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Register vcell-su download-vcml subcommand and resolve users by id #1675

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Register vcell-su download-vcml subcommand and resolve users by id #1675

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2 changes: 2 additions & 0 deletions vcell-admin/src/main/java/org/vcell/admin/cli/AdminCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
import org.vcell.admin.cli.sim.JobInfoCommand;
import org.vcell.admin.cli.sim.ResultSetCrawlerCommand;
import org.vcell.admin.cli.sim.SimDataVerifierCommand;
import org.vcell.admin.cli.tools.DatabaseCommand;
import org.vcell.admin.cli.tools.UsageCommand;
import org.vcell.admin.cli.tools.UsersQueryCommand;
import org.vcell.db.DatabaseSyntax;
Expand All @@ -33,6 +34,7 @@
DatabaseCreateScriptCommand.class,
UsageCommand.class,
UsersQueryCommand.class,
DatabaseCommand.class,
ResultSetCrawlerCommand.class,
SimDataVerifierCommand.class,
JobInfoCommand.class,
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9 changes: 9 additions & 0 deletions vcell-admin/src/main/java/org/vcell/admin/cli/CLIDatabaseService.java
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Expand Up @@ -170,6 +170,15 @@ public BioModelInfo queryBiomodelInfo(User owner, KeyValue biomodelId) throws Da
return getDatabaseServer().getBioModelInfo(owner, biomodelId);
}

public User resolveUser(String userid) throws DataAccessException, SQLException {
AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(conFactory);
User user = adminDbTopLevel.getUser(userid, true);
if (user == null) {
throw new DataAccessException("user '" + userid + "' not found");
}
return user;
}

public MathModelInfo queryMathmodelInfo(User owner, KeyValue mathmodelId) throws DataAccessException {
return getDatabaseServer().getMathModelInfo(owner, mathmodelId);
}
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7 changes: 7 additions & 0 deletions vcell-admin/src/main/java/org/vcell/admin/cli/tools/DatabaseCommand.java
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Expand Up @@ -35,6 +35,9 @@ public class DatabaseCommand implements Callable<Integer> {
@Option(names = "--user", description = "userid and key for private models --biomodel-id (format is 'userid:key')")
private User user = User.tempUser;

@Option(names = "--userid", description = "userid alone for private --biomodel-id; user key resolved via DB lookup")
private String userid;

@Option(names = {"-d", "--debug"}, description = "full application debug mode")
private boolean bDebug = false;

Expand All @@ -61,6 +64,10 @@ public Integer call() {
throw new RuntimeException("outputDir '" + (outputDir == null ? "" : outputDir) + "' is not a 'valid directory'");

try (CLIDatabaseService cliDatabaseService = new CLIDatabaseService()) {
if (userid != null) {
user = cliDatabaseService.resolveUser(userid);
logger.info("resolved userid '" + userid + "' to user " + user.getName() + ":" + user.getID());
}
if (biomodelsFile != null) {
List<String> lines = Files.readAllLines(biomodelsFile.toPath());
for (String line : lines) {
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