44ccfacbe3a3d4b300f80d48651c77837a4b571e
galt
Tue Apr 26 11:12:02 2022 -0700
SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix.
diff --git src/hg/hgGeneRing/hgGeneRing.c src/hg/hgGeneRing/hgGeneRing.c
index b5abcef..91fa664 100644
--- src/hg/hgGeneRing/hgGeneRing.c
+++ src/hg/hgGeneRing/hgGeneRing.c
@@ -1,949 +1,949 @@
/* hgGeneRing - Gene Network Browser. */
/* Copyright (C) 2013 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "cheapcgi.h"
#include "htmshell.h"
#include "obscure.h"
#include "web.h"
#include "cart.h"
#include "hdb.h"
#include "dbDb.h"
#include "hgFind.h"
#include "hCommon.h"
#include "hui.h"
#include "interaction.h"
#include "bdgpGeneInfo.h"
#include "portable.h"
char *errMsg = NULL;
char *geneList = NULL;
struct slName *geneNames = NULL;
struct hash *aliasHash = NULL;
struct interaction *interactions = NULL;
struct node {
char *name; /* name or id - use also as hash key */
char *alias; /* if used */
struct nodelist *xrays; /* out-going rays in directed graph */
struct nodelist *nrays; /* in-coming rays in directed graph */
boolean ring; /* member of gene-ring? */
int ringRank; /* number of ring members connected to by x or n rays */
int xpos; /* x position */
int ypos; /* y position */
};
struct nodelist {
struct nodelist *next; /* next in list */
struct node *node;
};
struct nodelist* allNodes = NULL;
struct hash *nodeHash = NULL;
int ringCount = 0;
int insideCount = 0;
int outsideCount = 0;
struct cart *cart = NULL;
struct hash *oldVars = NULL;
char *clade = NULL;
char *organism = NULL;
char *db = NULL;
/* ------ old junk cloned from hgGateway --------- */
void hgGateway()
/* hgGateway - Human Genome Browser Gateway. */
{
char *defaultPosition = hDefaultPos(db);
char *position = cloneString(cartUsualString(cart, "position", defaultPosition));
boolean gotClade = hGotClade();
/* JavaScript to copy input data on the change genome button to a hidden form
This was done in order to be able to flexibly arrange the UI HTML
*/
char *onChangeDB = "onchange=\"document.orgForm.db.value = document.mainForm.db.options[document.mainForm.db.selectedIndex].value; document.orgForm.submit();\"";
char *onChangeOrg = "onchange=\"document.orgForm.org.value = document.mainForm.org.options[document.mainForm.org.selectedIndex].value; document.orgForm.db.value = 0; document.orgForm.submit();\"";
char *onChangeClade = "onchange=\"document.orgForm.clade.value = document.mainForm.clade.options[document.mainForm.clade.selectedIndex].value; document.orgForm.org.value = 0; document.orgForm.db.value = 0; document.orgForm.submit();\"";
if (sameString(position, "genome") || sameString(position, "hgBatch"))
position = defaultPosition;
puts("<FORM ACTION=\"/cgi-bin/hgTracks\" NAME=\"mainForm\" METHOD=\"GET\">\n"
"<CENTER>"
"<TABLE CELLPADDING=1 style='background-color:#FFFEF3; border-style:none;'>\n"
"<TR><TD style='text-align:center; font-size:small;'>\n"
"The UCSC Genome Browser was created by the \n"
"<A HREF=\"/staff.html\">Genome Bioinformatics Group of UC Santa Cruz</A>.\n"
"<BR>"
"Software Copyright (c) The Regents of the University of California.\n"
"All rights reserved.\n"
"</TD></TR></TABLE></CENTER>\n");
puts("<input TYPE=\"IMAGE\" BORDER=\"0\" NAME=\"hgt.dummyEnterButton\" src=\"/images/DOT.gif\" WIDTH=1 HEIGHT=1 ALT=dot>\n"
"<CENTER>\n"
"<table bgcolor='#CCCC99' border=0 CELLPADDING=1 CELLSPACING=0>\n"
"<tr><td>\n"
"<table CELLPADDING=0 CELLSPACING=0 style='background-color:#FEFDEF; border-style:none;'>\n"
"<tr><td>\n"
"<table bgcolor='#FFFEF3' border=0>\n"
"<tr>\n"
"<td>\n"
"<table><tr>");
if (gotClade)
