How to expand wildcard inside shell code block in a Makefile? - shell

I got this script which reads a delimited part of my .gitignore file and remove all files after the given mark # #:
# https://stackoverflow.com/questions/55527923/how-to-stop-makefile-from-expanding-my-shell-output
RAW_GITIGNORE_CONTENTS := $(shell while read -r line; do printf "$$line "; done < ".gitignore")
GITIGNORE_CONTENTS := $(shell echo "$(RAW_GITIGNORE_CONTENTS)" | sed -E $$'s/[^\#]+\# //g')
# https://stackoverflow.com/questions/4210042/exclude-directory-from-find-command
DIRECTORIES_TO_CLEAN := $(shell /bin/find -not -path "./**.git**" -not -path "./pictures**" -type d)
clean:
# https://stackoverflow.com/questions/10586153/split-string-into-an-array-in-bash
# https://stackoverflow.com/questions/11289551/argument-list-too-long-error-for-rm-cp-mv-commands
readarray -td' ' GARBAGE_DIRECTORIES <<<"$(DIRECTORIES_TO_CLEAN) "; \
unset 'GARBAGE_DIRECTORIES[-1]'; \
declare -p GARBAGE_DIRECTORIES; \
readarray -td' ' GARBAGE_EXTENSIONS <<<"$(GITIGNORE_CONTENTS) "; \
unset 'GARBAGE_EXTENSIONS[-1]'; \
declare -p GARBAGE_EXTENSIONS; \
for filename in "$${GARBAGE_DIRECTORIES[#]}"; \
do \
arraylength="$${#GARBAGE_EXTENSIONS[#]}"; \
printf 'Cleaning %s extensions on %s\n' "$${arraylength}" "$$filename"; \
for extension in "$${GARBAGE_EXTENSIONS[#]}"; \
do \
[[ ! -z "$$filename" ]] || continue; \
[[ ! -z "$$extension" ]] || continue; \
full_expression="$${filename}/$${extension}" ;\
printf '%s\n' "$$full_expression"; \
rm -v "$$full_expression"; \
done; \
done;
Running it with the following .gitignore file:
*.txt
*.var
# Comment #
*.aux
The rm command is not expanding the wildcards and keeps telling me rm: cannot remove './*.aux': No such file or directory and do not remove the *.aux files from the ./ directory.
Update
After asked on a comment by #Beta, I simplified the Makefile to this:
GITIGNORE_CONTENTS := "*.aux" "*.lof"
DIRECTORIES_TO_CLEAN := "./setup/cache" "./setup/cache/chapters"
clean:
readarray -td' ' GARBAGE_DIRECTORIES <<<"$(DIRECTORIES_TO_CLEAN) "; \
unset 'GARBAGE_DIRECTORIES[-1]'; \
declare -p GARBAGE_DIRECTORIES; \
readarray -td' ' GARBAGE_EXTENSIONS <<<"$(GITIGNORE_CONTENTS) "; \
unset 'GARBAGE_EXTENSIONS[-1]'; \
declare -p GARBAGE_EXTENSIONS; \
for filename in "$${GARBAGE_DIRECTORIES[#]}"; \
do \
arraylength="$${#GARBAGE_EXTENSIONS[#]}"; \
printf 'Cleaning %s extensions on %s\n' "$${arraylength}" "$$filename"; \
for extension in "$${GARBAGE_EXTENSIONS[#]}"; \
do \
[[ ! -z "$$filename" ]] || continue; \
[[ ! -z "$$extension" ]] || continue; \
full_expression="$${filename}/$${extension}" ;\
printf '%s\n' "$$full_expression"; \
rm -vf "$$full_expression"; \
done; \
done;
Which results on this output after running it:
$ make
readarray -td' ' GARBAGE_DIRECTORIES <<<""./setup/cache" "./setup/cache/chapters" "; \
unset 'GARBAGE_DIRECTORIES[-1]'; \
declare -p GARBAGE_DIRECTORIES; \
readarray -td' ' GARBAGE_EXTENSIONS <<<""*.aux" "*.lof" "; \
unset 'GARBAGE_EXTENSIONS[-1]'; \
declare -p GARBAGE_EXTENSIONS; \
for filename in "${GARBAGE_DIRECTORIES[#]}"; \
do \
arraylength="${#GARBAGE_EXTENSIONS[#]}"; \
printf 'Cleaning %s extensions on %s\n' "${arraylength}" "$filename"; \
for extension in "${GARBAGE_EXTENSIONS[#]}"; \
do \
[[ ! -z "$filename" ]] || continue; \
[[ ! -z "$extension" ]] || continue; \
full_expression="${filename}/${extension}" ;\
printf '%s\n' "$full_expression"; \
rm -vf "$full_expression"; \
done; \
done;
declare -a GARBAGE_DIRECTORIES=([0]="./setup/cache" [1]="./setup/cache/chapters")
declare -a GARBAGE_EXTENSIONS=([0]="*.aux" [1]="*.lof")
Cleaning 2 extensions on ./setup/cache
./setup/cache/*.aux
./setup/cache/*.lof
Cleaning 2 extensions on ./setup/cache/chapters
./setup/cache/chapters/*.aux
./setup/cache/chapters/*.lof
More simplification
I reduced to the more simple version it could be:
clean:
rm -v "./setup/cache/*.aux";
Running this, also do not remove the files:
$ make
rm -v "./setup/cache/*.aux";
rm: cannot remove './setup/cache/*.aux': No such file or directory
make: *** [Makefile:3: clean] Error 1
$ ls ./setup/cache/*.aux
./setup/cache/main.aux
On above, after running ls, you can see the file still exists and it is there.

