Updating anvil-edge README for edge-24-09-03-06-11-1

anvilproject · Sep 3, 2024 · 880372a · 880372a
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diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json
@@ -7,11 +7,11 @@
         "date2": "Mon Aug 26 18:31:46 2024"
     },
     "2": {
-        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-27-06-11-1/results.html",
-        "date1": "Tue Aug 27 06:26:39 2024",
-        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-27-06-11-1/tools.yml",
-        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-20-06-10-1/results.html",
-        "date2": "Tue Aug 20 06:25:04 2024"
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.html",
+        "date1": "Tue Sep 03 06:25:36 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/tools.yml",
+        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-27-06-11-1/results.html",
+        "date2": "Tue Aug 27 06:26:39 2024"
     },
     "3": {
         "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-27-18-16-1/results.html",

diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/chunk.json
@@ -0,0 +1,7 @@
+{
+    "2": {
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.html",
+        "date1": "Tue Sep 03 06:25:36 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/tools.yml"
+    }
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/chunk.txt
@@ -0,0 +1,20 @@
+-t miniasm --tool-version 8dee0218ac7d
+-t deeptools_bigwig_compare --tool-version 26e7304d6737
+-t fastq_groomer --tool-version 47e5dbc3e790
+-t sra_tools --tool-version 83c7d564b128
+-t mummer_mummerplot --tool-version ebe3b0f84de9
+-t poretools_qualpos --tool-version 4fe6b96aff72
+-t kallisto_pseudo --tool-version 5ae5c312d718
+-t sam_pileup --tool-version a3b4ad6858ff
+-t samtools_calmd --tool-version 06dc50b7b711
+-t music_manipulate_eset --tool-version 22232092be53
+-t droplet_barcode_plot --tool-version 8f605643ccfd
+-t scater_plot_exprs_freq --tool-version 058b40656107
+-t scanpy_parameter_iterator --tool-version 0387a2179f88
+-t query_tabular --tool-version cf34c344508d
+-t column_remove_by_header --tool-version 372967836e98
+-t snpsift --tool-version 2e497a770bca
+-t bcftools_plugin_mendelian --tool-version bf235558f2cf
+-t bcftools_csq --tool-version fdd127bd4a32
+-t vcfcommonsamples --tool-version f1852ecef841
+-t vcfdistance --tool-version c506b8275b1a
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/101b56dd69096d11.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/101b56dd69096d11.json
@@ -0,0 +1,101 @@
+{
+    "model_class": "Job",
+    "id": "101b56dd69096d11",
+    "history_id": "c5fe43971bba42f1",
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3",
+    "state": "error",
+    "exit_code": 127,
+    "create_time": "2024-09-03T06:52:31.325977",
+    "update_time": "2024-09-03T06:52:46.150783",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-kc4wx",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "ln -s '/galaxy/server/database/objects/0/6/5/dataset_06523432-b9d1-4891-b7d3-e4f400182d1f.dat' input1.bam && ln -s '/galaxy/server/database/objects/_metadata_files/8/5/3/metadata_853b3ca5-b2b1-4b83-8363-91890d787490.dat' 'input1.bam.bai' && ln -s '/galaxy/server/database/objects/3/b/b/dataset_3bb2da50-e1ca-44ce-a322-d63f5df29347.dat' reference.fasta && samtools faidx reference.fasta && samtools pileup -M 60 -f reference.fasta input1.bam > '/galaxy/server/database/objects/6/e/a/dataset_6eae9bca-de3a-49f3-a1fe-3848034e3fd9.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": "",
+    "params": {
+        "__input_ext": "\"input\"",
+        "dbkey": "\"equCab2\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/equCab2.len\"",
+        "c": "{\"__current_case__\": 0, \"consensus\": \"no\"}",
+        "mapCap": "\"60\"",
+        "indels": "\"no\"",
+        "lastCol": "\"no\"",
+        "refOrHistory": "{\"__current_case__\": 1, \"input1\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}, \"ownFile\": {\"values\": [{\"id\": 128, \"src\": \"hda\"}]}, \"reference\": \"history\"}"
+    },
+    "inputs": {
+        "refOrHistory|input1": {
+            "id": "519c268d6e571334",
+            "src": "hda",
+            "uuid": "06523432-b9d1-4891-b7d3-e4f400182d1f"
+        },
+        "refOrHistory|ownFile": {
+            "id": "f9ab1f8db539c4c2",
+            "src": "hda",
+            "uuid": "3bb2da50-e1ca-44ce-a322-d63f5df29347"
+        }
+    },
+    "outputs": {
+        "output1": {
+            "id": "156ba8706e2576b1",
+            "src": "hda",
+            "uuid": "6eae9bca-de3a-49f3-a1fe-3848034e3fd9"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n",
