src/hg/hgTracks/searchTracks.c 1.4
1.4 2010/05/27 17:14:12 larrym
fix build problem (mapName -> track)
Index: src/hg/hgTracks/searchTracks.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/searchTracks.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/hgTracks/searchTracks.c 26 May 2010 20:36:39 -0000 1.3
+++ src/hg/hgTracks/searchTracks.c 27 May 2010 17:14:12 -0000 1.4
@@ -1,348 +1,348 @@
/* Track search code used by hgTracks CGI */
#include "common.h"
#include "hCommon.h"
#include "memalloc.h"
#include "obscure.h"
#include "dystring.h"
#include "hash.h"
#include "cheapcgi.h"
#include "hPrint.h"
#include "htmshell.h"
#include "cart.h"
#include "hgTracks.h"
#include "versionInfo.h"
#include "web.h"
#include "cds.h"
#include "ra.h"
static int gCmpGroup(const void *va, const void *vb)
/* Compare groups based on label. */
{
const struct group *a = *((struct group **)va);
const struct group *b = *((struct group **)vb);
return strcmp(a->label, b->label);
}
static int gCmpTrack(const void *va, const void *vb)
/* Compare tracks based on longLabel. */
{
const struct slRef *aa = *((struct slRef **)va);
const struct slRef *bb = *((struct slRef **)vb);
const struct track *a = ((struct track *) aa->val);
const struct track *b = ((struct track *) bb->val);
return strcmp(a->longLabel, b->longLabel);
}
// XXXX make a matchString function to support "contains", "is" etc. and wildcards in contains
// ((sameString(op, "is") && !strcasecmp(track->shortLabel, str)) ||
static boolean isNameMatch(struct track *track, char *str, char *op)
{
return str && strlen(str) &&
((sameString(op, "is") && !strcasecmp(track->shortLabel, str)) ||
(sameString(op, "is") && !strcasecmp(track->longLabel, str)) ||
(sameString(op, "contains") && containsStringNoCase(track->shortLabel, str) != NULL) ||
(sameString(op, "contains") && containsStringNoCase(track->longLabel, str) != NULL));
}
static boolean isDescriptionMatch(struct track *track, char *str, char *op)
{
// XXXX obviously very primitive; s/d ignore html markup and do stemming etc.
char *html = track->tdb->html;
if((!html || !strlen(html)) && track->tdb->parent)
{
// XXXX is there a cleaner way to find parent?
html = track->tdb->parent->html;
}
// fprintf(stderr, "description: %s; %s\n", str, html);
return str && strlen(str) && sameString(op, "contains") && (strstrNoCase(html, str) != NULL);
}
static boolean isMetaMatch(struct track *track, char *name, char *op, char *val)
{
boolean retVal = FALSE;
char *setting = NULL;
char buf[100];
char *metadata = trackDbSetting(track->tdb, "metadata");
if(metadata)
{
char *ptr;
safef(buf, sizeof(buf), "%s=", name);
ptr = strstr(metadata, buf);
if(ptr)
{
ptr += strlen(buf);
setting = ptr;
ptr = skipToSpaces(ptr);
if(*ptr)
*ptr = 0;
}
}
// fprintf(stderr, "%s; setting: %s\n", track->track, setting);
retVal = setting && strlen(setting) &&
((sameString(op, "is") && !strcasecmp(setting, val)) ||
(sameString(op, "contains") && containsStringNoCase(setting, val) != NULL));
return retVal;
}
// XXXX got this code from hgEncodeVocab.c; it should be moved into a library (kent/src/hg/lib/encode.c?)
static char *cv_file()
{
static char filePath[PATH_LEN];
safef(filePath, sizeof(filePath), "%s/encode/cv.ra", hCgiRoot());
if(!fileExists(filePath))
errAbort("Error: can't locate cv.ra; %s doesn't exist\n", filePath);
return filePath;
}
static int termCmp(const void *va, const void *vb)
/* Compare controlled vocab based on term value */
{
const struct hash *a = *((struct hash **)va);
const struct hash *b = *((struct hash **)vb);
char *termA = hashMustFindVal((struct hash *)a, "term");
char *termB = hashMustFindVal((struct hash *)b, "term");
return (strcasecmp(termA, termB));
}
static int getTermList(struct hash *cvHash, char ***terms, char *type)
{
// Pull out all term fields from ra entries with given type
// Returns count of items found and items via the terms argument.
