7355201a77e934e6e7f28242d4beb15d694e7c8d
braney
  Sun Oct 11 13:21:05 2020 -0700
initial work on Clinvar Submissions track #26330

diff --git src/hg/lib/clinvarSub.c src/hg/lib/clinvarSub.c
new file mode 100644
index 0000000..75a7362
--- /dev/null
+++ src/hg/lib/clinvarSub.c
@@ -0,0 +1,211 @@
+/* clinvarSub.c was originally generated by the autoSql program, which also 
+ * generated clinvarSub.h and clinvarSub.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 "clinvarSub.h"
+
+
+
+char *clinvarSubCommaSepFieldNames = "varId,clinSign,dateLastEval,description,subPhenoInfo,repPhenoInfo,revStatus,collMethod,originCounts,submitter,scv,subGeneSymbol,explOfInterp";
+
+void clinvarSubStaticLoad(char **row, struct clinvarSub *ret)
+/* Load a row from clinvarSub table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->varId = sqlSigned(row[0]);
+ret->clinSign = row[1];
+ret->dateLastEval = row[2];
+ret->description = row[3];
+ret->subPhenoInfo = row[4];
+ret->repPhenoInfo = row[5];
+ret->revStatus = row[6];
+ret->collMethod = row[7];
+ret->originCounts = row[8];
+ret->submitter = row[9];
+ret->scv = row[10];
+ret->subGeneSymbol = row[11];
+ret->explOfInterp = row[12];
+}
+
+struct clinvarSub *clinvarSubLoad(char **row)
+/* Load a clinvarSub from row fetched with select * from clinvarSub
+ * from database.  Dispose of this with clinvarSubFree(). */
+{
+struct clinvarSub *ret;
+
+AllocVar(ret);
+ret->varId = sqlSigned(row[0]);
+ret->clinSign = cloneString(row[1]);
+ret->dateLastEval = cloneString(row[2]);
+ret->description = cloneString(row[3]);
+ret->subPhenoInfo = cloneString(row[4]);
+ret->repPhenoInfo = cloneString(row[5]);
+ret->revStatus = cloneString(row[6]);
+ret->collMethod = cloneString(row[7]);
+ret->originCounts = cloneString(row[8]);
+ret->submitter = cloneString(row[9]);
+ret->scv = cloneString(row[10]);
+ret->subGeneSymbol = cloneString(row[11]);
+ret->explOfInterp = cloneString(row[12]);
+return ret;
+}
+
+struct clinvarSub *clinvarSubLoadAll(char *fileName) 
+/* Load all clinvarSub from a whitespace-separated file.
+ * Dispose of this with clinvarSubFreeList(). */
+{
+struct clinvarSub *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[13];
+
+while (lineFileRow(lf, row))
+    {
+    el = clinvarSubLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct clinvarSub *clinvarSubLoadAllByChar(char *fileName, char chopper) 
+/* Load all clinvarSub from a chopper separated file.
+ * Dispose of this with clinvarSubFreeList(). */
+{
+struct clinvarSub *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[13];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = clinvarSubLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct clinvarSub *clinvarSubCommaIn(char **pS, struct clinvarSub *ret)
+/* Create a clinvarSub out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new clinvarSub */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->varId = sqlSignedComma(&s);
+ret->clinSign = sqlStringComma(&s);
+ret->dateLastEval = sqlStringComma(&s);
+ret->description = sqlStringComma(&s);
+ret->subPhenoInfo = sqlStringComma(&s);
+ret->repPhenoInfo = sqlStringComma(&s);
+ret->revStatus = sqlStringComma(&s);
+ret->collMethod = sqlStringComma(&s);
+ret->originCounts = sqlStringComma(&s);
+ret->submitter = sqlStringComma(&s);
+ret->scv = sqlStringComma(&s);
+ret->subGeneSymbol = sqlStringComma(&s);
+ret->explOfInterp = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void clinvarSubFree(struct clinvarSub **pEl)
+/* Free a single dynamically allocated clinvarSub such as created
+ * with clinvarSubLoad(). */
+{
+struct clinvarSub *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->clinSign);
+freeMem(el->dateLastEval);
+freeMem(el->description);
+freeMem(el->subPhenoInfo);
+freeMem(el->repPhenoInfo);
+freeMem(el->revStatus);
+freeMem(el->collMethod);
+freeMem(el->originCounts);
+freeMem(el->submitter);
+freeMem(el->scv);
+freeMem(el->subGeneSymbol);
+freeMem(el->explOfInterp);
+freez(pEl);
+}
+
+void clinvarSubFreeList(struct clinvarSub **pList)
+/* Free a list of dynamically allocated clinvarSub's */
+{
+struct clinvarSub *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    clinvarSubFree(&el);
+    }
+*pList = NULL;
+}
+
+void clinvarSubOutput(struct clinvarSub *el, FILE *f, char sep, char lastSep) 
+/* Print out clinvarSub.  Separate fields with sep. Follow last field with lastSep. */
+{
+fprintf(f, "%d", el->varId);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->clinSign);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->dateLastEval);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->description);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->subPhenoInfo);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->repPhenoInfo);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->revStatus);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->collMethod);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->originCounts);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->submitter);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->scv);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->subGeneSymbol);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->explOfInterp);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+