{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/fiss/issues/39","repository_url":"https://api.github.com/repos/broadinstitute/fiss","labels_url":"https://api.github.com/repos/broadinstitute/fiss/issues/39/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/fiss/issues/39/comments","events_url":"https://api.github.com/repos/broadinstitute/fiss/issues/39/events","html_url":"https://github.com/broadinstitute/fiss/issues/39","id":243539978,"number":39,"title":"BUG: config_get does not return valid json on the CLI for String and File variables","user":{"login":"dheiman","id":1229253,"avatar_url":"https://avatars1.githubusercontent.com/u/1229253?v=4","gravatar_id":"","url":"https://api.github.com/users/dheiman","html_url":"https://github.com/dheiman","followers_url":"https://api.github.com/users/dheiman/followers","following_url":"https://api.github.com/users/dheiman/following{/other_user}","gists_url":"https://api.github.com/users/dheiman/gists{/gist_id}","starred_url":"https://api.github.com/users/dheiman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dheiman/subscriptions","organizations_url":"https://api.github.com/users/dheiman/orgs","repos_url":"https://api.github.com/users/dheiman/repos","events_url":"https://api.github.com/users/dheiman/events{/privacy}","received_events_url":"https://api.github.com/users/dheiman/received_events","type":"User","site_admin":false},"labels":[{"id":450102825,"url":"https://api.github.com/repos/broadinstitute/fiss/labels/bug","name":"bug","color":"ee0701","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-07-17T21:57:11Z","updated_at":"2017-07-17T23:54:34Z","closed_at":null,"body":"`String` and `File` outputs and inputs should be delimited like so: `\"\\\"<value>\\\"\"` and are as such when accessed via the API via either the [documentation](https://api.firecloud.org/#!/Method_Configurations/getWorkspaceMethodConfig) or curl command.\r\n\r\n`config_get` removes the escape characters from the inner double quotes in the CLI, resulting in JSON files that are invalid, and thus not usable by `config_put`.\r\n\r\ne.g.\r\n `https://api.firecloud.org/api/workspaces/nci-dheiman-b-org/analyses_packaging/method_configs/broadgdac/mRNA_Preprocess`\r\n```js\r\n{\r\n  \"name\": \"CopyNumber_Gistic2\",\r\n  \"methodRepoMethod\": {\r\n    \"methodNamespace\": \"broadgdac\",\r\n    \"methodName\": \"copy_number_gistic2\",\r\n    \"methodVersion\": 18\r\n  },\r\n  \"outputs\": {\r\n    \"copy_number_gistic2.report_gistic2.del_o\": \"this.gistic2__del\",\r\n    \"copy_number_gistic2.report_gistic2.amp_o\": \"this.gistic2__amp\",\r\n    \"copy_number_gistic2.tool_gistic2.broad_values_by_arm\": \"this.gistic2__broad_values_by_arm\",\r\n    \"copy_number_gistic2.tool_gistic2.all_data_by_genes\": \"this.gistic2__all_data_by_genes\",\r\n    \"copy_number_gistic2.tool_gistic2.all_lesions\": \"this.gistic2__all_lesions\",\r\n    \"copy_number_gistic2.tool_gistic2.all_thresholded_by_genes\": \"this.gistic2__all_thresholded_by_genes\",\r\n    \"copy_number_gistic2.report_gistic2.report_gistic2_pkg\": \"this.pkg__CopyNumber_Gistic2\",\r\n    \"copy_number_gistic2.report_gistic2.broad_sig_res_o\": \"this.gistic2__broad_sig_res\"\r\n  },\r\n  \"inputs\": {\r\n    \"copy_number_gistic2.tool_gistic2.seg_file\": \"this.CNV__snp6\",\r\n    \"copy_number_gistic2.tool_gistic2.do_gene_gistic\": \"1\",\r\n    \"copy_number_gistic2.tool_gistic2.remove_X\": \"0\",\r\n    \"copy_number_gistic2.tool_gistic2.refgene_file\": \"\\\"gs://broad-institute-gdac/gdc/reference/gistic/gistic2.refgene.hg38.UCSC.add_miR.160920.mat\\\"\",\r\n    \"copy_number_gistic2.tool_gistic2.amp_thresh\": \"0.1\",\r\n    \"copy_number_gistic2.tool_gistic2.markers_file\": \"\\\"gs://broad-institute-gdac/gdc/reference/gistic/gistic2.markers.snp6.na35.liftoverhg38.txt\\\"\",\r\n    \"copy_number_gistic2.report_gistic2.type\": \"\",\r\n    \"copy_number_gistic2.tool_gistic2.cnv_files\": \"\\\"gs://broad-institute-gdac/gdc/reference/gistic/hg38_GDC_SNP6_CNV_list.161107.txt\\\"\",\r\n    \"copy_number_gistic2.tool_gistic2.arm_peel\": \"1\",\r\n    \"copy_number_gistic2.tool_gistic2.cap\": \"1.5\",\r\n    \"copy_number_gistic2.report_gistic2.package\": \"true\",\r\n    \"copy_number_gistic2.tool_gistic2.join_segment_size\": \"4\",\r\n    \"copy_number_gistic2.tool_gistic2.max_sample_segs\": \"2000\",\r\n    \"copy_number_gistic2.tool_gistic2.del_thresh\": \"0.1\",\r\n    \"copy_number_gistic2.tool_gistic2.qv_thresh\": \"0.25\",\r\n    \"copy_number_gistic2.tool_gistic2.conf_level\": \"0.99\",\r\n    \"copy_number_gistic2.tool_gistic2.broad_length_cutoff\": \"0.98\",\r\n    \"copy_number_gistic2.tool_gistic2.gene_collapse_method\": \"\\\"extreme\\\"\"\r\n  },\r\n  \"rootEntityType\": \"sample_set\",\r\n  \"prerequisites\": {},\r\n  \"methodConfigVersion\": 3,\r\n  \"deleted\": false,\r\n  \"namespace\": \"broadgdac\"\r\n}\r\n```\r\n`% fissfc config_get -w analyses_packaging -c CopyNumber_Gistic2`\r\n```js\r\n{\r\n  \"name\": \"CopyNumber_Gistic2\",\r\n  \"methodRepoMethod\": {\r\n    \"methodNamespace\": \"broadgdac\",\r\n    \"methodName\": \"copy_number_gistic2\",\r\n    \"methodVersion\": 18\r\n  },\r\n  \"outputs\": {\r\n    \"copy_number_gistic2.report_gistic2.del_o\": \"this.gistic2__del\",\r\n    \"copy_number_gistic2.report_gistic2.amp_o\": \"this.gistic2__amp\",\r\n    \"copy_number_gistic2.tool_gistic2.broad_values_by_arm\": \"this.gistic2__broad_values_by_arm\",\r\n    \"copy_number_gistic2.tool_gistic2.all_data_by_genes\": \"this.gistic2__all_data_by_genes\",\r\n    \"copy_number_gistic2.tool_gistic2.all_lesions\": \"this.gistic2__all_lesions\",\r\n    \"copy_number_gistic2.tool_gistic2.all_thresholded_by_genes\": \"this.gistic2__all_thresholded_by_genes\",\r\n    \"copy_number_gistic2.report_gistic2.report_gistic2_pkg\": \"this.pkg__CopyNumber_Gistic2\",\r\n    \"copy_number_gistic2.report_gistic2.broad_sig_res_o\": \"this.gistic2__broad_sig_res\"\r\n  },\r\n  \"inputs\": {\r\n    \"copy_number_gistic2.tool_gistic2.seg_file\": \"this.CNV__snp6\",\r\n    \"copy_number_gistic2.tool_gistic2.do_gene_gistic\": \"1\",\r\n    \"copy_number_gistic2.tool_gistic2.remove_X\": \"0\",\r\n    \"copy_number_gistic2.tool_gistic2.refgene_file\": \"\"gs://broad-institute-gdac/gdc/reference/gistic/gistic2.refgene.hg38.UCSC.add_miR.160920.mat\"\",\r\n    \"copy_number_gistic2.tool_gistic2.amp_thresh\": \"0.1\",\r\n    \"copy_number_gistic2.tool_gistic2.markers_file\": \"\"gs://broad-institute-gdac/gdc/reference/gistic/gistic2.markers.snp6.na35.liftoverhg38.txt\"\",\r\n    \"copy_number_gistic2.report_gistic2.type\": \"\",\r\n    \"copy_number_gistic2.tool_gistic2.cnv_files\": \"\"gs://broad-institute-gdac/gdc/reference/gistic/hg38_GDC_SNP6_CNV_list.161107.txt\"\",\r\n    \"copy_number_gistic2.tool_gistic2.arm_peel\": \"1\",\r\n    \"copy_number_gistic2.tool_gistic2.cap\": \"1.5\",\r\n    \"copy_number_gistic2.report_gistic2.package\": \"true\",\r\n    \"copy_number_gistic2.tool_gistic2.join_segment_size\": \"4\",\r\n    \"copy_number_gistic2.tool_gistic2.max_sample_segs\": \"2000\",\r\n    \"copy_number_gistic2.tool_gistic2.del_thresh\": \"0.1\",\r\n    \"copy_number_gistic2.tool_gistic2.qv_thresh\": \"0.25\",\r\n    \"copy_number_gistic2.tool_gistic2.conf_level\": \"0.99\",\r\n    \"copy_number_gistic2.tool_gistic2.broad_length_cutoff\": \"0.98\",\r\n    \"copy_number_gistic2.tool_gistic2.gene_collapse_method\": \"\"extreme\"\"\r\n  },\r\n  \"rootEntityType\": \"sample_set\",\r\n  \"prerequisites\": {\r\n\r\n  },\r\n  \"methodConfigVersion\": 3,\r\n  \"deleted\": false,\r\n  \"namespace\": \"broadgdac\"\r\n}\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/fiss/issues/comments/315918102","html_url":"https://github.com/broadinstitute/fiss/issues/39#issuecomment-315918102","issue_url":"https://api.github.com/repos/broadinstitute/fiss/issues/39","id":315918102,"user":{"login":"noblem","id":3883143,"avatar_url":"https://avatars3.githubusercontent.com/u/3883143?v=4","gravatar_id":"","url":"https://api.github.com/users/noblem","html_url":"https://github.com/noblem","followers_url":"https://api.github.com/users/noblem/followers","following_url":"https://api.github.com/users/noblem/following{/other_user}","gists_url":"https://api.github.com/users/noblem/gists{/gist_id}","starred_url":"https://api.github.com/users/noblem/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/noblem/subscriptions","organizations_url":"https://api.github.com/users/noblem/orgs","repos_url":"https://api.github.com/users/noblem/repos","events_url":"https://api.github.com/users/noblem/events{/privacy}","received_events_url":"https://api.github.com/users/noblem/received_events","type":"User","site_admin":false},"created_at":"2017-07-17T23:54:34Z","updated_at":"2017-07-17T23:54:34Z","body":"Also, if you ARE intending to address this yourself ... please tweak the highlevel regression test to exercise this edge case and ensure it never reappears, ok?"}}
{"actor":{"display_login":"noblem"}}