Merge pull request #75 from datajoint/stage

Added support for {} in comments when creating tables

LNX-docker-compose.yml

@@ -11,7 +11,7 @@ services:
       - MYSQL_ROOT_PASSWORD=simple
   fakeservices.datajoint.io:
     <<: *net
-    image: raphaelguzman/nginx:v0.0.10
+    image: datajoint/nginx:v0.0.16
     environment:
     - ADD_db_TYPE=DATABASE
     - ADD_db_ENDPOINT=db:3306

local-docker-compose.yml

@@ -16,7 +16,7 @@ services:
     #   - ./mysql/data:/var/lib/mysql
   fakeservices.datajoint.io:
     <<: *net
-    image: raphaelguzman/nginx:v0.0.10
+    image: datajoint/nginx:v0.0.16
     environment:
     - ADD_db_TYPE=DATABASE
     - ADD_db_ENDPOINT=db:3306

src/mym.cpp

@@ -354,7 +354,7 @@ static void updateplugindir() {
     mxDestroyArray(mym_fileparts[2]);
 }
 /**********************************************************************
- *mysql():  Execute the actual action
+ * mysql():  Execute the actual action
  * Which action we perform is based on the first input argument,
  * which must be present and must be a character string:
  *   'open', 'close', 'use', 'status', or a legitimate MySQL query.
@@ -694,11 +694,11 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
         }
         //******************PLACEHOLDER PROCESSING******************
         // global placeholders variables and constant
-        const unsigned nex = nrhs-jarg-1;   // expected number of placeholders
+        const unsigned expectedNumberOfPlaceholders = nrhs-jarg-1;   // expected number of placeholders
         unsigned query_flags = 0;
         unsigned nb_flags = 0;
         unsigned nac = 0;                                   // actual number
-        size_t lq = strlen(query);  // original query length, needed at some point
+        size_t lengthOfQuery = strlen(query);  // Length of the query which is needed for mysql_real_query later
         // Check for presence of query flags. This needs to be expanded once we have additional flags
         for (int i=nrhs-1; i > jarg; --i) {
             if (mxIsChar(prhs[i]) && (strcasecmp(getstring(prhs[i]), ML_FLAG_BIGINT_TO_DOUBLE)==0)) {
@@ -709,7 +709,8 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
             }
         }
 
