struct tenFields *parseTenFields(char *fileName) /* Return list of partially parsed lines from GFF. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); struct tenFields *tfList = NULL, *tf; char *words[11]; int wordCount, i; while ((wordCount = lineFileChopNextTab(lf, words, ArraySize(words))) != 0) { if (wordCount != 10) errAbort("Expecting 10 tab separated fields got %d line %d of %s", wordCount, lf->lineIx, lf->fileName); AllocVar(tf); for (i=0; i<10; ++i) { char *s = words[i]; if (i == 0 && sameString(s, "17")) /* 17 is a synonym for mitochondria */ s = cloneString("M"); if (i != 6) cgiDecode(s, s, strlen(s)); tf->fields[i] = cloneString(s); } tf->lineIx = lf->lineIx; slAddHead(&tfList, tf); } lineFileClose(&lf); slReverse(&tfList); return tfList; }
void noteIds(struct tenFields *tfList, char *inGff, FILE *cdsFile, FILE *otherFile) /* Look for cases where tenth field is of form * ID=XXX;Note=YYY. In these cases move XXX to * the ninth field, and store the ID, the * third (type) field, and the YYY in f */ { struct tenFields *tf; struct hash *uniqHash = newHash(19); for (tf = tfList; tf != NULL; tf = tf->next) { char *s = tf->fields[9]; if (startsWith("ID=", s)) { char *id = s+3, *note = ""; char *e = strchr(s, ';'); if (!hashLookup(uniqHash, id)) { hashAdd(uniqHash, id, NULL); if (e != NULL) { *e++ = 0; s = stringIn("Note=", e); if (s != NULL) { note = s+5; cgiDecode(note, note, strlen(note)); } } } tf->fields[8] = id; } } hashFree(&uniqHash); }
void doDocIdReport(struct cart *theCart) { char *docId = cartString(theCart, "docId"); cartWebStart(cart, database, "ENCODE DCC: Validation report for docId %s",docId); struct sqlConnection *conn = sqlConnect(database); char query[10 * 1024]; struct sqlResult *sr; char **row; boolean beenHere = FALSE; printf("<a href=docIdView?db=%s> Return </a><BR>", database); safef(query, sizeof query, "select * from %s where ix=%s", docIdTable,docId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (beenHere) errAbort("found more than one record with ix value %s in table %s", docId, docIdTable); beenHere = TRUE; struct docIdSub *docIdSub = docIdSubLoad(row); cgiDecode(docIdSub->valReport, docIdSub->valReport, strlen(docIdSub->valReport)); //printf("tempFile is %s\n<BR>", tempFile); printf("<pre>%s", docIdSub->valReport); } cartWebEnd(); }
void docIdReport(char *database) /* docIdReport - generate report from docIdSub table. */ { struct sqlConnection *conn = sqlConnect(database); struct docIdSub *docIdSub; char query[10 * 1024]; struct sqlResult *sr; char **row; safef(query, sizeof query, "select * from %s", docIdTable); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { docIdSub = docIdSubLoad(row); verbose(2, "ix %d\n", docIdSub->ix); verbose(2, "submitDate %s\n", docIdSub->submitDate); verbose(2, "md5sum %s\n", docIdSub->md5sum); verbose(2, "valReport %s\n", docIdSub->valReport); verbose(2, "metaData %s\n", docIdSub->metaData); verbose(2, "submitPath %s\n", docIdSub->submitPath); verbose(2, "submitter %s\n", docIdSub->submitter); cgiDecode(docIdSub->metaData, docIdSub->metaData, strlen(docIdSub->metaData)); char *tempFile = "temp"; FILE *f = mustOpen(tempFile, "w"); fwrite(docIdSub->metaData, strlen(docIdSub->metaData), 1, f); fclose(f); boolean validated; struct mdbObj *mdbObj = mdbObjsLoadFromFormattedFile(tempFile, &validated); printf("%s %s %s %s %s\n", docIdDecorate(docIdSub->ix), mdbObjFindValue(mdbObj, "dataType"), mdbObjFindValue(mdbObj, "view"), mdbObjFindValue(mdbObj, "cell"), mdbObjFindValue(mdbObj, "lab")); } sqlFreeResult(&sr); sqlDisconnect(&conn); }
