ae3969602106c0229160648f6ff6c87c3ad0de2d
giardine
  Tue Dec 7 14:13:12 2010 -0800
Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
diff --git src/hg/lib/variome.c src/hg/lib/variome.c
new file mode 100644
index 0000000..5e1e740
--- /dev/null
+++ src/hg/lib/variome.c
@@ -0,0 +1,424 @@
+/* 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. */
+
+#include "common.h"
+#include "linefile.h"
+#include "dystring.h"
+#include "jksql.h"
+#include "variome.h"
+#include "hdb.h"
+#include "binRange.h"
+
+static char const rcsid[] = "$Id:$";
+
+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. Note that strings must be escaped to allow insertion into the database.
+ * For example "autosql's features include" --> "autosql\'s features include" 
+ * If worried about this use variomeSaveToDbEscaped() */
+{
+struct dyString *update = newDyString(updateSize);
+dyStringPrintf(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);
+}
+
+void variomeSaveToDbEscaped(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. Automatically 
+ * escapes all simple strings (not arrays of string) but may be slower than variomeSaveToDb().
+ * For example automatically copies and converts: 
+ * "autosql's features include" --> "autosql\'s features include" 
+ * before inserting into database. */ 
+{
+struct dyString *update = newDyString(updateSize);
+char  *chrom, *name, *strand, *db, *owner, *color, *class, *creationDate, *lastModifiedDate, *descriptionKey, *geneSymbol;
+chrom = sqlEscapeString(el->chrom);
+name = sqlEscapeString(el->name);
+strand = sqlEscapeString(el->strand);
+db = sqlEscapeString(el->db);
+owner = sqlEscapeString(el->owner);
+color = sqlEscapeString(el->color);
+class = sqlEscapeString(el->class);
+creationDate = sqlEscapeString(el->creationDate);
+lastModifiedDate = sqlEscapeString(el->lastModifiedDate);
+descriptionKey = sqlEscapeString(el->descriptionKey);
+geneSymbol = sqlEscapeString(el->geneSymbol);
+
+dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s','%s',%u,'%s')", 
+	tableName,  el->bin,  chrom,  el->chromStart,  el->chromEnd,  name,  el->score,  strand,  db,  owner,  color,  class,  creationDate,  lastModifiedDate,  descriptionKey,  el->id,  geneSymbol);
+sqlUpdate(conn, update->string);
+freeDyString(&update);
+freez(&chrom);
+freez(&name);
+freez(&strand);
+freez(&db);
+freez(&owner);
+freez(&color);
+freez(&class);
+freez(&creationDate);
+freez(&lastModifiedDate);
+freez(&descriptionKey);
+freez(&geneSymbol);
+}
+
+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();
+
+safef(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);
+
+variomeSaveToDbEscaped(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];
+safef(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();
+
+safef(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();
+safef(query, ArraySize(query), "DELETE FROM %s WHERE id='%d'",
+        "variome", id);
+sqlUpdate(conn,query);
+wikiDisconnect(&conn);
+}
+
+/* prefixComments and addDescription used from wikiTrack.c */
+