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/omicia.c src/hg/cgilib/omicia.c new file mode 100644 index 0000000..a83d23b --- /dev/null +++ src/hg/cgilib/omicia.c @@ -0,0 +1,690 @@ +/* omicia.c was originally generated by the autoSql program, which also + * generated omicia.h and omicia.sql. This module links the database and + * the RAM representation of objects. */ + +/* Copyright (C) 2014 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + +#include "common.h" +#include "linefile.h" +#include "dystring.h" +#include "jksql.h" +#include "omicia.h" + + +void omiciaAutoStaticLoad(char **row, struct omiciaAuto *ret) +/* Load a row from omiciaAuto table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->bin = sqlUnsigned(row[0]); +ret->chrom = row[1]; +ret->chromStart = sqlUnsigned(row[2]); +ret->chromEnd = sqlUnsigned(row[3]); +ret->name = row[4]; +ret->score = sqlUnsigned(row[5]); +safecpy(ret->strand, sizeof(ret->strand), row[6]); +} + +struct omiciaAuto *omiciaAutoLoad(char **row) +/* Load a omiciaAuto from row fetched with select * from omiciaAuto + * from database. Dispose of this with omiciaAutoFree(). */ +{ +struct omiciaAuto *ret; + +AllocVar(ret); +ret->bin = sqlUnsigned(row[0]); +ret->chrom = cloneString(row[1]); +ret->chromStart = sqlUnsigned(row[2]); +ret->chromEnd = sqlUnsigned(row[3]); +ret->name = cloneString(row[4]); +ret->score = sqlUnsigned(row[5]); +safecpy(ret->strand, sizeof(ret->strand), row[6]); +return ret; +} + +struct omiciaAuto *omiciaAutoLoadAll(char *fileName) +/* Load all omiciaAuto from a whitespace-separated file. + * Dispose of this with omiciaAutoFreeList(). */ +{ +struct omiciaAuto *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[7]; + +while (lineFileRow(lf, row)) + { + el = omiciaAutoLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct omiciaAuto *omiciaAutoLoadAllByChar(char *fileName, char chopper) +/* Load all omiciaAuto from a chopper separated file. + * Dispose of this with omiciaAutoFreeList(). */ +{ +struct omiciaAuto *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[7]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = omiciaAutoLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct omiciaAuto *omiciaAutoLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all omiciaAuto 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 omiciaAutoFreeList(). */ +{ +struct omiciaAuto *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = omiciaAutoLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void omiciaAutoSaveToDb(struct sqlConnection *conn, struct omiciaAuto *el, char *tableName, int updateSize) +/* Save omiciaAuto 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. Strings are automatically escaped to allow insertion into the database. */ +{ +struct dyString *update = newDyString(updateSize); +sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s')", + tableName, el->bin, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct omiciaAuto *omiciaAutoCommaIn(char **pS, struct omiciaAuto *ret) +/* Create a omiciaAuto out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new omiciaAuto */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->bin = sqlUnsignedComma(&s); +ret->chrom = sqlStringComma(&s); +ret->chromStart = sqlUnsignedComma(&s); +ret->chromEnd = sqlUnsignedComma(&s); +ret->name = sqlStringComma(&s); +ret->score = sqlUnsignedComma(&s); +sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); +*pS = s; +return ret; +} + +void omiciaAutoFree(struct omiciaAuto **pEl) +/* Free a single dynamically allocated omiciaAuto such as created + * with omiciaAutoLoad(). */ +{ +struct omiciaAuto *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freez(pEl); +} + +void omiciaAutoFreeList(struct omiciaAuto **pList) +/* Free a list of dynamically allocated omiciaAuto's */ +{ +struct omiciaAuto *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + omiciaAutoFree(&el); + } +*pList = NULL; +} + +void omiciaAutoOutput(struct omiciaAuto *el, FILE *f, char sep, char lastSep) +/* Print out omiciaAuto. Separate fields with sep. Follow last field with lastSep. */ +{ +fprintf(f, "%u", el->bin); +fputc(sep,f); +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->strand); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +void omiciaHandStaticLoad(char **row, struct omiciaHand *ret) +/* Load a row from omiciaHand table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->bin = sqlUnsigned(row[0]); +ret->chrom = row[1]; +ret->chromStart = sqlUnsigned(row[2]); +ret->chromEnd = sqlUnsigned(row[3]); +ret->name = row[4]; +ret->score = sqlUnsigned(row[5]); +safecpy(ret->strand, sizeof(ret->strand), row[6]); +} + +struct omiciaHand *omiciaHandLoad(char **row) +/* Load a omiciaHand from row fetched with select * from omiciaHand + * from database. Dispose of this with omiciaHandFree(). */ +{ +struct omiciaHand *ret; + +AllocVar(ret); +ret->bin = sqlUnsigned(row[0]); +ret->chrom = cloneString(row[1]); +ret->chromStart = sqlUnsigned(row[2]); +ret->chromEnd = sqlUnsigned(row[3]); +ret->name = cloneString(row[4]); +ret->score = sqlUnsigned(row[5]); +safecpy(ret->strand, sizeof(ret->strand), row[6]); +return ret; +} + +struct omiciaHand *omiciaHandLoadAll(char *fileName) +/* Load all omiciaHand from a whitespace-separated file. + * Dispose of this with omiciaHandFreeList(). */ +{ +struct omiciaHand *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[7]; + +while (lineFileRow(lf, row)) + { + el = omiciaHandLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct omiciaHand *omiciaHandLoadAllByChar(char *fileName, char chopper) +/* Load all omiciaHand from a chopper separated file. + * Dispose of this with omiciaHandFreeList(). */ +{ +struct omiciaHand *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[7]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = omiciaHandLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct omiciaHand *omiciaHandLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all omiciaHand 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 omiciaHandFreeList(). */ +{ +struct omiciaHand *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = omiciaHandLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void omiciaHandSaveToDb(struct sqlConnection *conn, struct omiciaHand *el, char *tableName, int updateSize) +/* Save omiciaHand 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. Strings are automatically escaped to allow insertion into the database. */ +{ +struct dyString *update = newDyString(updateSize); +sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s')", + tableName, el->bin, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct omiciaHand *omiciaHandCommaIn(char **pS, struct omiciaHand *ret) +/* Create a omiciaHand out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new omiciaHand */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->bin = sqlUnsignedComma(&s); +ret->chrom = sqlStringComma(&s); +ret->chromStart = sqlUnsignedComma(&s); +ret->chromEnd = sqlUnsignedComma(&s); +ret->name = sqlStringComma(&s); +ret->score = sqlUnsignedComma(&s); +sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); +*pS = s; +return ret; +} + +void omiciaHandFree(struct omiciaHand **pEl) +/* Free a single dynamically allocated omiciaHand such as created + * with omiciaHandLoad(). */ +{ +struct omiciaHand *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freez(pEl); +} + +void omiciaHandFreeList(struct omiciaHand **pList) +/* Free a list of dynamically allocated omiciaHand's */ +{ +struct omiciaHand *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + omiciaHandFree(&el); + } +*pList = NULL; +} + +void omiciaHandOutput(struct omiciaHand *el, FILE *f, char sep, char lastSep) +/* Print out omiciaHand. Separate fields with sep. Follow last field with lastSep. */ +{ +fprintf(f, "%u", el->bin); +fputc(sep,f); +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->strand); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +void omiciaLinkStaticLoad(char **row, struct omiciaLink *ret) +/* Load a row from omiciaLink table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->id = row[0]; +ret->attrType = row[1]; +ret->raKey = row[2]; +ret->acc = row[3]; +ret->displayVal = row[4]; +} + +struct omiciaLink *omiciaLinkLoad(char **row) +/* Load a omiciaLink from row fetched with select * from omiciaLink + * from database. Dispose of this with omiciaLinkFree(). */ +{ +struct omiciaLink *ret; + +AllocVar(ret); +ret->id = cloneString(row[0]); +ret->attrType = cloneString(row[1]); +ret->raKey = cloneString(row[2]); +ret->acc = cloneString(row[3]); +ret->displayVal = cloneString(row[4]); +return ret; +} + +struct omiciaLink *omiciaLinkLoadAll(char *fileName) +/* Load all omiciaLink from a whitespace-separated file. + * Dispose of this with omiciaLinkFreeList(). */ +{ +struct omiciaLink *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[5]; + +while (lineFileRow(lf, row)) + { + el = omiciaLinkLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct omiciaLink *omiciaLinkLoadAllByChar(char *fileName, char chopper) +/* Load all omiciaLink from a chopper separated file. + * Dispose of this with omiciaLinkFreeList(). */ +{ +struct omiciaLink *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[5]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = omiciaLinkLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct omiciaLink *omiciaLinkLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all omiciaLink 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 omiciaLinkFreeList(). */ +{ +struct omiciaLink *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = omiciaLinkLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void omiciaLinkSaveToDb(struct sqlConnection *conn, struct omiciaLink *el, char *tableName, int updateSize) +/* Save omiciaLink 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. Strings are automatically escaped to allow insertion into the database. */ +{ +struct dyString *update = newDyString(updateSize); +sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s')", + tableName, el->id, el->attrType, el->raKey, el->acc, el->displayVal); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct omiciaLink *omiciaLinkCommaIn(char **pS, struct omiciaLink *ret) +/* Create a omiciaLink out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new omiciaLink */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->id = sqlStringComma(&s); +ret->attrType = sqlStringComma(&s); +ret->raKey = sqlStringComma(&s); +ret->acc = sqlStringComma(&s); +ret->displayVal = sqlStringComma(&s); +*pS = s; +return ret; +} + +void omiciaLinkFree(struct omiciaLink **pEl) +/* Free a single dynamically allocated omiciaLink such as created + * with omiciaLinkLoad(). */ +{ +struct omiciaLink *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->id); +freeMem(el->attrType); +freeMem(el->raKey); +freeMem(el->acc); +freeMem(el->displayVal); +freez(pEl); +} + +void omiciaLinkFreeList(struct omiciaLink **pList) +/* Free a list of dynamically allocated omiciaLink's */ +{ +struct omiciaLink *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + omiciaLinkFree(&el); + } +*pList = NULL; +} + +void omiciaLinkOutput(struct omiciaLink *el, FILE *f, char sep, char lastSep) +/* Print out omiciaLink. Separate fields with sep. Follow last field with lastSep. */ +{ +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->id); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->attrType); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->raKey); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->acc); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->displayVal); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +void omiciaAttrStaticLoad(char **row, struct omiciaAttr *ret) +/* Load a row from omiciaAttr table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->id = row[0]; +ret->attrType = row[1]; +ret->attrVal = row[2]; +} + +struct omiciaAttr *omiciaAttrLoad(char **row) +/* Load a omiciaAttr from row fetched with select * from omiciaAttr + * from database. Dispose of this with omiciaAttrFree(). */ +{ +struct omiciaAttr *ret; + +AllocVar(ret); +ret->id = cloneString(row[0]); +ret->attrType = cloneString(row[1]); +ret->attrVal = cloneString(row[2]); +return ret; +} + +struct omiciaAttr *omiciaAttrLoadAll(char *fileName) +/* Load all omiciaAttr from a whitespace-separated file. + * Dispose of this with omiciaAttrFreeList(). */ +{ +struct omiciaAttr *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[3]; + +while (lineFileRow(lf, row)) + { + el = omiciaAttrLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct omiciaAttr *omiciaAttrLoadAllByChar(char *fileName, char chopper) +/* Load all omiciaAttr from a chopper separated file. + * Dispose of this with omiciaAttrFreeList(). */ +{ +struct omiciaAttr *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[3]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = omiciaAttrLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct omiciaAttr *omiciaAttrLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all omiciaAttr 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 omiciaAttrFreeList(). */ +{ +struct omiciaAttr *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = omiciaAttrLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void omiciaAttrSaveToDb(struct sqlConnection *conn, struct omiciaAttr *el, char *tableName, int updateSize) +/* Save omiciaAttr 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. Strings are automatically escaped to allow insertion into the database. */ +{ +struct dyString *update = newDyString(updateSize); +sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s')", + tableName, el->id, el->attrType, el->attrVal); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct omiciaAttr *omiciaAttrCommaIn(char **pS, struct omiciaAttr *ret) +/* Create a omiciaAttr out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new omiciaAttr */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->id = sqlStringComma(&s); +ret->attrType = sqlStringComma(&s); +ret->attrVal = sqlStringComma(&s); +*pS = s; +return ret; +} + +void omiciaAttrFree(struct omiciaAttr **pEl) +/* Free a single dynamically allocated omiciaAttr such as created + * with omiciaAttrLoad(). */ +{ +struct omiciaAttr *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->id); +freeMem(el->attrType); +freeMem(el->attrVal); +freez(pEl); +} + +void omiciaAttrFreeList(struct omiciaAttr **pList) +/* Free a list of dynamically allocated omiciaAttr's */ +{ +struct omiciaAttr *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + omiciaAttrFree(&el); + } +*pList = NULL; +} + +void omiciaAttrOutput(struct omiciaAttr *el, FILE *f, char sep, char lastSep) +/* Print out omiciaAttr. Separate fields with sep. Follow last field with lastSep. */ +{ +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->id); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->attrType); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->attrVal); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +