diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d1d73e5..011d7b5 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -18,15 +18,15 @@ jobs: run: | pip3 install jsonschema pip3 install requests - - name: Check validity of traces + - name: Check validity of instances run: | - find . -type f -name "*.json" > traces.txt && err=0 + find . -type f -name "*.json" > instances.txt && err=0 git clone https://github.com/wfcommons/workflow-schema err_report() { - echo "Error on trace file $1" + echo "Error on instance file $1" } - trap 'err_report ${trace_file}' ERR; - for trace_file in `cat traces.txt`; do - python3 ./workflow-schema/wfcommons-validator.py -d ${trace_file}; + trap 'err_report ${instance_file}' ERR; + for instance_file in `cat instances.txt`; do + python3 ./workflow-schema/wfcommons-validator.py -d ${instance_file}; echo ""; done diff --git a/1000genome/README.md b/1000genome/README.md index 7d38e42..7a00196 100644 --- a/1000genome/README.md +++ b/1000genome/README.md @@ -1,7 +1,7 @@ - + -# Execution Traces for 1000Genome Workflow +# Execution Instances for 1000Genome Workflow ## Workflow Description @@ -42,14 +42,14 @@ performance metrics can be found in the following research publication: Future Generation Computer Systems, 95, 615–628. https://doi.org/10.1016/j.future.2019.01.015. -## Execution Traces +## Execution Instances -Execution traces are formatted according to the +Execution instances are formatted according to the [WfCommons JSON format](https://github.com/wfcommons/workflow-schema) for -describing workflow executions. Execution traces from different computing +describing workflow executions. Execution instances from different computing platforms are organized into sub-folders. -Trace files are named using the following convention: +Instance files are named using the following convention: `1000genome--ch--.json`, where: - ``: The compute platform where the actual Pegasus workflow diff --git a/cycles/README.md b/cycles/README.md index b938b70..9ccb85c 100644 --- a/cycles/README.md +++ b/cycles/README.md @@ -1,7 +1,7 @@ - + -# Execution Traces for Cycles Workflow +# Execution Instances for Cycles Workflow ## Workflow Description @@ -40,14 +40,14 @@ performance metrics can be found in the following research publication: Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD) (pp. 4545–4552). https://doi.org/10.1109/BigData47090.2019.9006107 -## Execution Traces +## Execution Instances -Execution traces are formatted according to the +Execution instances are formatted according to the [WfCommons JSON format](https://github.com/wfcommons/workflow-schema) -for describing workflow executions. Execution traces from different +for describing workflow executions. Execution instances from different computing platforms are organized into sub-folders. -Trace files are named using the following convention: +Instance files are named using the following convention: `cycles-----.json`, where: - ``: The compute platform where the actual Pegasus workflow diff --git a/epigenomics/README.md b/epigenomics/README.md index 83e04b6..fd5e537 100644 --- a/epigenomics/README.md +++ b/epigenomics/README.md @@ -1,7 +1,7 @@ - + -# Execution Traces for Epigenomics Workflow +# Execution Instances for Epigenomics Workflow ## Workflow Description @@ -38,14 +38,14 @@ performance metrics can be found in the following research publication: "Characterizing and Profiling Scientific Workflows," Future Generation Computer Systems, vol. 29, iss. 3, pp. 682-692, 2013. -## Execution Traces +## Execution Instances -Execution traces are formatted according to the +Execution instances are formatted according to the [WfCommons JSON format](https://github.com/wfcommons/workflow-schema) -for describing workflow executions. Execution traces from different +for describing workflow executions. Execution instances from different computing platforms are organized into sub-folders. -Trace files are named using the following convention: +Instance files are named using the following convention: `epigenomics-----.json`, where: - ``: The compute platform where the actual Pegasus workflow diff --git a/montage/README.md b/montage/README.md index 3947063..270bbb2 100644 --- a/montage/README.md +++ b/montage/README.md @@ -1,5 +1,5 @@ - + # Execution Instances for Montage Workflow diff --git a/seismology/README.md b/seismology/README.md index 9e1a7da..eab2c9f 100644 --- a/seismology/README.md +++ b/seismology/README.md @@ -1,13 +1,13 @@ - + -# Execution Traces for Seismic Cross Correlation Workflow +# Execution Instances for Seismic Cross Correlation Workflow ## Workflow Description The Seismic Cross Correlation workflow represents a common data-intensive analysis pattern used by many seismologists. The workflow preprocesses and -cross-correlates traces (sequences of measurements of acceleration in three +cross-correlates instances (sequences of measurements of acceleration in three dimensions) from multiple seismic stations. The workflow is composed of two different tasks: @@ -34,14 +34,14 @@ publication: science. In 7th International Workshop on Data-Intensive Computing in the Clouds (pp. 1–8). https://doi.org/10.1109/DataCloud.2016.004 -## Execution Traces +## Execution Instances -Execution traces are formatted according to the +Execution instances are formatted according to the [WfCommons JSON format](https://github.com/wfcommons/workflow-schema) -for describing workflow executions. Execution traces from different +for describing workflow executions. Execution instances from different computing platforms are organized into sub-folders. -Trace files are named using the following convention: +Instance files are named using the following convention: `seismology--p-.json`, where: - ``: The compute platform where the actual Pegasus workflow diff --git a/soykb/README.md b/soykb/README.md index 40695bd..d1bb8ba 100644 --- a/soykb/README.md +++ b/soykb/README.md @@ -1,7 +1,7 @@ - + -# Execution Traces for Soybean Workflow (SoyKB) +# Execution Instances for Soybean Workflow (SoyKB) ## Workflow Description @@ -45,14 +45,14 @@ performance metrics can be found in the following research publication: workflow and browser in SoyKB,” BMC Bioinformatics, vol. 17, iss. 13, p. 337, 2016. https://doi.org/10.1186/s12859-016-1227-y -## Execution Traces +## Execution Instances -Execution traces are formatted according to the +Execution instances are formatted according to the [WfCommons JSON format](https://github.com/wfcommons/workflow-schema) -for describing workflow executions. Execution traces from different +for describing workflow executions. Execution instances from different computing platforms are organized into sub-folders. -Trace files are named using the following convention: +Instance files are named using the following convention: `soykb----.json`, where: - ``: The compute platform where the actual Pegasus workflow diff --git a/srasearch/README.md b/srasearch/README.md index 967e617..76bdd05 100644 --- a/srasearch/README.md +++ b/srasearch/README.md @@ -1,7 +1,7 @@ - + -# Execution Traces for SRA Search Workflow +# Execution Instances for SRA Search Workflow ## Workflow Description @@ -24,14 +24,14 @@ The figure below shows an overview of the SRA Search workflow structure: -## Execution Traces +## Execution Instances -Execution traces are formatted according to the +Execution instances are formatted according to the [WfCommons JSON format](https://github.com/wfcommons/workflow-schema) for -describing workflow executions. Execution traces from different computing +describing workflow executions. Execution instances from different computing platforms are organized into sub-folders. -Trace files are named using the following convention: +Instance files are named using the following convention: `srasearch---.json`, where: - ``: The compute platform where the actual Pegasus workflow