I managed to fix it by changing:
rm -vf "$$full_expression"; \
To:
rm -vf $${full_expression}; \

Related

Makefile cache creating false positive outcome

I have a make target, which i usually need to run twice to get accurate outcome. I.e the 1st run if accurate thenn on the 2nd run, if the variable is changed, it still displays the previous output, which is wrong, is there a way to get rid of cache or clear it in between.
.PHONY:check-tf-lint
check-tf-lint: configure ## TF Linting
$(eval list_of_dir := $(shell cd ${deployment} && ls -ld */ | awk '{print $$NF}'| grep -v 'test_cases'| sed 's|/||g'))
$(shell touch ${quality-metrics}/formatting.txt)
#for i in aws_bot; do \
make set-tf-version -e infra_module_path=$$i; \
terraform fmt -check -list=false ${deployment}/$$i ; \
if [ "$$?" != "0" ]; then \
echo "Need Formatting in $$i" >> ${quality-metrics}/formatting.txt; \
terraform fmt -check ${deployment}/$$i >> ${quality-metrics}/formatting.txt; \
echo "" >> ${quality-metrics}/formatting.txt; \
fi \
done
$(eval TMP := $(shell (cat ${quality-metrics}/formatting.txt | wc -l)))
echo "${TMP}"
#if [ "$(TMP)" = "0" ]; then \
echo "All Good! No Formatting Needed."; \
else \
echo "Kindly Format Below Mentioned code and check in Again"; \
cat ${quality-metrics}/formatting.txt; \
fi
$(shell rm -rf ${quality-metrics}/formatting.txt)
#if [ "$(TMP)" != "0" ]; then \
exit 1; \
fi
Rule of thumb: you should never use eval or shell functions in a make recipe. If you are doing that it's a pretty sure sign that something has gone wrong somewhere.
In your case the reason you see this behavior is that make will expand ALL variables and functions for all lines in a recipe before the first line in the recipe is invoked. So as far as make is concerned your recipe is handled like this:
.PHONY:check-tf-lint
check-tf-lint: configure ## TF Linting
$(eval list_of_dir := $(shell cd ${deployment} && ls -ld */ | awk '{print $$NF}'| grep -v 'test_cases'| sed 's|/||g'))
$(shell touch ${quality-metrics}/formatting.txt)
$(eval TMP := $(shell (cat ${quality-metrics}/formatting.txt | wc -l)))
$(shell rm -rf ${quality-metrics}/formatting.txt)
#for i in aws_bot; do \
make set-tf-version -e infra_module_path=$$i; \
terraform fmt -check -list=false ${deployment}/$$i ; \
if [ "$$?" != "0" ]; then \
echo "Need Formatting in $$i" >> ${quality-metrics}/formatting.txt; \
terraform fmt -check ${deployment}/$$i >> ${quality-metrics}/formatting.txt; \
echo "" >> ${quality-metrics}/formatting.txt; \
fi \
done
echo "${TMP}"
#if [ "$(TMP)" = "0" ]; then \
echo "All Good! No Formatting Needed."; \
