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/lib/omicia.c src/hg/lib/omicia.c deleted file mode 100644 index a83d23b..0000000 --- src/hg/lib/omicia.c +++ /dev/null @@ -1,690 +0,0 @@ -/* 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 -------------------------------- */ -