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/ccdsInfo.c src/hg/cgilib/ccdsInfo.c
new file mode 100644
index 0000000..1678112
--- /dev/null
+++ src/hg/cgilib/ccdsInfo.c
@@ -0,0 +1,297 @@
+/* ccdsInfo.c was originally generated by the autoSql program, which also 
+ * generated ccdsInfo.h and ccdsInfo.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 "ccdsInfo.h"
+#include "genbank.h"
+
+/* FIXME: database should really have an enum column */
+
+static enum ccdsInfoSrcDb parseSrcDb(char *srcDbStr, char *mrnaAcc)
+/* parse the srcDb string to an enum */
+{
+if (sameString(srcDbStr, "N"))
+    return ccdsInfoNcbi;
+else if (sameString(srcDbStr, "H"))
+    {
+    if (startsWith("OTT", mrnaAcc))
+        return ccdsInfoVega;
+    else
+        return ccdsInfoEnsembl;
+    }
+errAbort("invalid ccdsInfoSrcDb column \"%s\"", srcDbStr);
+return ccdsInfoNull;
+}
+
+static char *formatSrcDb(enum ccdsInfoSrcDb srcDb)
+/* format the srcDb string to an enum */
+{
+switch (srcDb)
+    {
+    case ccdsInfoNcbi:
+        return "N";
+    case ccdsInfoVega:
+    case ccdsInfoEnsembl:
+        return "H";
+    case ccdsInfoNull:
+        assert(FALSE);
+    }
+ return "?";
+}
+
+
+void ccdsInfoStaticLoad(char **row, struct ccdsInfo *ret)
+/* Load a row from ccdsInfo table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+strcpy(ret->ccds, row[0]);
+ret->srcDb = parseSrcDb(row[1], row[2]);
+strcpy(ret->mrnaAcc, row[2]);
+strcpy(ret->protAcc, row[3]);
+}
+
+struct ccdsInfo *ccdsInfoLoad(char **row)
+/* Load a ccdsInfo from row fetched with select * from ccdsInfo
+ * from database.  Dispose of this with ccdsInfoFree(). */
+{
+struct ccdsInfo *ret;
+
+AllocVar(ret);
+strcpy(ret->ccds, row[0]);
+ret->srcDb = parseSrcDb(row[1], row[2]);
+strcpy(ret->mrnaAcc, row[2]);
+strcpy(ret->protAcc, row[3]);
+return ret;
+}
+
+struct ccdsInfo *ccdsInfoLoadAll(char *fileName) 
+/* Load all ccdsInfo from a whitespace-separated file.
+ * Dispose of this with ccdsInfoFreeList(). */
+{
+struct ccdsInfo *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[4];
+
+while (lineFileRow(lf, row))
+    {
+    el = ccdsInfoLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct ccdsInfo *ccdsInfoLoadAllByChar(char *fileName, char chopper) 
+/* Load all ccdsInfo from a chopper separated file.
+ * Dispose of this with ccdsInfoFreeList(). */
+{
+struct ccdsInfo *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[4];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = ccdsInfoLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct ccdsInfo *ccdsInfoCommaIn(char **pS, struct ccdsInfo *ret)
+/* Create a ccdsInfo out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new ccdsInfo */
+{
+char *s = *pS;
+char srcDbBuf[2];
+
+if (ret == NULL)
+    AllocVar(ret);
+sqlFixedStringComma(&s, ret->ccds, sizeof(ret->ccds));
+sqlFixedStringComma(&s, srcDbBuf, sizeof(srcDbBuf));
+sqlFixedStringComma(&s, ret->mrnaAcc, sizeof(ret->mrnaAcc));
+ret->srcDb = parseSrcDb(srcDbBuf, ret->mrnaAcc);
+sqlFixedStringComma(&s, ret->protAcc, sizeof(ret->protAcc));
+*pS = s;
+return ret;
+}
+
+void ccdsInfoFree(struct ccdsInfo **pEl)
+/* Free a single dynamically allocated ccdsInfo such as created
+ * with ccdsInfoLoad(). */
+{
+struct ccdsInfo *el;
+
+if ((el = *pEl) == NULL) return;
+freez(pEl);
+}
+
+void ccdsInfoFreeList(struct ccdsInfo **pList)
+/* Free a list of dynamically allocated ccdsInfo's */
+{
+struct ccdsInfo *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    ccdsInfoFree(&el);
+    }
+*pList = NULL;
+}
+
+void ccdsInfoOutput(struct ccdsInfo *el, FILE *f, char sep, char lastSep) 
+/* Print out ccdsInfo.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ccds);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", formatSrcDb(el->srcDb));
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->mrnaAcc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->protAcc);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+static char *createSql =
