b7cb97d2942575d92f6385055e172dcbd979ee05
angie
  Tue Oct 1 13:09:29 2019 -0700
Adding new data type bigDbSnp.as with associated dbSnpDetails.as, for a track based on the new "dbSNP 2.0" schema and JSON downloads.  refs #23283

diff --git src/hg/lib/dbSnpDetails.c src/hg/lib/dbSnpDetails.c
new file mode 100644
index 0000000..bbe8a1a
--- /dev/null
+++ src/hg/lib/dbSnpDetails.c
@@ -0,0 +1,346 @@
+/* dbSnpDetails.c was originally generated by the autoSql program, which also 
+ * generated dbSnpDetails.h and dbSnpDetails.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 "dbSnpDetails.h"
+
+
+
+char *dbSnpDetailsCommaSepFieldNames = "name,freqSourceCount,alleleCounts,alleleTotals,soTermCount,soTerms,clinVarCount,clinVarAccs,clinVarSigs,submitterCount,submitters,pubMedIdCount,pubMedIds";
+
+struct dbSnpDetails *dbSnpDetailsLoad(char **row)
+/* Load a dbSnpDetails from row fetched with select * from dbSnpDetails
+ * from database.  Dispose of this with dbSnpDetailsFree(). */
+{
+struct dbSnpDetails *ret;
+
+AllocVar(ret);
+ret->freqSourceCount = sqlSigned(row[1]);
+ret->soTermCount = sqlSigned(row[4]);
+ret->clinVarCount = sqlSigned(row[6]);
+ret->submitterCount = sqlSigned(row[9]);
+ret->pubMedIdCount = sqlSigned(row[11]);
+ret->name = cloneString(row[0]);
+{
+int sizeOne;
+sqlStringDynamicArray(row[2], &ret->alleleCounts, &sizeOne);
+assert(sizeOne == ret->freqSourceCount);
+}
+{
+int sizeOne;
+sqlSignedDynamicArray(row[3], &ret->alleleTotals, &sizeOne);
+assert(sizeOne == ret->freqSourceCount);
+}
+{
+int sizeOne;
+sqlSignedDynamicArray(row[5], &ret->soTerms, &sizeOne);
+assert(sizeOne == ret->soTermCount);
+}
+{
+int sizeOne;
+sqlStringDynamicArray(row[7], &ret->clinVarAccs, &sizeOne);
+assert(sizeOne == ret->clinVarCount);
+}
+{
+int sizeOne;
+sqlStringDynamicArray(row[8], &ret->clinVarSigs, &sizeOne);
+assert(sizeOne == ret->clinVarCount);
+}
+{
+int sizeOne;
+sqlStringDynamicArray(row[10], &ret->submitters, &sizeOne);
+assert(sizeOne == ret->submitterCount);
+}
+{
+int sizeOne;
+sqlSignedDynamicArray(row[12], &ret->pubMedIds, &sizeOne);
+assert(sizeOne == ret->pubMedIdCount);
+}
+return ret;
+}
+
+struct dbSnpDetails *dbSnpDetailsLoadAll(char *fileName) 
+/* Load all dbSnpDetails from a whitespace-separated file.
+ * Dispose of this with dbSnpDetailsFreeList(). */
+{
+struct dbSnpDetails *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[13];
+
+while (lineFileRow(lf, row))
+    {
+    el = dbSnpDetailsLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct dbSnpDetails *dbSnpDetailsLoadAllByChar(char *fileName, char chopper) 
+/* Load all dbSnpDetails from a chopper separated file.