void doDocIdMeta(struct cart *theCart) { char *docId = cartString(theCart, "docId"); cartWebStart(cart, database, "ENCODE DCC: Metadata for docId %s",docId); struct sqlConnection *conn = sqlConnect(database); char query[10 * 1024]; struct sqlResult *sr; char **row; struct tempName tn; trashDirFile(&tn, "docId", "meta", ".txt"); char *tempFile = tn.forCgi; boolean beenHere = FALSE; printf("<a href=docIdView?db=%s> Return </a><BR>", database); safef(query, sizeof query, "select * from %s where ix=%s", docIdTable,docId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (beenHere) errAbort("found more than one record with ix value %s in table %s", docId, docIdTable); beenHere = TRUE; struct docIdSub *docIdSub = docIdSubLoad(row); cgiDecode(docIdSub->metaData, docIdSub->metaData, strlen(docIdSub->metaData)); //printf("tempFile is %s\n<BR>", tempFile); FILE *f = mustOpen(tempFile, "w"); fwrite(docIdSub->metaData, strlen(docIdSub->metaData), 1, f); fclose(f); boolean validated; struct mdbObj *mdbObj = mdbObjsLoadFromFormattedFile(tempFile, &validated); unlink(tempFile); if (mdbObj->next) errAbort("got more than one metaObj from metaData"); for(; mdbObj; mdbObj = mdbObj->next) { printf("<BR>object: %s\n", mdbObj->obj); struct mdbVar *vars = mdbObj->vars; for(; vars; vars = vars->next) { printf("<BR>%s %s\n", vars->var, vars->val); } } } cartWebEnd(); }
void doStandard(struct cart *theCart) { cart = theCart; cartWebStart(cart, database, "ENCODE DCC Submissions"); struct sqlConnection *conn = sqlConnect(database); struct docIdSub *docIdSub; char query[10 * 1024]; struct sqlResult *sr; char **row; struct tempName tn; trashDirFile(&tn, "docId", "meta", ".txt"); char *tempFile = tn.forCgi; //printf("tempFile is %s\n<BR>", tempFile); // <Data type> <Cell Type> <Key Metadata> <View> printf("<table border=1><tr>"); printf("<th>dataType</th>"); printf("<th>cell type</th>"); printf("<th>metadata</th>"); printf("<th>view</th>"); printf("<th>fileType</th>"); printf("<th>file</th>"); printf("<th>lab</th>"); printf("<th>assembly</th>"); printf("<th>subId</th>"); printf("<th>val-report</th>"); printf("</tr>\n"); safef(query, sizeof query, "select * from %s", docIdTable); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { docIdSub = docIdSubLoad(row); verbose(2, "ix %d\n", docIdSub->ix); verbose(2, "submitDate %s\n", docIdSub->submitDate); verbose(2, "md5sum %s\n", docIdSub->md5sum); verbose(2, "valReport %s\n", docIdSub->valReport); verbose(2, "metaData %s\n", docIdSub->metaData); verbose(2, "submitPath %s\n", docIdSub->submitPath); verbose(2, "submitter %s\n", docIdSub->submitter); cgiDecode(docIdSub->metaData, docIdSub->metaData, strlen(docIdSub->metaData)); //printf("tempFile %s\n", tempFile); FILE *f = mustOpen(tempFile, "w"); fwrite(docIdSub->metaData, strlen(docIdSub->metaData), 1, f); fclose(f); boolean validated; struct mdbObj *mdbObj = mdbObjsLoadFromFormattedFile(tempFile, &validated); unlink(tempFile); // <Data type> <Cell Type> <Key Metadata> <View> char *docIdType = mdbObjFindValue(mdbObj, "type"); char *docIdComposite = mdbObjFindValue(mdbObj, "composite"); char buffer[10 * 