puts("<td align=center valign=baseline>clade</td>");
puts("<td align=center valign=baseline>genome</td>\n"
"<td align=center valign=baseline>assembly</td>\n"
"<td align=center valign=baseline>position</td>\n"
"<td align=center valign=baseline>image width</td>\n"
"<td align=center valign=baseline> </td>\n"
"</tr>\n<tr>");
if (gotClade)
{
puts("<td align=center>\n");
printCladeListHtml(organism, onChangeClade);
puts("</td>\n");
}
puts("<td align=center>\n");
if (gotClade)
printGenomeListForCladeHtml(db, onChangeOrg);
else
printGenomeListHtml(db, onChangeOrg);
puts("</td>\n");
puts("<td align=center>\n");
/* HACK ALERT - Zoo needs to have different pulldown behavior - Hiram */
if ( startsWith( "Zoo", organism ) ) {
puts("<select NAME=\"db\" onchange=\"document.orgForm.db.value = document.mainForm.db.options[document.mainForm.db.selectedIndex].value; document.orgForm.submit();\">"
"\t<option SELECTED VALUE=\"zooHuman3\">June 2002</option>"
"\t</select>");
} else {
printAssemblyListHtml(db, onChangeDB);
}
puts("</td>\n");
puts("<td align=center>\n");
cgiMakeTextVar("position", addCommasToPos(position), 30);
printf("</td>\n");
#ifdef SORRY_GILL_I_HIT_INSTEAD_OF_SUBMIT_TOO_MANY_TIMES
puts("<td align=center>\n");
cgiMakeOnClickButton("document.mainForm.position.value=''","clear");
printf("</td>\n");
#endif /* SORRY_GILL_I_HIT_INSTEAD_OF_SUBMIT_TOO_MANY_TIMES */
cartSetString(cart, "position", position);
cartSetString(cart, "db", db);
cartSetString(cart, "org", organism);
if (gotClade)
cartSetString(cart, "clade", clade);
freez(&defaultPosition);
position = NULL;
puts("<td align=center>\n");
cgiMakeIntVar("pix", cartUsualInt(cart, "pix", hgDefaultPixWidth), 4);
cartSaveSession(cart);
printf("</td>\n");
printf("<td align=center>");
cgiMakeButton("Submit", "Submit");
printf("</td>\n");
puts("</tr></table>\n"
"</td></tr><tr><td><CENTER>\n"
"<a HREF=\"../cgi-bin/cartReset\">Click here to reset</a> the browser user interface settings to their defaults.<BR>\n"
"</CENTER>\n"
"</td></tr><tr><td><CENTER>\n");
cgiMakeButton("customTrackPage", "Add Your Own Custom Tracks");
puts("</CENTER>\n"
"</td></tr></table>\n"
"</td></tr></table>\n"
"</td></tr></table>\n");
puts("</CENTER>");
hgPositionsHelpHtml(organism, db);
puts("</FORM>\n"
);
puts("<FORM ACTION=\"/cgi-bin/hgGateway\" METHOD=\"GET\" NAME=\"orgForm\">");
if (gotClade)
printf("<input type=\"hidden\" name=\"clade\" value=\"%s\">\n", clade);
printf("<input type=\"hidden\" name=\"org\" value=\"%s\">\n", organism);
printf("<input type=\"hidden\" name=\"db\" value=\"%s\">\n", db);
cartSaveSession(cart);
puts("</FORM><BR>");
}
/* end of hgGateway junk that this code was cloned from */
/* ----------------------------------------------------------------------- */
boolean getGenesAsList()
/* create name-list from geneString,
so that we don't have to keep re-parsing
the cart string in different places
*/
{
char* ss = cloneString(geneList);
char* s = ss;
char* w = NULL;
int c=0;
char emsg[256];
/* clean up unwanted characters if any */
subChar(ss, ',' ,' ');
subChar(ss, '\t',' ');
subChar(ss, '\n',' ');
subChar(ss, '\r',' ');
while (1)
{
if (!(w = nextWord(&s))) break;
if (slNameInList(geneNames, w))
/* could be optimized, but not expecting large lists for ring */
{
safef(emsg,sizeof(emsg), "Duplicate gene id (%s) found in list.",w);
errMsg = cloneString(emsg);
freez(&ss);
return FALSE;
}
slNameAddHead(&geneNames, w);
c++;
}
slReverse(&geneNames);
if (c==0)
{
errMsg = "No genes in list. Please specify genes for ring.";
return FALSE;
}
freez(&ss);
return TRUE;
}
void updateGeneList()
