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How to use getrowcount method in pyatom

Best Python code snippet using pyatom_python

Matrix.py

Source:Matrix.py

1# Matrix.py2# This class represents matrix.3#from __future__ import division4from DataType import DataType5from Number import Number6import Vector7# Somehow this avoids import problems.8from types import IntType, FloatType, ListType9from mit.cadlab.dome3.objectmodel.dataobject import DomeMatrixData10from mit.cadlab.dome3.objectmodel.dataobject import DomeVectorData1112#Known Bugs::13#Odd rounding occurs if the value type is Integer/int and14#operations involve a Real/float151617from math import fabs, sqrt1819class Matrix(DataType, DomeMatrixData):20    # Object Creation and Representation Methods21    def __init__(self,value0=0, value1=1):22        self.dataType = "Matrix"23        # Input is a DomeMatrixData24        if isinstance(value0, DomeMatrixData):25            DomeMatrixData.__init__(self, value0)26        elif (type(value0)==IntType and type(value1)==IntType):27            # row and column size specified28            DomeMatrixData.__init__(self, value0, value1)2930    #def __del__(self):3132    def __repr__(self):33        return str(self.getData())3435    def __str__(self):36        return str(self.getData())3738    def __cmp__(self,other):39        raise TypeError(str(self)+' cmp '+str(other))4041    #def __hash__(self):4243    def __nonzero__(self):44        # Return 0 if all elements are 045        for i in range(self.getRowCount()):46            for j in range(self.getColumnCount()):47                if self[i][j] != 0:48                    return 149        return 05051    # Methods for Attribute Access52    #def __getattr__(self, name):53    #def __setattr__(self, name, value):54    #def __delattr__(self, name):5556    # Methods for Sequence and Mapping57    #def __len__(self):5859    def __getitem__(self, key):60        #print ' key: ' + str(key)61        if key < self.getRowCount():62            #return self.getRow(key)63            #return Vector.Vector(v[key])64            #return self.getData()[key]65            # KJT: changed return type from that above to that below66            return self.getData()[key]67        else:68            raise IndexError('Index '+str(key)+' out of range')6970    #def __setitem__(self, key, value):71     #   print '...... setitem key: ' + str(key)72      #  if key < self.getRowCount():73       #     print '.... 2! setitem key: ' + str(key)74       #     self.setItem(key, value)75        #else:76         #   raise IndexError('Index '+str(key)+' out of range')7778    #def __delitem__(self, key):79    #def __getslice__(self,i,j,s):80    #def __setslice__(self,i,j,s):81    #def __delslice__(self,i,j):82    #def __contains__(self,obj):83848586    # Mathematical Operations methods87    def __add__(self,other):88        try:89            return self._add(other)90        except TypeError, e:91            try:92                return other.__radd__(self)93            except:94                raise e9596    def __sub__(self,other):97        try:98            return self._sub(other)99        except TypeError, e:100            try:101                return other.__rsub__(self)102            except:103                raise e104105    def __mul__(self,other):106        try:107            return self._mul(other)108        except TypeError, e:109            try:110                return other.__rmul__(self)111            except:112                raise e113114    def __div__(self,other):115        try:116            return self._div(other)117        except TypeError, e:118            try:119                return other.__rdiv__(self)120            except:121                raise e122123    #def __mod__(self,other):124    #def __divmod__(self,other):125    #def __pow__(self,other):126    #def __lshift__(self,other):127    #def __rshift__(self,other):128    #def __and__(self,other):129    #def __or__(self,other):130    #def __xor__(self,other):131    #def __radd__(self,other):132    #def __rsub__(self,other):133134    def __radd__(self,other):135        try:136            return self._add(other)137        except TypeError, e:138            try:139                return other.__radd__(self)140            except:141                raise e142143    def __rsub__(self,other):144        try:145            return self._sub(other)146        except TypeError, e:147            try:148                return other.__rsub__(self)149            except:150                raise e151152    def __rmul__(self,other):153        # case of scalar multiplication154        try:155            return self._mul(other)156        except TypeError, e:157            try:158                # is this a loop?159                return other.__rmul__(self)160            except:161                raise e162163164    def __rdiv__(self,other):165        raise TypeError("Cannot divide by a matrix.")166167    #def __rmod__(self,other):168    #def __rdivmod__(self,other):169    #def __rpow__(self,other):170    #def __rlshift__(self,other):171    #def __rrshift__(self,other):172    #def __rand__(self,other):173    #def __ror__(self,other):174    #def __rxor__(self,other):175    #def __iadd__(self,other):176    #def __isub__(self,other):177    #def __imul__(self,other):178    #def __idiv__(self,other):179    #def __imod__(self,other):180    #def __ipow__(self,other):181    #def __ilshift__(self,other):182    #def __irshift__(self,other):183    #def __iand__(self,other):184    #def __ior__(self,other):185    #def __ixor__(self,other):186187    def __neg__(self):188        return self*-1189190    #def __pos__(self):191    #def __abs__(self):192    #def __invert__(self):193    #def __int__(self):194    #def __long__(self):195    #def __float__(self):196    #def __complex__(self):197    #def __oct__(self):198    #def __hex__(self):199    #def __coerce__(self,other):200201202    # Comparison Operations203    #def __lt__(self,other):204    #def __le__(self,other):205    #def __gt__(self,other):206    #def __ge__(self,other):207208    def __eq__(self,other):209        #print '__eq__'210        if (isinstance(other,Matrix)) and (self.getRowCount()==other.getRowCount()) and (self.getColumnCount()==other.getColumnCount()):211            for i in range(self.getRowCount()):212                for j in range(self.getColumnCount()):213                    if self[i][j] != other[i][j]:214                        #print '... mismatch: ' + ' i=' + str(i) + ' j=' + str(j) + ' ' +str(self[i][j]) + ' ' + str(other[i][j])215                        return 0216            return 1217        else:218            return 0219220    def __ne__(self,other):221        if (isinstance(other,Matrix)) and (self.getRowCount()==other.getRowCount()) and (self.getColumnCount()==other.getColumnCount()):222            for i in range(self.getRowCount()):223                for j in range(self.getColumnCount()):224                    if self[i][j] != other[i][j]:225                        return 1226            return 0227        else:228            return 1229230    # Overidding methods of DataType231    def _copyTo(self,other):232        # not implemented233        #if isinstance(other,Matrix):234        #   other.value=self.value235        #else:236        DataType._copyTo(self,other)237238    # shallow copy239    def _copyFrom(self,other):240        if isinstance(other,Matrix):241            # check the size of other matrix if it's important.242            if self.isFixedSize() and ((self.getRowCount()!