Final Review #6
Final Review #6
Conversation
1. Insert data into workflowdb dabatase 2. Create output directory (with date/time stamp) 3. Several imrpvements on json and xml parsing. 4. Updated job monitoring 5. Updated iteration strategies 6. Updated arguments to include and workflowId and match with the command line arguments
Updated Moteurlite.java for the review comments
1. Combined setter methods into corresponding getter methods, eliminating the need for class-level variables. 2. The class now directly returns the parsed values when needed.
1. Modified the constructor to directly use the refactored getter methods of BoutiquesService. 2. This makes the class more streamlined by fetching values directly without maintaining class-level variables. 3. createJob method - Instead of passing arguments to this method, created class level fields and used inside the method.
1. Updated the boutiques parsing classes. 2. Updated moteurlite class 3. Updated InputFileParser class
Moteur lite
improve pom + add ci
| * | ||
| */ | ||
|
|
||
| public class InputDownloads { |
There was a problem hiding this comment.
Merge the 3 files :
- InputDownloads
- InputParser
- InputsFileParser
into a single Class InputsFileService
| } | ||
| } | ||
| } catch (Exception e) { | ||
| e.printStackTrace(); |
There was a problem hiding this comment.
Do not catch all Exception, only the ones necessary.
Either :
- log with a logger and rethrow a custom Exception
- do not catch it and let it bubble up
| * This method parses the types of inputs from the XML file and returns a Map where the key is | ||
| * the source name and the value is the type of the input (e.g., String, URI). | ||
| */ | ||
| public static Map<String, String> parseInputType(String fileName) { |
There was a problem hiding this comment.
not used, can be deleted
| return inputsMap; | ||
| } | ||
|
|
||
| public Map<String, String> getInputTypeMap() { |
There was a problem hiding this comment.
The 3 last methods are not used and can be deleted.
| } | ||
|
|
||
| // Fetch download files using InputsFileParser | ||
| List<URI> downloads = InputsFileParser.getDownloadFiles(inputsMap); |
There was a problem hiding this comment.
Instead of parsing each value for a specific regex, we should rely on the File types in the boutiques files to build the list of downloads.
| value = new File(System.getProperty("user.dir")).toURI().relativize(new File(value).toURI()).getPath(); | ||
| URI uri = new URI(value); | ||
| String basename = Paths.get(uri.getPath()).getFileName().toString(); | ||
| jsonNode.put(key, basename); |
There was a problem hiding this comment.
I get that we want to extract the filename from value.
I would do Paths.get(new URI(value).getPath()).getFileName(). To test
| else { | ||
| URI uri = new URI(value); | ||
| String basename = Paths.get(uri.getPath()).getFileName().toString(); | ||
| jsonNode.put(key, basename); |
There was a problem hiding this comment.
Normally the else case here is for simple Strings. Why not put the value in the jsonNode ?
| String type = map2.get(key); | ||
|
|
||
| if ("Integer".equals(type) || "Number".equals(type)) { | ||
| jsonNode.put(key, Integer.parseInt(value)); |
There was a problem hiding this comment.
Boutiques only support Number, and that can be a float.
| URI resultsDirectoryURI = new URI(inputsMap.get("results-directory")); | ||
|
|
||
| // Use BoutiquesService to fetch the input types | ||
| String invocationString = CreateInvocation.convertMapToJson(invocation, boutiquesService.getInputType(descriptor)); |
There was a problem hiding this comment.
i think we can move the convertMapToJson method in this class. It will be short.
src/main/java/fr/insalyon/creatis/moteurlite/WorkflowsDbRepository.java
Outdated
Show resolved
Hide resolved
Moteurlite support
No description provided.