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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 02 Jun 2025 10:29:28 +0000
parents c7a7520afb4b
children
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4:c7a7520afb4b 5:f934215bdb78
1 { 1 {
2 "summary": { 2 "summary": {
3 "num_errors": 0, 3 "num_errors": 0,
4 "num_failures": 0, 4 "num_failures": 1,
5 "num_skips": 0, 5 "num_skips": 0,
6 "num_tests": 1 6 "num_tests": 2
7 }, 7 },
8 "tests": [ 8 "tests": [
9 { 9 {
10 "data": { 10 "data": {
11 "inputs": { 11 "inputs": {
12 "adv|json_conf": { 12 "adv|json_conf": {
13 "id": "1895a93fdf3c72e9", 13 "id": "c9e99bc7539b08e5",
14 "src": "hda" 14 "src": "hda"
15 }, 15 },
16 "genbank_files": { 16 "genbank_files": {
17 "id": "c0d7a43ba58f94b5", 17 "id": "c804608f95de6282",
18 "src": "hdca" 18 "src": "hdca"
19 } 19 }
20 }, 20 },
21 "job": { 21 "job": {
22 "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpxct9x70x/files/3/0/f/dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat,/tmp/tmpxct9x70x/files/b/f/b/dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat,/tmp/tmpxct9x70x/files/1/e/5/dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat,/tmp/tmpxct9x70x/files/a/b/a/dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat,/tmp/tmpxct9x70x/files/7/b/7/dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat' --file_name_mapping '/tmp/tmpxct9x70x/files/3/0/f/dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat:p7_L7Ae-Weiss.gb,/tmp/tmpxct9x70x/files/b/f/b/dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpxct9x70x/files/1/e/5/dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat:p6_Kozak-ATG.gb,/tmp/tmpxct9x70x/files/a/b/a/dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpxct9x70x/files/7/b/7/dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpxct9x70x/files/f/4/f/dataset_f4fd59e8-f8d6-4be2-8b00-9e12ca8319ef.dat'", 22 "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpgfe8mdmw/files/a/5/a/dataset_a5a56a5c-573a-4b34-8c98-27b2edff54f3.dat,/tmp/tmpgfe8mdmw/files/1/7/7/dataset_1779bfb3-ff31-4b6d-8c6f-82172c987fee.dat,/tmp/tmpgfe8mdmw/files/4/c/c/dataset_4cc83056-e7b7-4dcd-9360-cde2bc1978f1.dat,/tmp/tmpgfe8mdmw/files/9/6/9/dataset_969b7b35-4f05-48bc-92f5-4e2f5ce375ca.dat,/tmp/tmpgfe8mdmw/files/7/b/4/dataset_7b47f46b-3e00-4a65-9c9a-6a25e3c30b04.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpgfe8mdmw/job_working_directory/000/7/outputs/dataset_89f2f3f4-04a0-4998-a3f6-d065b9e1f365.dat' --file_name_mapping '/tmp/tmpgfe8mdmw/files/a/5/a/dataset_a5a56a5c-573a-4b34-8c98-27b2edff54f3.dat:p7_L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/1/7/7/dataset_1779bfb3-ff31-4b6d-8c6f-82172c987fee.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpgfe8mdmw/files/4/c/c/dataset_4cc83056-e7b7-4dcd-9360-cde2bc1978f1.dat:p6_Kozak-ATG.gb,/tmp/tmpgfe8mdmw/files/9/6/9/dataset_969b7b35-4f05-48bc-92f5-4e2f5ce375ca.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/7/b/4/dataset_7b47f46b-3e00-4a65-9c9a-6a25e3c30b04.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpgfe8mdmw/files/b/3/e/dataset_b3e3a95b-dd84-41de-b53b-ea44d034e11b.dat'",
23 "command_version": "", 23 "command_version": "",
24 "copied_from_job_id": null, 24 "copied_from_job_id": null,
25 "create_time": "2025-06-02T09:46:35.368351", 25 "create_time": "2025-06-02T10:25:46.744304",
26 "dependencies": [], 26 "dependencies": [],
27 "exit_code": 0, 27 "exit_code": 0,
28 "external_id": "129989", 28 "external_id": "148807",
29 "galaxy_version": "24.2", 29 "galaxy_version": "24.2",
30 "handler": null, 30 "handler": null,