= other.getRowCount()) or (self.getColumnCount() != other.getColumnCount())):243                raise ValueError(str(self)+' copyFrom '+str(other)+': mis-matched sizes')244            else:245                self.setValueType(other.getValueType())246                # setData updates the units, initialValue, isFixedSize,247                self.setData(other)248        elif isinstance(other, Vector.Vector):249            if self.isFixedSize() and (self.getRowCount()!=other.getSize()) or (self.getColumnCount()!=1):250                raise ValueError(str(self)+' copyFrom '+str(other)+': mis-matched sizes')251            elif self.isFixedSize() and (self.getColumnCount()!=other.getSize()) or (self.getRowCount()!=1):252                raise ValueError(str(self)+' copyFrom '+str(other)+': mis-matched sizes')253            elif (self.isFixedSize() and self.getColumnCount()==1):254                self.setValueType(other.getValueType())255                self.setUnit(other.getUnit())256                self.setInitialValue(other.getInitialValue())257                self.setFixedSize(other.getFixedSize())258                for i in range(other.getSize()):259                    self[i][0] = other[i]260            elif (self.isFixedSize() and self.getRowCount()==1):261                self.setValueType(other.getValueType())262                self.setUnit(other.getUnit())263                self.setInitialValue(other.getInitialValue())264                self.setFixedSize(other.getFixedSize())265                for i in range(other.getSize()):266                    self[0][i] = other[i]267            else:268                self.setValueType(other.getValueType())269                self.setRowCount(1);270                self.setColumnCount(other.getSize());271                self.setUnit(other.getUnit())272                self.setInitialValue(other.getInitialValue())273                self.setFixedSize(other.getFixedSize())274                for i in range(other.getSize()):275                    self[0][i] = other[i]276        elif isinstance(other, ListType):277            if self.isFixedSize() and (self.getRowCount()!=len(other)) or (self.getColumnCount()!=1):278                raise ValueError(str(self)+' copyFrom '+str(other)+': mis-matched sizes')279            elif self.isFixedSize() and (self.getColumnCount()!=len(other)) or (self.getRowCount()!=1):280                raise ValueError(str(self)+' copyFrom '+str(other)+': mis-matched sizes')281            elif (self.isFixedSize() and self.getColumnCount()==1):282                self.setValueType(other.getValueType())283                self.setUnit(other.getUnit())284                self.setInitialValue(other.getInitialValue())285                self.setFixedSize(other.getFixedSize())286                for i in range(len(other)):287                    self[i][0] = other[i]288            elif (self.isFixedSize() and self.getRowCount()==1):289                self.setValueType(other.getValueType())290                self.setUnit(other.getUnit())291                self.setInitialValue(other.getInitialValue())292                self.setFixedSize(other.getFixedSize())293                for i in range(len(other)):294                    self[0][i] = other[i]295            else:296                self.setValueType(other.getValueType())297                self.setRowCount(1);298                self.setColumnCount(len(other));299                self.setUnit(other.getUnit())300                self.setInitialValue(other.getInitialValue())301                self.setFixedSize(other.getFixedSize())302                for i in range(len(other)):303                    self[0][i] = other[i]304        else:305            # raises TypeError306            DataType._copyFrom(self,other)307308309    def dup(self):310        # return a copy of one self311        #return Matrix(self.duplicate())312        # !!!!!!!! deep copy in Java is broken !!!!!!313        returnMatrix=Matrix(self.getRowCount(),self.getColumnCount())314        for i in range(self.getRowCount()):315            for j in range(self.getColumnCount()):316                if isNumberType(self[i][j]):317                    returnMatrix[i][j]=self[i][j]318                else:319                    returnMatrix[i][j]=self[i][j].dup()320        returnMatrix.setUnit(self.getUnit())321        returnMatrix.setInitialValue(self.getInitialValue())322        returnMatrix.setFixedSize(self.isFixedSize())323        returnMatrix.setValueType(self.getValueType())324        return returnMatrix325326327    # Matrix specific functions, probably will move to DMath.py328    def inverse(self):329        # eee... implement Gauss-Jordan elimination?330        # first matrix must be square331        if (not self.isSquare()):332            raise ValueError(str(self)+' must be sqaure to have an inverse.')333        elif (self.det()==0):334            raise ValueError(str(self)+' is not invertible, determinant == 0.')335        else:336            dim = self.getRowCount();337            augMatrix = self.catH(self.IdentityMatrix(dim,338                                                      dim))339340            gauss = augMatrix.gaussianElimination()341            #print '.....Finished gaussian Elimination(): ' + str(gauss)342            # divide through by pivots343            #print '..... size of gauss, rows:' + str(gauss.getRowCount()) + ' cols:' + str(gauss.getColumnCount())344            for i in range(dim):345                pivot = gauss[i][i]346                #print '....pivot=' + str(pivot) + '  i=' + str(i)347                for j in range(2*dim):348                    #print '.... j=' + str(j)349                    #print '.......' + str(gauss[i][j])350                    gauss[i][j]=gauss[i][j]/pivot351                    if gauss[i][j] == 0:352                        gauss[i][j] = 0353            return gauss.subMatrix(0, dim, dim-1, 2*dim-1)354355    def gaussianElimination(self):356        returnMatrix = self.dup()357        if (returnMatrix.getValueType()=='Integer'):358            returnMatrix.setValueType('real')359        diagonal = self.getColumnCount()360        if (self.getRowCount()<self.getColumnCount()):361            diagonal = self.getRowCount()362        for j in range(diagonal):363            rowIndex = returnMatrix._rowMax(j)364            returnMatrix._rowSwap(j, rowIndex)365            if (returnMatrix[j][j]==0.0):366                return Matrix(0,0)367            for k in range(self.getRowCount()):368                if (k!