+    "job_stdout": "",
+    "job_stderr": "",
+    "stdout": "",
+    "stderr": "samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n",
+    "job_messages": [
+        {
+            "code_desc": "",
+            "desc": "Fatal error: Exit code 127 ()",
+            "error_level": 3,
+            "exit_code": 127,
+            "type": "exit_code"
+        }
+    ],
+    "dependencies": [],
+    "job_metrics": [
+        {
+            "title": "Job Runtime (Wall Clock)",
+            "value": "0 seconds",
+            "plugin": "core",
+            "name": "runtime_seconds",
+            "raw_value": "0E-7"
+        },
+        {
+            "title": "Job End Time",
+            "value": "2024-09-03 06:52:35",
+            "plugin": "core",
+            "name": "end_epoch",
+            "raw_value": "1725346355.0000000"
+        },
+        {
+            "title": "Job Start Time",
+            "value": "2024-09-03 06:52:35",
+            "plugin": "core",
+            "name": "start_epoch",
+            "raw_value": "1725346355.0000000"
+        },
+        {
+            "title": "Memory Allocated (MB)",
+            "value": "4080",
+            "plugin": "core",
+            "name": "galaxy_memory_mb",
+            "raw_value": "4080.0000000"
+        },
+        {
+            "title": "Cores Allocated",
+            "value": "1",
+            "plugin": "core",
+            "name": "galaxy_slots",
+            "raw_value": "1.0000000"
+        }
+    ]
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/60dc8ed2ca8581ac.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/60dc8ed2ca8581ac.json
@@ -0,0 +1,60 @@
+{
+    "model_class": "Job",
+    "id": "60dc8ed2ca8581ac",
+    "history_id": "c5fe43971bba42f1",
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-09-03T06:58:10.264162",
+    "update_time": "2024-09-03T06:58:14.627333",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-44j2j",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "cat '/galaxy/server/database/jobs_directory/000/130/configs/tmp7_jrxnls' && cp '/galaxy/server/database/objects/e/1/0/dataset_e106e609-955c-4b07-8741-017cc91a020e.dat' 'workdb.sqlite' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/130/configs/tmpy5o6f8gl' -Q '/galaxy/server/database/jobs_directory/000/130/configs/tmp7_jrxnls'   --comment_char='#'   -o '/galaxy/server/database/objects/8/c/8/dataset_8c882cff-dcfc-4326-b285-ddc57cecc7db.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "__input_ext": "\"sqlite\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "addqueries": "{\"queries\": []}",
+        "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}",
+        "sqlquery": "\"SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\"",
+        "save_db": "false",
+        "modify_database": "{\"sql_stmts\": []}",
+        "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"^\\\\d+\"}}, {\"__index__\": 1, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}, {\"__index__\": 2, \"filter\": {\"__current_case__\": 3, \"filter_type\": \"append_line_num\"}}, {\"__index__\": 3, \"filter\": {\"__current_case__\": 9, \"columns\": \"7,2,3,4,1\", \"filter_type\": \"select_columns\"}}, {\"__index__\": 4, \"filter\": {\"__current_case__\": 11, \"add\": null, \"column\": \"c4\", \"filter_type\": \"replace\", \"regex_pattern\": \"(\\\\d+)/(\\\\d+)/(\\\\d+)\", \"regex_replace\": \"19\\\\3-\\\\2-\\\\1\"}}]}, \"table\": {\"values\": [{\"id\": 153, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"id,first,last,dob,pets\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"people\"}}]",
+        "add_to_database": "{\"withdb\": {\"values\": [{\"id\": 152, \"src\": \"hda\"}]}}",
+        "workdb": "\"workdb.sqlite\""
+    },
+    "inputs": {
+        "add_to_database|withdb": {
+            "id": "5cfa2c742a69011a",
+            "src": "hda",
+            "uuid": "e106e609-955c-4b07-8741-017cc91a020e"
+        },
+        "tables_0|table": {
+            "id": "b17c5c82cd3ecfce",
+            "src": "hda",
+            "uuid": "b746cd5b-f442-4c12-9a2d-08f780790990"
+        }
+    },
+    "outputs": {
+        "output": {
+            "id": "ac7f57a7a56a19b0",
+            "src": "hda",
+            "uuid": "8c882cff-dcfc-4326-b285-ddc57cecc7db"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "\nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n        ",
+    "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n          \nrowcount: None\n",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "\nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n        ",
