My environment created a variable that looks like this:
SM_TRAINING_ENV={"additional_framework_parameters":{},"channel_input_dirs":{"training":"/opt/ml/input/data/training"},"current_host":"algo-1","framework_module":"sagemaker_tensorflow_container.training:main","hosts":["algo-1"],"hyperparameters":{"bool_param":true,"float_param":1.25,"int_param":5,"model_dir":"s3://bucket/detection/prefix/testing-2019-04-06-02-24-20-194/model","str_param":"bla"},"input_config_dir":"/opt/ml/input/config","input_data_config":{"training":{"RecordWrapperType":"None","S3DistributionType":"FullyReplicated","TrainingInputMode":"File"}},"input_dir":"/opt/ml/input","is_master":true,"job_name":"testing-2019-04-06-02-24-20-194","log_level":20,"master_hostname":"algo-1","model_dir":"/opt/ml/model","module_dir":"s3://bucket/prefix/testing-2019-04-06-02-24-20-194/source/sourcedir.tar.gz","module_name":"launcher.sh","network_interface_name":"ethwe","num_cpus":8,"num_gpus":1,"output_data_dir":"/opt/ml/output/data","output_dir":"/opt/ml/output","output_intermediate_dir":"/opt/ml/output/intermediate","resource_config":{"current_host":"algo-1","hosts":["algo-1"],"network_interface_name":"ethwe"},"user_entry_point":"launcher.sh"}
EDIT by Ed Morton: per the OPs comment below, this is what (s)he is trying to describe above as the sample input:
$ SM_TRAINING_ENV='{"additional_framework_parameters":{},"channel_input_dirs":{"training":"/opt/ml/input/data/training"},"current_host":"algo-1","framework_module":"sagemaker_tensorflow_container.training:main","hosts":["algo-1"],"hyperparameters":{"bool_param":true,"float_param":1.25,"int_param":5,"model_dir":"s3://bucket/detection/prefix/testing-2019-04-06-02-24-20-194/model","str_param":"bla"},"input_config_dir":"/opt/ml/input/config","input_data_config":{"training":{"RecordWrapperType":"None","S3DistributionType":"FullyReplicated","TrainingInputMode":"File"}},"input_dir":"/opt/ml/input","is_master":true,"job_name":"testing-2019-04-06-02-24-20-194","log_level":20,"master_hostname":"algo-1","model_dir":"/opt/ml/model","module_dir":"s3://bucket/prefix/testing-2019-04-06-02-24-20-194/source/sourcedir.tar.gz","module_name":"launcher.sh","network_interface_name":"ethwe","num_cpus":8,"num_gpus":1,"output_data_dir":"/opt/ml/output/data","output_dir":"/opt/ml/output","output_intermediate_dir":"/opt/ml/output/intermediate","resource_config":{"current_host":"algo-1","hosts":["algo-1"],"network_interface_name":"ethwe"},"user_entry_point":"launcher.sh"}'
$ echo "$SM_TRAINING_ENV"
{"additional_framework_parameters":{},"channel_input_dirs":{"training":"/opt/ml/input/data/training"},"current_host":"algo-1","framework_module":"sagemaker_tensorflow_container.training:main","hosts":["algo-1"],"hyperparameters":{"bool_param":true,"float_param":1.25,"int_param":5,"model_dir":"s3://bucket/detection/prefix/testing-2019-04-06-02-24-20-194/model","str_param":"bla"},"input_config_dir":"/opt/ml/input/config","input_data_config":{"training":{"RecordWrapperType":"None","S3DistributionType":"FullyReplicated","TrainingInputMode":"File"}},"input_dir":"/opt/ml/input","is_master":true,"job_name":"testing-2019-04-06-02-24-20-194","log_level":20,"master_hostname":"algo-1","model_dir":"/opt/ml/model","module_dir":"s3://bucket/prefix/testing-2019-04-06-02-24-20-194/source/sourcedir.tar.gz","module_name":"launcher.sh","network_interface_name":"ethwe","num_cpus":8,"num_gpus":1,"output_data_dir":"/opt/ml/output/data","output_dir":"/opt/ml/output","output_intermediate_dir":"/opt/ml/output/intermediate","resource_config":{"current_host":"algo-1","hosts":["algo-1"],"network_interface_name":"ethwe"},"user_entry_point":"launcher.sh"}
How can I create a new bash variable that is equal to the value of SM_TRAINING_ENV["hyperparameters"]["model_dir"]?