else \
echo "Kindly Format Below Mentioned code and check in Again"; \
cat ${quality-metrics}/formatting.txt; \
fi
#if [ "$(TMP)" != "0" ]; then \
exit 1; \
fi
You should always write your recipes using shell facilities and not make facilities. Set shell variables, don't use eval to set make variables, and run shell commands directly (you're in a recipe after all!) rather than using make's shell function.
You may need to put all the lines in a single script (with semicolon / backslash) to allow this to work. Or consider .ONESHELL but that's a much bigger set of changes.
This worked for me !
.PHONY:check-tf-lint
check-tf-lint: ## TF Linting
$(eval list_of_dir := $(shell cd ${deployment} && ls -ld */ | awk '{print $$NF}'| grep -v 'test_cases'| sed 's|/||g'))
#for i in $(list_of_dir); do \
make set-tf-version -e infra_module_path=$$i; \
terraform fmt -check -list=false ${deployment}/$$i ; \
if [ "$$?" != "0" ]; then \
echo "Need Formatting in $$i" >> ${quality-metrics}/formatting.txt; \
terraform fmt -check ${deployment}/$$i >> ${quality-metrics}/formatting.txt; \
echo "" >> ${quality-metrics}/formatting.txt; \
fi \
done
#if [ -e "${quality-metrics}/formatting.txt" ]; then \
export MNC=`cat ${quality-metrics}/formatting.txt | wc -l`; \
if [ "$${MNC}" = "0" ]; then \
echo "All Good! No Formatting Needed."; \
else \
echo ""; \
echo "Kindly Format Below Mentioned code and check in Again"; \
cat ${quality-metrics}/formatting.txt; \
fi; \
rm -rf ${quality-metrics}/formatting.txt; \
if [ "$${MNC}" != "0" ]; then \
exit 1; \
fi \
fi

Interpolate variable in command substitution in Makefile

I am trying to do variable interpolation inside a command substitution in a Makefile.
I have this code:
setup:
mkdir -p data_all ; \
for i in $(shell jq -r 'keys | #tsv' assets.json) ; do \
git_url=$(shell jq -r ".$$i" assets.json) ; \
git clone $$git_url data_all/$$i ; \
done
The code is failing, however, because $$i does not expand in the "shell" line that sets git_url.
How do I interpolate the variable $i in the "shell" line that sets git_url?
You mixed up make functions ($(shell ...)) and true shell constructs. When writing a recipe the simplest is to write it first in plain shell:
mkdir -p data_all ; \
for i in $( jq -r 'keys | #tsv' assets.json ) ; do \
git_url=$( jq -r ".$i" assets.json ) ; \
git clone $git_url data_all/$i ; \
done
And then escaping the unwanted $ expansion by make:
mkdir -p data_all ; \
for i in $$( jq -r 'keys | #tsv' assets.json ) ; do \
git_url=$$( jq -r ".$$i" assets.json ) ; \
git clone $$git_url data_all/$$i ; \
done