=j):369                    returnMatrix._rowZero(j,j,k)370        return returnMatrix371372373    def catH(self, other):374        # return matrix of [self, other]375        # make sure the number of rows are equal376        ### MAYBE should use the java super's appendHorizontally()377        if not(isinstance(other, Matrix)):378            raise TypeError(str(other)+' is not a Matrix and cannnot be used in catH.')379        elif (self.getRowCount() != other.getRowCount()):380            raise ValueError(str(self)+' catH '+str(other)+' row number not the same.')381        else:382            tRow = self.getRowCount()383            tCol = self.getColumnCount() + other.getColumnCount()384            returnMatrix = Matrix(tRow, tCol)385            for i in range(tRow):386               for j in range(tCol):387                   if j < self.getColumnCount():388                       returnMatrix[i][j] = self[i][j]389                   else:390                       returnMatrix[i][j]=other[i][j-self.getColumnCount()]391            return returnMatrix392393    def catV(self, other):394        # return matrix of [self; other]395        # make sure the number of rows are equal396        ### MAYBE should use the java super's appendVertically()397        if not(isinstance(other, Matrix)):398            raise TypeError(str(other)+' is not a Matrix and cannnot be used in catV.')399        elif (self.getColumnCount() != other.getColumnCount()):400            raise ValueError(str(self)+' catV '+str(other)+' column number not the same.')401        else:402            tRow = self.getRowCount() + other.getRowCount()403            tCol = self.getColumnCount()404            returnMatrix = Matrix(tRow, tCol)405            for i in range(tRow):406               for j in range(tCol):407                   if i < self.getRowCount():408                       returnMatrix[i][j] = self[i][j]409                   else:410                       returnMatrix[i][j]=other[i-self.getRowCount()][j]411            return returnMatrix412413414415    def IdentityMatrix(self, rowCount, colCount):416        # errr, as close as it can get if it's not nxn.417        if (not(type(rowCount)==IntType) or not(type(colCount)==IntType)):418            raise TypeError(str(rowCount)+' or '+str(colCount)+' are not integer types')419        returnMatrix = Matrix(rowCount, colCount)420        cC=0421        for rC in range(rowCount):422            returnMatrix[rC][cC]=1423            cC=cC+1424            if cC >= colCount:425                return returnMatrix426        return returnMatrix427428    def transpose(self):429        # rows vs. columns.430        returnMatrix = Matrix(self.getColumnCount(), self.getRowCount())431        for i in range(self.getRowCount()):432            for j in range(self.getColumnCount()):433                returnMatrix[j][i] = self[i][j]434        return returnMatrix435436    def rowEchelon(self):437        numSwaps = 0438        return self._fwdElimination(numSwaps)[0]439440441442    def subMatrix(self, r1, c1, r2, c2):443        if r2 < r1:444            rHold = r2445            r2 = r1446            r1 = rHold447        if c2 < c1:448            cHold = c2449            c2 = c1450            c1 = cHold451        subRow = r2-r1+1452        subCol = c2-c1+1453        if (r2 < self.getRowCount()) and (c2 < self.getColumnCount()) and r1>=0 and r2 >=0:454            returnMatrix = Matrix(subRow, subCol)455            i2 = 0456            for i in range(r1,r2+1):457                j2 = 0458                for j in range(c1,c2+1):459                    returnMatrix[i2][j2] = self[i][j]460                    j2 = j2+1461                i2 = i2+1462            return returnMatrix463        else:464            raise IndexError('Indices not in range.')465466    def det(self):467        changedType = 0;468        if (self.isEmpty() or (not self.isSquare())):469            #print ' self is empty or not square'470            return 0.0471        if (self.getRowCount()==1):472            #print ' row count == 1'473            return self[0][0]474        if (self.getRowCount()==2):475            #print ' row count == 2'476            return ((self[0][0]*self[1][1])-(self[1][0]*self[0][1]))477        # matrix is not Empty, is Square, rows>2, use fwdElimination478        numSwaps = 0479        mtmp = self._fwdElimination(numSwaps)480        m = mtmp[0]481        numSwaps = mtmp[1]482        #print 'numSwaps: ' + str(numSwaps)483        if (m.isEmpty()):484            #print 'm is empty'485            return 0.0486        result = 1.0487        for i in range(self.getColumnCount()):488            result *= m[i][i]489        factor = -1490        if (numSwaps%2)==0:491            1492        result *= factor493        #print ' result: ' + str(result)494        return result495496497    def trace(self):498        result = 0.0499        diagonal = self.getColumnCount()500        if (self.getRowCount()<self.getColumnCount()):501            diagonal = self.getRowCount()502        for i in range(diagonal):503            result += self[i][i]504        return result505506507    def euclidNorm(self):508        return sqrt(self.sumOfSquares())509510511    def sumOfSquares(self):512        result = 0.0513        rows = self.getRowCount()514        cols = self.getColumnCount()515        value = 0.0516        for i in range(rows):517            for j in range(cols):518                value = self[i][j]519                result += value*value520        return result521522523    def absSum(self):524        result = 0.0525        for i in range(self.getRowCount()):526            for j in range(self.getColumnCount()):527                result += abs(self[i][j])528        return result529530531    def fill(self, value):532        # integer, real, float, int533        rows = self.getRowCount()534        cols = self.getColumnCount()535        if (isinstance(value, Number)):536            value = value.getValue()537        try:538            #print '...fill value: ' + str(value)539            for i in range(rows):540                for j in range(cols):541                    #self.setItem(i,j,value)542                    self[i][j] = value543        except TypeError, e:544            raise e545546    def getRow(self, index):547        # KJT, replaced following with line below: returnRow = self[index].dup()548        returnRow = DomeMatrixData.getRow(self, index)549        returnRow.setUnit(self.getUnit())550        return returnRow551552    def getCol(self, index):553        returnCol = DomeMatrixData.getCol(self, index)554        returnCol.setUnit(self.getUnit())555        return returnCol556        #KJT: changed implementation from that below to that above557        #returnVector = Vector.Vector()558        #returnVector.setSize(self.getRowCount())559        #returnVector.setValueType(self.getValueType())560        #returnVector.setInitialValue(self.getInitialValue())561        #returnVector.setUnit(self.getUnit())562        # assuming this is a column vector563        #for i in range(self.getRowCount()):564        #    returnVector[i] = self[i][index]565        #return returnVector566567568    def numRows(self):569        return self.getRowCount()570571    def numCols(self):572        return self.getRowCount()573574    def size(self):575        return [self.getRowCount(), self.getColumnCount()]576        #KJT return self.getRowCount() * self.getColumnCount()577578    #def setSize(self, rows, cols):579     #   self.setRowCount(rows)580      #  self.setColumnCount(cols)581582    def setSize(self, rows, cols, value=0):583        oldRow = self.getRowCount()584        oldCol = self.getColumnCount()585        self.setRowCount(rows)586        self.setColumnCount(cols)587        if rows > oldRow:588            #print '...... set value of extra row'589            for i in range(oldRow, rows):590                for j in range(cols):591                    #print 'i='+str(i)+' j='+str(j)+' val='+str(value)592                    self[i][j] = value593        if cols > oldCol:594            #print '.... set value of extra col'595            for j in range(oldCol, cols):596                for i in range(rows):597                    #print 'i='+str(i)+ ' j=' + str(j) + ' val=' + str(value)598                    self[i][j] = value599600601    def setNumRows(self, rows, value=0):602        oldRow = self.getRowCount()603        self.setRowCount(rows)604        if rows > oldRow:605            for i in range(oldRow, rows):606                for j in range(self.getColumnCount()):607                    self[i][j] = value608                    #print 'i='+str(i)+' j='+ str(j)+' val='+str(value)609610611    def setNumCols(self, cols, value=0):612        oldCol = self.getColumnCount()613        self.setColumnCount(cols)614        if cols > oldCol:615            for j in range(oldCol, cols):616                for i in range(self.getRowCount()):617                    self[i][j] = value618                    #print 'i='+str(i)+' j='+str(j)+' val='+str(value)619620621    def setRow(self, index, value):622        if (not (isinstance(value, Vector.Vector))):623            raise TypeError('setRow(), ' +str(value)+': is not a Vector')624        if (value.getSize() != self.getColumnCount()) :625            raise ValueError('setRow(), '+str(value)+': mis-matched sizes')626        if (index >= self.getRowCount()):627            raise ValueError('setRow(), '+str(index)+': index out of range')628        else:629            for j in range(self.getColumnCount()):630                self[index][j] = value[j]631632633    def setCol(self, index, value):634        if (not (isinstance(value, Vector.Vector))):635            raise TypeError('setCol(), ' +str(value)+': is not a Vector')636        if (value.getSize() != self.getRowCount()) :637            raise ValueError('setCol(), '+str(value)+': mis-matched sizes')638        if (index >= self.getColumnCount()):639            raise ValueError('setCol(), '+str(index)+': index out of range')640        else:641            for i in range(self.getRowCount()):642                self[i][index] = value[i]643644    # Undefined645    def euclideanNorm():646        return sqrt(self.sumOfSquares())647648649650    # Actually implementation of mathematical operators651    def _add(self,other):652        if (isinstance(other, Number)):653            # scalar add654            returnMatrix = self.dup()655            if (isinstance(other, Real)):656                # automatically change return matrix type to real657                returnMatrix.setValueType("real")658            for i in range(returnMatrix.getRowCount()):659                for j in range(returnMatrix.getColumnCount()):660                    returnMatrix[i][j] = returnMatrix[i][j]+other.value661        elif isNumberType(other):662            #scalar add663            returnMatrix = self.dup()664            if (type(other)==FloatType):665                # automatically change return matrix type to real666                returnMatrix.setValueType("real")667            for i in range(returnMatrix.getRowCount()):668                for j in range(returnMatrix.getColumnCount()):669                    returnMatrix[i][j] = returnMatrix[i][j]+other670            return returnMatrix671        elif isinstance(other, Matrix):672            # check the size of other matrix673            if (self.getRowCount()== other.getRowCount()) and (self.getColumnCount() == other.getColumnCount()):674                returnMatrix = self.dup()675                for i in range(returnMatrix.getRowCount()):676                    for j in range(returnMatrix.getColumnCount()):677                        returnMatrix[i][j] = returnMatrix[i][j]+other[i][j]678                if (other.getValueType()=='real'):679                    returnMatrix.setValueType('real')680                return returnMatrix681            else:682                raise ValueError(str(self)+' + '+str(other)+': mis-matched sizes')683        elif isinstance(other, Vector.Vector):684            if (self.getRowCount()==other.getSize()) and (self.getColumnCount()==1):685                returnMatrix = self.dup()686                for i in range(other.getSize()):687                    returnMatrix[i][0] = returnMatrix[i][0] + other[i]688                return returnMatrix689            elif (self.getColumnCount()==other.getSize()) and (self.getRowCount()==1):690                