For completeness, I was trying simple things like echo ${SM_TRAINING_ENV} | jq . and kept getting errors with everything I tried.
Edit: I've been informed that this value isn't a proper json, so rewording the question. I think the environment sets it to the value of a python dictionary, so jq seems not usable. Removed json tag. Maybe this is a job for awk?
It looks like I can match the value I want if I assume the structure doesn't change with the regex pattern s3.*?model, but not sure how to set a regex pattern to a new variable.
First, you need to quote the JSON value so that the double quotes will be included in the value.
SM_TRAINING_ENV='{"additional_framework_parameters":{},"channel_input_dirs":{"training":"/opt/ml/input/data/training"},"current_host":"algo-1","framework_module":"sagemaker_tensorflow_container.training:main","hosts":["algo-1"],"hyperparameters":{"bool_param":true,"float_param":1.25,"int_param":5,"model_dir":"s3://bucket/detection/prefix/testing-2019-04-06-02-24-20-194/model","str_param":"bla"},"input_config_dir":"/opt/ml/input/config","input_data_config":{"training":{"RecordWrapperType":"None","S3DistributionType":"FullyReplicated","TrainingInputMode":"File"}},"input_dir":"/opt/ml/input","is_master":true,"job_name":"testing-2019-04-06-02-24-20-194","log_level":20,"master_hostname":"algo-1","model_dir":"/opt/ml/model","module_dir":"s3://bucket/prefix/testing-2019-04-06-02-24-20-194/source/sourcedir.tar.gz","module_name":"launcher.sh","network_interface_name":"ethwe","num_cpus":8,"num_gpus":1,"output_data_dir":"/opt/ml/output/data","output_dir":"/opt/ml/output","output_intermediate_dir":"/opt/ml/output/intermediate","resource_config":{"current_host":"algo-1","hosts":["algo-1"],"network_interface_name":"ethwe"},"user_entry_point":"launcher.sh"}'
Then you can use the jq utility to extract the value you want.
new_var=$(echo "$SM_TRAINING_ENV" | jq '.hyperparameters.model_dir')
This doesn't really index but it works if order is always the same:
NEW_VAR=$(echo $SM_TRAINING_ENV | egrep -o s3.*?model | head -1)
Would much prefer something not dependent on order though.
Related
I did check the ABS, but it was hard to find a reference to my problem/question there.
Here it is. Consider the following code (Which extracts the first character of OtherVar and then converts MyVar to uppercase):
OtherVar=foobar
MyChar=${OtherVar:0:1} # get first character of OtherVar string variable
MyChar=${MyChar^} # first character to upper case
Could I somehow condense the second and third line into one statement?
P.S.: As was pointed out below, not needs to have a named variable. I should add, I would like to not add any sub-shells or so and would also accept a somehow hacky way to achieve the desired result.
P.P.S.: The question is purely educational.
You could do it all-in-one without forking sub-shell or running external command:
printf -v MyChar %1s "${OtherVar^}"
Or:
read -n1 MyChar <<<"${OtherVar^}"
Another option:
declare -u MyChar=${OtherVar:0:1}
But I can't see the point in such optimization in a bash script.
There are more suitable text processing interpreters, like awk, sed, even perl or python if performance matters.
You could use the cut command and put it in a complex expression to get it on one line, but I'm not sure it makes the code too much clearer:
OtherVar=foobar
MyChar=$(echo ${OtherVar^} | cut -c1-1) # uppercase first character and cut string
I'm trying to extract a tag value of an HTML node that I already have in a variable.