-        if (nex) {
+        // If there is placeholders, parse them accordingly
+        if (expectedNumberOfPlaceholders) {
             // local placeholders variables and constant
             char** po = 0;                              // pointer to placeholders openning symbols
             char** pc = 0;                              // pointer to placeholders closing symbols
@@ -718,10 +719,10 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
             unsigned* ps = 0;                           // pointer to placeholders size (in bytes)
             pfserial* pf = 0;                           // pointer to serialization function
             // LOOK FOR THE PLACEHOLDERS
-            po = (char**)mxCalloc(nex+1, sizeof(char*));
-            pc = (char**)mxCalloc(nex+1, sizeof(char*));
+            po = (char**)mxCalloc(expectedNumberOfPlaceholders+1, sizeof(char*));
+            pc = (char**)mxCalloc(expectedNumberOfPlaceholders+1, sizeof(char*));
             if ((po[nac++] = strstr(query, PH_OPEN)))
-                while (po[nac-1]&&nac<=nex) {
+                while (po[nac-1]&&nac<=expectedNumberOfPlaceholders) {
                     pc[nac-1] = strstr(po[nac-1]+1, PH_CLOSE);
                     if (pc[nac-1]==0)
                         mexErrMsgTxt("Placeholders are not correctly closed!");
@@ -730,10 +731,10 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
                 }
             nac--;
             // Adjust placeholders based on the number of flags present
-            if ((nac < nex) && (nac >= (nex-nb_flags))) {
-                nb_flags = nex-nac;
+            if ((nac < expectedNumberOfPlaceholders) && (nac >= (expectedNumberOfPlaceholders-nb_flags))) {
+                nb_flags = expectedNumberOfPlaceholders-nac;
             }
-            else if (nac != nex) {
+            else if (nac != expectedNumberOfPlaceholders) {
                 mexErrMsgTxt("The number of placeholders differs from that of additional arguments!");
             }
             // now we have the correct number of placeholders
@@ -789,7 +790,7 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
                 nb += plen[i];
             }
             // create new query
-            char* nq = (char*)mxCalloc(2*nb+lq+1, sizeof(char));  // new query
+            char* nq = (char*)mxCalloc(2*nb+lengthOfQuery+1, sizeof(char));  // new query
             char* pnq = nq; // running pointer to new query
             const char* poq = query; // running pointer to old query
             for (unsigned i = 0; i<nac; i++) {
@@ -800,12 +801,12 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
                 pd[i]=NULL;
                 mxFree(pd[i]);
             }
-            memcpy(pnq, poq, lq-(poq-query)+1);
+            memcpy(pnq, poq, lengthOfQuery-(poq-query)+1);
             // replace the old query by the new one
-            pnq += lq-(poq-query)+1;
+            pnq += lengthOfQuery-(poq-query)+1;
             mxFree(query);
             query = nq;
-            lq = (ulong)(pnq-nq);
+            lengthOfQuery = (ulong)(pnq-nq);
             mxFree(po);
             mxFree(pc);
             mxFree(pec);
@@ -816,13 +817,41 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
             if (pcmp!=NULL)
                 mxFree(pcmp);
         }
-        else {
-            // check that no placeholders are present in the query
-            char*p_tmp_o = strstr(query, PH_OPEN);
-            char*p_tmp_c = strstr(query, PH_CLOSE);
-            if (p_tmp_o||p_tmp_c)
-                mexErrMsgTxt("The query contains placeholders, but no additional arguments!");
+        // Check that no placeholders are present in the query except for \{ and \}
+        char* parsedQueryString = (char*)mxCalloc(strlen(query), sizeof(char)); // Query string with escape character removed
+        size_t parsedQueryStringCurrentIndex = 0;
+
+        // Loop through the query string character by character
+        for (size_t i = 0; query[i] != '\0'; i++) {
+
+            if ((query[i] == '{' || query[i] == '}') && i != 0) {
+                if (query[i - 1] != '\\') {
+                    // Curley bracket doesn't seem to be escaped thus throw and error
+                    mxFree(parsedQueryString);
+                    mexErrMsgTxt("The query contains placeholders, but no additional arguments!");
+                }
+                else {
+                    // Valid curley bracket thus add it to the parsedQueryString with the \ removed
+                    parsedQueryStringCurrentIndex--;
+                    parsedQueryString[parsedQueryStringCurrentIndex] = query[i];
+                }
+            }
+            else {
+                // Non curley bracket thus add it to the parsedQueryString
+                parsedQueryString[parsedQueryStringCurrentIndex] = query[i];
+            }
+
+            // Increment the currentIndex counter
+            parsedQueryStringCurrentIndex++;
         }
+        // Add ending character
+        parsedQueryString[parsedQueryStringCurrentIndex] = '\0';
+
+        // Update the query string
+        mxFree(query); // Free up the old string allocation
+        query = parsedQueryString;
+        lengthOfQuery = strlen(query); // Update the length of the query
+
         // Process flags
         for (int i=nrhs-nb_flags; i < nrhs; ++i) {
             if  (strcasecmp(getstring(prhs[i]), ML_FLAG_BIGINT_TO_DOUBLE)==0) {
@@ -832,7 +861,7 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
 
         //  Execute the query (data stays on server)
         if (nac!=0) {
-            if (mysql_real_query(conn, query, lq))
+            if (mysql_real_query(conn, query, lengthOfQuery))
                 mexErrMsgTxt(mysql_error(conn));
         }
         else if (mysql_query(conn, query))
@@ -980,14 +1009,14 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
         // serialize the matlab variable, it can be an array, cell, struct etc
         //******************PLACEHOLDER PROCESSING******************
         // global placeholders variables and constant
-        const unsigned nex = nrhs-jarg-1;   // expected number of placeholders
+        const unsigned expectedNumberOfPlaceholders = nrhs-jarg-1;   // expected number of placeholders
         unsigned query_flags = 0;
         unsigned nb_flags = 0;
         unsigned nac = 0;                                   // actual number
         if (debug)
-            mexPrintf("Num of args = %d\n", (int) nex) ;
+            mexPrintf("Num of args = %d\n", (int) expectedNumberOfPlaceholders) ;
 
