From 3314598800fc92bf7e31e35464d2eb461898ee12 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 29 Mar 2016 12:52:19 -0400 Subject: [PATCH] Check .shed.yml owner against credentials during shed creation. Fixes #246. Rebased with advice from @nsoranzo - as always thanks eagle eyes. --- planemo/shed/__init__.py | 8 +++ .../repos/single_tool_other_owner/.shed.yml | 8 +++ .../repos/single_tool_other_owner/cat.xml | 24 +++++++ .../single_tool_other_owner/related_file | 2 + .../single_tool_other_owner/test-data/1.bed | 65 +++++++++++++++++++ .../1_bed_random_lines_1_seed_asdf_out.bed | 1 + tests/test_shed_create.py | 6 ++ 7 files changed, 114 insertions(+) create mode 100644 tests/data/repos/single_tool_other_owner/.shed.yml create mode 100644 tests/data/repos/single_tool_other_owner/cat.xml create mode 100644 tests/data/repos/single_tool_other_owner/related_file create mode 100644 tests/data/repos/single_tool_other_owner/test-data/1.bed create mode 100644 tests/data/repos/single_tool_other_owner/test-data/1_bed_random_lines_1_seed_asdf_out.bed diff --git a/planemo/shed/__init__.py b/planemo/shed/__init__.py index 021de3df0..b189316bb 100644 --- a/planemo/shed/__init__.py +++ b/planemo/shed/__init__.py @@ -61,6 +61,8 @@ "in .shed.yml and --name on the command-line.") REALIZAION_PROBLEMS_MESSAGE = ("Problem encountered executing action for one or more " "repositories.") +INCORRECT_OWNER_MESSAGE = ("Attempting to create a repository with configured " + "owner [%s] that does not matche API user [%s].") # Planemo generated or consumed files that do not need to be uploaded to the # tool shed. PLANEMO_FILES = [ @@ -1191,6 +1193,12 @@ def find_repository_id(self, ctx, shed_context): def create(self, ctx, shed_context): """Wrapper for creating the endpoint if it doesn't exist """ + context_owner = shed_context.owner() + config_owner = self.config.get("owner", None) + if context_owner and config_owner and context_owner != config_owner: + message = INCORRECT_OWNER_MESSAGE % (config_owner, context_owner) + raise Exception(message) + def _create(): repo = create_repository_for( ctx, diff --git a/tests/data/repos/single_tool_other_owner/.shed.yml b/tests/data/repos/single_tool_other_owner/.shed.yml new file mode 100644 index 000000000..4d67da9a7 --- /dev/null +++ b/tests/data/repos/single_tool_other_owner/.shed.yml @@ -0,0 +1,8 @@ +name: "single_tool" +owner: "notiuc" +description: "a simple tool" +type: "unrestricted" +remote_repository_url: "https://github.com/galaxyproject/planemo/tree/master/tests/data/repos/single_tool" +homepage_url: "http://planemo.readthedocs.org/en/latest/" +categories: + - "Text Manipulation" diff --git a/tests/data/repos/single_tool_other_owner/cat.xml b/tests/data/repos/single_tool_other_owner/cat.xml new file mode 100644 index 000000000..5d71cceb0 --- /dev/null +++ b/tests/data/repos/single_tool_other_owner/cat.xml @@ -0,0 +1,24 @@ + + tail-to-head + + cat $input1 #for $q in $queries# ${q.input2} #end for# > $out_file1 + + + + + + + + + + + + + + + + + + Concatenate datasets. + + diff --git a/tests/data/repos/single_tool_other_owner/related_file b/tests/data/repos/single_tool_other_owner/related_file new file mode 100644 index 000000000..f44288327 --- /dev/null +++ b/tests/data/repos/single_tool_other_owner/related_file @@ -0,0 +1,2 @@ +A related non-tool file. + diff --git a/tests/data/repos/single_tool_other_owner/test-data/1.bed b/tests/data/repos/single_tool_other_owner/test-data/1.bed new file mode 100644 index 000000000..eb4c30e34 --- /dev/null +++ b/tests/data/repos/single_tool_other_owner/test-data/1.bed @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff --git a/tests/data/repos/single_tool_other_owner/test-data/1_bed_random_lines_1_seed_asdf_out.bed b/tests/data/repos/single_tool_other_owner/test-data/1_bed_random_lines_1_seed_asdf_out.bed new file mode 100644 index 000000000..7b8da5dbf --- /dev/null +++ b/tests/data/repos/single_tool_other_owner/test-data/1_bed_random_lines_1_seed_asdf_out.bed @@ -0,0 +1 @@ +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + diff --git a/tests/test_shed_create.py b/tests/test_shed_create.py index 6b04386d6..446b84f49 100644 --- a/tests/test_shed_create.py +++ b/tests/test_shed_create.py @@ -15,6 +15,12 @@ def test_create_single(self): create_command.extend(self._shed_args()) self._check_exit_code(create_command) + def test_create_wrong_owner(self): + with self._isolate_repo("single_tool_other_owner"): + create_command = ["shed_create", "--skip_upload"] + create_command.extend(self._shed_args()) + self._check_exit_code(create_command, exit_code=-1) + def test_create_multiple(self): with self._isolate_repo("multi_repos_nested"): create_command = ["shed_create", "--skip_upload", "-r"]