struct hashCookie hc;
struct hashEl *hEl;
struct slList *termList = NULL;
struct hash *ra;
int i, count = 0;
char **retval;
hc = hashFirst(cvHash);
while ((hEl = hashNext(&hc)) != NULL)
{
ra = (struct hash *) hEl->val;
if(sameString(hashMustFindVal(ra, "type"), type))
{
slAddTail(&termList, ra);
count++;
}
}
slSort(&termList, termCmp);
retval = needMem(sizeof(char *) * (count + 1));
retval[0] = cloneString("Any");
for(i=0; termList != NULL;termList = termList->next, i++)
{
ra = (struct hash *) termList;
retval[i+1] = cloneString(hashMustFindVal(ra, "term"));
}
*terms = retval;
return count + 1;
}
void doSearchTracks(struct group *groupList)
{
struct group *group;
char *ops[] = {"is", "contains"};
char *op_labels[] = {"is", "contains"};
char *metaNames[] = {"antibody", "cell line"};
char *metaValues[] = {"antibody", "cell"};
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = "any";
labels[0] = "Any";
char *nameSearch = cartOptionalString(cart, "hgt.nameSearch");
char *nameOp = cartOptionalString(cart, "hgt.nameOp");
char *descSearch = cartOptionalString(cart, "hgt.descSearch");
char *descOp = cartOptionalString(cart, "hgt.descOp");
char *groupSearch = cartOptionalString(cart, "hgt.groupSearch");
char *metaName = cartOptionalString(cart, "hgt.metaName");
char *metaOp = cartOptionalString(cart, "hgt.metaOp");
char *metaSearch = cartOptionalString(cart, "hgt.metaSearch");
char *antibodySearch = cartOptionalString(cart, "hgt.antibodySearch");
char *cellSearch = cartOptionalString(cart, "hgt.cellSearch");
char **terms;
int len;
struct hash *cvHash = raReadAll(cv_file(), "term");
// struct track *trackList =
getTrackList(&groupList, -2);
slSort(&groupList, gCmpGroup);
for (group = groupList; group != NULL; group = group->next)
{
if (group->trackList != NULL)
{
groups[numGroups] = cloneString(group->name);
labels[numGroups] = cloneString(group->label);
numGroups++;
if (numGroups >= ArraySize(groups))
internalErr();
}
}
cartWebStart(cart, database, "Search/Select Annotation Tracks (very rough prototype!)");
hPrintf("<form action='%s' name='SearchTracks' method='post'>\n\n", hgTracksName());
hPrintf("<table>\n");
hPrintf("<tr><td></td><td><b>Name:</b></td><td>\n");
cgiMakeDropListFull("hgt.nameOp", op_labels, ops, ArraySize(ops), nameOp == NULL ? "contains" : nameOp, NULL);
hPrintf("</td>\n<td><input type='text' name='hgt.nameSearch' value='%s'></td></tr>\n", nameSearch == NULL ? "" : nameSearch);
hPrintf("<tr><td>and</td><td><b>Description:</b></td><td>\n");
cgiMakeDropListFull("hgt.descOp", op_labels, ops, ArraySize(ops), descOp == NULL ? "contains" : descOp, NULL);
hPrintf("</td>\n<td><input type='text' name='hgt.descSearch' value='%s'></td></tr>\n", descSearch == NULL ? "" : descSearch);
hPrintf("<tr><td>and</td>\n");
hPrintf("<td><b>Group</b></td><td>is</td>\n<td>\n");
cgiMakeDropListFull("hgt.groupSearch", labels, groups, numGroups, groupSearch, NULL);
hPrintf("</td></tr>\n");
hPrintf("<tr><td>and</td>\n");
hPrintf("<td><b>Antibody</b></td><td>is</td>\n<td>\n");
len = getTermList(cvHash, &terms, "Antibody");
cgiMakeDropListFull("hgt.antibodySearch", terms, terms, len, antibodySearch, NULL);
hPrintf("</td></tr>\n");
hPrintf("<tr><td>and</td>\n");
hPrintf("<td><b>Cell Line</b></td><td>is</td>\n<td>\n");
len = getTermList(cvHash, &terms, "Cell Line");
cgiMakeDropListFull("hgt.cellSearch", terms, terms, len, cellSearch, NULL);
hPrintf("</td></tr>\n");
hPrintf("<tr><td>and</td><td>\n");
cgiMakeDropListFull("hgt.metaName", metaNames, metaValues, ArraySize(metaNames), metaName, NULL);
hPrintf("</td><td>\n");
cgiMakeDropListFull("hgt.metaOp", op_labels, ops, ArraySize(ops), metaOp == NULL ? "contains" : metaOp, NULL);
hPrintf("</td><td>\n");
hPrintf("<input type='text' name='hgt.metaSearch' value='%s'></td></tr>\n", metaSearch == NULL ? "" : metaSearch);
hPrintf("</td></tr>\n");
hPrintf("</table>\n");
hPrintf("<input type='submit' name='%s' value='Search'>\n", searchTracks);