I'm currently using Zsh but I'm trying to make it work in Bash as well.
The current variable has the value:
<span class="alter" fill="#ffedf0" data-count="0" data-more="none"/>
and I would like to get the value of data-count (in this case 0, but could be any length integer).
I have tried using cut, sed and the variables expansion as explained in this question but I haven't managed to adapt the regexs, or maybe it has to be done differently for Zsh.
There is no reason why sed would not work in this situation. For your specific case, I would do something like this:
sed 's/.*data-count="\([0-9]*\)".*/\1/g' file_name.txt
Basically, it just states that sed is looking for the a pattern that contains data-count=, then saves everything within the paranthesis \(...\) into \1, which is subsequently printed in place of the match (full line due to the .*)
Could you please try following.
awk 'match($0,/data-count=[^ ]*/){print substr($0,RSTART+12,RLENGTH-13)}' Input_file
Explanation: Using match function of awk to match regex data-count=[^ ]* means match everything from data-count till a space comes, if this regex is TRUE(a match is found) then out of the box variables RSTART and RLENGTH will be set. Later I am printing current line's sub-string as per these variables values to get only value of data-count.
With sed could you please try following.
sed 's/.*data-count=\"\([^"]*\).*/\1/' Input_file
Explanation: Using sed's capability of group referencing and saving regex value in first group after data-count=\" which is its length, then since using s(substitution) with sed so mentioning 1 will replace all with \1(which is matched regex value in temporary memory, group referencing).
As was said before, to be on the safe side and handle any syntactically valid HTML tag, a parser would be strongly advised. But if you know in advance, what the general format of your HTML element will look like, the following hack might come handy:
Assume that your variable is called "html"
html='<span class="alter" fill="#ffedf0" data-count="0" data-more="none"/>'
First adapt it a bit:
htmlx="tag ${html%??}"
This will add the string tag in front and remove the final />
Now make an associative array:
declare -A fields
fields=( ${=$(tr = ' ' <<<$htmlx)} )
The tr turns the equal sign into a space and the ${= handles word splitting. You can now access the values of your attributes by, say,
echo $fields[data-count]
Note that this still has the surrounding double quotes. Yuo can easily remove them by
echo ${${fields[data-count]%?}#?}
Of course, once you do this hack, you have access to all attributes in the same way.
So, I am writing a shell script and I am running a command that gives me an output like:
{"a":"some_text","b":some_other_text","c":"even_more_text"}
Now, I am not sure how to parse it, I basically need the value of "c", i.e. "ever_more_text" in a variable, but finding out results on internet have not worked yet! TIA.
the output which you paste here is not valid json. Check with https://jsonformatter.curiousconcept.com/ There is missing first double quote in "some_other_text". If you add it, you can then easily parse with jq:
./your_script.sh | jq -r ".c"
I have a shell script where I have a statement:
isPartial = $searchCurl| grep -Po '\"partialSearch\":(true|false)'|sed 's/\\\"partialSearch\\\"://'
now, if I just echo the RHS
$searchCurl| grep -Po '\"partialSearch\":(true|false)'|sed 's/\\\"partialSearch\\\"://'
it prints "partialSearch":true, but the variable isPartial doesn't get initialized .
Why is this happening and how can I fix it ?
Since the number of backslashes in your examples varies, it is not clear to me if the double quotes are already escaped in the input text. I’ll assume they are not, i.e. the input text looks something like:
sometext... "partialSearch":true ... sometext...
..bla bla bla... "partialsearch":false ...
and my examples below will work under this assumption.
There are a number of points to be made.
You seem to be trying to parse JSON input with regular expressions. While this could be acceptable for quick-and-dirty one-time jobs where you know the exact format of the data being processed, in general it is a very bad idea. You should use a JSON parser like jq.
You obviously have stored some bash code in the variable searchCurl. This is considered bad practice. Instead of searchCurl="... code ..." you should do function searchCurl () { ... code ... } and call searchCurl without prefixing it with a dollar sign. Variables are for values, functions are for code.
