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Fix unicycler datatype comparisons (galaxyproject#6131)
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Fixes
https://sentry.galaxyproject.org/share/issue/f5ec29350256422da159e25b0875b7ee/
when users attempt to run jobs with unexpected fastq datatypes like
fastqcssanger.gz, which is alloed because basic fastq/fastq.gz are
allowd (this is a mistake IMO ...):
```
NotFound: cannot find 'lr'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
NotFound: cannot find 'lr'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
NotFound: cannot find 'lr'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
NotFound: cannot find 'lr'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
NotFound: cannot find 'lr'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
NotFound: cannot find 'lr'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
NotFound: cannot find 'lr'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
NotFound: cannot find 'lr'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
NotFound: cannot find 'lr'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
NotFound: cannot find 'lr'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
NotFound: cannot find 'lr'
  File "galaxy/jobs/runners/__init__.py", line 297, in prepare_job
    job_wrapper.prepare()
  File "galaxy/jobs/__init__.py", line 1260, in prepare
    ) = tool_evaluator.build()
  File "galaxy/tools/evaluation.py", line 588, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "galaxy/tools/evaluation.py", line 98, in global_tool_logs
    raise e
  File "galaxy/tools/evaluation.py", line 94, in global_tool_logs
    return func()
  File "galaxy/tools/evaluation.py", line 611, in _build_command_line
    command_line = fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 123, in fill_template
    raise first_exception or e
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py", line 172, in respond
```
This is hopefully an uncontroversial fix.
  • Loading branch information
@mvdbeek
mvdbeek authored Jul 7, 2024
1 parent df9c285 commit bc94851
Showing 1 changed file with 19 additions and 21 deletions.
40 changes: 19 additions & 21 deletions tools/unicycler/unicycler.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<description>pipeline for bacterial genomes</description>
<macros>
<token name="@TOOL_VERSION@">0.5.0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
</macros>
<edam_topics>
<edam_topic>topic_0196</edam_topic>
Expand All @@ -23,48 +23,46 @@
#end for
## Preparing files
#set $uncompressed = ('fastqsanger','fastq')
#set $compressed = ('fastqsanger.gz','fastq.gz')
#if str( $paired_unpaired.fastq_input_selector ) == "paired"
#if $paired_unpaired.fastq_input1.file_ext in $uncompressed
#set fq1 = "fq1.fastq"
#elif $paired_unpaired.fastq_input1.file_ext in $compressed
#if $paired_unpaired.fastq_input1.is_of_type("fastq.gz"):
#set fq1 = "fq1.fastq.gz"
#else
#set fq1 = "fq1.fastq"
#end if
#if $paired_unpaired.fastq_input2.file_ext in $uncompressed
#set fq2 = "fq2.fastq"
#elif $paired_unpaired.fastq_input2.file_ext in $compressed
#if $paired_unpaired.fastq_input2.is_of_type("fastq.gz"):
#set fq2 = "fq2.fastq.gz"
#else
#set fq2 = "fq2.fastq"
#end if
ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
ln -s '${paired_unpaired.fastq_input2}' $fq2 &&
#elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
#if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed
#set fq1 = "fq1.fastq"
#elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed
#if $paired_unpaired.fastq_input1.forward.is_of_type("fastq.gz"):
#set fq1 = "fq1.fastq.gz"
#else
#set fq1 = "fq1.fastq"
#end if
#if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed
#set fq2 = "fq2.fastq"
#elif $paired_unpaired.fastq_input1.reverse.file_ext in $compressed
#if $paired_unpaired.fastq_input1.reverse.is_of_type("fastq.gz"):
#set fq2 = "fq2.fastq.gz"
#else
#set fq2 = "fq2.fastq"
#end if
ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 &&
#elif str( $paired_unpaired.fastq_input_selector ) == "single"
#if $paired_unpaired.fastq_input1.file_ext in $uncompressed
#set fq = "fq.fastq"
#elif $paired_unpaired.fastq_input1.file_ext in $compressed
#if $paired_unpaired.fastq_input1.is_of_type("fastqsanger.gz"):
#set fq = "fq.fastq.gz"
#else
#set fq = "fq.fastq"
#end if
ln -s '${paired_unpaired.fastq_input1}' '$fq' &&
#end if
#if $long
#if $long.file_ext in $uncompressed
#if $long.is_of_type("fastq"):
#set lr = "lr.fastq"
#elif $long.file_ext in $compressed
#elif $long.is_of_type("fastq.gz"):
#set lr = "lr.fastq.gz"
#elif $long.is_of_type('fasta')
#elif $long.is_of_type("fasta")
#set lr = "lr.fasta"
#end if
ln -s '${long}' '$lr' &&
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