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/lib/variome.c src/hg/lib/variome.c
deleted file mode 100644
index 7af4cd5..0000000
--- src/hg/lib/variome.c
+++ /dev/null
@@ -1,385 +0,0 @@
-/* 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. */
-
-#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 */
-