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();
}
struct docIdSub *docIdSubLoadAllByChar(char *fileName, char chopper)
/* Load all docIdSub from a chopper separated file.
* Dispose of this with docIdSubFreeList(). */
{
struct docIdSub *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[10];
while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
{
el = docIdSubLoad(row);
slAddHead(&list, el);
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
struct docIdSub *docIdSubLoadAll(char *fileName)
/* Load all docIdSub from a whitespace-separated file.
* Dispose of this with docIdSubFreeList(). */
{
struct docIdSub *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[10];
while (lineFileRow(lf, row))
{
el = docIdSubLoad(row);
slAddHead(&list, el);
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
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);
}