31 "history_id": "c0d7a43ba58f94b5", 31 "history_id": "c804608f95de6282",
32 "id": "92e9df4c7abf24ab", 32 "id": "91a273dde5f46de6",
33 "inputs": { 33 "inputs": {
34 "adv|json_conf": { 34 "adv|json_conf": {
35 "id": "1895a93fdf3c72e9", 35 "id": "c9e99bc7539b08e5",
36 "src": "hda", 36 "src": "hda",
37 "uuid": "f4fd59e8-f8d6-4be2-8b00-9e12ca8319ef" 37 "uuid": "b3e3a95b-dd84-41de-b53b-ea44d034e11b"
38 }, 38 },
39 "genbank_files1": { 39 "genbank_files1": {
40 "id": "c0d7a43ba58f94b5", 40 "id": "c804608f95de6282",
41 "src": "hda", 41 "src": "hda",
42 "uuid": "30fc2017-6620-4a80-a60e-0c795c89f106" 42 "uuid": "a5a56a5c-573a-4b34-8c98-27b2edff54f3"
43 }, 43 },
44 "genbank_files2": { 44 "genbank_files2": {
45 "id": "1e3e46a5cbeec338", 45 "id": "dc78a71e9d46a610",
46 "src": "hda", 46 "src": "hda",
47 "uuid": "bfb54321-8ad0-4e42-b307-f32e47e0618a" 47 "uuid": "1779bfb3-ff31-4b6d-8c6f-82172c987fee"
48 }, 48 },
49 "genbank_files3": { 49 "genbank_files3": {
50 "id": "81fab13a93a3da95", 50 "id": "32d06e9182be9fe5",
51 "src": "hda", 51 "src": "hda",
52 "uuid": "1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3" 52 "uuid": "4cc83056-e7b7-4dcd-9360-cde2bc1978f1"
53 }, 53 },
54 "genbank_files4": { 54 "genbank_files4": {
55 "id": "a9ff23755d49e4b6", 55 "id": "a50e356be1f2db6f",
56 "src": "hda", 56 "src": "hda",
57 "uuid": "aba8d5b4-a4f3-4487-803c-be5dee1445cd" 57 "uuid": "969b7b35-4f05-48bc-92f5-4e2f5ce375ca"
58 }, 58 },
59 "genbank_files5": { 59 "genbank_files5": {
60 "id": "2ca788c708559c16", 60 "id": "64d80998680b05e1",
61 "src": "hda", 61 "src": "hda",
62 "uuid": "7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968" 62 "uuid": "7b47f46b-3e00-4a65-9c9a-6a25e3c30b04"
63 } 63 }
64 }, 64 },
65 "job_messages": [], 65 "job_messages": [],
66 "job_metrics": [], 66 "job_metrics": [],
67 "job_runner_name": null, 67 "job_runner_name": null,
69 "job_stdout": "", 69 "job_stdout": "",
70 "model_class": "Job", 70 "model_class": "Job",
71 "output_collections": {}, 71 "output_collections": {},
72 "outputs": { 72 "outputs": {
73 "output": { 73 "output": {
74 "id": "92e9df4c7abf24ab", 74 "id": "91a273dde5f46de6",
75 "src": "hda", 75 "src": "hda",
76 "uuid": "41b844ab-5a85-46cd-8367-7ad1fbee7d3c" 76 "uuid": "89f2f3f4-04a0-4998-a3f6-d065b9e1f365"
77 } 77 }
78 }, 78 },
79 "params": { 79 "params": {
80 "__input_ext": "\"input\"", 80 "__input_ext": "\"input\"",
81 "adv": "{\"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}}", 81 "adv": "{\"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}}",
82 "annotation_column": null, 82 "annotation_column": null,
83 "chromInfo": "\"/tmp/tmpxct9x70x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 83 "chromInfo": "\"/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
84 "db_uri": null, 84 "db_uri": null,
85 "dbkey": "\"?\"", 85 "dbkey": "\"?\"",
86 "fragment_column": null, 86 "fragment_column": null,
87 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", 87 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
88 "sequence_column": null, 88 "sequence_column": null,
89 "table": null 89 "table": null
90 }, 90 },
91 "state": "ok", 91 "state": "ok",
92 "stderr": "", 92 "stderr": "",
93 "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat\nProcessing file: dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat\nProcessing file: dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat\nProcessing file: dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat\nProcessing file: dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat'.\n", 93 "stdout": "Execution was blocked by config (execution = false)\n",