Bash - pass argument from array

I am using bash to call tool written in java (gatk) and I need to pass multiple arguments from array as input arguments. I tried it this way, but it seems not working. Could you please help me, how to solve it?
Code:
java $GATK \
-T GenotypeGVCFs \
-R $ref \
-o output.vcf \
for foo in array
do
--variant $foo \
done
What i want to be called:
java $GATK \
-T GenotypeGVCFs \
-R $ref \
-o output.vcf \
for foo in array
do
--variant file1 \
--variant file2 \
--variant file3 ...etc
done
edit: sorry for misunderstandings
array=("file1","file2","file3"...)
Thanks
I assume that what you actually want is that if array contains a b c, to have the command
java $GATK \
-T GenotypeGVCFs \
-R $ref \
-o output.vcf \
--variant a --variant b --variant c
If that is so, you can prepare a second array:
array=("file 1" "file 2" "file 3")
declare -a fullarray
for i in "${array[#]}"
do
fullarray+=( --variant "$i" )
done
And then
java $GATK \
-T GenotypeGVCFs \
-R $ref \
-o output.vcf \
"${fullarray[#]}"
This will also make sure that if any of the names in array contains a space, it will still be passed as a proper parameter and not split into two (assuming that you didn't mess it up when you added it to the array).
With echo and $():
array=(file1 file2 file3)
java $GATK \
-T GenotypeGVCFs \
-R $ref \
-o output.vcf \
$(for foo in ${array[*]}
do
echo -n " --variant $foo"
done)
You can do this with the following:
java $GATK \
-T GenotypeGVCFs \
-R $ref \
-o output.vcf \
${array[*]/#/ --variant }
#RealSkeptic's answer is the best. I'd write, for readability:
array=( "file 1" "file 2" "file 3" )
args=(
"$GATK"
-T GenotypeGVCFs
-R "$ref"
-o output.vcf
)
for foo in "${array[#]}"; do args+=( --variant "$foo" ); done
java "${args[#]}"

makefile giving unexpected end of file error

HOMEDIR = $(shell pwd)
DEFAULT = 4.0.3
YESDIR = $(shell echo $(#:install-%=%) | tr A-Z a-z)
NODIR = $(shell echo $(#:clean-%=%) | tr A-Z a-z)
install:
#$(MAKE) install-$(DEFAULT)
install-%:
#cd $(HOMEDIR);\
if [ ! -e $(YESDIR) ]; then \
echo "Library $(#:install-%=%) Version=$(YESDIR) does not exist"; \
elif [ -e $(YESDIR)/Install.sh ]; then \
echo "Installing $(PKGNAM) version=$(YESDIR)" ; \
cd $(YESDIR) ;\
$(SHELL) Install.sh $(HOMEDIR) 1 ;\
elif [ -e $(YESDIR)/Makefile ]; then \
cd $(YESDIR); \
$(MAKE); \
else \
echo "Installation instruction for $(#:install-%=%) Version=$(YESDIR) does not exist"; \
fi;
the above makefile gives me the following error
line 6: syntax error: unexpected end of file
Remove trailing blanks in this line:
$(SHELL) Install.sh $(HOMEDIR) 1 ;\

Makefile (running outside scripts that have makefile macros)