hPrintf("<input type='submit' name='submit' value='Cancel'>\n");
hPrintf("</form>\n");
struct slRef *tracks = NULL;
int tracksFound = 0;
struct hash *parents = newHash(4);
if(groupSearch != NULL && sameString(groupSearch, "any"))
{
groupSearch = NULL;
}
if(metaSearch != NULL && !strlen(metaSearch))
{
metaSearch = NULL;
}
if(antibodySearch != NULL && sameString(antibodySearch, "Any"))
{
antibodySearch = NULL;
}
if(cellSearch != NULL && sameString(cellSearch, "Any"))
{
cellSearch = NULL;
}
if((nameSearch != NULL && strlen(nameSearch)) || descSearch != NULL || groupSearch != NULL || metaSearch != NULL || antibodySearch != NULL || cellSearch != NULL)
{
for (group = groupList; group != NULL; group = group->next)
{
if(groupSearch == NULL || !strcmp(group->name, groupSearch))
{
if (group->trackList != NULL)
{
struct trackRef *tr;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
if((isEmpty(nameSearch) || isNameMatch(track, nameSearch, nameOp)) &&
(isEmpty(descSearch) || isDescriptionMatch(track, descSearch, descOp)) &&
(isEmpty(antibodySearch) || isMetaMatch(track, "antibody", "is", antibodySearch)) &&
(isEmpty(cellSearch) || isMetaMatch(track, "cell", "is", cellSearch)) &&
(isEmpty(metaName) || isEmpty(metaSearch) || isMetaMatch(track, metaName, metaOp, metaSearch)))
{
tracksFound++;
if(tracks == NULL)
tracks = slRefNew(track);
else
refAdd(&tracks, track);
}
if (track->subtracks != NULL)
{
struct track *subTrack;
for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next)
{
// fprintf(stderr, "search track: %s\n", subTrack->shortLabel);
if((isEmpty(nameSearch) || isNameMatch(subTrack, nameSearch, nameOp)) &&
(isEmpty(descSearch) || isDescriptionMatch(subTrack, descSearch, descOp)) &&
(isEmpty(antibodySearch) || isMetaMatch(subTrack, "antibody", "is", antibodySearch)) &&
(isEmpty(cellSearch) || isMetaMatch(subTrack, "cell", "is", cellSearch)) &&
(isEmpty(metaName) || isEmpty(metaSearch) || isMetaMatch(subTrack, metaName, metaOp, metaSearch)))
{
// XXXX to parent hash. - use tdb->parent instead.
hashAdd(parents, subTrack->track, track);
// fprintf(stderr, "found subtrack: %s\n", subTrack->shortLabel);
tracksFound++;
if(tracks == NULL)
tracks = slRefNew(subTrack);
else
refAdd(&tracks, subTrack);
}
}
}
}
}
}
}
slSort(&tracks, gCmpTrack);
if(tracksFound)
{
hPrintf("<p>%d tracks found:</p>\n", tracksFound);
hPrintf("<form action='%s' name='SearchTracks' method='post'>\n\n", hgTracksName());
hButton("submit", "save");
hButtonWithOnClick("hgt.ignoreme", "show all", "show all found tracks", "alert('show all not yet implemented'); return false;");
hPrintf("<table>\n");
hPrintf("<tr bgcolor='#666666'><td><b>Name</b></td><td><b>Description</b></td><td><b>Group</b></td><td><br /></td></tr>\n");
struct slRef *ptr;
while((ptr = slPopHead(&tracks)))
{
struct track *track = (struct track *) ptr->val;
// trackDbOutput(track->tdb, stderr, ',', '\n');
hPrintf("<tr bgcolor='#EEEEEE'>\n");
hPrintf("<td>%s</td>\n", track->shortLabel);
- hPrintf("<td><a target='_top' href='%s'>%s</a></td>\n", trackUrl(track->mapName, NULL), track->longLabel);
+ hPrintf("<td><a target='_top' href='%s'>%s</a></td>\n", trackUrl(track->track, NULL), track->longLabel);
// How do we get subtrack's parent?
struct track *parent = NULL;
if(hashLookup(parents, track->track) != NULL)
parent = (struct track *) hashLookup(parents, track->track)->val;
hPrintf("<td>%s</td>\n", parent != NULL ? parent->longLabel : track->group != NULL ? track->group->label : "");
hPrintf("<td>\n");
if (tdbIsSuper(track->tdb))
{
superTrackDropDown(cart, track->tdb,
superTrackHasVisibleMembers(track->tdb));
}
else
{
hTvDropDownClassVisOnly(track->track, track->visibility,
track->canPack, (track->visibility == tvHide) ?
"hiddenText" : "normalText",
trackDbSetting(track->tdb, "onlyVisibility"));
}
hPrintf("</td></tr>\n");
}
hPrintf("</table>\n");
hButton("submit", "save");
hPrintf("</form>\n");
}
else
{
hPrintf("<p>No tracks found</p>\n");
}
}
}