533112afe2a2005e80cdb1f82904ea65032d4302 braney Sat Oct 2 11:37:34 2021 -0700 split hg/lib into two separate libaries, one only used by the cgis diff --git src/hg/cgilib/gtexEqtlCluster.c src/hg/cgilib/gtexEqtlCluster.c new file mode 100644 index 0000000..157064e --- /dev/null +++ src/hg/cgilib/gtexEqtlCluster.c @@ -0,0 +1,327 @@ +/* gtexEqtlCluster.c was originally generated by the autoSql program, which also + * generated gtexEqtlCluster.h and gtexEqtlCluster.sql. This module links the database and + * the RAM representation of objects. */ + +#include "common.h" +#include "linefile.h" +#include "dystring.h" +#include "jksql.h" +#include "gtexEqtlCluster.h" + + + +char *gtexEqtlClusterCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,targetId,target,distance,maxEffect,effectType,maxPvalue,expCount,expNames,expScores,expPvals,expProbs"; + +struct gtexEqtlCluster *gtexEqtlClusterLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all gtexEqtlCluster from table that satisfy the query given. + * Where query is of the form 'select * from example where something=something' + * or 'select example.* from example, anotherTable where example.something = + * anotherTable.something'. + * Dispose of this with gtexEqtlClusterFreeList(). */ +{ +struct gtexEqtlCluster *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = gtexEqtlClusterLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void gtexEqtlClusterSaveToDb(struct sqlConnection *conn, struct gtexEqtlCluster *el, char *tableName, int updateSize) +/* Save gtexEqtlCluster as a row to the table specified by tableName. + * As blob fields may be arbitrary size updateSize specifies the approx size + * of a string that would contain the entire query. Arrays of native types are + * converted to comma separated strings and loaded as such, User defined types are + * inserted as NULL. This function automatically escapes quoted strings for mysql. */ +{ +struct dyString *update = newDyString(updateSize); +char *expNamesArray, *expScoresArray, *expPvalsArray, *expProbsArray; +expNamesArray = sqlStringArrayToString(el->expNames, el->expCount); +expScoresArray = sqlFloatArrayToString(el->expScores, el->expCount); +expPvalsArray = sqlFloatArrayToString(el->expPvals, el->expCount); +expProbsArray = sqlFloatArrayToString(el->expProbs, el->expCount); +sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s',%d,%g,'%s',%g,%u,'%s','%s','%s','%s')", + tableName, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->targetId, el->target, el->distance, el->maxEffect, el->effectType, el->maxPvalue, el->expCount, expNamesArray , expScoresArray , expPvalsArray , expProbsArray ); +sqlUpdate(conn, update->string); +freeDyString(&update); +freez(&expNamesArray); +freez(&expScoresArray); +freez(&expPvalsArray); +freez(&expProbsArray); +} + +struct gtexEqtlCluster *gtexEqtlClusterLoad(char **row) +/* Load a gtexEqtlCluster from row fetched with select * from gtexEqtlCluster + * from database. Dispose of this with gtexEqtlClusterFree(). */ +{ +struct gtexEqtlCluster *ret; + +AllocVar(ret); +ret->expCount = sqlUnsigned(row[11]); +ret->chrom = cloneString(row[0]); +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = cloneString(row[3]); +ret->score = sqlUnsigned(row[4]); +ret->targetId = cloneString(row[5]); +ret->target = cloneString(row[6]); +ret->distance = sqlSigned(row[7]); +ret->maxEffect = sqlFloat(row[8]); +safecpy(ret->effectType, sizeof(ret->effectType), row[9]); +ret->maxPvalue = sqlFloat(row[10]); +{ +int sizeOne; +sqlStringDynamicArray(row[12], &ret->expNames, &sizeOne); +assert(sizeOne == ret->expCount); +} +{ +int sizeOne; +sqlFloatDynamicArray(row[13], &ret->expScores, &sizeOne); +assert(sizeOne == ret->expCount); +} +{ +int sizeOne; +sqlFloatDynamicArray(row[14], &ret->expPvals, &sizeOne); +assert(sizeOne == ret->expCount); +} +{ +int sizeOne; +sqlFloatDynamicArray(row[15], &ret->expProbs, &sizeOne); +assert(sizeOne == ret->expCount); +} +return ret; +} + +struct gtexEqtlCluster *gtexEqtlClusterLoadAll(char *fileName) +/* Load all gtexEqtlCluster from a whitespace-separated file. + * Dispose of this with gtexEqtlClusterFreeList(). */ +{ +struct gtexEqtlCluster *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[16]; + +while (lineFileRow(lf, row)) + { + el = gtexEqtlClusterLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct gtexEqtlCluster *gtexEqtlClusterLoadAllByChar(char *fileName, char chopper) +/* Load all gtexEqtlCluster from a chopper separated file. + * Dispose of this with gtexEqtlClusterFreeList(). */ +{ +struct gtexEqtlCluster *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[16]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = gtexEqtlClusterLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct gtexEqtlCluster *gtexEqtlClusterCommaIn(char **pS, struct gtexEqtlCluster *ret) +/* Create a gtexEqtlCluster out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new gtexEqtlCluster */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->chrom = sqlStringComma(&s); +ret->chromStart = sqlUnsignedComma(&s); +ret->chromEnd = sqlUnsignedComma(&s); +ret->name = sqlStringComma(&s); +ret->score = sqlUnsignedComma(&s); +ret->targetId = sqlStringComma(&s); +ret->target = sqlStringComma(&s); +ret->distance = sqlSignedComma(&s); +ret->maxEffect = sqlFloatComma(&s); +sqlFixedStringComma(&s, ret->effectType, sizeof(ret->effectType)); +ret->maxPvalue = sqlFloatComma(&s); +ret->expCount = sqlUnsignedComma(&s); +{ +int i; +s = sqlEatChar(s, '{'); +AllocArray(ret->expNames, ret->expCount); +for (i=0; i<ret->expCount; ++i) + { + ret->expNames[i] = sqlStringComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +{ +int i; +s = sqlEatChar(s, '{'); +AllocArray(ret->expScores, ret->expCount); +for (i=0; i<ret->expCount; ++i) + { + ret->expScores[i] = sqlFloatComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +{ +int i; +s = sqlEatChar(s, '{'); +AllocArray(ret->expPvals, ret->expCount); +for (i=0; i<ret->expCount; ++i) + { + ret->expPvals[i] = sqlFloatComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +{ +int i; +s = sqlEatChar(s, '{'); +AllocArray(ret->expProbs, ret->expCount); +for (i=0; i<ret->expCount; ++i) + { + ret->expProbs[i] = sqlFloatComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +*pS = s; +return ret; +} + +void gtexEqtlClusterFree(struct gtexEqtlCluster **pEl) +/* Free a single dynamically allocated gtexEqtlCluster such as created + * with gtexEqtlClusterLoad(). */ +{ +struct gtexEqtlCluster *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->targetId); +freeMem(el->target); +/* All strings in expNames are allocated at once, so only need to free first. */ +if (el->expNames != NULL) + freeMem(el->expNames[0]); +freeMem(el->expNames); +freeMem(el->expScores); +freeMem(el->expPvals); +freeMem(el->expProbs); +freez(pEl); +} + +void gtexEqtlClusterFreeList(struct gtexEqtlCluster **pList) +/* Free a list of dynamically allocated gtexEqtlCluster's */ +{ +struct gtexEqtlCluster *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + gtexEqtlClusterFree(&el); + } +*pList = NULL; +} + +void gtexEqtlClusterOutput(struct gtexEqtlCluster *el, FILE *f, char sep, char lastSep) +/* Print out gtexEqtlCluster. Separate fields with sep. Follow last field with lastSep. */ +{ +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->chrom); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->chromStart); +fputc(sep,f); +fprintf(f, "%u", el->chromEnd); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->name); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->score); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->targetId); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->target); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%d", el->distance); +fputc(sep,f); +fprintf(f, "%g", el->maxEffect); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->effectType); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%g", el->maxPvalue); +fputc(sep,f); +fprintf(f, "%u", el->expCount); +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<el->expCount; ++i) + { + if (sep == ',') fputc('"',f); + fprintf(f, "%s", el->expNames[i]); + if (sep == ',') fputc('"',f); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<el->expCount; ++i) + { + fprintf(f, "%g", el->expScores[i]); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<el->expCount; ++i) + { + fprintf(f, "%g", el->expPvals[i]); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<el->expCount; ++i) + { + fprintf(f, "%g", el->expProbs[i]); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +