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/near/hgNear/customColumn.c src/hg/near/hgNear/customColumn.c index 7d35b6a..79b171f 100644 --- src/hg/near/hgNear/customColumn.c +++ src/hg/near/hgNear/customColumn.c @@ -1,765 +1,765 @@ /* customColumn - handle columns put in by users. */ /* Copyright (C) 2012 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 "hash.h" #include "localmem.h" #include "cheapcgi.h" #include "obscure.h" #include "portable.h" #include "net.h" #include "cart.h" #include "hgNear.h" static char *customFileName() /* Return file name associated with custom column if any. * Delete cart var if it's grown stale. */ { char *fileName = NULL; if (cartVarExists(cart, customFileVarName)) { fileName = cartString(cart, customFileVarName); if (!fileExists(fileName)) { cartRemove(cart, customFileVarName); fileName = NULL; } } return fileName; } static char *newCustomFileName() /* Create new custom file name. */ { struct tempName tn; makeTempName(&tn, "near", ".col"); return cloneString(tn.forCgi); } void doCustomPage(struct sqlConnection *conn, struct column *colList) /* Put up page to input custom columns. */ { makeTitle("Setup Custom Columns for Gene Sorter", "hgNearHelp.html#Custom"); hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\">\n"); cartSaveSession(cart); /* Put up descriptive text. */ controlPanelStart(); hPrintf( "Add your own custom columns to the Gene Sorter using the " "<A HREF=\"../goldenPath/help/customColumn.html\">" "format described here</A>."); controlPanelEnd(); /* Put up various buttons. */ controlPanelStart(); hPrintf("<TABLE><TR><TD>"); hPrintf("Custom column action: "); hPrintf("</TD><TD>"); cgiMakeOptionalButton(customClearDoName, "clear", customFileName() == NULL); hPrintf("</TD><TD>"); cgiMakeButton(customPasteDoName, "paste in"); hPrintf("</TD><TD>"); cgiMakeButton(customUploadDoName, "from file"); hPrintf("</TD><TD>"); cgiMakeButton(customFromUrlDoName, "from URL"); hPrintf("</TD><TD>"); cgiMakeButton(confVarName, "cancel"); hPrintf("</TD></TR></TABLE>"); controlPanelEnd(); hPrintf("</FORM>"); } static void submitCancel() /* Put up little table with submit and cancle buttons. */ { hPrintf("<TABLE><TR><TD>"); cgiMakeButton(customSubmitDoName, "submit"); hPrintf("</TD><TD>"); hPrintf(" "); hPrintf("</TD><TD>"); cgiMakeButton(customPageDoName, "cancel"); hPrintf("</TD></TR></TABLE>"); } void doCustomUpload(struct sqlConnection *conn, struct column *colList) /* Put up page to upload custom columns. */ { makeTitle("Upload Custom Columns", "hgNearHelp.html#Custom"); hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=\"POST\" ENCTYPE=\"multipart/form-data\">\n"); cartSaveSession(cart); controlPanelStart(); hPrintf( "Upload a file with custom columns in the " "<A HREF=\"../goldenPath/help/customColumn.html\">" "format described here</A>."); hPrintf("<BR>"); hPrintf("Column File: <INPUT TYPE=FILE NAME=%s> ", customUploadVarName); hPrintf("<BR>"); submitCancel(); controlPanelEnd(); hPrintf("</FORM>"); } void doCustomPaste(struct sqlConnection *conn, struct column *colList) /* Put up page to paste custom columns. */ { makeTitle("Paste in Custom Columns", "hgNearHelp.html#Custom"); hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=\"POST\">\n"); cartSaveSession(cart); controlPanelStart(); hPrintf( "Paste in custom columns in the " "<A HREF=\"../goldenPath/help/customColumn.html\">" "format described here</A>."); hPrintf("<BR>"); cgiMakeTextArea(customPasteVarName, "", 10, 70); submitCancel(); controlPanelEnd(); hPrintf("</FORM>"); } void doCustomFromUrl(struct sqlConnection *conn, struct column *colList) /* Put up page to paste in URLS with custom columns. */ { makeTitle("Paste in Custom Columns", "hgNearHelp.html#Custom"); hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=\"POST\">\n"); cartSaveSession(cart); controlPanelStart(); hPrintf( "Paste