returnMatrix = self.dup()691                for i in range(other.getSize()):692                    returnMatrix[0][i] = returnMatrix[0][i] + other[i]693                return returnMatrix694            else:695                raise ValueError(str(self)+' + '+str(other)+': mis-matched sizes')696        elif isinstance(other, ListType):697            if ((self.getRowCount()==len(other)) and (self.getColumnCount()==1)):698                returnMatrix = self.dup()699                for i in range(len(other)):700                    returnMatrix[i][0] = returnMatrix[i][0]+other[i]701                return returnMatrix702            elif (self.getColumnCount()==len(other)) and (self.getRowCount()==1):703                returnMatrix = self.dup()704                for i in range(len(other)):705                    returnMatrix[0][i] = returnMatrix[0][i]+other[i]706                return returnMatrix707            else:708                raise ValueError(str(self)+' + '+str(other)+': mis-matched sizes')709710        else:711            raise TypeError('Matrix cannot be added to with '+712                            other.getClass().getName())713714    def _sub(self,other):715        if isinstance(other, Number):716            #scalar sub717            returnMatrix = self.dup()718            for i in range(returnMatrix.getRowCount()):719                for j in range(returnMatrix.getColumnCount()):720                    returnMatrix[i][j] = returnMatrix[i][j]-other.value721        elif isNumberType(other):722            #scalar sub723            returnMatrix = self.dup()724            for i in range(returnMatrix.getRowCount()):725                for j in range(returnMatrix.getColumnCount()):726                    returnMatrix[i][j] = returnMatrix[i][j]-other727            return returnMatrix728        elif isinstance(other, Matrix):729            # check the size of other matrix730            if (self.getRowCount()== other.getRowCount()) and (self.getColumnCount() == other.getColumnCount()):731                returnMatrix = self.dup()732                for i in range(returnMatrix.getRowCount()):733                    for j in range(returnMatrix.getColumnCount()):734                        returnMatrix[i][j] = returnMatrix[i][j]-other[i][j]735                return returnMatrix736            else:737                raise ValueError(str(self)+' - '+str(other)+': mis-matched sizes')738        elif isinstance(other, Vector.Vector):739            if (self.getRowCount()==other.getSize()) and (self.getColumnCount()==1):740                returnMatrix = self.dup()741                for i in range(other.getSize()):742                    returnMatrix[i][0] = returnMatrix[i][0] - other[i]743                return returnMatrix744            elif (self.getColumnCount()==other.getSize()) and (self.getRowCount()==1):745                returnMatrix = self.dup()746                for i in range(other.getSize()):747                    returnMatrix[0][i] = returnMatrix[0][i] - other[i]748                return returnMatrix749            else:750                raise ValueError(str(self)+' - '+str(other)+': mis-matched sizes')751        elif isinstance(other, ListType):752            if ((self.getRowCount()==len(other)) and (self.getColumnCount()==1)):753                returnMatrix = self.dup()754                for i in range(len(other)):755                    returnMatrix[i][0] = returnMatrix[i][0]-other[i]756                return returnMatrix757            elif (self.getColumnCount()==len(other)) and (self.getRowCount()==1):758                returnMatrix = self.dup()759                for i in range(len(other)):760                    returnMatrix[0][i] = returnMatrix[0][i]-other[i]761                return returnMatrix762            else:763                raise ValueError(str(self)+' - '+str(other)+': mis-matched sizes')764        else:765            raise TypeError('Matrix cannot be subtracted to with a '+766                            other.getClass().getName())767768    def _mul(self,other):769        if isinstance(other, Number):770            #scalar multiplication771            returnMatrix = self.dup()772            for i in range(returnMatrix.getRowCount()):773                for j in range(returnMatrix.getColumnCount()):774                    returnMatrix[i][j] = returnMatrix[i][j]*other.value775        elif isNumberType(other):776            #scalar multiplication777            returnMatrix = self.dup()778779            for i in range(returnMatrix.getRowCount()):780                for j in range(returnMatrix.getColumnCount()):781                    returnMatrix[i][j] = returnMatrix[i][j]*other782            return returnMatrix783        elif isinstance(other, Matrix):784            # check the size of other matrix, size of rows == size of columns785            # or number of columns == # of rows786            if (self.getColumnCount()== other.getRowCount()):787                # return has self # rows and other # columns788                returnMatrix = Matrix(self.getRowCount(),789                                      other.getColumnCount())790                for i in range(returnMatrix.getRowCount()):791                    for j in range(returnMatrix.getColumnCount()):792                        entry = 0793                        for sC in range(selfMatrix.getColumnCount()):794                            for oR in range(selfMatrix.getRowCount()):795                                entry = self[i][sC]*other[oR][j]+entry796                        returnMatrix[i][j] = entry797                return returnMatrix798            else:799                raise ValueError(str(self)+' * '+str(other)+': mis-matched sizes')800        elif isinstance(other, Vector.Vector):801            # !!!! Need to worry about reverse, Vector * Matrix802            if (self.getColumnCount()==other.getSize()):803                returnMatrix = Matrix(self.getRowCount(),804                                      1)805806                for i in range(returnMatrix.getRowCount()):807                    entry = 0808                    for sC in range(returnMatrix.getColumnCount()):809                        entry = self[0][sC]*other[sC] + entry810                    returnMatrix[i][0] = entry811                return returnMatrix812            else:813                raise ValueError(str(self)+' * '+str(other)+': mis-matched sizes')814        elif isinstance(other, ListType):815            if (self.getColumnCount()==len(other)):816                returnMatrix = Matrix(self.getRowCount(),817                                      1)818                