+    "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n          \nrowcount: None\n",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/95e5dec2fbf26496.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/95e5dec2fbf26496.json
@@ -0,0 +1,49 @@
+{
+    "model_class": "Job",
+    "id": "95e5dec2fbf26496",
+    "history_id": "c5fe43971bba42f1",
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-09-03T06:46:14.137222",
+    "update_time": "2024-09-03T06:46:19.068042",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-7l5xz",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/4/6/2/dataset_46264658-3f70-4f21-8bc4-767b9965501a.dat' sanger.gz '/galaxy/server/database/objects/0/2/c/dataset_02ce87b3-3454-4ad3-83df-7d3fd4f7d3f5.dat' sanger ascii summarize_input",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "__input_ext": "\"fastq.gz\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}",
+        "input_type": "\"sanger\""
+    },
+    "inputs": {
+        "input_file": {
+            "id": "6f9ddc11486f4483",
+            "src": "hda",
+            "uuid": "46264658-3f70-4f21-8bc4-767b9965501a"
+        }
+    },
+    "outputs": {
+        "output_file": {
+            "id": "95e5dec2fbf26496",
+            "src": "hda",
+            "uuid": "02ce87b3-3454-4ad3-83df-7d3fd4f7d3f5"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "Groomed 2 sanger.gz reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "Groomed 2 sanger.gz reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/98623284f686bc7c.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/98623284f686bc7c.json
@@ -0,0 +1,60 @@
+{
+    "model_class": "Job",
+    "id": "98623284f686bc7c",
+    "history_id": "c5fe43971bba42f1",
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2024-09-03T06:59:45.209611",
+    "update_time": "2024-09-03T06:59:49.873153",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-mpbcg",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "cat '/galaxy/server/database/jobs_directory/000/137/configs/tmpljwbu6nc' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/137/configs/tmpmsqj69lx' -Q '/galaxy/server/database/jobs_directory/000/137/configs/tmpljwbu6nc'   --comment_char='#'   -o '/galaxy/server/database/objects/6/0/d/dataset_60da0121-d131-4f09-8906-54a9df5c81a7.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "__input_ext": "\"tabular\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "addqueries": "{\"queries\": [{\"__index__\": 0, \"query_result\": {\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}, \"sqlquery\": \"SELECT * FROM psms WHERE confidence > 97.0\"}]}",
+        "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}",
+        "sqlquery": "\"SELECT scan,\\\"m/z\\\", \\\"Precursor m/z Error [ppm]\\\", Sequence, \\\"Protein(s)\\\", confidence FROM PSMs WHERE NOT re_search(', ',\\\"Protein(s)\\\")\"",
+        "save_db": "false",
+        "modify_database": "{\"sql_stmts\": [{\"__index__\": 0, \"sqlstmt\": \"UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0\"}]}",
+        "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19,23\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 160, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"scan,,,,,,confidence\", \"column_names_from_first_line\": true, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]",
+        "add_to_database": "{\"withdb\": null}",
+        "workdb": "\"workdb.sqlite\""
+    },
+    "inputs": {
+        "tables_0|table": {
+            "id": "f88cf8ee998749f2",
+            "src": "hda",
+            "uuid": "06d6bda3-00a4-44af-bf95-4105b34dca77"
+        }
+    },
+    "outputs": {
+        "output": {
+            "id": "4306367a50dd42eb",
+            "src": "hda",
+            "uuid": "60da0121-d131-4f09-8906-54a9df5c81a7"
+        },
+        "output1": {
+            "id": "287c916884dcddd5",
+            "src": "hda",
+            "uuid": "af560828-98a1-4e90-a79c-bb812ced1a2b"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "\nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n        ",
+    "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0  \nrowcount: <sqlite3.Cursor object at 0x7c7aacb5f3b0>\n\nSQL: SELECT * FROM psms WHERE confidence > 97.0  \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n          \nrowcount: None\n",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "\nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n        ",
+    "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0  \nrowcount: <sqlite3.Cursor object at 0x7c7aacb5f3b0>\n\nSQL: SELECT * FROM psms WHERE confidence > 97.0  \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n          \nrowcount: None\n",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}