In most cases, if you are going to use sed, it’s better to use it for everything without invoking grep. Sometimes it can be simpler to have both. See below for an example.
To assign the output of a command to a variable, you have to use command substitution.
In short, if in your input text you have only one match of '"partialSearch":(true|false)', this is what you want:
isPartial=$(searchCurl|sed -rn 's/^.*"partialSearch":(true|false).*$/\1/p')
If you have more and the input text is one big line as I suppose, usage of grep -o might simplify the task of splitting the input into one match per line, so that
isPartial=$(searchCurl|grep -Po '"partialSearch":(true|false)'|sed -e 's/^.*://')
might be what you want (and in this case, isPartial will hold a space-separated list of true and false).
Apologies for a seemingly inane question. But I have spent the whole day trying to figure it out and it drives me up the walls. I'm trying to write a seemingly simple bash script that would take a list of files in the directory from ls, replace part of the file names using sed, get unique names from the list and pass them onto some command. Like so:
inputs=`ls *.ext`
echo $inputs
test1_R1.ext test1_R2.ext test2_R1.ext test2_R2.ext
Now I would like to put it through sed to replace 1.ext and 2.ext with * to get test1_R* etc. Then I'd like to remove resulting duplicates by running sort -u to arrive to the following $outputs variable:
echo $outputs
test1_R* test2_R*
And pass this onto a command, like so
cat $outputs
I can do something like this in a command line:
ls *.ext | sed s/..ext/\*/g | sort -u
But if I try to assign the above to a variable in the script it just returns the output from the ls. I have tried several ways to do it: including the whole pipe in the script. Running each command separately and assigning it to a variable, then passing that variable to the next command and writing the outputs to files then passing the file to the next command. But so far none of this managed to achieve what I aimed to. I think my problem lies in (except general cluelessness aroung bash scripting) inability to run seq on a variable within script. There seems to be a lot of advice around in how to pass variables to pattern or replacement string in sed, but they all seem to take files as input. But I understand that it might not be the proper way of doing it anyway. Therefore I would really appreciate if someone could suggest an elegant way to achieve, what I'm trying to.
Many thanks!
Update 2/06/2014
Hi Barmar, thanks for your answer. Can't say it solved the problem, but it helped pin-pointing it. Seems like the problem is in me using the asterisk. I have to say, I'm very puzzled. The actual file names I've got are:
test1_R1.fastq.gz test1_R2.fastq.gz test2_R1.fastq.gz test2_R2.fastq.gz
If I'm using the code you suggested, which seems to me the right way do to it:
ins=$(ls *.fastq.gz | sed 's/..fastq.gz/\*/g' | sort -u)
Sed doesn't seem to do anything and I'm getting the output of ls:
test1_R1.fastq.gz test1_R2.fastq.gz test2_R1.fastq.gz test2_R2.fastq.gz
Now if I replace that backslash with anything else, the sed works, but it also returns whatever character I'm putting in front (or after) the asteriks:
ins=$(ls *.fastq.gz | sed 's/..fastq.gz/"*/g' | sort -u)
test1_R"* test2_R"*
That's odd enough, but surely I can just put an "R" in front of the asteriks and then replace R in the search pattern string, right? Wrong! If I do that whichever way: 's/R..fastq.gz/R*/g' 's/...fastq.gz/R*/g' 's/[A-Z]..fastq.gz/R*/g' I'm back to the original names! And even if I end up with something like test1_RR* test2_RR* and try to run it through sed again and replace "_R" for "_" or "RR" for "R", I'm having no luck and I'm back to the original names. And yet I can replace the rest of the file name no problem, just not to get me test1_R* I need.
I have a feeling I should be escaping that * in some very clever way, but nothing I've tried seems to work. Thanks again for your help!
This is how you capture the result of the whole pipeline in a variable:
var=$(ls *.ext | sed s/..ext/\*/g | sort -u)