change test to make it fail #5

lldelisle · 2023-11-16T12:13:32Z

No description provided.

github-actions · 2024-01-11T16:58:25Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	1
Error	0
Failure	1
Skipped	0

Failed Tests

❌ parallel-accession-download.ga_0

Problems:

Output with path /tmp/tmpquzmltfa/SRR044777__1f7bfb65-f951-4191-ad52-4786ba81c88c different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/data-fetching/parallel-accession-download/test-data/SRR044777_head.fastq v. /tmp/tmpknh59paySRR044777_head.fastq )
Failed to find 'b'@F47USSH02H1LGA/4'' in history data. (lines_diff=0).

Workflow invocation details

Invocation Messages

Steps

Step 1: Run accessions:
- step_state: scheduled

Step 2: Split accessions to collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir ./out && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/baabc30154cd/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/tmp/tmp8_14wfun/files/c/b/f/dataset_cbfa874e-8e4e-4102-b65f-e29063a8faae.dat' --ftype 'txt' --chunksize 1 --file_names 'split_file' --file_ext 'txt'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"52942787b0a211ee9f24237fad8a8bfc"`
chromInfo	`"/tmp/tmp8_14wfun/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
split_parms	`{"__current_case__": 5, "input": {"values": [{"id": 1, "src": "hda"}]}, "newfilenames": "split_file", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_ftype": "txt", "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}}`

Step 3: to parameter:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"52942787b0a211ee9f24237fad8a8bfc"`
chromInfo	`"/tmp/tmp8_14wfun/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 4: fasterq-dump:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  mkdir -p ~/.ncbi && cp '/tmp/tmp8_14wfun/job_working_directory/000/4/configs/tmpbfj_9r3d' ~/.ncbi/user-settings.mkfg &&   export SRA_PREFETCH_RETRIES=3 && export SRA_PREFETCH_ATTEMPT=1 &&   echo 'SRR044777' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&  while [ $SRA_PREFETCH_ATTEMPT -le $SRA_PREFETCH_RETRIES ] ; do fasterq-dump "$acc" -e ${GALAXY_SLOTS:-1} --seq-defline '@$sn/$ri' --qual-defline '+' --split-3 --skip-technical 2>&1 | tee -a '/tmp/tmp8_14wfun/job_working_directory/000/4/outputs/dataset_3f7a3a89-9f7f-4d76-a80c-79709e5e14e6.dat'; if [ $? == 0 ] && [ $(ls *.fastq | wc -l) -ge 1 ]; then break ; else echo "Prefetch attempt $SRA_PREFETCH_ATTEMPT of $SRA_PREFETCH_RETRIES exited with code $?" ; SRA_PREFETCH_ATTEMPT=`expr $SRA_PREFETCH_ATTEMPT + 1` ; sleep 1 ; fi ; done && mkdir -p output && mkdir -p outputOther && count="$(ls *.fastq | wc -l)" && echo "There are $count fastq files" && data=($(ls *.fastq)) && if [ "$count" -eq 1 ]; then pigz -cqp ${GALAXY_SLOTS:-1} "${data[0]}" > output/"${acc}"__single.fastqsanger.gz && rm "${data[0]}"; elif [ "--split-3" = "--split-3" ]; then if [ -e "${acc}".fastq ]; then pigz -cqp ${GALAXY_SLOTS:-1} "${acc}".fastq > outputOther/"${acc}"__single.fastqsanger.gz; fi && pigz -cqp ${GALAXY_SLOTS:-1} "${acc}"_1.fastq > output/"${acc}"_forward.fastqsanger.gz && pigz -cqp ${GALAXY_SLOTS:-1} "${acc}"_2.fastq > output/"${acc}"_reverse.fastqsanger.gz && rm "${acc}"*.fastq; elif [ "$count" -eq 2 ]; then pigz -cqp ${GALAXY_SLOTS:-1} "${data[0]}" > output/"${acc}"_forward.fastqsanger.gz && pigz -cqp ${GALAXY_SLOTS:-1} "${data[1]}" > output/"${acc}"_reverse.fastqsanger.gz && rm "${data[0]}" && rm "${data[1]}"; else for file in ${data[*]}; do pigz -cqp ${GALAXY_SLOTS:-1} "$file" > outputOther/"$file"sanger.gz && rm "$file"; done; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Output:

Downloading accession: SRR044777...
spots read      : 7,882
reads read      : 31,528
reads written   : 7,882
technical reads : 23,646
There are 1 fastq files
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"52942787b0a211ee9f24237fad8a8bfc"`
adv	`{"minlen": null, "seq_defline": "@$sn/$ri", "skip_technical": true, "split": "--split-3"}`
chromInfo	`"/tmp/tmp8_14wfun/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "SRR044777", "input_select": "accession_number"}`

Step 5: flatten paired output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"52942787b0a211ee9f24237fad8a8bfc"`
input	`{"values": [{"id": 3, "src": "hdca"}]}`
rules	{"mapping": [{"collapsible_value": {"__class__": "RuntimeValue"}, "columns": [1], "connectable": true, "editing": false, "is_workflow": false, "type": "list_identifiers"}, {"collapsible_value": {"__class__": "RuntimeValue"}, "columns": [2], "connectable": true, "is_workflow": false, "type": "paired_identifier"}], "rules": [{"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier1", "warn": null}, {"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier2", "warn": null}]}

Step 6: flatten single end output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"52942787b0a211ee9f24237fad8a8bfc"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
rules	{"mapping": [{"collapsible_value": {"__class__": "RuntimeValue"}, "columns": [1], "connectable": true, "editing": false, "is_workflow": false, "type": "list_identifiers"}], "rules": [{"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier1", "warn": null}]}

Other invocation details
- history_id
  - 1239dd3e295ce541
- history_state
  - ok
- invocation_id
  - 1239dd3e295ce541
- invocation_state
  - scheduled
- workflow_id
  - 642fb8db1d7b0e74

Passed Tests

✅ parallel-accession-download.ga_1

Workflow invocation details

Invocation Messages

Steps

Step 1: Run accessions:
- step_state: scheduled

Step 2: Split accessions to collection:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir ./out && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/baabc30154cd/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/tmp/tmp8_14wfun/files/1/8/7/dataset_187b6885-da55-4529-9e61-0c05dd01acd6.dat' --ftype 'txt' --chunksize 1 --file_names 'split_file' --file_ext 'txt'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"7210c601b0a211ee9f24237fad8a8bfc"`
chromInfo	`"/tmp/tmp8_14wfun/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
split_parms	`{"__current_case__": 5, "input": {"values": [{"id": 7, "src": "hda"}]}, "newfilenames": "split_file", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_ftype": "txt", "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}}`

Step 3: to parameter:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"7210c601b0a211ee9f24237fad8a8bfc"`
chromInfo	`"/tmp/tmp8_14wfun/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 4: fasterq-dump:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  mkdir -p ~/.ncbi && cp '/tmp/tmp8_14wfun/job_working_directory/000/10/configs/tmpqjn48nuw' ~/.ncbi/user-settings.mkfg &&   export SRA_PREFETCH_RETRIES=3 && export SRA_PREFETCH_ATTEMPT=1 &&   echo 'SRR11953971' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&  while [ $SRA_PREFETCH_ATTEMPT -le $SRA_PREFETCH_RETRIES ] ; do fasterq-dump "$acc" -e ${GALAXY_SLOTS:-1} --seq-defline '@$sn/$ri' --qual-defline '+' --split-3 --skip-technical 2>&1 | tee -a '/tmp/tmp8_14wfun/job_working_directory/000/10/outputs/dataset_110f93be-8ebd-4ec1-ac74-359df98c9209.dat'; if [ $? == 0 ] && [ $(ls *.fastq | wc -l) -ge 1 ]; then break ; else echo "Prefetch attempt $SRA_PREFETCH_ATTEMPT of $SRA_PREFETCH_RETRIES exited with code $?" ; SRA_PREFETCH_ATTEMPT=`expr $SRA_PREFETCH_ATTEMPT + 1` ; sleep 1 ; fi ; done && mkdir -p output && mkdir -p outputOther && count="$(ls *.fastq | wc -l)" && echo "There are $count fastq files" && data=($(ls *.fastq)) && if [ "$count" -eq 1 ]; then pigz -cqp ${GALAXY_SLOTS:-1} "${data[0]}" > output/"${acc}"__single.fastqsanger.gz && rm "${data[0]}"; elif [ "--split-3" = "--split-3" ]; then if [ -e "${acc}".fastq ]; then pigz -cqp ${GALAXY_SLOTS:-1} "${acc}".fastq > outputOther/"${acc}"__single.fastqsanger.gz; fi && pigz -cqp ${GALAXY_SLOTS:-1} "${acc}"_1.fastq > output/"${acc}"_forward.fastqsanger.gz && pigz -cqp ${GALAXY_SLOTS:-1} "${acc}"_2.fastq > output/"${acc}"_reverse.fastqsanger.gz && rm "${acc}"*.fastq; elif [ "$count" -eq 2 ]; then pigz -cqp ${GALAXY_SLOTS:-1} "${data[0]}" > output/"${acc}"_forward.fastqsanger.gz && pigz -cqp ${GALAXY_SLOTS:-1} "${data[1]}" > output/"${acc}"_reverse.fastqsanger.gz && rm "${data[0]}" && rm "${data[1]}"; else for file in ${data[*]}; do pigz -cqp ${GALAXY_SLOTS:-1} "$file" > outputOther/"$file"sanger.gz && rm "$file"; done; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Output:

