Given the following simple palindrome grammar,
the resulting parser seems to accept any combination
of a's and b's rather than just palindromes.
[well, that was true when I incorrectly specified the start symbol; now I've revised to fix that but still don't get the desired behavior, so I'm adding my exact commands to run as well]
[and revised again, displaying suggested changes and resulting problems.]
// test1.g4
grammar test1;
palindrome
: 'z' entry EOF ;
entry
: 'a' entry 'a'
| 'b' entry 'b'
| 'a'
| 'b'
|
;
WS : [ \t\r\n]+ -> skip ;
Given this exact test1.g, I then execute the following shell script:
#!bash
# script for running ANTLR tests
ANTLR4="java -jar /usr/local/lib/antlr-4.1-complete.jar"
$ANTLR4 test1.g4
echo "grammar compiled"
x=/usr/local/lib/antlr-4.1-complete.jar
javac -classpath $x *.java 2>&1
echo "parser compiled"
#java -cp $x:. org.antlr.v4.runtime.misc.TestRig test1 start -tokens -trace -diagnost
java -cp $x:. org.antlr.v4.runtime.misc.TestRig test1 palindrome -tokens
And then running it on input "aab" gives:
aab
[#0,0:0='a',<2>,1:0]
[#1,1:1='a',<2>,1:1]
[#2,2:2='b',<1>,1:2]
[#3,4:3='<EOF>',<-1>,2:0]
No method for rule palindrome or it has arguments
If I pass aab to it, I get the following output:
line 1:3 no viable alternative at input 'b'
Are you sure you're telling it to start with entry instead of start now? If you start with entry, the generated code literally does not contain a code flow path that will not produce a syntax error for the input aab. You could hide the message by overriding the output listener, piping stdout somewhere you can't see, or terminating the process before parsing completes, but the syntax error will happen otherwise.
Related
I am struggling to find out is there a way to feed input
to the interactive command of gst a.st b.st ... -
and redirect the output. Normally, the interactive buffer will
have st> ... and when you type a command it will output something by calling
the default/override displayString method to the interactive output. How to get the input
and feed the output using linux command or maybe a tiny smalltalk test script to do that.
Thank you.
Here's a contrived demonstration program. It reads in strings from standard input until EOF, sorts them, then prints them out:
input := stdin nextLine.
c := OrderedCollection new.
[ input ~= nil ] whileTrue: [
c add: input.
input := stdin nextLine.
].
c sort do: [ :each | each printNl ]
You can run it interactively (pressed Ctrl-D after entering hhh):
$ gst sortprog.st
tttt
aaa
vvvv
hhh
'aaa'
'hhh'
'tttt'
'vvvv'
Or I can create a text file test.in with the following contents:
tttt
aaa
vvvv
hhh
Then run:
$ gst sortprog.st < test.in > test.out
And then check the contents of the output file:
$ cat test.out
'aaa'
'hhh'
'tttt'
'vvvv'
If your program has prompts, they will appear in the output file, of course. Anything going to stdout will go to that file.
Adding .g.vcf instead of .vcf after the variable in expand rule is somehow adding the .g to a wildcard in another module
I have tried the following in the all rule :
{stuff}.g.vcf
{stuff}"+"g.vcf"
{stuff}_var"+".g.vcf"
{stuff}.t.vcf
all fail but {stuff}.gvcf or {stuff}.vcf work
Error:
InputFunctionException in line 21 of snake_modules/mark_duplicates.snakefile:
KeyError: 'Mother.g'
Wildcards:
lane=Mother.g
Code:
LANES = config["list2"].split()
rule all:
input:
expand(projectDir+"results/alignments/variants/{stuff}.g.vcf", stuff=LANES)
rule mark_duplicates:
""" this will mark duplicates for bam files from the same sample and library """
input:
get_lanes
output:
projectDir+"results/alignments/markdups/{lane}.markdup.bam"
log:
projectDir+"logs/"+stamp+"_{lane}_markdup.log"
shell:
" input=$(echo '{input}' |sed -e s'/ / I=/g') && java -jar /home/apps/pipelines/picard-tools/CURRENT MarkDuplicates I=$input O={projectDir}results/alignments/markdups/{wildcards.lane}.markdup.bam M={projectDir}results/alignments/markdups/{wildcards.lane}.markdup_metrics.txt &> {log}"
I want my final output to have the {stuff}.g.vcf notation. Please note this output is created in another snake module but the error appears in the mark duplicates which is before the other module.
I have tried multiple changes but it is the .g.vcf in the all rule that causes the issue.