for i in range(returnMatrix.getRowCount()):819                    entry = 0820                    for sC in range(returnMatrix.getColumnCount):821                        entry = self[0][sC]*other[sC] + entry822                    returnMatrix[i][0] = entry823                return returnMatrix824            else:825                raise ValueError(str(self)+' * '+str(other)+': mis-matched sizes')826        else:827            raise TypeError('Matrix cannot be multiplied by a '+828                            other.getClass().getName())829830831    def _div(self,other):832        if isinstance(other, Number):833            #scalar multiplication834            returnMatrix = self.dup()835            for i in range(returnMatrix.getRowCount()):836                for j in range(returnMatrix.getColumnCount()):837                    returnMatrix[i][j] = returnMatrix[i][j]/other.value838        elif isNumberType(other):839            #like scalar multiplication840            returnMatrix = self.dup()841842            for i in range(returnMatrix.getRowCount()):843                for j in range(returnMatrix.getColumnCount()):844                    returnMatrix[i][j] = returnMatrix[i][j]/other845            return returnMatrix846        else:847            raise TypeError('Matrix cannot be divided by a '+848                            other.getClass().getName())849850851    # Need to change852    #def _pow(self,other):853    #def __radd__(self,other):854    #def __rsub__(self,other):855    #def __rmul__(self,other):856    #def __rdiv__(self,other):857    #def __rmod__(self,other):858    #def __rpow__(self,other):859    #def __neg__(self):860    #def __pos__(self):861    #def __abs__(self):862    #def __int__(self):863    #def __float__(self):864    #def __long__(self):865    #def __complex__(self):866867868    # Undocumented helper functions869    def isEmpty(self):870        return (self.getRowCount()==0) or (self.getColumnCount()==0)871872    def isSquare(self):873        return self.getRowCount()==self.getColumnCount()874875    def isUpperTriangular(self):876        if (self.isEmpty()):877            return false878        rows = self.getRowCount()879        cols = self.getColumnCount()880        for i in range(1,rows):881            #if ((i<cols)&&((self[i][i]==0)) return false882            j = 0883            while (j<i) and (j<cols):884                if (self[i][j]!=0):885                    return false886                j=j+1887        return true888889    def isNonSingular(self):890        if (self.isEmpty()):891            return false892        if (self.isUpperTriangular()):893            diagonal = self.getColumnCount()894            if (self.getRowCount()<self.getColumnCount()):895                diagonal = self.getRowCount()896            index = 0897            while (index<diagonal):898                if (self[index][index]==0):899                    return false900                index=index+1901            return true902        rowEchelonForm = self.rowEchelon()903        rowEchelonForm.isNonSingular()904905906907908    # private helper functions doing row manipulations909910    def _fwdElimination(self, numSwaps):911        # numSwaps should be an int912        returnMatrix = self.dup()913        if (returnMatrix.getValueType() == 'Integer'):914            returnMatrix.setValueType('real')915        rows = self.getRowCount()916        cols = self.getColumnCount()917        diagonal = cols918        if (rows<cols):919            diagonal = rows920        numSwaps=0921        for j in range(diagonal):922            numSwaps += returnMatrix._rowSwap(j, returnMatrix._rowMax(j))923            if (returnMatrix[j][j]==0):924                #print 'found a 0 on the diagonal'925                # Not certain if this is what we really want to return...926                return [Matrix(0,0), numSwaps]927            for k in range(j+1, rows):928                #print '.... returnMatrix after rowSwap:' + str(returnMatrix)929                returnMatrix._rowZero(j,j,k)930                #print 'k=' + str(k) + ' matrix:' + str(returnMatrix)931            #print '???? ' + str(returnMatrix)932        return [returnMatrix, numSwaps]933934    def _rowSwap(self, r1, r2):935        # r1, r2 are int936        # assert r1 and r2 are valid937        if (r1==r2):938            return 0939        numCols = self.getColumnCount()940        tmp = 0.0941        for j in range(numCols):942            tmp = self[r1][j]943            self[r1][j]=self[r2][j]944            self[r2][j]=tmp945        return 1946947    def _rowScale(self, rIndex, factor):948        # rIndex is int, factor is real949        numCols = self.getColumnCount()950        for j in range(numCols):951            self[rIndex][j]*=factor952953    def _rowZero(self, col, r1, r2):954        # assert col, r1 and r2 are valid955        # adding a multiple of r1 to r2, r1 is left unchanged956        #print ' numerator: ' + str(self[r2][col])957        #print ' denominator ' + str(self[r1][col])958        numerator = float(self[r2][col])959        denominator = float(self[r1][col])960        factor = -1.0*(numerator/denominator)961        #print '_rowZero factor=' + str(factor) +' col=' + str(col) + ' r1='+ str(r1) + ' r2=' + str(r2)962        numCols = self.getColumnCount()963        for j in range(numCols):964            self[r2][j] += self[r1][j]*factor965        #print ' after rowZero: ' + str(self)966967968    def _rowMax(self, c):969        # returns number of row with highest absolute value in specified970        # column971        # starts searching at r=c972        # assert c is valid973        # c is an int974        r = c975        result = r976        #print '_rowMax c = ' + str(c)977        maxValue = fabs(self[result][c])978        #print '.... init maxValue ' + str(maxValue) + ' init result ' +  str(result)979        for i in range(r, self.getRowCount()):980        #while r<self.getRowCount():981            currentValue = fabs(self[i][c])982            #print '...... currentValue at ' + str(i) + ' is:' + str(currentValue)983            if (currentValue > maxValue):984                result = i985                maxValue = currentValue986        #print '_rowMax result=' + str(result)987        return result988989990991    # Conversion functions992993    def array(self):994        returnList = []995        for i in range(self.getRowCount()):996            returnList.append(self[i].array())997        return returnList9989991000100110021003#Helper functions1004def isNumberType(x):1005    return type(x)==IntType or type(x)==FloatType100610071008
...

