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/oreganno.c src/hg/cgilib/oreganno.c new file mode 100644 index 0000000..7644e15 --- /dev/null +++ src/hg/cgilib/oreganno.c @@ -0,0 +1,531 @@ +/* oreganno.c was originally generated by the autoSql program, which also + * generated oreganno.h and oreganno.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 "oreganno.h" + + +void oregannoStaticLoad(char **row, struct oreganno *ret) +/* Load a row from oreganno 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->id = row[4]; +strcpy(ret->strand, row[5]); +ret->name = row[6]; +} + +struct oreganno *oregannoLoad(char **row) +/* Load a oreganno from row fetched with select * from oreganno + * from database. Dispose of this with oregannoFree(). */ +{ +struct oreganno *ret; + +AllocVar(ret); +ret->bin = sqlUnsigned(row[0]); +ret->chrom = cloneString(row[1]); +ret->chromStart = sqlUnsigned(row[2]); +ret->chromEnd = sqlUnsigned(row[3]); +ret->id = cloneString(row[4]); +strcpy(ret->strand, row[5]); +ret->name = cloneString(row[6]); +return ret; +} + +struct oreganno *oregannoLoadAll(char *fileName) +/* Load all oreganno from a whitespace-separated file. + * Dispose of this with oregannoFreeList(). */ +{ +struct oreganno *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[7]; + +while (lineFileRow(lf, row)) + { + el = oregannoLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct oreganno *oregannoLoadAllByChar(char *fileName, char chopper) +/* Load all oreganno from a chopper separated file. + * Dispose of this with oregannoFreeList(). */ +{ +struct oreganno *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[7]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = oregannoLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct oreganno *oregannoLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all oreganno 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 oregannoFreeList(). */ +{ +struct oreganno *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = oregannoLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void oregannoSaveToDb(struct sqlConnection *conn, struct oreganno *el, char *tableName, int updateSize) +/* Save oreganno 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','%s','%s')", + tableName, el->bin, el->chrom, el->chromStart, el->chromEnd, el->id, el->strand, el->name); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct oreganno *oregannoCommaIn(char **pS, struct oreganno *ret) +/* Create a oreganno out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new oreganno */ +{ +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->id = sqlStringComma(&s); +sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); +ret->name = sqlStringComma(&s); +*pS = s; +return ret; +} + +void oregannoFree(struct oreganno **pEl) +/* Free a single dynamically allocated oreganno such as created + * with oregannoLoad(). */ +{ +struct oreganno *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->id); +freeMem(el->name); +freez(pEl); +} + +void oregannoFreeList(struct oreganno **pList) +/* Free a list of dynamically allocated oreganno's */ +{ +struct oreganno *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + oregannoFree(&el); + } +*pList = NULL; +} + +void oregannoOutput(struct oreganno *el, FILE *f, char sep, char lastSep) +/* Print out oreganno. 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->id); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->strand); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->name); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +void oregannoAttrStaticLoad(char **row, struct oregannoAttr *ret) +/* Load a row from oregannoAttr table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->id = row[0]; +ret->attribute = row[1]; +ret->attrVal = row[2]; +} + +struct oregannoAttr *oregannoAttrLoad(char **row) +/* Load a oregannoAttr from row fetched with select * from oregannoAttr + * from database. Dispose of this with oregannoAttrFree(). */ +{ +struct oregannoAttr *ret; + +AllocVar(ret); +ret->id = cloneString(row[0]); +ret->attribute = cloneString(row[1]); +ret->attrVal = cloneString(row[2]); +return ret; +} + +struct oregannoAttr *oregannoAttrLoadAll(char *fileName) +/* Load all oregannoAttr from a whitespace-separated file. + * Dispose of this with oregannoAttrFreeList(). */ +{ +struct oregannoAttr *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[3]; + +while (lineFileRow(lf, row)) + { + el = oregannoAttrLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct oregannoAttr *oregannoAttrLoadAllByChar(char *fileName, char chopper) +/* Load all oregannoAttr from a chopper separated file. + * Dispose of this with oregannoAttrFreeList(). */ +{ +struct oregannoAttr *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[3]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = oregannoAttrLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct oregannoAttr *oregannoAttrLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all oregannoAttr 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 oregannoAttrFreeList(). */ +{ +struct oregannoAttr *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = oregannoAttrLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void oregannoAttrSaveToDb(struct sqlConnection *conn, struct oregannoAttr *el, char *tableName, int updateSize) +/* Save oregannoAttr 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->attribute, el->attrVal); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct oregannoAttr *oregannoAttrCommaIn(char **pS, struct oregannoAttr *ret) +/* Create a oregannoAttr out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new oregannoAttr */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->id = sqlStringComma(&s); +ret->attribute = sqlStringComma(&s); +ret->attrVal = sqlStringComma(&s); +*pS = s; +return ret; +} + +void oregannoAttrFree(struct oregannoAttr **pEl) +/* Free a single dynamically allocated oregannoAttr such as created + * with oregannoAttrLoad(). */ +{ +struct oregannoAttr *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->id); +freeMem(el->attribute); +freeMem(el->attrVal); +freez(pEl); +} + +void oregannoAttrFreeList(struct oregannoAttr **pList) +/* Free a list of dynamically allocated oregannoAttr's */ +{ +struct oregannoAttr *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + oregannoAttrFree(&el); + } +*pList = NULL; +} + +void oregannoAttrOutput(struct oregannoAttr *el, FILE *f, char sep, char lastSep) +/* Print out oregannoAttr. 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->attribute); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->attrVal); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +void oregannoLinkStaticLoad(char **row, struct oregannoLink *ret) +/* Load a row from oregannoLink table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->id = row[0]; +ret->attribute = row[1]; +ret->raKey = row[2]; +ret->attrAcc = row[3]; +} + +struct oregannoLink *oregannoLinkLoad(char **row) +/* Load a oregannoLink from row fetched with select * from oregannoLink + * from database. Dispose of this with oregannoLinkFree(). */ +{ +struct oregannoLink *ret; + +AllocVar(ret); +ret->id = cloneString(row[0]); +ret->attribute = cloneString(row[1]); +ret->raKey = cloneString(row[2]); +ret->attrAcc = cloneString(row[3]); +return ret; +} + +struct oregannoLink *oregannoLinkLoadAll(char *fileName) +/* Load all oregannoLink from a whitespace-separated file. + * Dispose of this with oregannoLinkFreeList(). */ +{ +struct oregannoLink *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[4]; + +while (lineFileRow(lf, row)) + { + el = oregannoLinkLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct oregannoLink *oregannoLinkLoadAllByChar(char *fileName, char chopper) +/* Load all oregannoLink from a chopper separated file. + * Dispose of this with oregannoLinkFreeList(). */ +{ +struct oregannoLink *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[4]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = oregannoLinkLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct oregannoLink *oregannoLinkLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all oregannoLink 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 oregannoLinkFreeList(). */ +{ +struct oregannoLink *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = oregannoLinkLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void oregannoLinkSaveToDb(struct sqlConnection *conn, struct oregannoLink *el, char *tableName, int updateSize) +/* Save oregannoLink 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')", + tableName, el->id, el->attribute, el->raKey, el->attrAcc); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct oregannoLink *oregannoLinkCommaIn(char **pS, struct oregannoLink *ret) +/* Create a oregannoLink out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new oregannoLink */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->id = sqlStringComma(&s); +ret->attribute = sqlStringComma(&s); +ret->raKey = sqlStringComma(&s); +ret->attrAcc = sqlStringComma(&s); +*pS = s; +return ret; +} + +void oregannoLinkFree(struct oregannoLink **pEl) +/* Free a single dynamically allocated oregannoLink such as created + * with oregannoLinkLoad(). */ +{ +struct oregannoLink *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->id); +freeMem(el->attribute); +freeMem(el->raKey); +freeMem(el->attrAcc); +freez(pEl); +} + +void oregannoLinkFreeList(struct oregannoLink **pList) +/* Free a list of dynamically allocated oregannoLink's */ +{ +struct oregannoLink *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + oregannoLinkFree(&el); + } +*pList = NULL; +} + +void oregannoLinkOutput(struct oregannoLink *el, FILE *f, char sep, char lastSep) +/* Print out oregannoLink. 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->attribute); +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->attrAcc); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ + +struct hash *oregannoLoadAttrHash(struct sqlConnection *conn) +/* Construct a hash table of the entries in the oregannoAttr table, indexed by ID. + * Free with hashFreeWithVals(&attrHash, oregannoAttrFree). + */ +{ +struct hash *attrHash = hashNew(0); +struct sqlResult *result = NULL; +struct oregannoAttr *attr = NULL; +char query[2048], **row = NULL; + +sqlSafef(query, sizeof(query), "select * from oregannoAttr where attribute = 'type'"); +result = sqlGetResult (conn, query); +while ((row = sqlNextRow(result)) != NULL) + { + attr = oregannoAttrLoad(row); + hashAdd (attrHash, attr->id, attr); + } +sqlFreeResult(&result); +return attrHash; +}