My guess is that {lane} is interpreted as a regular expression and it's capturing more than it should. Try adding before rule all:
wildcard_constraints:
stuff= '|'.join([re.escape(x) for x in LANES]),
lane= '|'.join([re.escape(x) for x in LANES])
(See also this thread https://groups.google.com/forum/#!topic/snakemake/wVlJW9X-9EU)
We are currently using sed to filter output of regression runs. Sometimes we have a filter that looks like this:
/copyright/,/end copyright/d
If that end copyright is ever missing, the rest of the file is deleted. I'm wondering if there's some way to generate an error for this? awk would also be okay to use. I don't really want to add code that reads the file line by line and issues an error if it hits EOF.
here's a string
copyright
2016 jan 15
end copyright
date 2016 jan 5 time 15:36
last one
I'd like to get an error if end copyright is missing. The real filter also would replace the date line with DATE, so it's more that just ripping out the copyright.
You can persuade sed to generate an error if you reach end of input (i.e. see address $) between your start and end, but it won't be a very helpful message:
/copyright/,/end copyright/{
$s//\1/ # here
d
}
This will error if end copyright is missing or on the last line, with an exit status of 1 and the helpful message:
sed: -e expression #1, char 0: invalid reference \1 on `s' command's RHS
If you're using this in a makefile, you might want to echo a helpful message first, or (better) to wrap this in something that catches the error and produces a more useful one.
I tested this with GNU sed; though if you are using GNU sed, you could more easily use its useful extension:
q [EXIT-CODE]
This command only accepts a single address.
Exit 'sed' without processing any more commands or input. Note
that the current pattern space is printed if auto-print is not
disabled with the -n options. The ability to return an exit code
from the 'sed' script is a GNU 'sed' extension.
Q [EXIT-CODE]
This command only accepts a single address.
This command is the same as 'q', but will not print the contents of
pattern space. Like 'q', it provides the ability to return an exit
code to the caller.
So you could simply write
/copyright/,/end copyright/{
$Q 42
d
}
Never use range expressions /start/,/end/ as they make trivial code very slightly briefer but require a complete rewrite or duplicate conditions when you have the tiniest requirements change. Always use a flag instead. Note that since sed doesn't support variables, it doesn't support flag variables, and so you shouldn't be using sed you should be using awk instead.
In this case your original code would be:
awk '/copyright/{f=1} !f; /end copyright/{f=0}' file
And your modified code would be:
awk '/copyright/{f=1} !f; /end copyright/{f=0} END{if (f) print "Missing end copyright"}' file
The above is obviously untested since you didn't provide any sample input/output we could test a potential solution against.
With sed you can build a loop:
sed -e '/copyright/{:a;/end copyright/d;N;ba;};' file
:a defines the label "a"
/copyright end/d deletes the pattern space, only when "end copyright" matches
N appends the next line to the pattern space
ba jumps to the label "a"
Note that d ends the loop.
In this way you can avoid to delete the text until the end.
If you don't want the text to be displayed at all and prefer an error message when a "copyright" block stays unclosed, you obviously need to wait the end of the file. You can do it with sed too storing all the lines in the buffer space until the end:
sed -n -e '/copyright/{:a;/end copyright/d;${c\ERROR MESSAGE
;};N;ba;};H;${g;p};' file
H appends the current line to the buffer space
g put the content of the buffer space to the pattern space
The file content is only displayed once the last line reached with ${g;p} otherwise when the closing "end copyright" is missing, the current line is changed in the error message with ${c\ERROR MESSAGE\n;} inside the loop.
This way you can test what returns sed before redirecting it to whatever you want.
I want to save the output of a program to a variable.
I use the following approach ,but fail.
$ PIPE RUN TEST | DEFINE/JOB VALUE #SYS$PIPE
$ x = f$logical("VALUE")
I got an error:%DCL-W-MAXPARM, too many parameters - reenter command with fewer parameters
\WORLD\
reference :
How to assign the output of a program to a variable in a DCL com script on VMS?
The usual way to do this is to write the output to a file and read from the file and put that into a DCL symbol (or logical). Although not obvious, you can do this with the PIPE command was well:
$ pipe r 2words
hello world
$ pipe r 2words |(read sys$pipe line ; line=""""+line+"""" ; def/job value &line )
$ sh log value
"VALUE" = "hello world" (LNM$JOB_85AB4440)
$
IF you are able to change the program, add some code to it to write the required values into symbols or logicals (see LIB$ routines)
If you can modify the program, using LIB$SET_SYMBOL in the program defines a DCL symbol (what you are calling a variable) for DCL. That's the cleanest way to do this. If it really needs to be a logical, then there are system calls that define logicals.
Im having an issue writing a DCL in OpenVMS in that I need the DCL to call a command and capture its output (but not output the output to the screen) Later on in the DCL I then need to print that output I stored.
Heres an example:
ICE SET FASTER !This command sets my environment to the "Faster" environment.