/* update the cart list of genes */
{
char *sep = "";
struct slName *sn = geneNames;
-struct dyString *geneList=newDyString(512);
+struct dyString *geneList=dyStringNew(512);
while(sn)
{
dyStringPrintf(geneList,"%s%s",sep,sn->name);
sep=" ";
sn=sn->next;
}
cartSetString(cart, "ring_geneList", geneList->string);
-freeDyString(&geneList);
+dyStringFree(&geneList);
}
struct bdgpGeneInfo *bdgpGeneInfoLoadByQuery(struct sqlConnection *conn, char *query)
/* Load all interaction 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 bdgpGeneInfoFreeList(). */
{
struct bdgpGeneInfo *list = NULL, *el;
struct sqlResult *sr;
char **row;
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
el = bdgpGeneInfoLoad(row);
slAddHead(&list, el);
}
slReverse(&list);
sqlFreeResult(&sr);
return list;
}
void getGeneAliasesFromTable(char* table)
/* read all the gene aliases from database, return bdgpGeneInfo-list */
{
struct bdgpGeneInfo *result = NULL, *this=NULL;
-struct dyString *query=newDyString(512);
+struct dyString *query=dyStringNew(512);
char *sep = "where";
struct slName *sn = geneNames;
sqlDyStringPrintf(query,"select * from %s",table);
while(sn)
{
char * nm = sn->name;
if (startsWith("CG",nm))
{
sqlDyStringPrintf(query," %s bdgpName='%s'",sep,nm);
sep = "or";
}
else if (!startsWith("FBgn",nm))
{
sqlDyStringPrintf(query," %s symbol='%s'",sep,nm);
sep = "or";
}
sn = sn->next;
}
//uglyf("<br>SQL=%s<br><br>\n",query->string);
struct sqlConnection* conn = hAllocConn();
result = bdgpGeneInfoLoadByQuery(conn, query->string);
for(this=result;this;this=this->next)
{
//uglyf("<br>adding %s=%s<br>\n",this->bdgpName,this->flyBaseId); // debug
hashAdd(aliasHash,this->bdgpName,cloneString(this->flyBaseId));
//uglyf("<br>adding %s=%s<br>\n",this->symbol,this->flyBaseId); // debug
hashAdd(aliasHash,this->symbol,cloneString(this->flyBaseId));
}
// Mysterious crashes if I free this list:
//bdgpGeneInfoFreeList(&result);
hFreeConn(&conn);
-freeDyString(&query);
+dyStringFree(&query);
}
struct interaction *getGenesFromTable(char* table)
/* read all the gene interactions from database, returns interaction-list */
{
struct interaction *result = NULL;
-struct dyString *query=newDyString(512);
+struct dyString *query=dyStringNew(512);
char *sep = "where";
struct slName *sn = geneNames;
getGeneAliasesFromTable("bdgpGeneInfo"); /* load aliases into hash */
sqlDyStringPrintf(query,"select * from %s",table);
while(sn)
{
struct hashEl *hel = NULL, *hf=NULL;
char * nm = sn->name;
char * alias = NULL;
if (!startsWith("FBgn",nm))
{
if (hf = hashLookup(aliasHash,nm))
{
alias = sn->name;
//uglyf("<br>aliasing %s with %s<br>\n",nm,(char *)hf->val); // debug
nm = (char *)hf->val;
}
}
hel = hashStore(nodeHash,nm);
if (!hel->val) /* add geneList elements to the hash */
{
struct node *n;
struct nodelist *nl;
AllocVar(n);
AllocVar(nl);
n->name = cloneString(nm);
n->alias = cloneString(alias);
n->ring = TRUE; /* this is a special ring member */
nl->node = n;
slAddHead(&allNodes,nl); /* all nodes going in hash are added to all-nodes list */
hel->val = n;
}
sqlDyStringPrintf(query," %s fromX='%s' or toY='%s'",sep,nm,nm);
sep = "or";
sn = sn->next;
}
//uglyf("<br>SQL=%s<br><br>\n",query->string);
struct sqlConnection* conn = hAllocConn();
result = interactionLoadByQuery(conn, query->string);
hFreeConn(&conn);
-freeDyString(&query);
+dyStringFree(&query);
return result;
}
void getGeneList()
/* hgGeneRing - Gene Network Browser. */
{
/* not much point in this, though called old it's the same as current
at this point. It is not the old value from before the last submit.