-        if (nex) {
+        if (expectedNumberOfPlaceholders) {
             // local placeholders variables and constant
             char** po = 0;                      // pointer to placeholders openning symbols
             char** pc = 0;                      // pointer to placeholders closing symbols
@@ -996,10 +1025,10 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
             unsigned* ps = 0;                   // pointer to placeholders size (in bytes)
             pfserial* pf = 0;                   // pointer to serialization function
             // LOOK FOR THE PLACEHOLDERS
-            po = (char**)mxCalloc(nex+1, sizeof(char*));
-            pc = (char**)mxCalloc(nex+1, sizeof(char*));
+            po = (char**)mxCalloc(expectedNumberOfPlaceholders+1, sizeof(char*));
+            pc = (char**)mxCalloc(expectedNumberOfPlaceholders+1, sizeof(char*));
             if ((po[nac++] = strstr(query, PH_OPEN)))
-            while (po[nac-1]&&nac<=nex) {
+            while (po[nac-1]&&nac<=expectedNumberOfPlaceholders) {
                 pc[nac-1] = strstr(po[nac-1]+1, PH_CLOSE);
                 if (pc[nac-1]==0)
                     mexErrMsgIdAndTxt("mYm:Serialization:Placeholders",
@@ -1008,7 +1037,7 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
                 nac++;
             }
             nac--; // utilized to find {}s
-            if (nac != nex) {
+            if (nac != expectedNumberOfPlaceholders) {
                 mexErrMsgIdAndTxt("mYm:Serialization:Placeholders",
                     "The number of placeholders differs from that of additional arguments!");
             }
@@ -1127,7 +1156,7 @@ void mexFunction(int nlhs, mxArray*plhs[], int nrhs, const mxArray*prhs[]) {
                 "There must be only one input and one output variable\n");
         }
     }
-    else if (q == VERSION) {
+    else if (q==VERSION) {
         if (nrhs > (jarg+1))
             mexErrMsgTxt("Version command does not take additional inputs");
         if (nlhs == 0) {
@@ -1423,7 +1452,6 @@ char* serializeArray(size_t &rnBytes, const mxArray *rpArray, const char *rpArg,
 
 
 
-
 // Serialize a sparse matrix
 char* serializeSparse(size_t &rnBytes, const mxArray *rpArray, 
                         const char *rpArg, const bool rhead) 

src/mym.h

@@ -34,7 +34,7 @@
 // mym version information
 #define MYM_VERSION_MAJOR 2
 #define MYM_VERSION_MINOR 8
-#define MYM_VERSION_BUGFIX 0
+#define MYM_VERSION_BUGFIX 1
 
 
 // some local defintion

tests/Main.m

@@ -1,5 +1,6 @@
 classdef Main < ...
     TestConnection & ...
+    TestDeclare & ...
     TestExternal & ...
     TestInsertFetch & ...
     TestTls

tests/TestDeclare.m

@@ -0,0 +1,25 @@
+classdef TestDeclare < Prep
+    % TestDeclare tests typical connection scenarios.
+    methods (Test)
+        function TestDeclare_delcareTable(testCase)
+            % Test table declare with comments that has \{ or \}
+            st = dbstack;
+            disp(['---------------' st(1).name '---------------']);
+            conn1 = mym(-1, 'open', testCase.CONN_INFO.host, ...
+                testCase.CONN_INFO.user, testCase.CONN_INFO.password, ...
+                'false');
+
+            mym(conn1, ['create database `' testCase.PREFIX '_declare`']);
+            mym(['create table {S}(id int, data varchar(30) default null) COMMENT "\{username\}_\{subject_nickname\}"'], ...
+                sprintf('`%s_%s`.`%s`', testCase.PREFIX, 'declare', 'test_table'));
+            query_string = mym(sprintf('SHOW CREATE TABLE `%s_%s`.`%s`', testCase.PREFIX, 'declare', 'test_table'));
+
+            if ~strfind(query_string.('Create Table'){1}, 'COMMENT=''{username}_{subject_nickname}''')
+                throw(MException('TestDeclare:invalidDeclareTable',...
+                    'Table comments got inserted incorrectly'));
+            end
+            mym(conn1, ['drop database `' testCase.PREFIX '_declare`']);
+            mym(conn1, 'close');
+        end
+    end
+end