1024]; safef(buffer, sizeof buffer, "%d", docIdSub->ix); if (sameString(database, "encpipeline_beta")) docIdDir = docIdDirBeta; printf("<tr>"); printf("<td>%s</td> ", mdbObjFindValue(mdbObj, "dataType")); printf("<td>%s</td> ", mdbObjFindValue(mdbObj, "cell")); struct dyString *str = newDyString(100); addValue(str, mdbObjFindValue(mdbObj, "antibody")); addValue(str, mdbObjFindValue(mdbObj, "treatment")); addValue(str, mdbObjFindValue(mdbObj, "rnaExtract")); addValue(str, mdbObjFindValue(mdbObj, "localization")); printf("<td>%s<a href=docIdView?docId=%s&db=%s&meta=\"\"> ...</a></td>", str->string,buffer, database); freeDyString(&str); printf("<td>%s</td> ", mdbObjFindValue(mdbObj, "view")); printf("<td>%s</td> ", mdbObjFindValue(mdbObj, "type")); printf("<td><a href=%s> %s</a></td>", docIdGetPath(buffer, docIdDir, docIdType, NULL) , docIdDecorate(docIdComposite,docIdSub->ix)); char *lab = mdbObjFindValue(mdbObj, "lab"); char *subId = mdbObjFindValue(mdbObj, "subId"); printf("<td><a href=docIdView?docId=%s&db=%s&lab=\"%s\"> %s</a></td>",buffer, database, subId, lab); printf("<td>%s</td> ", mdbObjFindValue(mdbObj, "assembly")); printf("<td>%s</td> ", subId); printf("<td><a href=docIdView?docId=%s&db=%s&report=\"\"> report</a></td>", buffer, database); printf("</tr>\n"); } printf("</table>"); sqlFreeResult(&sr); sqlDisconnect(&conn); cartWebEnd(); }
void docIdTidy(char *database, char *docIdDir) /* docIdTidy - tidy up the docId library by compressing and md5suming where appropriate. */ { char query[10 * 1024]; struct sqlResult *sr; char **row; struct sqlConnection *conn = sqlConnect(database); struct tempName tn; trashDirFile(&tn, "docId", "meta", ".txt"); char *tempFile = tn.forCgi; struct toDoList *toDoList = NULL; safef(query, sizeof query, "select * from %s", docIdTable); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct docIdSub *docIdSub = docIdSubLoad(row); cgiDecode(docIdSub->metaData, docIdSub->metaData, strlen(docIdSub->metaData)); FILE *f = mustOpen(tempFile, "w"); fwrite(docIdSub->metaData, strlen(docIdSub->metaData), 1, f); fclose(f); boolean validated; //printf("metadata is %s\n", docIdSub->metaData); struct mdbObj *mdbObj = mdbObjsLoadFromFormattedFile(tempFile, &validated); unlink(tempFile); char *docIdType = mdbObjFindValue(mdbObj, "type"); char buffer[10 * 1024]; safef(buffer, sizeof buffer, "%d", docIdSub->ix); char *path = docIdGetPath(buffer, docIdDir, docIdType, NULL); //docIdDecorate(docIdSub->ix)); printf("path %s\n", path); struct toDoList *toDoItem = NULL; if (!fileIsCompressed(path)) { if (toDoItem == NULL) AllocVar(toDoItem); printf("foo\n"); toDoItem->needs |= NEEDS_COMPRESSION; toDoItem->path = path; toDoItem->docId = docIdSub->ix; } printf("docId %d md5sum %s valReport %s\n",docIdSub->ix, docIdSub->md5sum, docIdSub->valReport); //if (docIdSub->md5sum == NULL) if (sameString(docIdSub->md5sum, "")) { printf("mdsum\n"); if (toDoItem == NULL) AllocVar(toDoItem); toDoItem->needs |= NEEDS_MD5SUM; toDoItem->path = path; toDoItem->docId = docIdSub->ix; } //if (docIdSub->valReport == NULL) if (sameString(docIdSub->valReport,"")) { printf("report\n"); if (toDoItem == NULL) AllocVar(toDoItem); toDoItem->needs |= NEEDS_REPORT; toDoItem->path = path; toDoItem->docId = docIdSub->ix; } if (toDoItem) slAddHead(&toDoList, toDoItem); } sqlFreeResult(&sr); doCompression(toDoList); doReports(toDoList); doMd5Summing(toDoList); }