char *oldGeneList = hashFindVal(oldVars, "ring_geneList");
*/
if (!sameString(errMsg,""))
{
printf("<CENTER>%s</CENTER>\n",errMsg);
}
puts("<FORM ACTION=\"/cgi-bin/hgGeneRing\" NAME=\"mainForm\" METHOD=\"GET\">\n"
"<CENTER>"
"<TABLE CELLPADDING=1 style='background-color:#FFFEF3; border-style:none;'>\n"
"<TR><TD style='text-align:center; font-size:x-small;'>\n"
"Enter gene list for gene network ring.\n"
"</TD></TR></TABLE></CENTER>\n");
puts("<CENTER>"
"<table bgcolor='#CCCC99' border=0 CELLPADDING=1 CELLSPACING=0>\n"
"<tr>\n");
puts("<td align=center>\n");
cgiMakeTextArea("ring_geneList", geneList, 25, 30);
printf("</td>\n");
puts("</tr><tr>\n");
printf("<td align=center>");
cgiMakeButton("Submit", "Submit");
printf("</td>\n");
puts("</tr></table></CENTER>\n");
puts("</FORM>\n");
cartSetString(cart, "ring_action", "saveGeneList");
cartSetString(cart, "ring_errMsg", "");
}
int compareNodes(const void *va, const void *vb)
{
const struct nodelist *a = *((struct nodelist **)va);
const struct nodelist *b = *((struct nodelist **)vb);
if (a->node->ring && !b->node->ring) return -1;
if (!a->node->ring && b->node->ring) return 1;
if (a->node->ring && b->node->ring)
{
return differentWord(a->node->name,b->node->name)*-1;
}
if (a->node->ringRank == b->node->ringRank)
{
return differentWord(a->node->name,b->node->name)*-1;
}
else
{
return (b->node->ringRank - a->node->ringRank);
}
}
boolean saveGeneList(boolean showAll)
/* Check for valid gene-list: parse and save.
If list not ok, return to getGeneList page.
Otherwise, show user's list and offer some links.
*/
{
struct interaction* intr;
struct nodelist *nl;
if (!getGenesAsList())
{
getGeneList();
return FALSE;
}
if (showAll)
{
puts("<CENTER>"
"<table bgcolor='#CCCC99' border=0 CELLPADDING=1 CELLSPACING=0>\n"
"<tr><td>\n");
printf("geneList: %s<br>\n", geneList );
puts("</td></tr><tr><td>"
"<a href=\"/cgi-bin/hgGeneRing?ring_action=getGeneList\">gene-list</a>\n"
"</td></tr><tr><td>"
"<a href=\"/cgi-bin/hgGeneRing?ring_action=drawScreen\">screen</a>\n");
puts("</td></tr></table></CENTER>\n");
}
interactions = getGenesFromTable("intrP2P"); /* adds geneList elements to hash */
if (showAll)
{
uglyf("slCount = %d for result list for %s.<br><br>\n",slCount(interactions),geneList);
}
/* this might get moved later */
/* add to hash the remaining interactions members */
for(intr=interactions;intr;intr=intr->next)
{
//uglyf("%s %s %f.<br>\n",intr->fromX,intr->toY,intr->score);
struct hashEl *helX = hashStore(nodeHash,intr->fromX);
struct hashEl *helY = hashStore(nodeHash,intr->toY);
struct node *x, *y;
struct nodelist *nl;
if (!helX->val) /* add X to hash for 1st time */
{
AllocVar(x);
AllocVar(nl);
x->name = cloneString(intr->fromX);
nl->node = x;
slAddHead(&allNodes,nl); /* add X to list of all nodes */
helX->val = x;
}
if (!helY->val) /* do same stuff for Y */
{
AllocVar(y);
AllocVar(nl);
y->name = cloneString(intr->toY);
nl->node = y;
slAddHead(&allNodes,nl);
helY->val = y;
}
x = helX->val; /* get X,Y from hash */
y = helY->val;
if (x->ring) y->ringRank++; /* increment ringRank counts */
if (y->ring) x->ringRank++;
AllocVar(nl);
nl->node = y;
slAddHead(&x->xrays,nl); /* add Y to X's list of x-rays */
AllocVar(nl);
nl->node = x;
slAddHead(&y->nrays,nl); /* likewise */
}
interactionFreeList(&interactions);
slReverse(&allNodes);