in URL or list of URLs that refer to files in the " "<A HREF=\"../goldenPath/help/customColumn.html\">" "format described here</A>."); hPrintf("<BR>"); cgiMakeTextArea(customFromUrlVarName, "", 10, 70); submitCancel(); controlPanelEnd(); hPrintf("</FORM>"); } /* ---- Parse custom columns. ---- */ static void addIfMissing(struct hash *settings, char *var, char *val) /* Add var to hash if it's not there already. */ { if (!hashLookup(settings, var)) hashAdd(settings, var, cloneString(val)); } static void outputSetting(FILE *f, char *name, char *val) /* Output name=val pair, adding quotes if val has spaces. */ { fprintf(f, "%s=", name); if (hasWhiteSpace(val)) { if (strchr(val, '"') != NULL) { char *s = makeEscapedString(val, '"'); fprintf(f, "\"%s\"", s); freez(&s); } else { fprintf(f, "\"%s\"", val); } } else fprintf(f, "%s", val); } static void outputSettings(FILE *f, struct hash *settings) /* Output settings hash as a var=val set. */ { struct hashEl *list, *el; list = hashElListHash(settings); for (el = list; el != NULL; el = el->next) { fprintf(f, " "); outputSetting(f, el->name, el->val); } hashElFreeList(&list); } struct column *parseColumnLine(struct lineFile *lf, char *line) /* Parse out column header line and return a column based on it. */ { struct hash *settings; struct column *col; AllocVar(col); settings = col->settings = hashVarLine(line, lf->lineIx); addIfMissing(settings, "name", "custom"); addIfMissing(settings, "shortLabel", "User Column"); addIfMissing(settings, "longLabel", "User custom column"); addIfMissing(settings, "visibility", "on"); addIfMissing(settings, "priority", "2.01"); addIfMissing(settings, "org", genome); addIfMissing(settings, "db", database); hashAdd(settings, "type", cloneString("custom")); columnVarsFromSettings(col, lf->fileName); return col; } struct column *verifyCopyColumn(struct sqlConnection *conn, struct lineFile *lf, FILE *output, char *line, struct column *builtInList, struct hash *uniqHash) /* Parse out column from line file. If output is non-NULL * then also save it to output. */ { char *word, *name; struct column *col = parseColumnLine(lf, line); struct hash *lookupHash = NULL, *gpHash = newHash(16); char *lookup = NULL; int hitCount = 0, missCount = 0, badGeneCount = 0; struct genePos *gpList, *gp; char *oneMiss = NULL, *oneBadGene = NULL; /* Build up hash & list of all known genes. */ gpList = knownPosAll(conn); for (gp = gpList; gp != NULL; gp = gp->next) hashAdd(gpHash, gp->name, gp); /* Deal with non-uniq names. */ if (hashLookup(uniqHash, col->name)) { int ix = 1; char buf[256]; for (;;) { safef(buf, sizeof(buf), "%s%d", col->name, ++ix); if (!hashLookup(uniqHash, buf)) { col->name = cloneString(buf); break; } } hashRemove(col->settings, "name"); hashAdd(col->settings, "name", col->name); } hashAdd(uniqHash, col->name, col); /* If there's a idLookup setting then make lookup hash. */ if ((lookup = hashFindVal(col->settings, "idLookup")) != NULL) { struct column *lookupCol = findNamedColumn(lookup); if (lookupCol == NULL) errAbort("Couldn't find column %s for idLookup line %d of %s", lookup, lf->lineIx, lf->fileName); lookupHash = hashNew(16); for (gp = gpList; gp != NULL; gp = gp->next) { char *cell = lookupCol->cellVal(lookupCol, gp, conn); if (cell != NULL) { hashAdd(lookupHash, cell, gp->name); freez(&cell); } } } /* Allocate structure and fill in from header. */ fprintf(output, "column"); outputSettings(output, col->settings); fprintf(output, "\n"); /* Make hash of lines. */ while (lineFileNext(lf, &line, NULL)) { line = trimSpaces(line); if (line[0] == '#') continue; if (line[0] == 0) break; if (startsWith("column ", line)) { lineFileReuse(lf); break; } name = word = nextWord(&line); line = skipLeadingSpaces(line); if (line == NULL || line[0] == 0) { errAbort("Expecting at least two words in line %d of %s", lf->lineIx, lf->fileName); } if (lookupHash != NULL) { name = hashFindVal(lookupHash, word); if (name == NULL) { ++missCount; if (oneMiss == NULL) oneMiss = cloneString(word); continue; } } else { if (!hashLookup(gpHash, name)) { ++badGeneCount; if (oneBadGene == NULL) { oneBadGene = cloneString(name); continue; } } } ++hitCount; fprintf(output, "%s %s\n", name, line); } fprintf(output, "\n"); if (missCount > 0) { warn("%d items including '%s' not found (and %d found) in %s", missCount, oneMiss, hitCount, lookup); } if (badGeneCount > 0) { warn("%d gene ID's including '%s' not found (and %d found)", badGeneCount, oneBadGene, hitCount); } hashFree(&lookupHash); return col; } static struct hash *hashColumns(struct column *colList) /* Return a hash of columns keyed by name. */ { struct column *col; struct hash *hash = hashNew(9); for (col = colList; col != NULL; col = col->next) hashAdd(hash, col->name, col); return hash; } static struct column *verifyCopyColumns(struct sqlConnection *conn, struct lineFile *lf, FILE *output, struct column *builtInList, struct hash *uniqHash) /* Read in custom columns. Verify that they are ok. Copy * version after lookup if any to output. */ { char *line, *word; struct column *colList = NULL; while (lineFileNextReal(lf, &line)) { word = nextWord(&line); if (sameString("column", word)) { struct column *col = verifyCopyColumn(conn, lf, output, line, builtInList, uniqHash); if (col != NULL) { slAddHead(&colList, col); } } else { errAbort("Unrecognized word '%s' line %d of %s", word, lf->lineIx, lf->fileName); break; } } return colList; } static void removeOldCustomColumns(struct column **pColList) /* Remove any existing custom columns. */ { struct column *list = NULL, *col, *next; for (col = *pColList; col != NULL; col = next) { next = col->next; if (!startsWith("custom", col->type)) { slAddHead(&list, col); } } slReverse(&list); *pColList = list; } static void customFromText(struct sqlConnection *conn, char *text, struct column **pColList) /* Convert custom column text to lineFile, and call custom column * updater. */ { struct lineFile *lf = lineFileOnString("custom column", TRUE, text); char *outFileName = newCustomFileName(); struct column *newList; FILE *f; struct hash *uniqHash = NULL; /* Remove file name from cart for better error recovery. */ cartRemove(cart, customFileVarName); /* Copy and verify output. */ f = mustOpen(outFileName, "w"); removeOldCustomColumns(pColList); uniqHash = hashColumns(*pColList); newList = verifyCopyColumns(conn, lf, f, *pColList, uniqHash); *pColList = slCat(*pColList, newList); lf->buf = NULL; /* Don't let lineFileClose free this */ lineFileClose(&lf); carefulClose(&f); /* Put back file name in cart , looks like we must have succeeded. */ cartSetString(cart, customFileVarName, outFileName); freez(&outFileName); freeHash(&uniqHash); } static void customFromUrls(struct sqlConnection *conn, char *urlList, struct column **pColList) /* Grab custom columns from a list of URLs. */ { char *outFileName = newCustomFileName(); struct column *customCols = NULL; FILE *f; char *url; struct hash *uniqHash = NULL; /* Remove file name from cart for better error recovery. */ cartRemove(cart, customFileVarName); /* Copy and verify output. */ f = mustOpen(outFileName, "w"); removeOldCustomColumns(pColList); uniqHash = hashColumns(*pColList); /* Loop through and add columns from each URL. */ while ((url = nextWord(&urlList)) != NULL) { if (!