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DEIB-GECO / GMQL

GMQL - GenoMetric Query Language
http://www.bioinformatics.deib.polimi.it/geco/
Apache License 2.0
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GMQL-PythonAPI Compilation Fails #71

Closed andreagulino closed 7 years ago

andreagulino commented 7 years ago

I cloned the project and compiled all modules, but GMQL-PythonAPI module fails:

[INFO] Compiling 7 source files to /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/target/classes at 1505122245319 [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/PythonManager.scala:239: error: value COLLECT is not a member of it.polimi.genomics.GMQLServer.GmqlServer [INFO] val result = this.server COLLECT variableToCollect.get [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:173: error: not found: type MetaExtension [INFO] def createMetaExtension(name: String, node: MENode): MetaExtension = { [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:173: error: not found: type MENode [INFO] def createMetaExtension(name: String, node: MENode): MetaExtension = { [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:174: error: value metaExtensionFactory is not a member of it.polimi.genomics.GMQLServer.Implementation [INFO] val metaExtensionFactory = PythonManager.getServer.implementation.metaExtensionFactory [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:178: error: not found: type MENode [INFO] def getMENode(name: String) : MENode = { [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:179: error: not found: value MEName [INFO] MEName(name) [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:182: error: not found: type MENode [INFO] def getMEType(typename: String, value: String) : MENode = { [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:184: error: not found: value MEStringConstant [INFO] case "string" => MEStringConstant(value) [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:185: error: not found: value MEFloat [INFO] case _ => MEFloat(value.toDouble) [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:189: error: not found: type MENode [INFO] def getBinaryMetaExpression(node1: MENode, operator: String, node2: MENode): MENode = { [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:189: error: not found: type MENode [INFO] def getBinaryMetaExpression(node1: MENode, operator: String, node2: MENode): MENode = { [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:189: error: not found: type MENode [INFO] def getBinaryMetaExpression(node1: MENode, operator: String, node2: MENode): MENode = { [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:191: error: not found: value MEADD [INFO] case "ADD" => MEADD(node1, node2) [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:192: error: not found: value MEDIV [INFO] case "DIV" => MEDIV(node1, node2) [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:193: error: not found: value MESUB [INFO] case "SUB" => MESUB(node1, node2) [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:194: error: not found: value MEMUL [INFO] case "MUL" => MEMUL(node1, node2) [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:199: error: not found: type MENode [INFO] def getUnaryMetaExpression(node: MENode, operator: String) : MENode = { [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:199: error: not found: type MENode [INFO] def getUnaryMetaExpression(node: MENode, operator: String) : MENode = { [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:201: error: not found: value MENegate [INFO] case "NEG" => MENegate(node) [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/ExpressionBuilder.scala:266: error: not found: value RENegate [INFO] case "NEG" => RENegate(node) [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/OperatorManager.scala:9: error: object MetaExtension is not a member of package it.polimi.genomics.core.DataStructures.MetaAggregate [INFO] import it.polimi.genomics.core.DataStructures.MetaAggregate.{MetaAggregateStruct, MetaExtension} [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/OperatorManager.scala:116: error: not found: type MetaExtension [INFO] extended_meta : Option[MetaExtension], [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/OperatorManager.scala:161: error: too many arguments for method PROJECT: (projected_meta: Option[List[String]], extended_meta: Option[it.polimi.genomics.core.DataStructures.MetaAggregate.MetaAggregateStruct], projected_values: Option[List[Int]], extended_values: Option[List[it.polimi.genomics.core.DataStructures.RegionAggregate.RegionFunction]])it.polimi.genomics.core.DataStructures.IRVariable [INFO] val nv = v.PROJECT(projected_meta_scala, extended_meta, all_but_meta, [INFO] ^ [ERROR] /Users/andreagulino/GMQL/GMQL/GMQL-PythonAPI/src/main/scala/it/polimi/genomics/pythonapi/operators/OperatorManager.scala:188: error: not enough arguments for constructor N: (n: Int)it.polimi.genomics.core.DataStructures.CoverParameters.N. [INFO] Unspecified value parameter n. [INFO] new N { [INFO] ^ [ERROR] 24 errors found [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------