I have some .PHONY targets such as 'clean', 'backup', and 'help'
the rule for some of these targets is very large.
For example:
.PHONY: backup
backup:
#$(GREEN)
#mkdir -p backup/include #make an backup include folder if it doesn't already exist
#mkdir -p backup/src #make a backup src folder if it doesn't already exist
#mkdir -p backup/docs #make a backup docs folder if it doesn't already exist
#total=0; headerCount=0; sourceCount=0; documentCount=0; \
for file in $(HEADER_PATH)*; do \
if ls $$file[~] >/dev/null 2>&1; then \
mv -fu $$file[~] backup/$$file; \
let "headerCount+=1"; \
echo $(DATE)[Backed Up] $$file~ >> $(LOG); \
fi; \
done; \
for file in $(SOURCE_PATH)*; do \
if ls $$file[~] >/dev/null 2>&1; then \
mv -fu $$file[~] backup/$$file; \
let "sourceCount+=1"; \
echo $(DATE)[Backed Up] $$file~ >> $(LOG); \
fi; \
done; \
for file in $(DOC_PATH)*; do \
if ls $$file[~] >/dev/null 2>&1; then \
mv -fu $$file[~] backup/$$file; \
let "documentCount+=1"; \
echo $(DATE)[Backed Up] $$file~ >> $(LOG); \
fi; \
done; \
let "total= headerCount + sourceCount + documentCount"; \
echo -n $(OUTPUT_PROMPT)" "; \
if test $$total -eq 0; then \
echo Nothing To Back up; \
else \
if test $$headerCount -eq $$total; then \
echo -n $$total" "; \
echo -n "Header"; \
if test $$total -ge 2; then \
echo -n "s"; \
fi; \
echo " Backed Up"; \
elif test $$sourceCount -eq $$total; then \
echo -n $$total" "; \
echo -n "Source"; \
if test $$total -ge 2; then \
echo -n "s"; \
fi; \
echo " Backed Up"; \
elif test $$documentCount -eq $$total; then \
echo -n $$total" "; \
echo -n "Document"; \
if test $$total -ge 2; then \
echo -n "s"; \
fi; \
echo " Backed Up"; \
else \
$(UNDERLINE); echo $$total " Files Backed Up"; $(UNUNDERLINE); \
if test $$headerCount -eq 1; then \
echo $(OUTPUT_PROMPT)" "$$headerCount header; \
elif test $$headerCount -ge 2; then \
echo $(OUTPUT_PROMPT)" "$$headerCount headers; \
fi; \
if test $$sourceCount -eq 1; then \
echo $(OUTPUT_PROMPT)" "$$sourceCount source; \
elif test $$sourceCount -ge 2; then \
echo $(OUTPUT_PROMPT)" "$$sourceCount sources; \
fi; \
if test $$documentCount -eq 1; then \
echo $(OUTPUT_PROMPT)" "$$documentCount document; \
elif test $$documentCount -ge 2; then \
echo $(OUTPUT_PROMPT)" "$$documentCount documents; \
fi; \
fi; \
fi;
#$(DEFAULT_TEXT)
what the code does is not important, but I wanted to illustrate that it has macros in which 'make' must expand, and that it also performs shell code (bash), and that some indication on what the script did, is displayed in the terminal.
I want to put this script outside of 'make' in another directory, and turn that code into something like this:
.PHONY: backup
backup:
#run scripts/backup.scr
#or something similar to that
How can I put the rule of my target (which is makefile/bash code) into a separate file, and have make practically paste it in so that it runs how I had it originally?
I thought I might be able to use the "include" command inside 'make'.
It looks like it is used to include other makefiles though..
maybe I should just paste the entire target/rule into another makefile, and then include that makefile into my main one?
Would that be the best way?
In your case, you have quite few output variables. It might be worth the hassle to separate the generation and execution, like:
clean : clean-script
sh clean-script
rm -f clean-script
clean-script : clean-script.in
sed -e 's:[#]HEADER_PATH[#]:$(HEADER_PATH):g' $<.in > $#
And write clean-script.in as a clean sh script with a few substitutions.
If you use GNU make, you can of course build a list of output varables like:
clean-script : clean-script.in
sed $(foreach var,$(SUBSTVARS),-e 's:[#]$(var)[#]:$($(var)):g') $<.in > $#
I don't know if it can help you, but you can run make inside some Makefile usually with a command (inside a rule) e.g.
$(MAKE) subtarget
See the section Recursive use of Make in the GNU make documentation.
I tend to dislike using make for complex projects (but unfortunately, I have to). If you are free to chose some other tool, you might consider omake and many others (cmake, scons, bake, ...)

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