removing .env files

[RoanKanninga]

Removing out of
generators/impl/TaskGenerator.java

// source its environment
						scriptBuilder.append(Parameters.SOURCE_COMMAND).append(" ")
								.append(Parameters.ENVIRONMENT_DIR_VARIABLE).append(File.separator).append(prevJobName)
								.append(Parameters.ENVIRONMENT_EXTENSION).append("\n");

scriptBuilder.append("\n\n# Connect parameters to environment\n");

// append footer that appends the task's parameters to
			// environment of this task
			String myEnvironmentFile = Parameters.ENVIRONMENT_DIR_VARIABLE + File.separator + task.getName()
					+ Parameters.ENVIRONMENT_EXTENSION;
			scriptBuilder.append("\n#\n## End of your protocol template\n#\n");
			scriptBuilder.append("\n# Save output in environment file: '" + myEnvironmentFile
					+ "' with the output vars of this step\n");

			Iterator<Output> itOutput = step.getProtocol().getOutputs().iterator();
			while (itOutput.hasNext())
			{
				String parameterName = itOutput.next().getName();
				if (dataEntityValues.containsKey(parameterName))
				{
					// If parameter not set at runtime then ERROR
					String line = "if [[ -z \"$" + parameterName + "\" ]]; then echo \"In step '" + step.getName()
							+ "', parameter '" + parameterName + "' has no value! Please assign a value to parameter '"
							+ parameterName + "'." + "\" >&2; exit 1; fi\n";

					// Else set parameters at right indexes.
					// Explanation: if param file is collapsed in this
					// template, then we should not output a single
					// value but a list of values because next step may
					// be run in uncollapsed fashion

					List<String> rowIndex = dataEntity.getList(Parameters.ID_COLUMN);
					for (int i = 0; i < rowIndex.size(); i++)
					{
						Object rowIndexObject = rowIndex.get(i);
						String rowIndexString = rowIndexObject.toString();
						line += "echo \"" + step.getName() + Parameters.STEP_PARAM_SEP_SCRIPT + parameterName + "["
								+ rowIndexString + "]=\\\"${" + parameterName + "[" + i + "]}\\\"\" >> "
								+ myEnvironmentFile + "\n";
					}

					scriptBuilder.append(line);
				}

			}
			scriptBuilder.append("\necho \"\" >> " + myEnvironmentFile + "\nchmod 755 " + myEnvironmentFile + "\n");```

[pneerincx]

Why disabling the creation of .env files. This would kill the feature to pass dynamic values computed at runtime of the script from one analysis step to the next. I would prefer a fix to make sure the .env files are created only when necessarry (and actually used) and with the correct permissions.

[freerkvandijk]

You only want to have/create the *.env files when needed in an analysis step. So I would assume you only check if the *.env files are present in your generated script when you actually need parameters values from them, instead of completely removing the dynamic values feature.

…

On 17 October 2017 at 10:06, Pieter Neerincx ***@***.***> wrote: Why disabling the creation of .env files. This would kill the feature to pass dynamic values computed at runtime of the script from one analysis step to the next. I would prefer a fix to make sure the .env files are created only when necessarry (and actually used) and with the correct permissions. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#277 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABxneW9781Tbz17_GTqAX4aXCx7ipc6pks5stGAegaJpZM4P7ox6> .

[RoanKanninga]

Fine by me, but you can already pass dynamic values from the generatedscript as a parameter via the -o argument in compute. Where do you want to set other dynamic values?