error when loading fasta

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error when loading fasta

Sofia Robb
Hi,

I am getting this error again when loading a fasta. I am running 7.x-2.0+37-dev. Should I install 7.x-2.1-beta2+22-dev instead? Last time I had this error (quite a while ago), I changed from the stable to the dev version.


WD trp-fasta:                                                                                                                                  [error]
array_keys() expects parameter 1 to be array, string given tripal_core.tripal.api.inc:117                                                      [warning]
[site http://default] [TRIPAL ] [TRP-FASTA] Array
strtr() expects parameter 1 to be string, array given syslog.module:115                                                                        [warning]
syslog() expects parameter 1 to be long, string given syslog.module:118                                                                        [warning]
html_entity_decode() expects parameter 1 to be string, array given unicode.inc:463                                                             [warning]
WD trp-fasta:



Thanks!
Sofia

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Re: error when loading fasta

Stephen Ficklin-2
HI Sofia,

That's an odd message for the FASTA loader as it's coming from the Drupal system logger.   Do you have any other information in the Drupal recent logs?

Stephen

On 3/10/2016 12:03 PM, Sofia Robb wrote:
Hi,

I am getting this error again when loading a fasta. I am running 7.x-2.0+37-dev. Should I install 7.x-2.1-beta2+22-dev instead? Last time I had this error (quite a while ago), I changed from the stable to the dev version.


WD trp-fasta:                                                                                                                                  [error]
array_keys() expects parameter 1 to be array, string given tripal_core.tripal.api.inc:117                                                      [warning]
[site http://default] [TRIPAL ] [TRP-FASTA] Array
strtr() expects parameter 1 to be string, array given syslog.module:115                                                                        [warning]
syslog() expects parameter 1 to be long, string given syslog.module:118                                                                        [warning]
html_entity_decode() expects parameter 1 to be string, array given unicode.inc:463                                                             [warning]
WD trp-fasta:



Thanks!
Sofia


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Re: error when loading fasta

Sofia Robb
Hi Stephen,

I am using a regex to extract the name and id from the fasta header. I was using the '>' in my regex. When I removed this character it loaded just fine. 

Thanks,
Sofia




On Mon, Mar 14, 2016 at 6:18 PM, Stephen Ficklin <[hidden email]> wrote:
HI Sofia,

That's an odd message for the FASTA loader as it's coming from the Drupal system logger.   Do you have any other information in the Drupal recent logs?

Stephen


On 3/10/2016 12:03 PM, Sofia Robb wrote:
Hi,

I am getting this error again when loading a fasta. I am running 7.x-2.0+37-dev. Should I install 7.x-2.1-beta2+22-dev instead? Last time I had this error (quite a while ago), I changed from the stable to the dev version.


WD trp-fasta:                                                                                                                                  [error]
array_keys() expects parameter 1 to be array, string given tripal_core.tripal.api.inc:117                                                      [warning]
[site http://default] [TRIPAL ] [TRP-FASTA] Array
strtr() expects parameter 1 to be string, array given syslog.module:115                                                                        [warning]
syslog() expects parameter 1 to be long, string given syslog.module:118                                                                        [warning]
html_entity_decode() expects parameter 1 to be string, array given unicode.inc:463                                                             [warning]
WD trp-fasta:



Thanks!
Sofia


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Re: error when loading fasta

Stephen Ficklin-2
Hi Sofia,

Thanks for the follow-up. It seems like we have a bit of bug in that if the regex is not appropriate for the string it causes this problem.   It really should provide a more useful message in this case.  I've added an issue to our tracking queue: https://www.drupal.org/node/2691787.  Feel free to follow it if you want updates when we are able to fix it.

I'm glad you were able to fix it.

Stephen

On 3/21/2016 8:38 AM, Sofia Robb wrote:
Hi Stephen,

I am using a regex to extract the name and id from the fasta header. I was using the '>' in my regex. When I removed this character it loaded just fine. 

Thanks,
Sofia




On Mon, Mar 14, 2016 at 6:18 PM, Stephen Ficklin <[hidden email]> wrote:
HI Sofia,

That's an odd message for the FASTA loader as it's coming from the Drupal system logger.   Do you have any other information in the Drupal recent logs?

Stephen


On 3/10/2016 12:03 PM, Sofia Robb wrote:
Hi,

I am getting this error again when loading a fasta. I am running 7.x-2.0+37-dev. Should I install 7.x-2.1-beta2+22-dev instead? Last time I had this error (quite a while ago), I changed from the stable to the dev version.


WD trp-fasta:                                                                                                                                  [error]
array_keys() expects parameter 1 to be array, string given tripal_core.tripal.api.inc:117                                                      [warning]
[site http://default] [TRIPAL ] [TRP-FASTA] Array
strtr() expects parameter 1 to be string, array given syslog.module:115                                                                        [warning]
syslog() expects parameter 1 to be long, string given syslog.module:118                                                                        [warning]
html_entity_decode() expects parameter 1 to be string, array given unicode.inc:463                                                             [warning]
WD trp-fasta:



Thanks!
Sofia


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Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
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