+ * Dispose of this with dbSnpDetailsFreeList(). */
+{
+struct dbSnpDetails *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[13];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = dbSnpDetailsLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct dbSnpDetails *dbSnpDetailsCommaIn(char **pS, struct dbSnpDetails *ret)
+/* Create a dbSnpDetails out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new dbSnpDetails */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->name = sqlStringComma(&s);
+ret->freqSourceCount = sqlSignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->alleleCounts, ret->freqSourceCount);
+for (i=0; i<ret->freqSourceCount; ++i)
+    {
+    ret->alleleCounts[i] = sqlStringComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->alleleTotals, ret->freqSourceCount);
+for (i=0; i<ret->freqSourceCount; ++i)
+    {
+    ret->alleleTotals[i] = sqlSignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->soTermCount = sqlSignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->soTerms, ret->soTermCount);
+for (i=0; i<ret->soTermCount; ++i)
+    {
+    ret->soTerms[i] = sqlSignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->clinVarCount = sqlSignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->clinVarAccs, ret->clinVarCount);
+for (i=0; i<ret->clinVarCount; ++i)
+    {
+    ret->clinVarAccs[i] = sqlStringComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->clinVarSigs, ret->clinVarCount);
+for (i=0; i<ret->clinVarCount; ++i)
+    {
+    ret->clinVarSigs[i] = sqlStringComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->submitterCount = sqlSignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->submitters, ret->submitterCount);
+for (i=0; i<ret->submitterCount; ++i)
+    {
+    ret->submitters[i] = sqlStringComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->pubMedIdCount = sqlSignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->pubMedIds, ret->pubMedIdCount);
+for (i=0; i<ret->pubMedIdCount; ++i)
+    {
+    ret->pubMedIds[i] = sqlSignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+*pS = s;
+return ret;
+}
+
+void dbSnpDetailsFree(struct dbSnpDetails **pEl)
+/* Free a single dynamically allocated dbSnpDetails such as created
+ * with dbSnpDetailsLoad(). */
+{
+struct dbSnpDetails *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->name);
+/* All strings in alleleCounts are allocated at once, so only need to free first. */
+if (el->alleleCounts != NULL)
+    freeMem(el->alleleCounts[0]);
+freeMem(el->alleleCounts);
+freeMem(el->alleleTotals);
+freeMem(el->soTerms);
+/* All strings in clinVarAccs are allocated at once, so only need to free first. */
+if (el->clinVarAccs != NULL)
+    freeMem(el->clinVarAccs[0]);
+freeMem(el->clinVarAccs);
+/* All strings in clinVarSigs are allocated at once, so only need to free first. */
+if (el->clinVarSigs != NULL)
+    freeMem(el->clinVarSigs[0]);
+freeMem(el->clinVarSigs);
+/* All strings in submitters are allocated at once, so only need to free first. */
+if (el->submitters != NULL)
+    freeMem(el->submitters[0]);
+freeMem(el->submitters);
+freeMem(el->pubMedIds);
+freez(pEl);
+}
+
+void dbSnpDetailsFreeList(struct dbSnpDetails **pList)
+/* Free a list of dynamically allocated dbSnpDetails's */
+{
+struct dbSnpDetails *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    dbSnpDetailsFree(&el);
+    }
+*pList = NULL;
+}
+
+void dbSnpDetailsOutput(struct dbSnpDetails *el, FILE *f, char sep, char lastSep) 
+/* Print out dbSnpDetails.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->name);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->freqSourceCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->freqSourceCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->alleleCounts[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->freqSourceCount; ++i)
+    {
+    fprintf(f, "%d", el->alleleTotals[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+fprintf(f, "%d", el->soTermCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->soTermCount; ++i)
+    {
+    fprintf(f, "%d", el->soTerms[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+fprintf(f, "%d", el->clinVarCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->clinVarCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->clinVarAccs[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->clinVarCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->clinVarSigs[i]);
+    if (sep == ',') fputc('"',f);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+fprintf(f, "%d", el->submitterCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->submitterCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->submitters[i]);
+    if (sep == ',') fputc('"',f);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+fprintf(f, "%d", el->pubMedIdCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->pubMedIdCount; ++i)
+    {
+    fprintf(f, "%d", el->pubMedIds[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+