slSort(&allNodes, compareNodes);
/* sum counts and if showAll, display our structure */
if (showAll)
{
uglyf("<pre>\n");
uglyf("name xrays nrays ring? ringRank \n");
uglyf("-------------------------------------- \n");
}
for(nl=allNodes;nl;nl=nl->next)
{
if (nl->node->ring)
{
ringCount++;
}
else
{
if (nl->node->ringRank > 1)
{
insideCount++;
}
else
{
outsideCount++;
}
}
if (showAll)
{
uglyf("%11s %4d %4d %4s %3d \n",
nl->node->name,
slCount(nl->node->xrays),
slCount(nl->node->nrays),
nl->node->ring ? "ring":"not!",
nl->node->ringRank
);
}
}
if (showAll)
{
uglyf("</pre>\n");
}
// TODO: add some real code for freeing these things properly
// e.g. for xrays and nrays lists, free up the nodelist list itself,
// but not the *node values themselves, which are allocated
// in the main nodelist/hash. If the nodelist is freed up
// properly then hash freeing should be easy enough.
// Do we use valgrind or some other util to verify mem-release?
return TRUE;
}
/* Count up elements in list that are outside ring. */
int slCountOutside(void *list)
{
struct slList *pt = (struct slList *)list;
int len = 0;
while (pt != NULL)
{
struct node *n = ((struct nodelist *)pt)->node;
if ((!n->ring) && (n->ringRank==1))
len += 1;
pt = pt->next;
}
return len;
}
#define NODE_SIZE 10
void addMap(struct nodelist *nl)
{
struct node *node = nl->node;
int x=node->xpos;
int y=node->ypos;
int r=NODE_SIZE;
char *name = node->name;
if (node->alias)
{
name = node->alias;
}
printf(
"<AREA SHAPE=CIRCLE COORDS=\"%d,%d,%d\""
" HREF=\"/cgi-bin/hgGeneRing?ring_action=geneFrame&ring_gene=%s&ring_position=%s\""
" ALT=\"%s\""
" TITLE=\"%s\">",
x,y,r,
name,
node->name,
name,
name
);
}
void drawScreen()
/*
Draw Gene Ring using given genes and interactions
and display it in a page as a .gif
*/
{
#define SCREEN_SIZE 800
#define RING_SIZE 200
#define INRING_SIZE 140
#define OUTRING_SIZE 340
struct tempName filename;
int width,height;
char *mapName="ring_map";
ZeroVar(&filename);
makeTempName(&filename, "hgGeneRing_screen", ".gif");
printf("<MAP Name=%s>\n", mapName);
struct memGfx *mg = mgNew(SCREEN_SIZE,SCREEN_SIZE);
int i;
double angle=0;
int xCen = SCREEN_SIZE/2, yCen = SCREEN_SIZE/2;
int x=0,y=0;
struct nodelist *nl, *saveNl;
/* draw the main RING */
mgCircle(mg, xCen, yCen, SCREEN_SIZE/4, MG_BLACK, FALSE);
/* draw the RING genes and assign position */
angle=(M_PI*2)/ringCount;
nl=allNodes;
for(i=0;i<ringCount;i++)
{
x = xCen + (int) RING_SIZE*cos(i*angle);
y = yCen + (int) RING_SIZE*sin(i*angle);
nl->node->xpos = x;
nl->node->ypos = y;
mgCircle(mg, x, y, NODE_SIZE, MG_BLACK, FALSE);
addMap(nl);
nl=nl->next;
}
/* draw the Inside genes, assign position, and draw rays */
angle=(M_PI*2)/insideCount;
for(i=0;i<insideCount;i++)
{
x = xCen + (int) INRING_SIZE*cos((i+.5)*angle);
y = yCen + (int) INRING_SIZE*sin((i+.5)*angle);
nl->node->xpos = x;
nl->node->ypos = y;
mgCircle(mg, x, y, NODE_SIZE, MG_BLACK, FALSE);
addMap(nl);
/* draw connections to ring */
{ /*local*/
struct nodelist *l;
for(l=nl->node->xrays;l;l=l->next)
{ /* blue = inward = to-ring */
mgDrawLine(mg, x, y, l->node->xpos, l->node->ypos, MG_BLUE);
}
for(l=nl->node->nrays;l;l=l->next)
{ /* red = outward = from-ring */
mgDrawLine(mg, x, y, l->node->xpos, l->node->ypos, MG_RED);
}
}
nl=nl->next;
}
/* draw the Outside genes, assign position, draw rays
do 1 ring member at a time.
