How to count TSLint errors?
I am working in a project with Angular where we changed the TSLint rules and we have massive output.
I would like to count the issues to see over the time if we progressively decrease them.
This command worked for me on Mac:
tslint 'src/**/*.ts' | wc -l
Output:
1953 errors.
Related
Anyone have a clean process for converting samples on macOS to FlameGraphs?
After a bit of fiddling I thought I could perhaps use a tool such as flamegraph-sample, but it seems to give me some trouble and so I thought perhaps there may be other more up-to-date options that I'm missing insomuch that this tool gives an error:
$ sudo sample PID -file ~/tmp/sample.txt -fullPaths 1
Sampling process 198 for 1 second with 1 millisecond of run time between samples
Sampling completed, processing symbols...
Sample analysis of process 35264 written to file ~/tmp/sample.txt
$ python stackcollapse-sample.py ~/tmp/sample.txt > ~/tmp/sample_collapsed.txt
$ flamegraph.pl ~/tmp/sample_collapsed.txt > ~/tmp/sample_collapsed_flamegraph.svg
Ignored 2335 lines with invalid format
ERROR: No stack counts found
There is this potentially useful but also pesky Pylint message which we would prefer to keep enabled and written to the console (and especially to the CI log), but only if Pylint can be told to return a 0 exit code if it finds nothing more severe (so we do not have to keep suppressing/unsuppressing it whenever adding/removing breakpoints or changing our workflow which requires 0 exit code from Pylint at a very early stage)
W1515: Leaving functions creating breakpoints in production code is not recommended (forgotten-debug-statement)
I checked the FAQ and the command-line help. There is the opposite switch --fail-on but no obvious way to reduce the severity. Also checked the changelog up to 2.13.0.
For now our poor people's workaround is to use grep instead of the one simple Pylint warning which we now disabled.
grep 'set_trace()\|breakpoint()' \
--dereference-recursive \
--include='*.py' \
$PYTHON_CODE_DIRECTORY \
||true
But the question is how to demote (reduce severity of) any specific Pylint warning.
Hi I can run the different steps of nanopolish with snakemake. But when I run it it will give an error that the index file created in the bwa rule isnt available yet. After it gives this error it creates the file it that the error was about. If I run snakemake again without removing files it works because the file is there. How can I tell snake make to wait with the next step until the first one is done? I have googled on any ways to solve this problem and all I could find was priority and ruleorder and I have used those but it still doesnt work. Here is the script that I use.
ruleorder: bwa > nanopolish
rule bwa:
input:
"nanopolish/assembly.fasta"
output:
"nanopolish/draft.fa"
conda:
"envs/nanopolish.yaml"
priority:
50
shell:
"bwa index {input} - > {output}"
rule nanopolish:
input:
"nanopolish/assembly.fasta",
"zipped/zipped.gz"
output:
"nanopolish/reads.sorted.bam"
conda:
"envs/nanopolish.yaml"
shell:
"bwa mem -x ont2d {input} | samtools sort -o {output} -T reads.tmp"
You should take a look again at the docs to properly understand the idea of SnakeMake.
Rules describe how to create output files from input files
A rule is not executed until all its input exists, so all you have to do is add the output of the bwa rule
rule nanopolish:
input:
"nanopolish/assembly.fasta",
"nanopolish/draft.fa", # <-- output of bwa
"zipped/zipped.gz"
Ruleorder and priority are not relevant solutions for your problem.
I use cut in one rule of my pipeline and always throws an error, but without any error description.
When I try this command with a simple bash script it is working without any errors.
Here is the rule:
rule convert_bamheader:
input: bam/SERUM-ACT/exon_tagged_trimmed_mapped_cleaned.bam, stats/SERUM-ACT/good_barcodes_clean_filter.txt
output: bam/SERUM-ACT/exon_tagged_trimmed_mapped_cleaned_header.txt, bam/SERUM-ACT/exon_tagged_trimmed_mapped_cleaned_header_filtered.tsv
jobid: 15
wildcards: sample=SERUM-ACT
threads: 4
mkdir -p stats/SERUM-ACT
mkdir -p log/SERUM-ACT
samtools view bam/SERUM-ACT/exon_tagged_trimmed_mapped_cleaned.bam > bam/SERUM-ACT/exon_tagged_trimmed_mapped_cleaned_header.txt
cut -f 12,13,18,20-24 bam/SERUM-ACT/exon_tagged_trimmed_mapped_cleaned_header.txt | grep -f stats/SERUM-ACT/good_barcodes_clean_filter.txt > bam/SERUM-ACT/exon_tagged_trimmed_mapped_cleaned_header_filtered.tsv
Submitted DRMAA job 15 with external jobid 7027806.
Error in rule convert_bamheader:
jobid: 15
output: bam/SERUM-ACT/exon_tagged_trimmed_mapped_cleaned_header.txt, bam/SERUM-ACT/exon_tagged_trimmed_mapped_cleaned_header_filtered.tsv
ClusterJobException in line 256 of */pipeline.snake:
Error executing rule convert_bamheader on cluster (jobid: 15, external: 7027806, jobscript: */.snakemake/tmp.ewej7q4e/snakejob.convert_bamheader.15.sh). For detailed error see the cluster log.
Job failed, going on with independent jobs.
Exiting because a job execution failed. Look above for error message
Complete log: */.snakemake/log/2018-12-18T104741.092698.snakemake.log
I thought that it has to do something with the number of threads provided and number of threads needed for the cut step, but I am not sure.
Perhaps someone can help me?
Cheers!
Hive query output that is using UDFs consists of these 2 warnings at the end. How do I suppress these 2 warnings. Please note that the 2 warnings come right after the output as part of output.
WARN: The method class org.apache.commons.logging.impl.SLF4JLogFactory#release() was invoked.
WARN: Please see http://www.slf4j.org/codes.html#release for an explanation.
hadoop version
Hadoop 2.6.0-cdh5.4.0
hive --version
Hive 1.1.0-cdh5.4.0
If you use beeline instead of Hive the error goes away. Not the best solution, but I'm planning to post to the CDH user group asking the same question to see if it's a bug that can be fixed.
This error occurs due to adding of assembly jar which which contains classes from icl-over-slf4j.jar (which is causing the stdout messages) and slf4j-log4j12.jar.
You can try couple of things to begin with:
Try removing the assembly jar, in case if using.
Look at the following link: https://issues.apache.org/jira/browse/HIVE-12179
This suggest that we can trigger a flag in Hive where spark-assembly is loaded only if HIVE_ADD_SPARK_ASSEMBLY = "true".
https://community.hortonworks.com/questions/34311/warning-message-in-hive-output-after-upgrading-to.html :
Although there is a workaround if to avoid any end time changes and that is to manually remove the 2 lines from the end of the files using shell script.
Have tried to set HIVE_ADD_SPARK_ASSEMBLY=false, but it didn't work.
Finally, I found a post question at Cloudera community. See: https://community.cloudera.com/t5/Support-Questions/Warning-message-in-Hive-output-after-upgrading-to-hive/td-p/157141
You could try the follow command, it works for me!
hive -S -d ns=$hiveDB -d tab=$t -d dunsCol=$c1 -d phase="$ph1" -d error=$c2 -d ts=$eColumnArray -d reporting_window=$rDate -f $dir'select_count.hsql' | grep -v "^WARN" > $gOutPut 2> /dev/null