void doGvf(struct trackDb *tdb, char *item) /* Show details for variants represented as GVF, stored in a bed8Attrs table */ { struct sqlConnection *conn = hAllocConn(database); int start = cartInt(cart, "o"); char query[1024]; sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, item, seqName, start); struct sqlResult *sr = sqlGetResult(conn, query); char **row; if ((row = sqlNextRow(sr)) == NULL) errAbort("doGvfDetails: can't find item '%s' in %s at %s:%d", item, database, seqName, start); int rowOffset = hOffsetPastBin(database, seqName, tdb->table); struct bed8Attrs *ba = bed8AttrsLoad(row+rowOffset); bedPrintPos((struct bed *)ba, 3, tdb); int i = 0; // Note: this loop modifies ba->attrVals[i], assuming we won't use them again: for (i = 0; i < ba->attrCount; i++) { // The ID is the bed8Attrs name and has already been displayed: if (sameString(ba->attrTags[i], "ID")) continue; cgiDecode(ba->attrVals[i], ba->attrVals[i], strlen(ba->attrVals[i])); char *tag = ba->attrTags[i]; // User-defined keywords used in dbVar's GVF: if (sameString(tag, "var_type")) // This one isn't anymore, but I add it back (hg18.txt). tag = "Variant type"; else if (sameString(tag, "clinical_int")) tag = "Clinical interpretation"; else if (sameString(tag, "var_origin")) tag = "Variant origin"; else if (islower(tag[0])) // Uppercase for nice display, assuming user doesn't care which keywords are // user-defined vs. GVF standard: tag[0] = toupper(tag[0]); // GVF standard Start_range and End_range tags (1-based coords): if (sameString(tag, "Start_range") || sameString(tag, "End_range")) { char *copy = cloneString(ba->attrVals[i]); char *words[3]; int wordCount = chopCommas(copy, words); if (wordCount == 2 && (sameString(".", words[0]) || isInteger(words[0])) && (sameString(".", words[1]) || isInteger(words[1]))) { boolean isStartRange = sameString(tag, "Start_range"); char *rangeStart = words[0], *rangeEnd = words[1]; if (sameString(".", rangeStart)) rangeStart = "unknown"; if (sameString(".", rangeEnd)) rangeEnd = "unknown"; if (isStartRange) printf("<B>Start range</B>: outer start %s, inner start %s<BR>\n", rangeStart, rangeEnd); else printf("<B>End range</B>: inner end %s, outer end %s<BR>\n", rangeStart, rangeEnd); } else // not formatted as expected, just print as-is: printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i])); } // Parent sounds like mom or dad (as in var_origin)... tweak it too: else if (sameString(tag, "Parent")) { printf("<B>Variant region:</B> " "<A HREF=\"http://www.ncbi.nlm.nih.gov/dbvar/variants/%s/\" " "TARGET=_BLANK>%s</A><BR>\n", ba->attrVals[i], htmlEncode(ba->attrVals[i])); } else if (sameString(tag, "Name")) { char *url = trackDbSetting(tdb, "url"); // Show the Name only if it hasn't already appeared in the URL: if (url == NULL || !stringIn("$$", url)) printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i])); } else if (sameWord(tag, "Phenotype_id") && startsWith("HPO:HP:", ba->attrVals[i])) { subChar(tag, '_', ' '); printf("<B>%s</B>: <A HREF=\"http://www.berkeleybop.org/obo/%s\" " "TARGET=_BLANK>%s</A><BR>\n", tag, ba->attrVals[i]+strlen("HPO:"), htmlEncode(ba->attrVals[i])); } else { subChar(tag, '_', ' '); printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i])); } } sqlFreeResult(&sr); hFreeConn(&conn); /* printTrackHtml is done in genericClickHandlerPlus. */ }