*/
angle=(M_PI*2)/ringCount;
nl=allNodes;
for(i=0;i<ringCount;i++)
{
double subAngle=0;
int numOutside=0, doneOutside=0;
numOutside += slCountOutside(nl->node->nrays);
numOutside += slCountOutside(nl->node->xrays);
subAngle = angle / (numOutside+1); /* add 1 to give a little space between ring groups */
/* draw connections to ring */
{ /*local*/
struct nodelist *l;
int j = 0;
struct nodelist *rays;
Color color;
for (j=0;j<2;j++)
{
if (j==0)
{
color = MG_BLUE;
rays = nl->node->xrays;
}
else
{
color = MG_RED;
rays = nl->node->nrays;
}
for(l=rays;l;l=l->next)
{
if (l->node->ring)
{ /* this ring-ring line gets draw twice but that's ok */
x = l->node->xpos;
y = l->node->ypos;
mgDrawLine(mg, x, y, nl->node->xpos, nl->node->ypos, MG_BLACK);
}
else if (l->node->ringRank==1)
{
doneOutside++;
x = xCen + (int) OUTRING_SIZE*cos((i-.5)*angle+(doneOutside*subAngle));
y = yCen + (int) OUTRING_SIZE*sin((i-.5)*angle+(doneOutside*subAngle));
l->node->xpos = x;
l->node->ypos = y;
mgCircle(mg, x, y, NODE_SIZE, MG_BLACK, FALSE);
addMap(l);
mgDrawLine(mg, x, y, nl->node->xpos, nl->node->ypos, color);
}
}
}
}
nl=nl->next;
}
printf("</MAP>\n");
mgSaveGif(mg, filename.forCgi, FALSE);
width=height=SCREEN_SIZE;
printf("<CENTER><TABLE BORDER=0 CELLPADDING=0>");
printf("<TR><TD HEIGHT=5></TD></TR>");
printf("<TR><TD><IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s >",
filename.forHtml, width, height, mapName);
printf("</TD></TR>");
printf("<TR><TD HEIGHT=5></TD></TR>");
printf(
"<TR><TD>"
"<a href = \"/cgi-bin/hgGeneRing?ring_action=saveGeneList\">back</a> "
"<a href = \"/cgi-bin/hgGeneRing?ring_action=getGeneList\">gene-list</a> "
"<a href = \"/cgi-bin/hgGeneRing?ring_action=drawScreen\">refresh</a> "
"</TD></TR>");
printf("<TR><TD HEIGHT=5></TD></TR></TABLE></CENTER>");
}
char *unAlias(char *gene)
/* deal with alias mapping for gene names, return FBgn */
{
struct hashEl *hf=NULL;
if (!startsWith("FBgn",gene))
{
if (hf=hashLookup(aliasHash,gene))
{
gene=(char *)hf->val;
}
}
return gene;
}
void drawDetails()
{
char *gene = cartUsualString(cart, "ring_gene", "");
char *targ = unAlias(gene);
struct hashEl *hel = NULL;
struct node *n;
hel = hashLookup(nodeHash,targ);
if (hel)
{
n = hel->val;
printf(
"Details page for gene %s "
"<A HREF=\"/cgi-bin/hgGeneRing?ring_action=%s&ring_gene=%s\" target=\"_parent\" >"
"%s Ring</A> "
" (rank=%d) "
"<A HREF=\"/cgi-bin/hgGeneRing?ring_action=drawScreen\" target=\"_parent\" > return </A>"
"\n",
gene,
n->ring?"removeFromRing":"addToRing",
gene,
n->ring?"Remove From ":"Add To ",
n->ringRank
);
}
else
{
printf("Unknown gene %s",gene);
}
}
void hgGeneRing()
/* hgGeneRing - Gene Network Browser. */
{
char *action = cartUsualString(cart, "ring_action", "");
if (sameWord(action,""))
{
action = "getGeneList";
}