+    /* SQL to create ccdsInfo format table */
+    "CREATE TABLE %s (\n"
+    "    ccds char(12) not null,     # CCDS id\n"
+    "    srcDb char(1) not null,     # source database: N=NCBI, H=Hinxton\n"
+    "    mrnaAcc char(18) not null,  # mRNA accession (NCBI or Hinxton)\n"
+    "    protAcc char(18) not null,  # protein accession (NCBI or Hinxton)\n"
+    "              #Indices\n"
+    "    INDEX(ccds),\n"
+    "    INDEX(mrnaAcc)\n"
+    ");\n";
+
+char *ccdsInfoGetCreateSql(char *table)
+/* Get sql command to create ccdsInfo table. Result should be freed. */
+{
+char sql[1024];
+sqlSafef(sql, sizeof(sql), createSql, table);
+return cloneString(sql);
+}
+
+static int cmpMRna(const void *va, const void *vb)
+/* Compare to sort based on mrnaAcc. */
+{
+const struct ccdsInfo *a = *((struct ccdsInfo **)va);
+const struct ccdsInfo *b = *((struct ccdsInfo **)vb);
+return strcmp(a->mrnaAcc, b->mrnaAcc);
+}
+
+void ccdsInfoMRnaSort(struct ccdsInfo **ccdsInfos)
+/* Sort list by mrnaAcc */
+{
+slSort(ccdsInfos, cmpMRna);
+}
+
+static int cmpCcdsMRna(const void *va, const void *vb)
+/* Compare to sort based on CCDS id and mrnaAcc. */
+{
+const struct ccdsInfo *a = *((struct ccdsInfo **)va);
+const struct ccdsInfo *b = *((struct ccdsInfo **)vb);
+
+
+int dif = strcmp(a->ccds, b->ccds);
+if (dif == 0)
+    dif = strcmp(a->mrnaAcc, b->mrnaAcc);
+return dif;
+}
+
+void ccdsInfoCcdsMRnaSort(struct ccdsInfo **ccdsInfos)
+/* Sort list by CCDS id and mrnaAcc */
+{
+slSort(ccdsInfos, cmpCcdsMRna);
+}
+
+static char *getSrcDbWhere(enum ccdsInfoSrcDb srcDb)
+/* generate where expression for CCDS srcDb.  Note: static return!! */
+{
+static char extraWhere[64];
+switch (srcDb) {
+case ccdsInfoNull:
+    extraWhere[0] = '\0';
+    break;
+case ccdsInfoNcbi:
+    safef(extraWhere, sizeof(extraWhere), " and srcDb = 'N'");
+    break;
+case ccdsInfoVega:
+    safef(extraWhere, sizeof(extraWhere), " and srcDb = 'H' and mrnaAcc like 'OTT%%'");
+    break;
+case ccdsInfoEnsembl:
+    safef(extraWhere, sizeof(extraWhere), " and srcDb = 'H' and mrnaAcc not like 'OTT%%'");
+    break;
+}
+return extraWhere;
+}
+
+struct ccdsInfo *ccdsInfoSelectByCcds(struct sqlConnection *conn, char *ccdsId,
+                                      enum ccdsInfoSrcDb srcDb)
+/* Obtain list of ccdsInfo object for the specified id and srcDb.  If srcDb is
+ * ccdsInfoNull, return all srcDbs.  Return NULL if ccdsId it's not valid */
+{
+char query[256];
+struct sqlResult *sr;
+char **row;
+struct ccdsInfo *ccdsInfos = NULL;
+
+sqlSafef(query, sizeof(query), "select * from ccdsInfo where ccds = '%s'%-s",
+      ccdsId, getSrcDbWhere(srcDb));
+sr = sqlGetResult(conn, query);
+
+while ((row = sqlNextRow(sr)) != NULL)
+    slSafeAddHead(&ccdsInfos, ccdsInfoLoad(row));
+sqlFreeResult(&sr);
+
+return ccdsInfos;
+}
+
+struct ccdsInfo *ccdsInfoSelectByMrna(struct sqlConnection *conn, char *mrnaAcc)
+/* Obtain of ccdsInfo object for the specified mRNA or NULL if mrna is not
+ * associated with a CCDS.  Version number is optional for RefSeq mrnaAcc */
+{
+char query[256];
+struct sqlResult *sr;
+char **row;
+struct ccdsInfo *ccdsInfo = NULL;
+
+if (genbankIsRefSeqAcc(mrnaAcc) && (strchr(mrnaAcc, '.') == NULL))
+    sqlSafef(query, sizeof(query), "select * from ccdsInfo where mrnaAcc like '%s.%%'",
+          mrnaAcc);
+else
+    sqlSafef(query, sizeof(query), "select * from ccdsInfo where mrnaAcc = '%s'",
+          mrnaAcc);
+sr = sqlGetResult(conn, query);
+
+/* should only get one, but this is easier to code */
+while ((row = sqlNextRow(sr)) != NULL)
+    slSafeAddHead(&ccdsInfo, ccdsInfoLoad(row));
+sqlFreeResult(&sr);
+
+if ((ccdsInfo != NULL) && (ccdsInfo->next != NULL))
+    errAbort("obtained multiple CCDSs for mRNA %s", mrnaAcc);
+
+return ccdsInfo;
+}