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/gtexEqtlCluster.c src/hg/cgilib/gtexEqtlCluster.c
new file mode 100644
index 0000000..157064e
--- /dev/null
+++ src/hg/cgilib/gtexEqtlCluster.c
@@ -0,0 +1,327 @@
+/* gtexEqtlCluster.c was originally generated by the autoSql program, which also 
+ * generated gtexEqtlCluster.h and gtexEqtlCluster.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 "gtexEqtlCluster.h"
+
+
+
+char *gtexEqtlClusterCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,targetId,target,distance,maxEffect,effectType,maxPvalue,expCount,expNames,expScores,expPvals,expProbs";
+
+struct gtexEqtlCluster *gtexEqtlClusterLoadByQuery(struct sqlConnection *conn, char *query)
+/* Load all gtexEqtlCluster 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 gtexEqtlClusterFreeList(). */
+{
+struct gtexEqtlCluster *list = NULL, *el;
+struct sqlResult *sr;
+char **row;
+
+sr = sqlGetResult(conn, query);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = gtexEqtlClusterLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+return list;
+}
+
+void gtexEqtlClusterSaveToDb(struct sqlConnection *conn, struct gtexEqtlCluster *el, char *tableName, int updateSize)
+/* Save gtexEqtlCluster 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. This function automatically escapes quoted strings for mysql. */
+{
+struct dyString *update = newDyString(updateSize);
+char  *expNamesArray, *expScoresArray, *expPvalsArray, *expProbsArray;
+expNamesArray = sqlStringArrayToString(el->expNames, el->expCount);
+expScoresArray = sqlFloatArrayToString(el->expScores, el->expCount);
+expPvalsArray = sqlFloatArrayToString(el->expPvals, el->expCount);
+expProbsArray = sqlFloatArrayToString(el->expProbs, el->expCount);
+sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s',%d,%g,'%s',%g,%u,'%s','%s','%s','%s')", 
+	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->targetId,  el->target,  el->distance,  el->maxEffect,  el->effectType,  el->maxPvalue,  el->expCount,  expNamesArray ,  expScoresArray ,  expPvalsArray ,  expProbsArray );
+sqlUpdate(conn, update->string);
+freeDyString(&update);
+freez(&expNamesArray);
+freez(&expScoresArray);
+freez(&expPvalsArray);
+freez(&expProbsArray);
+}
+
+struct gtexEqtlCluster *gtexEqtlClusterLoad(char **row)
+/* Load a gtexEqtlCluster from row fetched with select * from gtexEqtlCluster
+ * from database.  Dispose of this with gtexEqtlClusterFree(). */
+{
+struct gtexEqtlCluster *ret;
+
+AllocVar(ret);
+ret->expCount = sqlUnsigned(row[11]);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+ret->score = sqlUnsigned(row[4]);
+ret->targetId = cloneString(row[5]);
+ret->target = cloneString(row[6]);
+ret->distance = sqlSigned(row[7]);
+ret->maxEffect = sqlFloat(row[8]);
+safecpy(ret->effectType, sizeof(ret->effectType), row[9]);
+ret->maxPvalue = sqlFloat(row[10]);
+{
+int sizeOne;
+sqlStringDynamicArray(row[12], &ret->expNames, &sizeOne);
+assert(sizeOne == ret->expCount);
+}
+{
+int sizeOne;
+sqlFloatDynamicArray(row[13], &ret->expScores, &sizeOne);
+assert(sizeOne == ret->expCount);
+}
+{
+int sizeOne;
+sqlFloatDynamicArray(row[14], &ret->expPvals, &sizeOne);
+assert(sizeOne == ret->expCount);
+}
+{
+int sizeOne;
+sqlFloatDynamicArray(row[15], &ret->expProbs, &sizeOne);
+assert(sizeOne == ret->expCount);
+}
+return ret;
+}
+
+struct gtexEqtlCluster *gtexEqtlClusterLoadAll(char *fileName) 
+/* Load all gtexEqtlCluster from a whitespace-separated file.
+ * Dispose of this with gtexEqtlClusterFreeList(). */
+{
+struct gtexEqtlCluster *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[16];
+
+while (lineFileRow(lf, row))
+    {
+    el = gtexEqtlClusterLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gtexEqtlCluster *gtexEqtlClusterLoadAllByChar(char *fileName, char chopper) 
+/* Load all gtexEqtlCluster from a chopper separated file.
+ * Dispose of this with gtexEqtlClusterFreeList(). */
+{
+struct gtexEqtlCluster *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[16];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = gtexEqtlClusterLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gtexEqtlCluster *gtexEqtlClusterCommaIn(char **pS, struct gtexEqtlCluster *ret)
+/* Create a gtexEqtlCluster out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gtexEqtlCluster */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->chrom = sqlStringComma(&s);
+ret->chromStart = sqlUnsignedComma(&s);
+ret->chromEnd = sqlUnsignedComma(&s);
+ret->name = sqlStringComma(&s);
+ret->score = sqlUnsignedComma(&s);
+ret->targetId = sqlStringComma(&s);
+ret->target = sqlStringComma(&s);
+ret->distance = sqlSignedComma(&s);
+ret->maxEffect = sqlFloatComma(&s);
+sqlFixedStringComma(&s, ret->effectType, sizeof(ret->effectType));
+ret->maxPvalue = sqlFloatComma(&s);
+ret->expCount = sqlUnsignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->expNames, ret->expCount);
+for (i=0; i<ret->expCount; ++i)
+    {
+    ret->expNames[i] = sqlStringComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->expScores, ret->expCount);
+for (i=0; i<ret->expCount; ++i)
+    {
+    ret->expScores[i] = sqlFloatComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->expPvals, ret->expCount);
+for (i=0; i<ret->expCount; ++i)
+    {
+    ret->expPvals[i] = sqlFloatComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->expProbs, ret->expCount);
+for (i=0; i<ret->expCount; ++i)
+    {
+    ret->expProbs[i] = sqlFloatComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+*pS = s;
+return ret;
+}
+
+void gtexEqtlClusterFree(struct gtexEqtlCluster **pEl)
+/* Free a single dynamically allocated gtexEqtlCluster such as created
+ * with gtexEqtlClusterLoad(). */
+{
+struct gtexEqtlCluster *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->targetId);
+freeMem(el->target);
+/* All strings in expNames are allocated at once, so only need to free first. */
+if (el->expNames != NULL)
+    freeMem(el->expNames[0]);
+freeMem(el->expNames);
+freeMem(el->expScores);
+freeMem(el->expPvals);
+freeMem(el->expProbs);
+freez(pEl);
+}
+
+void gtexEqtlClusterFreeList(struct gtexEqtlCluster **pList)
+/* Free a list of dynamically allocated gtexEqtlCluster's */
+{
+struct gtexEqtlCluster *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    gtexEqtlClusterFree(&el);
+    }
+*pList = NULL;
+}
+
+void gtexEqtlClusterOutput(struct gtexEqtlCluster *el, FILE *f, char sep, char lastSep) 
+/* Print out gtexEqtlCluster.  Separate fields with sep. Follow last field with lastSep. */
+{
+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->targetId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->target);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->distance);
+fputc(sep,f);
+fprintf(f, "%g", el->maxEffect);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->effectType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%g", el->maxPvalue);
+fputc(sep,f);
+fprintf(f, "%u", el->expCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->expCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->expNames[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->expCount; ++i)
+    {
+    fprintf(f, "%g", el->expScores[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->expCount; ++i)
+    {
+    fprintf(f, "%g", el->expPvals[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->expCount; ++i)
+    {
+    fprintf(f, "%g", el->expProbs[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+