4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/cgilib/variome.c src/hg/cgilib/variome.c
index 7af4cd5..28e0431 100644
--- src/hg/cgilib/variome.c
+++ src/hg/cgilib/variome.c
@@ -1,385 +1,385 @@
 /* variome.c was originally generated by the autoSql program, which also 
  * generated variome.h and variome.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. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "variome.h"
 #include "hdb.h"
 #include "binRange.h"
 
 
 void variomeStaticLoad(char **row, struct variome *ret)
 /* Load a row from variome 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->name = row[4];
 ret->score = sqlUnsigned(row[5]);
 safecpy(ret->strand, sizeof(ret->strand), row[6]);
 ret->db = row[7];
 ret->owner = row[8];
 ret->color = row[9];
 ret->class = row[10];
 ret->creationDate = row[11];
 ret->lastModifiedDate = row[12];
 ret->descriptionKey = row[13];
 ret->id = sqlUnsigned(row[14]);
 ret->geneSymbol = row[15];
 }
 
 struct variome *variomeLoad(char **row)
 /* Load a variome from row fetched with select * from variome
  * from database.  Dispose of this with variomeFree(). */
 {
 struct variome *ret;
 
 AllocVar(ret);
 ret->bin = sqlUnsigned(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = cloneString(row[4]);
 ret->score = sqlUnsigned(row[5]);
 safecpy(ret->strand, sizeof(ret->strand), row[6]);
 ret->db = cloneString(row[7]);
 ret->owner = cloneString(row[8]);
 ret->color = cloneString(row[9]);
 ret->class = cloneString(row[10]);
 ret->creationDate = cloneString(row[11]);
 ret->lastModifiedDate = cloneString(row[12]);
 ret->descriptionKey = cloneString(row[13]);
 ret->id = sqlUnsigned(row[14]);
 ret->geneSymbol = cloneString(row[15]);
 return ret;
 }
 
 struct variome *variomeLoadAll(char *fileName) 
 /* Load all variome from a whitespace-separated file.
  * Dispose of this with variomeFreeList(). */
 {
 struct variome *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[16];
 
 while (lineFileRow(lf, row))
     {
     el = variomeLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct variome *variomeLoadAllByChar(char *fileName, char chopper) 
 /* Load all variome from a chopper separated file.
  * Dispose of this with variomeFreeList(). */
 {
 struct variome *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[16];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = variomeLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct variome *variomeLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all variome 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 variomeFreeList(). */
 {
 struct variome *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = variomeLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void variomeSaveToDb(struct sqlConnection *conn, struct variome *el, char *tableName, int updateSize)
 /* Save variome 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',%u,'%s','%s','%s','%s','%s','%s','%s','%s',%u,'%s')", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->db,  el->owner,  el->color,  el->class,  el->creationDate,  el->lastModifiedDate,  el->descriptionKey,  el->id,  el->geneSymbol);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct variome *variomeCommaIn(char **pS, struct variome *ret)
 /* Create a variome out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new variome */
 {
 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->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->db = sqlStringComma(&s);
 ret->owner = sqlStringComma(&s);
 ret->color = sqlStringComma(&s);
 ret->class = sqlStringComma(&s);
 ret->creationDate = sqlStringComma(&s);
 ret->lastModifiedDate = sqlStringComma(&s);
 ret->descriptionKey = sqlStringComma(&s);
 ret->id = sqlUnsignedComma(&s);
 ret->geneSymbol = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void variomeFree(struct variome **pEl)
 /* Free a single dynamically allocated variome such as created
  * with variomeLoad(). */
 {
 struct variome *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->db);
 freeMem(el->owner);
 freeMem(el->color);
 freeMem(el->class);
 freeMem(el->creationDate);
 freeMem(el->lastModifiedDate);
 freeMem(el->descriptionKey);
 freeMem(el->geneSymbol);
 freez(pEl);
 }
 
 void variomeFreeList(struct variome **pList)
 /* Free a list of dynamically allocated variome's */
 {
 struct variome *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     variomeFree(&el);
     }
 *pList = NULL;
 }
 
 void variomeOutput(struct variome *el, FILE *f, char sep, char lastSep) 
 /* Print out variome.  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->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 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->db);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->owner);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->color);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->class);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->creationDate);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->lastModifiedDate);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->descriptionKey);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->id);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneSymbol);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 #include "wikiTrack.h"
 #include "wikiLink.h"
 #include "web.h"
 #include "cheapcgi.h"
 #include "hPrint.h"
 #include "hgConfig.h"
 #include "hCommon.h"
 
 char *variomeClassList[] = {
     "substitution",
     "insertion",
     "duplication",
     "deletion",
     "inversion",
     "complex",
     ITEM_NOT_CLASSIFIED,
 };
 
 char *variomeCoorList[] = {
     "exact coordinates",
     "estimated coordinates",
 };
 
 int variomeClassCnt = ArraySize(variomeClassList);
 
 struct variome *findVariomeItemId(char *db, char *wikiItemId)
 /* given a wikiItemId return the row from the table */
 {
 struct variome *item;
 char query[256];
 struct sqlConnection *conn = wikiConnect();
 
 sqlSafef(query, ArraySize(query), "SELECT * FROM variome WHERE id='%s' limit 1",
         wikiItemId);
 
 item = variomeLoadByQuery(conn, query);
 if (NULL == item)
     errAbort("display wiki item: failed to load item '%s'", wikiItemId);
 
 wikiDisconnect(&conn);
 return item;
 }
 
 /* use functions from lib/wikiTrack.c, lib/wikiLink.c for accessing wiki pages */
 
 int addVariomeItem(char *db, char *chrom, int start, int end,
     char *name, int score, char *strand, char *owner, char *class,
         char *color, char *category, char *geneSymbol, char *wikiKey)
 /* create new Variome row with given parameters */
 {
 struct sqlConnection *conn = wikiConnect();
 struct variome *newItem;
 AllocVar(newItem);
 newItem->bin = binFromRange(start, end);
 newItem->chrom = cloneString(chrom);
 newItem->chromStart = start;
 newItem->chromEnd = end;
 newItem->name = cloneString(name);
 newItem->score = score;
 if (sameString(strand, "plus"))
     safef(newItem->strand, sizeof(newItem->strand), "%s", "+");
 else if (sameString(strand, "minus"))
     safef(newItem->strand, sizeof(newItem->strand), "%s", "-");
 else 
     safef(newItem->strand, sizeof(newItem->strand), "%s", " ");
 newItem->db = cloneString(db);
 newItem->owner = cloneString(owner);
 newItem->class = cloneString(class);
 newItem->color = cloneString(color);
 newItem->creationDate = cloneString("0");
 newItem->lastModifiedDate = cloneString("0");
 newItem->descriptionKey = cloneString("0");
 newItem->id = 0;
 newItem->geneSymbol = cloneString(geneSymbol);
 
 variomeSaveToDb(conn, newItem, "variome", 1024);
 
 int id = sqlLastAutoId(conn);
 char descriptionKey[256];
 /* when wikiKey is NULL, assign the default key of category:db-id,
  *      else, it is the proper key
  */
 if (wikiKey)
     safef(descriptionKey,ArraySize(descriptionKey), "%s", wikiKey);
 else
     safef(descriptionKey,ArraySize(descriptionKey),
         "%s:%s-%d", category, db, id);
 
 variomeFree(&newItem);
 
 char query[1024];
 sqlSafef(query, ArraySize(query), "UPDATE %s set creationDate=now(),lastModifiedDate=now(),descriptionKey='%s' WHERE id='%d'",
     "variome", descriptionKey, id);
 
 sqlUpdate(conn,query);
 wikiDisconnect(&conn);
 return (id);
 }
 
 void updateVariomeLastModifiedDate(char *db, int id)
 /* set lastModifiedDate to now() */
 {
 char query[512];
 struct sqlConnection *conn = wikiConnect();
 
 sqlSafef(query, ArraySize(query),
     "UPDATE %s set lastModifiedDate=now() WHERE id='%d'",
         "variome", id);
 sqlUpdate(conn,query);
 wikiDisconnect(&conn);
 }
 
 void deleteVariomeItem(char *db, int id)
 /* delete the item with specified id */
 {
 char query[512];
 struct sqlConnection *conn = wikiConnect();
 sqlSafef(query, ArraySize(query), "DELETE FROM %s WHERE id='%d'",
         "variome", id);
 sqlUpdate(conn,query);
 wikiDisconnect(&conn);
 }
 
 /* prefixComments and addDescription used from wikiTrack.c */