if (sameWord(action,"getGeneList"))
{
getGeneList();
}
else if (sameWord(action,"saveGeneList"))
{
saveGeneList(TRUE);
}
else if (sameWord(action,"drawScreen"))
{
if (saveGeneList(FALSE))
drawScreen();
}
else if (sameWord(action,"drawDetails"))
{
if (saveGeneList(FALSE))
drawDetails();
}
else if (sameWord(action,"addToRing"))
{
char *gene = cartUsualString(cart, "ring_gene", "");
getGenesAsList();
slNameAddTail(&geneNames, gene);
updateGeneList();
/* in lieue of actually just redirecting the browser */
cartSaveSession(cart);
geneList = cloneString(cartUsualString(cart, "ring_geneList", ""));
slFreeList(&geneNames); /* just reset everything */
if (saveGeneList(FALSE))
drawScreen();
}
else if (sameWord(action,"removeFromRing"))
{
char *gene = cartUsualString(cart, "ring_gene", "");
struct slName **psn = &geneNames;
getGenesAsList();
while(*psn)
{
if (sameString((*psn)->name,gene))
{
*psn = (*psn)->next;
break;
}
psn=&((*psn)->next);
}
updateGeneList();
/* in lieue of actually just redirecting the browser */
cartSaveSession(cart);
geneList = cloneString(cartUsualString(cart, "ring_geneList", ""));
slFreeList(&geneNames); /* just reset everything */
if (saveGeneList(FALSE))
drawScreen();
}
else
{
getGeneList();
}
}
void doMiddle(struct cart *theCart)
/* Set up pretty web display and save cart in global. */
{
char *action = cgiUsualString("ring_action", "");
cart = theCart;
getDbGenomeClade(cart, &db, &organism, &clade, oldVars);
if (! hDbIsActive(db))
{
db = hDefaultDb();
organism = hGenome(db);
clade = hClade(organism);
}
/* temporary hack, set db to dm1 fly */
db = "dm1";
organism = "D. melanogaster";
clade = "insect";
cartSetString(cart, "db", db);
cartSetString(cart, "org", organism);
cartSetString(cart, "clade", clade);
hSetDb(db);
if (sameWord(action,"geneFrame"))
{ /* special handling for frameset - can't use cartWebStart etc. */
char *gene = cartUsualString(cart, "ring_gene", "");
char *position = cartUsualString(cart, "ring_position", "");
printf(
"<frameset rows = \"18%%, *\">"
" <frame src =\"/cgi-bin/hgGeneRing?ring_action=drawDetails&ring_gene=%s\" />"
" <frame src =\"/cgi-bin/hgTracks?position=%s&db=%s\" />"
"</frameset>",
gene,
position,
db
);
}
else
{
cartWebStart(theCart, database, "%s Gene Network Browser \n", organism);
geneList = cloneString(cartUsualString(cart, "ring_geneList", ""));
errMsg = cartUsualString(cart, "ring_errMsg", ""); /* any error from last time */
hgGeneRing();
cartSaveSession(cart);
cartWebEnd();
}
freez(&geneList);
}
char *excludeVars[] = {NULL};
int main(int argc, char *argv[])
/* Process command line. */
{
oldVars = hashNew(10);
cgiSpoof(&argc, argv);
nodeHash = newHash(8);
aliasHash = newHash(8);
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
freeHashAndVals(&nodeHash);
return 0;
}