Downloading accession: SRR11953971...
spots read      : 2,057
reads read      : 4,114
reads written   : 4,114
There are 2 fastq files
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"7210c601b0a211ee9f24237fad8a8bfc"`
adv	`{"minlen": null, "seq_defline": "@$sn/$ri", "skip_technical": true, "split": "--split-3"}`
chromInfo	`"/tmp/tmp8_14wfun/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "SRR11953971", "input_select": "accession_number"}`

Step 5: flatten paired output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"7210c601b0a211ee9f24237fad8a8bfc"`
input	`{"values": [{"id": 11, "src": "hdca"}]}`
rules	{"mapping": [{"collapsible_value": {"__class__": "RuntimeValue"}, "columns": [1], "connectable": true, "editing": false, "is_workflow": false, "type": "list_identifiers"}, {"collapsible_value": {"__class__": "RuntimeValue"}, "columns": [2], "connectable": true, "is_workflow": false, "type": "paired_identifier"}], "rules": [{"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier1", "warn": null}, {"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier2", "warn": null}]}

Step 6: flatten single end output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"7210c601b0a211ee9f24237fad8a8bfc"`
input	`{"values": [{"id": 12, "src": "hdca"}]}`
rules	{"mapping": [{"collapsible_value": {"__class__": "RuntimeValue"}, "columns": [1], "connectable": true, "editing": false, "is_workflow": false, "type": "list_identifiers"}], "rules": [{"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier1", "warn": null}]}

Other invocation details
- history_id
  - 642fb8db1d7b0e74
- history_state
  - ok
- invocation_id
  - 642fb8db1d7b0e74
- invocation_state
  - scheduled
- workflow_id
  - 642fb8db1d7b0e74

change test to make it fail

84c953f

lldelisle mentioned this pull request Nov 16, 2023

PR between forks 8BitJonny/gh-get-current-pr#293

Open

lldelisle closed this Nov 22, 2023

lldelisle reopened this Nov 22, 2023

lldelisle force-pushed the main branch from 93eaf27 to 29beede Compare November 24, 2023 11:10

lldelisle closed this Jan 11, 2024

lldelisle reopened this Jan 11, 2024

lldelisle closed this Jan 11, 2024

lldelisle reopened this Jan 11, 2024

lldelisle force-pushed the main branch from 676d9bc to 389d7c9 Compare June 24, 2024 14:13

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change test to make it fail #5

change test to make it fail #5

lldelisle commented Nov 16, 2023

github-actions bot commented Jan 11, 2024

Workflow invocation details

Workflow invocation details

change test to make it fail #5

Are you sure you want to change the base?

change test to make it fail #5

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lldelisle commented Nov 16, 2023

github-actions bot commented Jan 11, 2024

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Workflow invocation details