Showing 87 of 87 total issues
Function main has a Cognitive Complexity of 284 (exceeds 20 allowed). Consider refactoring. Open
func main() {
// we want to load a config file named "irods_downloader_config.yaml" if it exists in WD or in ~/.config
viper.SetConfigName("irods_downloader_config")
viper.SetConfigType("yaml")
viper.AddConfigPath(".") // look for config in the working directory first- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Function main has 566 lines of code (exceeds 50 allowed). Consider refactoring. Open
func main() {
// we want to load a config file named "irods_downloader_config.yaml" if it exists in WD or in ~/.config
viper.SetConfigName("irods_downloader_config")
viper.SetConfigType("yaml")
viper.AddConfigPath(".") // look for config in the working directory firstFile irods_downloader.go has 686 lines of code (exceeds 500 allowed). Consider refactoring. Open
package main
import (
"bytes"
"encoding/json"Similar blocks of code found in 2 locations. Consider refactoring. Open
func indexBam(cram_list []cram_file, i int, samtools_exec string) {
cram := &cram_list[i]
bam_filename := cram.Realigned_bam_path
output, err := exec.Command(samtools_exec, "index", bam_filename).CombinedOutput()- Read upRead up
Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 154.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
func quickcheck_alignments(cram_list []cram_file, i int, samtools_exec string) {
cram := &cram_list[i]
bam_filename := cram.Realigned_bam_path
output, err := exec.Command(samtools_exec, "quickcheck", bam_filename).CombinedOutput()- Read upRead up
Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 154.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Function main has 8 return statements (exceeds 4 allowed). Open
func main() {
// we want to load a config file named "irods_downloader_config.yaml" if it exists in WD or in ~/.config
viper.SetConfigName("irods_downloader_config")
viper.SetConfigType("yaml")
viper.AddConfigPath(".") // look for config in the working directory firstAvoid deeply nested control flow statements. Open
if err != nil {
// Display everything we got if error.
log.Println("Error when running command. Output:")
log.Println(string(output))
log.Printf("Got command status: %s\n", err.Error())don't use underscores in Go names; func parameter submitted_jobs_map should be submittedJobsMap Open
submitted_jobs_map map[string]string,- Exclude checks
don't use underscores in Go names; func parameter attribute_name should be attributeName Open
attribute_name string,- Exclude checks
don't use underscores in Go names; struct field Cram_dl_path should be CramDlPath Open
Cram_dl_path string- Exclude checks
don't use underscores in Go names; var bwa_align_libraries should be bwaAlignLibraries Open
bwa_align_libraries := viper.GetStringSlice("bwa_align_libraries")- Exclude checks
don't use underscores in Go names; var genome_annot should be genomeAnnot Open
genome_annot := viper.GetString("genome_annot")- Exclude checks
don't use underscores in Go names; var sample_name should be sampleName Open
sample_name := ""- Exclude checks
don't use underscores in Go names; var fq_filename should be fqFilename Open
fq_filename := strings.ReplaceAll(cram.Filename, ".cram", "")- Exclude checks
don't use underscores in Go names; var rna_bams_featurecounts_input should be rnaBamsFeaturecountsInput Open
var rna_bams_featurecounts_input []string- Exclude checks
don't use underscores in Go names; func parameter cram_list should be cramList Open
func writeCheckpoint(cram_list []cram_file, step int) {- Exclude checks
don't use underscores in Go names; func parameter cram_list should be cramList Open
func quickcheck_alignments(cram_list []cram_file, i int, samtools_exec string) {- Exclude checks
don't use underscores in Go names; func parameter samtools_exec should be samtoolsExec Open
func indexBam(cram_list []cram_file, i int, samtools_exec string) {- Exclude checks
don't use underscores in Go names; struct field Realigned_bam_path should be RealignedBamPath Open
Realigned_bam_path string- Exclude checks
don't use underscores in Go names; var imeta_file should be imetaFile Open
imeta_file, err := os.Create(cram.Imeta_path)- Exclude checks