char *scanSettingsForCT(char *userName, char *sessionName, char *contents, int *pLiveCount, int *pExpiredCount) /* Parse the CGI-encoded session contents into {var,val} pairs and search * for custom tracks. If found, refresh the custom track. Parsing code * taken from cartParseOverHash. * If any nonexistent custom track files are found, return a SQL update * command that will remove those from this session. We can't just do * the update here because that messes up the caller's query. */ { int contentLength = strlen(contents); struct dyString *newContents = dyStringNew(contentLength+1); struct dyString *oneSetting = dyStringNew(contentLength / 4); char *updateIfAny = NULL; char *contentsToChop = cloneString(contents); char *namePt = contentsToChop; verbose(3, "Scanning %s %s\n", userName, sessionName); while (isNotEmpty(namePt)) { char *dataPt = strchr(namePt, '='); char *nextNamePt; if (dataPt == NULL) errAbort("Mangled session content string %s", namePt); *dataPt++ = 0; nextNamePt = strchr(dataPt, '&'); if (nextNamePt != NULL) *nextNamePt++ = 0; dyStringClear(oneSetting); dyStringPrintf(oneSetting, "%s=%s%s", namePt, dataPt, (nextNamePt ? "&" : "")); if (startsWith(CT_FILE_VAR_PREFIX, namePt)) { boolean thisGotLiveCT = FALSE, thisGotExpiredCT = FALSE; cgiDecode(dataPt, dataPt, strlen(dataPt)); verbose(3, "Found variable %s = %s\n", namePt, dataPt); /* If the file does not exist, omit this setting from newContents so * it doesn't get copied from session to session. If it does exist, * leave it up to customFactoryTestExistence to parse the file for * possible customTrash table references, some of which may exist * and some not. */ if (! fileExists(dataPt)) { verbose(3, "Removing %s from %s %s\n", oneSetting->string, userName, sessionName); thisGotExpiredCT = TRUE; } else { char *db = namePt + strlen(CT_FILE_VAR_PREFIX); dyStringAppend(newContents, oneSetting->string); customFactoryTestExistence(db, dataPt, &thisGotLiveCT, &thisGotExpiredCT); } if (thisGotLiveCT && pLiveCount != NULL) (*pLiveCount)++; if (thisGotExpiredCT && pExpiredCount != NULL) (*pExpiredCount)++; if (thisGotExpiredCT) { if (verboseLevel() >= 3) verbose(3, "Found expired custom track in %s %s: %s\n", userName, sessionName, dataPt); else verbose(2, "Found expired custom track: %s\n", dataPt); } if (thisGotLiveCT) verbose(4, "Found live custom track: %s\n", dataPt); } else dyStringAppend(newContents, oneSetting->string); namePt = nextNamePt; } if (newContents->stringSize != contentLength) { struct dyString *update = dyStringNew(contentLength*2); if (newContents->stringSize > contentLength) errAbort("Uh, why is newContents (%d) longer than original (%d)??", newContents->stringSize, contentLength); dyStringPrintf(update, "UPDATE %s set contents='", savedSessionTable); dyStringAppendN(update, newContents->string, newContents->stringSize); dyStringPrintf(update, "', lastUse=now(), useCount=useCount+1 " "where userName=\"%s\" and sessionName=\"%s\";", userName, sessionName); verbose(3, "Removing one or more dead CT file settings from %s %s " "(original length %d, now %d)\n", userName, sessionName, contentLength, newContents->stringSize); updateIfAny = dyStringCannibalize(&update); } dyStringFree(&oneSetting); dyStringFree(&newContents); freeMem(contentsToChop); return updateIfAny; }