94 "tool_id": "save_to_db", 94 "tool_id": "save_to_db",
95 "tool_stderr": "", 95 "tool_stderr": "",
96 "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat\nProcessing file: dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat\nProcessing file: dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat\nProcessing file: dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat\nProcessing file: dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat'.\n", 96 "tool_stdout": "Execution was blocked by config (execution = false)\n",
97 "update_time": "2025-06-02T09:46:41.929779", 97 "update_time": "2025-06-02T10:25:54.228017",
98 "user_email": "planemo@galaxyproject.org", 98 "user_email": "planemo@galaxyproject.org",
99 "user_id": "c0d7a43ba58f94b5" 99 "user_id": "c804608f95de6282"
100 }, 100 },
101 "status": "success", 101 "output_problems": [
102 "Output output: different than expected\nExpected 5+-0 lines in the output found 0"
103 ],
104 "status": "failure",
102 "test_index": 0, 105 "test_index": 0,
103 "time_seconds": 29.02011752128601, 106 "time_seconds": 28.49768567085266,
104 "tool_id": "save_to_db", 107 "tool_id": "save_to_db",
105 "tool_version": "0.1.0+galaxy1" 108 "tool_version": "0.2.0+galaxy2"
106 }, 109 },
107 "has_data": true, 110 "has_data": true,
108 "id": "save_to_db-0" 111 "id": "save_to_db-0"
112 },
113 {
114 "data": {
115 "inputs": {
116 "adv|json_conf": {
117 "id": "ba5e0bd88cc3030c",
118 "src": "hda"
119 },
120 "genbank_files": {
121 "id": "dc78a71e9d46a610",
122 "src": "hdca"
123 }
124 },
125 "job": {
126 "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpgfe8mdmw/files/3/6/2/dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat,/tmp/tmpgfe8mdmw/files/4/e/0/dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat,/tmp/tmpgfe8mdmw/files/6/d/a/dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat,/tmp/tmpgfe8mdmw/files/8/0/b/dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat,/tmp/tmpgfe8mdmw/files/3/8/7/dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat' --file_name_mapping '/tmp/tmpgfe8mdmw/files/3/6/2/dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat:p7_L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/4/e/0/dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpgfe8mdmw/files/6/d/a/dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat:p6_Kozak-ATG.gb,/tmp/tmpgfe8mdmw/files/8/0/b/dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/3/8/7/dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpgfe8mdmw/files/8/3/d/dataset_83ddd986-5a07-406e-91f8-fcc403a6e927.dat'",
127 "command_version": "",
128 "copied_from_job_id": null,
129 "create_time": "2025-06-02T10:26:14.771419",
130 "dependencies": [
131 {
132 "cacheable": false,
133 "dependency_resolver": {
134 "auto_init": true,
135 "auto_install": true,
136 "can_uninstall_dependencies": true,
137 "ensure_channels": "conda-forge,bioconda",
138 "model_class": "CondaDependencyResolver",
139 "prefix": "/home/rkhaled/miniconda3",
140 "read_only": false,
141 "resolver_type": "conda",
142 "resolves_simple_dependencies": true,
143 "use_local": false,
144 "versionless": false
145 },
146 "dependency_type": "conda",
147 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
148 "exact": true,
149 "model_class": "MergedCondaDependency",
150 "name": "pandas",
151 "version": "2.2.3"
152 },
153 {
154 "cacheable": false,
155 "dependency_resolver": {
156 "auto_init": true,
157 "auto_install": true,
158 "can_uninstall_dependencies": true,
159 "ensure_channels": "conda-forge,bioconda",
160 "model_class": "CondaDependencyResolver",
