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This commit is contained in:
yanggang 2019-03-28 10:52:33 +08:00
parent e0190d6f67
commit 3772d4868c
5 changed files with 284 additions and 0 deletions
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51
piflow-bundle/src/main/resources/microorganism/biopro.json Normal file
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{
"flow":{
"name":"test",
"uuid":"1234",
"stops":[
{
"uuid":"1111",
"name":"SelectFilesByName",
"bundle":"cn.piflow.bundle.hdfs.SelectFilesByName",
"properties":{
"HDFSUrl":"hdfs://master2.packone:8020",
"HDFSPath":"/yg/microo/biproject/",
"selectionConditions":"bioproject.xml"
}
},
{
"uuid":"2222",
"name":"BioProjetDataParse",
"bundle":"cn.piflow.bundle.microorganism.BioProjetData",
"properties":{
"cachePath": "/yg/microoCache/"
}
},
{
"uuid": "3333",
"name": "putEs",
"bundle": "cn.piflow.bundle.es.PutEs",
"properties": {
"es_nodes": "10.0.88.70,10.0.88.71,10.0.88.72",
"es_port": "9200",
"es_index": "test_10",
"es_type": "test_10"
}
}
],
"paths":[
{
"from":"SelectFilesByName",
"outport":"",
"inport":"",
"to":"BioProjetDataParse"
},
{
"from":"BioProjetDataParse",
"outport":"",
"inport":"",
"to":"putEs"
}
]
}
}

68
piflow-bundle/src/main/resources/microorganism/embl.json Normal file
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{
"flow":{
"name":"test",
"uuid":"1234",
"stops":[
{
"uuid":"1111",
"name":"SelectFilesByName",
"bundle":"cn.piflow.bundle.hdfs.SelectFilesByName",
"properties":{
"HDFSUrl":"hdfs://10.0.88.70:9000",
"HDFSPath":"/yqd/ftp/embl/",
"selectionConditions":"rel_exp_con_pro_26_r138.dat.gz"
}
},{
"uuid":"2222",
"name":"UnzipFilesOnHDFS",
"bundle":"cn.piflow.bundle.hdfs.UnzipFilesOnHDFS",
"properties":{
"isCustomize":"false",
"filePath":"",
"hdfsUrl":"hdfs://master2.packone:8020",
"savePath":"/yqd/test/embl/"
}
},
{
"uuid":"3333",
"name":"EmblParser",
"bundle":"cn.piflow.bundle.microorganism.EmblData",
"properties":{
"cachePath": "/yqd/test/embl/"
}
},{
"uuid":"4444",
"name":"PutEs",
"bundle":"cn.piflow.bundle.es.PutEs",
"properties":{
"es_nodes": "10.0.88.70,10.0.88.71,10.0.88.72",
"es_port": "9200",
"es_index": "test_22",
"es_type": "test_22"
}
}
],
"paths":[
{
"from":"SelectFilesByName",
"outport":"",
"inport":"",
"to":"UnzipFilesOnHDFS"
},
{
"from":"UnzipFilesOnHDFS",
"outport":"",
"inport":"",
"to":"EmblParser"
},
{
"from":"EmblParser",
"outport":"",
"inport":"",
"to":"PutEs"
}
]
}
}

48
piflow-bundle/src/main/resources/microorganism/microbe.json Normal file
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{
"flow":{
"name":"test",
"uuid":"1234",
"stops":[
{
"uuid":"1111",
"name":"SelectFilesByName",
"bundle":"cn.piflow.bundle.hdfs.SelectFilesByName",
"properties":{
"HDFSUrl":"hdfs://10.0.88.70:9000",
"HDFSPath":"/yqd/ftp/NCBI_Microbe_genome/",
"selectionConditions":".*.gbk"
}
},{
"uuid":"3333",
"name":"MicrobeGenomeDataParser",
"bundle":"cn.piflow.bundle.microorganism.MicrobeGenomeData",
"properties":{
"cachePath":"/yqd/test/microbe/"
}
},{
"uuid":"4444",
"name":"PutEs",
"bundle":"cn.piflow.bundle.es.PutEs",
"properties":{
"es_nodes": "10.0.88.70,10.0.88.71,10.0.88.72",
"es_port": "9200",
"es_index": "test_19",
"es_type": "test_19"
}
}
],
"paths":[
{
"from":"SelectFilesByName",
"outport":"",
"inport":"",
"to":"MicrobeGenomeDataParser"
},{
"from":"MicrobeGenomeDataParser",
"outport":"",
"inport":"",
"to":"PutEs"
}
]
}
}

50
piflow-bundle/src/main/resources/microorganism/pfam.json Normal file
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@ -0,0 +1,50 @@
{
"flow":{
"name":"test",
"uuid":"1234",
"stops":[
{
"uuid":"1111",
"name":"SelectFilesByName",
"bundle":"cn.piflow.bundle.hdfs.SelectFilesByName",
"properties":{
"HDFSUrl":"hdfs://10.0.88.70:9000",
"HDFSPath":"/yqd/test/pfam/",
"selectionConditions":".*full"
}
},
{
"uuid":"3333",
"name":"PfamData",
"bundle":"cn.piflow.bundle.microorganism.PfamData",
"properties":{
"cachePath":"/yqd/test/pfam/"
}
},
{
"uuid":"4444",
"name":"putEs",
"bundle":"cn.piflow.bundle.es.PutEs",
"properties":{
"es_nodes": "10.0.88.70,10.0.88.71,10.0.88.72",
"es_port": "9200",
"es_index": "test_15",
"es_type": "test_15"
}
}
],
"paths":[
{
"from":"SelectFilesByName",
"outport":"",
"inport":"",
"to":"PfamData"
},{
"from":"PfamData",
"outport":"",
"inport":"",
"to":"putEs"
}
]
}
}

67
piflow-bundle/src/main/resources/microorganism/refseq.json Normal file
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@ -0,0 +1,67 @@
{
"flow":{
"name":"test",
"uuid":"1234",
"stops":[
{
"uuid":"1111",
"name":"SelectFilesByName",
"bundle":"cn.piflow.bundle.hdfs.SelectFilesByName",
"properties":{
"HDFSUrl":"hdfs://10.0.88.70:9000",
"HDFSPath":"/yqd/ftp/refseq/",
"selectionConditions":"archaea.4.genomic.gbff.gz"
}
},{
"uuid":"2222",
"name":"UnzipFilesOnHDFS",
"bundle":"cn.piflow.bundle.hdfs.UnzipFilesOnHDFS",
"properties":{
"isCustomize":"false",
"filePath":"",
"hdfsUrl":"hdfs://10.0.88.70:9000",
"savePath":"/yqd/test/refseq/"
}
},
{
"uuid":"3333",
"name":"Refseq_genomeParser",
"bundle":"cn.piflow.bundle.microorganism.RefseqData",
"properties":{
"cachePath":"/yqd/test/refseq/"
}
},{
"uuid":"4444",
"name":"PutEs",
"bundle":"cn.piflow.bundle.es.PutEs",
"properties":{
"es_nodes": "10.0.88.70,10.0.88.71,10.0.88.72",
"es_port": "9200",
"es_index": "test_20",
"es_type": "test_20"
}
}
],
"paths":[
{
"from":"SelectFilesByName",
"outport":"",
"inport":"",
"to":"UnzipFilesOnHDFS"
},
{
"from":"UnzipFilesOnHDFS",
"outport":"",
"inport":"",
"to":"Refseq_genomeParser"
},
{
"from":"Refseq_genomeParser",
"outport":"",
"inport":"",
"to":"PutEs"
}
]
}
}