{"action":"created","issue":{"url":"https://api.github.com/repos/TheRoddyWMS/Roddy/issues/234","repository_url":"https://api.github.com/repos/TheRoddyWMS/Roddy","labels_url":"https://api.github.com/repos/TheRoddyWMS/Roddy/issues/234/labels{/name}","comments_url":"https://api.github.com/repos/TheRoddyWMS/Roddy/issues/234/comments","events_url":"https://api.github.com/repos/TheRoddyWMS/Roddy/issues/234/events","html_url":"https://github.com/TheRoddyWMS/Roddy/issues/234","id":309643210,"number":234,"title":"When input file and string parameters are not configured in the proper order, a job will not be executed","user":{"login":"dankwart-de","id":6582183,"avatar_url":"https://avatars0.githubusercontent.com/u/6582183?v=4","gravatar_id":"","url":"https://api.github.com/users/dankwart-de","html_url":"https://github.com/dankwart-de","followers_url":"https://api.github.com/users/dankwart-de/followers","following_url":"https://api.github.com/users/dankwart-de/following{/other_user}","gists_url":"https://api.github.com/users/dankwart-de/gists{/gist_id}","starred_url":"https://api.github.com/users/dankwart-de/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dankwart-de/subscriptions","organizations_url":"https://api.github.com/users/dankwart-de/orgs","repos_url":"https://api.github.com/users/dankwart-de/repos","events_url":"https://api.github.com/users/dankwart-de/events{/privacy}","received_events_url":"https://api.github.com/users/dankwart-de/received_events","type":"User","site_admin":false},"labels":[{"id":411780502,"url":"https://api.github.com/repos/TheRoddyWMS/Roddy/labels/bug","name":"bug","color":"ee0701","default":true}],"state":"open","locked":false,"assignee":{"login":"dankwart-de","id":6582183,"avatar_url":"https://avatars0.githubusercontent.com/u/6582183?v=4","gravatar_id":"","url":"https://api.github.com/users/dankwart-de","html_url":"https://github.com/dankwart-de","followers_url":"https://api.github.com/users/dankwart-de/followers","following_url":"https://api.github.com/users/dankwart-de/following{/other_user}","gists_url":"https://api.github.com/users/dankwart-de/gists{/gist_id}","starred_url":"https://api.github.com/users/dankwart-de/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dankwart-de/subscriptions","organizations_url":"https://api.github.com/users/dankwart-de/orgs","repos_url":"https://api.github.com/users/dankwart-de/repos","events_url":"https://api.github.com/users/dankwart-de/events{/privacy}","received_events_url":"https://api.github.com/users/dankwart-de/received_events","type":"User","site_admin":false},"assignees":[{"login":"dankwart-de","id":6582183,"avatar_url":"https://avatars0.githubusercontent.com/u/6582183?v=4","gravatar_id":"","url":"https://api.github.com/users/dankwart-de","html_url":"https://github.com/dankwart-de","followers_url":"https://api.github.com/users/dankwart-de/followers","following_url":"https://api.github.com/users/dankwart-de/following{/other_user}","gists_url":"https://api.github.com/users/dankwart-de/gists{/gist_id}","starred_url":"https://api.github.com/users/dankwart-de/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dankwart-de/subscriptions","organizations_url":"https://api.github.com/users/dankwart-de/orgs","repos_url":"https://api.github.com/users/dankwart-de/repos","events_url":"https://api.github.com/users/dankwart-de/events{/privacy}","received_events_url":"https://api.github.com/users/dankwart-de/received_events","type":"User","site_admin":false}],"milestone":null,"comments":0,"created_at":"2018-03-29T07:10:15Z","updated_at":"2018-03-29T11:32:06Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"e.g. you have 3 parameters in the following order:\r\ninput1: BaseFile\r\ninput2: String\r\ninput3: BaseFile\r\n=> Roddy will tell you, that there are not enough parameters for the tool and the tool will not be called.\r\nMessage: Not all input parameters were set for ${calledTool.id}. Expected ${calledTool.getInputParameters(context).size()}. Breaking loop and trying to go on. in GenericMethod\r\nOne possible error location might be in GenericMethod.assembleJobParameters(), because the list allInputValues does not have the right size after the method was called. \r\n\r\n``` Java\r\nprivate void assembleJobParameters() {\r\n        // Assemble initial parameters\r\n        parameters[PRM_WORKFLOW_ID] = context.analysis.configuration.getName()\r\n        if (toolName) {\r\n            parameters[PRM_TOOL_ID] = toolName\r\n            parameters[PRM_TOOLS_DIR] = configuration.getProcessingToolPath(context, toolName).getParent()\r\n        }\r\n\r\n        // Assemble additional parameters\r\n        for (Object entry in additionalInput) {\r\n            if (entry instanceof BaseFile)\r\n                // assert(((BaseFile) entry).isEvaluated)\r\n                allInputValues << (BaseFile) entry\r\n            else if (entry instanceof FileGroup) {\r\n                //Take a group and store all files in that group.\r\n                allInputValues << (FileGroup) entry\r\n            } else if (entry instanceof Map) {\r\n                (entry as Map).forEach { k, v ->\r\n                    parameters[k.toString()] = v.toString()\r\n                }\r\n            } else {               // Catch-all, in case one still wants to use a string with '=' to define a parameter (deprecated).\r\n                String[] split = entry.toString().split(\"=\")\r\n                if (split.length != 2)\r\n                    throw new RuntimeException(\"Unable to convert entry ${entry.toString()} to parameter.\")\r\n                parameters[split[0]] = split[1]\r\n            }\r\n        }\r\n    }\r\n```"},"comment":{"url":"https://api.github.com/repos/TheRoddyWMS/Roddy/issues/comments/377206880","html_url":"https://github.com/TheRoddyWMS/Roddy/issues/234#issuecomment-377206880","issue_url":"https://api.github.com/repos/TheRoddyWMS/Roddy/issues/234","id":377206880,"user":{"login":"dankwart-de","id":6582183,"avatar_url":"https://avatars0.githubusercontent.com/u/6582183?v=4","gravatar_id":"","url":"https://api.github.com/users/dankwart-de","html_url":"https://github.com/dankwart-de","followers_url":"https://api.github.com/users/dankwart-de/followers","following_url":"https://api.github.com/users/dankwart-de/following{/other_user}","gists_url":"https://api.github.com/users/dankwart-de/gists{/gist_id}","starred_url":"https://api.github.com/users/dankwart-de/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dankwart-de/subscriptions","organizations_url":"https://api.github.com/users/dankwart-de/orgs","repos_url":"https://api.github.com/users/dankwart-de/repos","events_url":"https://api.github.com/users/dankwart-de/events{/privacy}","received_events_url":"https://api.github.com/users/dankwart-de/received_events","type":"User","site_admin":false},"created_at":"2018-03-29T11:32:06Z","updated_at":"2018-03-29T11:32:06Z","author_association":"CONTRIBUTOR","body":"See pull request #235 "}}
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