161 "prefix": "/home/rkhaled/miniconda3",
162 "read_only": false,
163 "resolver_type": "conda",
164 "resolves_simple_dependencies": true,
165 "use_local": false,
166 "versionless": false
167 },
168 "dependency_type": "conda",
169 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
170 "exact": true,
171 "model_class": "MergedCondaDependency",
172 "name": "sqlalchemy",
173 "version": "2.0.40"
174 },
175 {
176 "cacheable": false,
177 "dependency_resolver": {
178 "auto_init": true,
179 "auto_install": true,
180 "can_uninstall_dependencies": true,
181 "ensure_channels": "conda-forge,bioconda",
182 "model_class": "CondaDependencyResolver",
183 "prefix": "/home/rkhaled/miniconda3",
184 "read_only": false,
185 "resolver_type": "conda",
186 "resolves_simple_dependencies": true,
187 "use_local": false,
188 "versionless": false
189 },
190 "dependency_type": "conda",
191 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
192 "exact": true,
193 "model_class": "MergedCondaDependency",
194 "name": "psycopg2",
195 "version": "2.9.9"
196 }
197 ],
198 "exit_code": 0,
199 "external_id": "149308",
200 "galaxy_version": "24.2",
201 "handler": null,
202 "history_id": "dc78a71e9d46a610",
203 "id": "c6ad8bbeb64086ff",
204 "inputs": {
205 "adv|json_conf": {
206 "id": "ba5e0bd88cc3030c",
207 "src": "hda",
208 "uuid": "83ddd986-5a07-406e-91f8-fcc403a6e927"
209 },
210 "genbank_files1": {
211 "id": "4da6c37b755c621f",
212 "src": "hda",
213 "uuid": "362bcc57-3b7e-4089-b9c7-33155498d352"
214 },
215 "genbank_files2": {
216 "id": "83933cf19817c19f",
217 "src": "hda",
218 "uuid": "4e03baea-fd7c-45b3-b808-4443adc60f91"
219 },
220 "genbank_files3": {
221 "id": "33ff3c6dc742881e",
222 "src": "hda",
223 "uuid": "6da90158-c02d-457e-8908-56b532b4b3c2"
224 },
225 "genbank_files4": {
226 "id": "8187d0d2b67e72bf",
227 "src": "hda",
228 "uuid": "80b64d26-b0b2-40df-ad9b-41446c172705"
229 },
230 "genbank_files5": {
231 "id": "a744ea399046e427",
232 "src": "hda",
233 "uuid": "38751000-4953-44bb-b142-81b4bc41ad97"
234 }
235 },
236 "job_messages": [],
237 "job_metrics": [],
238 "job_runner_name": null,
239 "job_stderr": "",
240 "job_stdout": "",
241 "model_class": "Job",
242 "output_collections": {},
243 "outputs": {
244 "output": {
245 "id": "c6ad8bbeb64086ff",
246 "src": "hda",
247 "uuid": "ee43072f-661d-47e0-b30f-d905aac37a4a"
248 }
249 },
250 "params": {
251 "__input_ext": "\"input\"",
252 "adv": "{\"json_conf\": {\"values\": [{\"id\": 13, \"src\": \"hda\"}]}}",
253 "annotation_column": null,
254 "chromInfo": "\"/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
255 "db_uri": null,
256 "dbkey": "\"?\"",
257 "fragment_column": null,
258 "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}",
259 "sequence_column": null,
260 "table": null
261 },
262 "state": "ok",
263 "stderr": "",
264 "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat(p6_Kozak-ATG)\nProcessing file: dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat'.\n",
265 "tool_id": "save_to_db",
266 "tool_stderr": "",
267 "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat(p6_Kozak-ATG)\nProcessing file: dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat'.\n",
268 "update_time": "2025-06-02T10:26:21.180586",
269 "user_email": "planemo@galaxyproject.org",
270 "user_id": "c804608f95de6282"
271 },
272 "status": "success",
273 "test_index": 1,
274 "time_seconds": 26.70093870162964,
275 "tool_id": "save_to_db",
276 "tool_version": "0.2.0+galaxy2"
277 },
278 "has_data": true,
279 "id": "save_to_db-1"
109 } 280 }
110 ], 281 ],
111 "version": "0.1" 282 "version": "0.1"
112 } 283 }