test_session.py

Source:test_session.py

1# Copyright (C) 2018-2021 CS GROUP - France. All Rights Reserved.2#3# This file is part of the Prewikka program.4#5# SPDX-License-Identifier: BSD-2-Clause6#7# Redistribution and use in source and binary forms, with or without8# modification, are permitted provided that the following conditions are met:9#10# 1. Redistributions of source code must retain the above copyright notice, this11#    list of conditions and the following disclaimer.12#13# 2. Redistributions in binary form must reproduce the above copyright notice,14#    this list of conditions and the following disclaimer in the documentation15#    and/or other materials provided with the distribution.16#17# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND18# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIEDi19# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE20# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR21# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES22# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;23# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND24# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT25# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS26# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.27"""28Tests for `prewikka.session.session`.29"""30from copy import deepcopy31import datetime32import time33from http import cookies34import pytest35from prewikka.config import ConfigSection36from prewikka.session.session import SessionInvalid, SessionExpired, SessionDatabase, Session37from prewikka.usergroup import User38from tests.fixtures import TEST_SESSION_ID39from tests.tests_session.utils import FakeAuthBackend, create_session, clean_sessions40def test_session_invalid():41    """42    Test `prewikka.session.session.SessionInvalid` error.43    """44    session_invalid = SessionInvalid()45    with pytest.raises(SessionInvalid):46        raise session_invalid47    session_invalid = SessionInvalid(login='test')48    with pytest.raises(SessionInvalid):49        raise session_invalid50def test_session_expired():51    """52    Test `prewikka.session.session.SessionExpired` error.53    """54    session_expired = SessionExpired()55    with pytest.raises(SessionExpired):56        raise session_expired57    session_expired = SessionExpired(login='test')58    with pytest.raises(SessionExpired):59        raise session_expired60def test_session_db_create_():61    """62    Test `prewikka.session.session.SessionDatabase.create_session` method.63    """64    user = User('anonymous')65    session_id = create_session(user)66    query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)67    assert query.getRowCount() == 168    assert session_id in query.toString()69    assert user.name in query.toString()70    clean_sessions()71def test_session_db_update():72    """73    Test `prewikka.session.session.SessionDatabase.update_session` method.74    """75    session_database = SessionDatabase()76    user = User('anonymous')77    session_id = create_session(user)78    old_query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)79    time_ = time.time() + 3600  # add 3600s80    session_database.update_session(session_id, time_)81    query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)82    assert old_query.toString() != query.toString()83    assert query.getRowCount() == 184    assert session_id in query.toString()85    assert user.name in query.toString()86    assert datetime.datetime.utcfromtimestamp(time_).strftime('%Y-%m-%d %H:%M:%S')in query.toString()87    # wrong session_id: nothing happening88    fake_session_id = 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'89    session_database.update_session(fake_session_id, time_)90    clean_sessions()91def test_session_db_get():92    """93    Test `prewikka.session.session.SessionDatabase.get_session` method.94    """95    session_database = SessionDatabase()96    user = User('anonymous')97    session_id = create_session(user)98    query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)99    assert query.getRowCount() == 1100    username, time_ = session_database.get_session(session_id)101    assert username == user.name102    assert datetime.datetime.utcfromtimestamp(time_).strftime('%Y-%m-%d %H:%M:%S')in query.toString()103    # wrong session_id: fail104    with pytest.raises(Exception):105        fake_session_id = 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'106        session_database.get_session(fake_session_id)107    clean_sessions()108def test_session_db_delete():109    """110    Test `prewikka.session.session.SessionDatabase.delete_session` method.111    """112    session_database = SessionDatabase()113    user = User('anonymous')114    # delete 1 session based on sessionid115    session_id = create_session(user)116    query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)117    assert query.getRowCount() == 1118    session_database.delete_session(sessionid=session_id)119    query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)120    assert query.getRowCount() == 0121    # delete 1 session based on userid122    session_id = create_session(user)123    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)124    assert session_id in query.toString()125    assert query.getRowCount() == 1126    session_database.delete_session(user=user)127    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)128    assert query.getRowCount() == 0129    # delete multiple sessions based on userid130    session_id_1 = create_session(user)131    session_id_2 = create_session(user)132    session_id_3 = create_session(user)133    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)134    assert session_id_1 in query.toString()135    assert session_id_2 in query.toString()136    assert session_id_3 in query.toString()137    assert query.getRowCount() == 3138    session_database.delete_session(user=user)139    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)140    assert query.getRowCount() == 0141    clean_sessions()142    # delete session based on invalid sessionid: nothing happening143    create_session(user)144    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)145    assert query.getRowCount() == 1146    fake_session_id = 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'147    session_database.delete_session(sessionid=fake_session_id)148    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)149    assert query.getRowCount() == 1150    # delete session based on invalid userid: nothing happening151    fake_user = User('fake')152    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', fake_user.id)153    assert query.getRowCount() == 0154    session_database.delete_session(user=fake_user)155    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)156    assert query.getRowCount() == 1157    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', fake_user.id)158    assert query.getRowCount() == 0159    # delete session with both userid and sessionid: fail160    with pytest.raises(Exception):161        fake_session_id = 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'162        fake_user_id = 'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb'163        session_database.delete_session(sessionid=fake_session_id, user=fake_user_id)164    # delete session without userid and sessionid: nothing165    session_database.delete_session(sessionid=None, user=None)166    clean_sessions()167def test_session_db_delete_expired_():168    """169    Test `prewikka.session.session.SessionDatabase.delete_expired_sessions` method.170    """171    session_database = SessionDatabase()172    user = User('anonymous')173    t_now = time.time()174    t_before = t_now - 3600175    t_after = t_now + 3600176    # without sessions in database177    session_database.delete_expired_sessions(t_now)178    # with 1 session expired in database179    session_id = create_session(user, t_before)180    session_database.delete_expired_sessions(t_now)181    query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)182    assert query.getRowCount() == 0183    # with 1 session NOT expired in database184    session_id = create_session(user, t_after)185    session_database.delete_expired_sessions(t_now)186    query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)187    assert query.getRowCount() == 1188    clean_sessions()189    # with 2 sessions expired and 1 not expired190    session_id_1 = create_session(user, t_before)191    session_id_2 = create_session(user, t_before)192    session_id_3 = create_session(user, t_after)193    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)194    assert query.getRowCount() == 3195    session_database.delete_expired_sessions(t_now)196    query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)197    assert query.getRowCount() == 1198    assert session_id_1 not in query.toString()199    assert session_id_2 not in query.toString()200    assert session_id_3 in query.toString()201    clean_sessions()202def test_session():203    """204    Test `prewikka.session.session.Session` class.205    """206    session_config = ConfigSection("")207    session_config.expiration = 60  # 1 hour208    create_session(env.request.user, session_id=TEST_SESSION_ID)209    req = deepcopy(env.request.web)210    # __init__()211    session = Session(session_config)212    # get_user()213    user_from_session = session.get_user(req)214    assert env.request.user == user_from_session215    # get_user() with old (but valid) cookie216    clean_sessions()217    create_session(env.request.user, time_=time.time()-3600, session_id=TEST_SESSION_ID)218    user_from_session = session.get_user(req)219    assert env.request.user == user_from_session220    # get_user() with invalid session (empty cookie)221    with pytest.raises(SessionInvalid):222        req = deepcopy(env.request.web)223        req.input_cookie = {}224        session.get_user(req)225    # get_user() with expired session (AJAX request)226    with pytest.raises(SessionExpired):227        req = deepcopy(env.request.web)228        req.input_cookie = {}229        req.is_xhr = True230        session.get_user(req)231    # get_user() with invalid session (bad session_id)232    with pytest.raises(SessionInvalid):233        req = deepcopy(env.request.web)234        req.input_cookie['sessionid'] = cookies.Morsel()235        req.input_cookie['sessionid'].value = 'invalid'236        session.get_user(req)237    # get_user() with expired session (cookie expired)238    with pytest.raises(SessionExpired):239        clean_sessions()240        req = deepcopy(env.request.web)241        create_session(env.request.user, time_=time.time()-3600*24, session_id=TEST_SESSION_ID)242        session = Session(session_config)243        session.get_user(req)244    # get_user() with invalid user245    backup_user = env.request.user246    with pytest.raises(SessionInvalid):247        req = deepcopy(env.request.web)248        env.request.user = User('test')249        session.get_user(req)250    env.request.user = backup_user251    # get_user() with changed backend252    backup_auth = env.auth253    with pytest.raises(SessionInvalid):254        req = deepcopy(env.request.web)255        clean_sessions()256        create_session(env.request.user, session_id=TEST_SESSION_ID)257        env.auth = FakeAuthBackend(ConfigSection(""))258        session.get_user(req)259    env.auth = backup_auth260    # logout()261    with pytest.raises(SessionInvalid):262        clean_sessions()263        create_session(env.request.user, session_id=TEST_SESSION_ID)264        session = Session(session_config)265        req = deepcopy(env.request.web)266        session.logout(req)267    # can_logout()268    assert session.can_logout()...

ParseBED.py

Source:ParseBED.py

1from __future__ import print_function2# This file is part of DQXServer - (C) Copyright 2014, Paul Vauterin, Ben Jeffery, Alistair Miles <info@cggh.org>3# This program is free software licensed under the GNU Affero General Public License.4# You can find a copy of this license in LICENSE in the top directory of the source code or at <http://opensource.org/licenses/AGPL-3.0>5from builtins import str6from DQXTableUtils import VTTable7import sys8basepath = '.'9#============= FAKE STUFF FOR DEBUGGING; REMOVE FOR PRODUCTION ==============10if True:11    basepath = '/Users/pvaut/Documents/Genome/SnpCrossData3'12    sys.argv = ['', 'genomeregions.bed']13#============= END OF FAKE STUFF ============================================14if len(sys.argv)<2:15    print('Usage: COMMAND BEDFileName')16    sys.exit()17sourcefile = sys.argv[1]18tb = VTTable.VTTable()19tb.AddColumn(VTTable.VTColumn('chromid', 'Text'))20tb.AddColumn(VTTable.VTColumn('fstart', 'Value'))21tb.AddColumn(VTTable.VTColumn('fend', 'Value'))22tb.AddColumn(VTTable.VTColumn('fname', 'Text'))23tb.AddColumn(VTTable.VTColumn('fid', 'Text'))24tb.AddColumn(VTTable.VTColumn('ftype', 'Text'))25tb.AddColumn(VTTable.VTColumn('fparentid', 'Text'))26tb.AddColumn(VTTable.VTColumn('fnames', 'Text'))27tb.AddColumn(VTTable.VTColumn('descr', 'Text'))28nr = 029with open(basepath + '/' + sourcefile, 'r') as fp:30    for line in fp:31        tokens = line.rstrip('\r\n').split('\t')32        print(str(tokens))33        tb.AddRowEmpty()34        tb.SetValue(tb.GetRowCount()-1, 0, tokens[0])35        tb.SetValue(tb.GetRowCount()-1, 1, int(tokens[1]))36        tb.SetValue(tb.GetRowCount()-1, 2, int(tokens[2]))37        tb.SetValue(tb.GetRowCount()-1, 3, tokens[3])38        tb.SetValue(tb.GetRowCount()-1, 4, str(nr))39        tb.SetValue(tb.GetRowCount()-1, 5, 'region')40        tb.SetValue(tb.GetRowCount()-1, 6, '')41        tb.SetValue(tb.GetRowCount()-1, 7, '')42        tb.SetValue(tb.GetRowCount()-1, 8, '')43        nr += 144tb.PrintRows(0, 9)45tb.SaveSQLCreation(basepath + '/' + sourcefile +'.create.sql', 'regions')...

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