The above command outputs this if executed directly in OpenVMS:
Initialising TEST Environment to FASTER
--------------------------------------------------------------------------------
Using Test Search rules FASTER
Using Test Search rules FASTER
--------------------------------------------------------------------------------
dcl>
So I created a DCL in an attempt to wrap this output in order to display a more simplified output. Heres my code so far:
!************************************************************************
$ !* Wrapper for setting ICE account. Outputs Environment
$ !************************************************************************
$ on error then goto ABORT_PROCESS
$ICE_DCL_MAIN:
$ ice set 'P1'
$ ICE SHOW
$ EXIT
$ABORT_PROCESS:
$ say "Error ICING to: " + P1
$ EXIT 2
[End of file]
In the lines above ICE SET 'P1' is setting the ice environment, but I dont want this output to be echoed to VMS. But what I do want is to write the output of $ICE SHOW into a variable and then echo that out later on in the DCL (most of which ive omitted for simplification purposes)
So what should be outputted should be:
current Test Environment is DISK$DEVELOPERS:[FASTER.DEVELOP]
Instead of:
Initialising TEST Environment to FASTER
--------------------------------------------------------------------------------
Using Test Search rules FASTER
Using Test Search rules FASTER
--------------------------------------------------------------------------------
current Test Environment is DISK$DEVELOPERS:[FASTER.DEVELOP]
Ive had a look through the manual and im getting a bit confused so I figured I tried here. Id appreciate any pointers. Thanks.
EDIT
Here is what ive come up with after the comments, the problem im having is when I connect to VMS using an emulator such as SecureCRT the correct output is echoed. But when I run the DCL via my SSH2 library in .NET it doesnt output anything. I guess thats because it closes the SYS$OUTPUT stream temporarily or something?
$ !************************************************************************
$ !* Wrapper for setting ICE account. Outputs Environment
$ !************************************************************************
$ on error then goto ABORT_PROCESS
$ICE_DCL_MAIN:
$ DEFINE SYS$OUTPUT NL:
$ ice set 'P1'
$ DEASSIGN SYS$OUTPUT
$ ice show
$ EXIT
$ABORT_PROCESS:
$ say "Error ICING to: " + P1
$ EXIT 2
[End of file]
EDIT 2
So I guess really I need to clarify what im trying to do here. Blocking the output doesnt so matter so much, im merely trying to capture it into a Symbol for example.
So in C# for example you can have a method that returns a string. So you'd have string myResult = vms.ICETo("FASTER"); and it would return that and store it in the variable.
I guess im looking for a similar thing in VMS so that once ive iced to the environment I can call:
$ environment == $ICE SHOW
But I of course get errors with that statement
The command $ assign/user_mode Thing Sys$Output will cause output to be redirected to Thing until you $ deassign/user_mode Sys$Output or next executable image exits. An assignment without the /USER_MODE qualifier will persist until deassigned.
Thing can be a logical name, a file specification (LOG.TXT) or the null device (NLA0:) if you simply want to flush the output.
When a command procedure is executed the output can be redirected using an /OUTPUT qualifier, e.g. $ #FOO/output=LOG.TXT.
And then there is piping ... .
You can redirect the output to a temp file and then print its content later:
$ pipe write sys$output "hi" > tmp.tmp
$ ty tmp.tmp
VMS is not Unix, DCL is not Bash: you can not easily set a DCL symbol from the output of a command.
Your ICE SHOW prints one line, correct? The first word is always "current", correct?
So you can create a hack.
First let me fake your ICE command:
$ create ice.com
$ write sys$output "current Test Environment is DISK$DEVELOPERS:[FASTER.DEVELOP]"
^Z
$
and I define a dcl$path pointing to the directory where this command procedure is
so that I can use/fake the command ICE
$ define dcl$path sys$disk[]
$ ice show
current Test Environment is DISK$DEVELOPERS:[FASTER.DEVELOP]
$
Now what you need, create a command procedure which sets a job logical
$ cre deflog.com
$ def/job/nolog mylog "current''p1'"
^Z
$
And I define a command "current" to run that command procedure:
$ current="#deflog """
Yes, you need three of the double quotes at the end of the line!
And finally:
$ pipe (ice show | #sys$pipe) && mysym="''f$log("mylog")'"
$ sh symb mysym
MYSYM = "current Test Environment is DISK$DEVELOPERS:[FASTER.DEVELOP]"
$
On the other hand, I don't know what you are referring to C# and Java. Can you elaborate on that and tell us what runs where?
You can try using: DEFINE /USER SYS$OUTPUT NL:.
It works only for the next command and you dont need to deassign.
Sharing some of my experience here. I used below methods to redirect outputs to files.
Define/Assign the user output and then execute the required command/script afterwards. Output will be written to .
$define /user sys$output <file_path>
execute your command/script
OR
assign /user <file_path> sys$output
execute your command/script
deassign sys$output
To re-direct in to null device like in Unix (mentioned in above answers), you can use 'nl:' instead of
define /user sys$output nl:
or
assign /user nl: sys$output