workaround this in the Cheetah template, but
> ideally the no-files case would be handled nicely in the framework.
>
> Peter
___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: Optional multiple file selectors,

Peter Cock
On Tue, Feb 25, 2014 at 2:50 PM, John Chilton <[hidden email]> wrote:
> Okay, known issue I guess. No inputs evaluates as a list with just
> "None" in it. This is less than ideal and there is an open Trello card
> on this (see top item of TODO list) https://trello.com/c/lp5YmA1O.
>
> I think vanilla (non-data) select tools work the same - but maybe not.
>
> -John

Thanks John - the workaround you suggested looks good,
https://github.com/peterjc/galaxy_blast/commit/2e5c9e2ea08532a530ac4588a1d01e1938f649d1

Tests passed on my local server (now just updated to galaxy-central),
waiting for TravisCI now...

Peter
___________________________________________________________
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/