(startsWith("http://" , url) || startsWith("https://", url) || startsWith("ftp://" , url))) errAbort("Invalid url [%s]. URLs must start with http://, https://, or ftp://", url); struct lineFile *lf = netLineFileOpen(url); struct column *newList = verifyCopyColumns(conn, lf, f, *pColList, uniqHash); customCols = slCat(newList, customCols); lineFileClose(&lf); } *pColList = slCat(customCols, *pColList); carefulClose(&f); /* Put back file name in cart , looks like we must have succeeded. */ cartSetString(cart, customFileVarName, outFileName); freez(&outFileName); hashFree(&uniqHash); } void doCustomSubmit(struct sqlConnection *conn, struct column *colList) /* Put up page to submit custom columns. */ { if (cartVarExists(cart, customUploadVarName)) { customFromText(conn, cartString(cart, customUploadVarName), &colList); cartRemove(cart, customUploadVarName); } else if (cartVarExists(cart, customPasteVarName)) { customFromText(conn, cartString(cart, customPasteVarName), &colList); cartRemove(cart, customPasteVarName); } else if (cartVarExists(cart, customFromUrlVarName)) { customFromUrls(conn, cartString(cart, customFromUrlVarName), &colList); cartRemove(cart, customFromUrlVarName); } else { warn("doCustomSubmit without recognized custom variable"); } slSort(&colList, columnCmpPriority); doConfigure(conn, colList, NULL); } void doCustomClear(struct sqlConnection *conn, struct column *colList) /* Put up page to clear custom columns. */ { removeOldCustomColumns(&colList); cartRemove(cart, customFileVarName); doConfigure(conn, colList, NULL); } struct column *quickParseColumn(struct lineFile *lf, char *colLine) /* Given column line, parse column until blank line with * minimal error checking. */ { struct column *col = parseColumnLine(lf, colLine); struct hash *idHash; char *line, *word; if (col == NULL) return NULL; col->customIdHash = idHash = hashNew(16); while (lineFileNext(lf, &line, NULL)) { if (line[0] == 0) break; word = nextWord(&line); line = skipLeadingSpaces(line); hashAdd(idHash, word, lmCloneString(idHash->lm, line)); } return col; } struct column *quickParseColumns(char *fileName) /* Parse column that's been validated and put into temp file. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); struct column *colList = NULL; char *line, *word; while (lineFileNextReal(lf, &line)) { word = nextWord(&line); if (sameString("column", word)) { struct column *col = quickParseColumn(lf, line); if (col != NULL) { slAddHead(&colList, col); } } else { warn("Unrecognized word '%s' line %d of %s", word, lf->lineIx, lf->fileName); break; } } lineFileClose(&lf); return colList; } struct column *customColumnsRead(struct sqlConnection *conn, char *org, char *db) /* Read in data for custom columns. */ { char *fileName = customFileName(); struct column *colList = NULL; if (fileName != NULL) colList = quickParseColumns(fileName); return colList; } /* ---- Implement column methods for custom types ---- */ static boolean colSettingOn(struct column *col, char *name) /* Return TRUE if setting exists and has value "on" */ { char *val = hashFindVal(col->settings, name); return val != NULL && sameString(val, "on"); } static boolean customExists(struct column *col, struct sqlConnection *conn) /* Custom column exists if we are in right database. */ { char *db = hashFindVal(col->settings, "db"); return db == NULL || sameString(db, database); } char *customCellVal(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Return value of custom field. */ { struct dyString *dy = NULL; char *retVal = NULL; struct hashEl *hel; for (hel = hashLookup(col->customIdHash, gp->name); hel != NULL; hel = hashLookupNext(hel)) { if (dy == NULL) dy = dyStringNew(256); else dyStringAppendC(dy, ','); dyStringAppend(dy, hel->val); } if (dy != NULL) retVal = dyStringCannibalize(&dy); return retVal; } static void customCellPrint(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Return value of custom field. */ { boolean gotAny = FALSE; struct hashEl *hel; hPrintf("<TD>"); for (hel = hashLookup(col->customIdHash, gp->name); hel != NULL; hel = hashLookupNext(hel)) { if (gotAny) hPrintf(", "); else gotAny = TRUE; if (col->itemUrl) { char *encoded = cgiEncode(hel->val); hPrintf("<A HREF=\""); hPrintf(col->itemUrl, encoded); hPrintf("\">"); hPrintEncodedNonBreak(hel->val); hPrintf("</A>"); freeMem(encoded); } else hPrintEncodedNonBreak(hel->val); } if (!gotAny) { hPrintf("n/a"); } hPrintf("</TD>"); } static void addSearchResult(struct searchResult **pList, struct hashEl *hel) /* Add given name to search result. */ { struct searchResult *res; AllocVar(res); res->gp.name = cloneString(hel->name); res->matchingId = cloneString(hel->val); slAddHead(pList, res); } struct searchResult *customSearch(struct column *col, struct sqlConnection *conn, char *search) /* Search lookup type column. */ { struct searchResult *resList = NULL; char *type = columnSetting(col, "search", "exact"); struct hashEl *helList, *hel; helList = hashElListHash(col->customIdHash); if (sameString(type, "prefix")) { for (hel = helList; hel != NULL; hel = hel->next) { if (startsWith(search, hel->val)) addSearchResult(&resList, hel); } } else if (sameString(type, "fuzzy")) { for (hel = helList; hel != NULL; hel = hel->next) { if (stringIn(search, hel->val) != NULL) addSearchResult(&resList, hel); } } else { for (hel = helList; hel != NULL; hel = hel->next) { if (sameString(search, hel->val)) addSearchResult(&resList, hel); } } hashElFreeList(&helList); return resList; } static void customFilterControls(struct column *col, struct sqlConnection *conn) /* Print out controls for filter. */ { if (colSettingOn(col, "isNumber")) minMaxAdvFilterControls(col, conn); else lookupAdvFilterControls(col, conn); } static struct genePos *customFilterText(struct column *col, struct sqlConnection *conn, struct genePos *list) /* Do advanced text filter on custom track. This works much like * lookup custom filter. */ { char *wild = advFilterVal(col, "wild"); struct hash *keyHash = keyFileHash(col); if (wild != NULL || keyHash != NULL) { boolean orLogic = advFilterOrLogic(col, "logic", TRUE); struct hash *hash = newHash(17); struct hashEl *hel, *helList = hashElListHash(col->customIdHash); struct slName *wildList = stringToSlNames(wild); for (hel = helList; hel != NULL; hel = hel->next) { if (keyHash == NULL || hashLookupUpperCase(keyHash, hel->val)) { if (wildList == NULL || wildMatchList(hel->val, wildList, orLogic)) hashAdd(hash, hel->name, NULL); } } list = weedUnlessInHash(list, hash); hashElFreeList(&helList); hashFree(&hash); } hashFree(&keyHash); return list; } static struct genePos *customFilterNum(struct column *col, struct sqlConnection *conn, struct genePos *list) /* Do advanced numerical filter on custom track. This * works much like floatAdvFilter. */ { char *minString = advFilterVal(col, "min"); char *maxString = advFilterVal(col, "max"); char *valString; if (minString != NULL || maxString != NULL) { struct genePos *gp, *next, *newList = NULL; double minVal = 0, maxVal = 0, val; if (minString != NULL) minVal = atof(minString); if (maxString != NULL) maxVal = atof(maxString); for (gp = list; gp != NULL; gp = next) { next = gp->next; valString = hashFindVal(col->customIdHash, gp->name); if (valString != NULL) { val = atof(valString); if (minString == NULL || val >= minVal) if (maxString == NULL || val <= maxVal) { slAddHead(&newList, gp); } } } slReverse(&newList); list = newList; } return list; } static struct genePos *customFilter(struct column *col, struct sqlConnection *conn, struct genePos *list) { if (colSettingOn(col, "isNumber")) return customFilterNum(col, conn, list); else return customFilterText(col, conn, list); } void setupColumnCustom(struct column *col, char *parameters) /* Set up custom column. */ { col->exists = customExists; col->cellVal = customCellVal; col->cellPrint = customCellPrint; if (columnSetting(col, "search", NULL)) col->simpleSearch = customSearch; col->filterControls = customFilterControls; col->advFilter = customFilter; }