| Previous changeset 11:0d0f7080b55c (2018-01-31) Next changeset 13:b5f070767ed4 (2018-02-01) |
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Commit message:
Uploaded 20180201 |
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modified:
query.py query.xml |
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added:
._.shed.yml ._example.tsv ._query.py ._query.xml |
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| diff -r 0d0f7080b55c -r 039e8e1e8b1f ._.shed.yml |
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| diff -r 0d0f7080b55c -r 039e8e1e8b1f ._example.tsv |
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| diff -r 0d0f7080b55c -r 039e8e1e8b1f ._query.py |
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| diff -r 0d0f7080b55c -r 039e8e1e8b1f ._query.xml |
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| diff -r 0d0f7080b55c -r 039e8e1e8b1f query.py --- a/query.py Wed Jan 31 17:29:13 2018 -0500 +++ b/query.py Thu Feb 01 16:23:17 2018 -0500 |
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| b'@@ -3,7 +3,7 @@\n # https://github.com/ross/requests-futures\n # http://docs.python-requests.org/en/master/user/quickstart/#more-complicated-post-requests\n \n-import os, uuid, optparse, requests, json, time\n+import sys, os, uuid, optparse, requests, json, time\n #from requests_futures.sessions import FuturesSession\n \n #### NN14 ####\n@@ -16,9 +16,17 @@\n QUERY_DELAY = 30;\n ##############\n \n+__version__ = "1.0.0";\n VALID_CHARS = \'.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ \'\n \n+# in the case of collections, exitcodes equal to 0 and 1 are not considered errors\n+def raiseException( exitcode, message, errorfilepath ):\n+ with open(errorfilepath, \'w\') as out:\n+ out.write(message);\n+ sys.exit(exitcode);\n+\n def query_request( options, args, payload ):\n+ output_dir_path = options.outputdir;\n # add additional parameters to the payload\n #payload["tree_id"] = str(options.treeid);\n payload["search_mode"] = str(options.search);\n@@ -32,7 +40,7 @@\n # make a synchronous post request to the query route\n req = session.post(QUERY_URL, headers=headers, json=payload);\n resp_code = req.status_code;\n- print(str(req.content)+"\\n\\n");\n+ #print(str(req.content)+"\\n\\n");\n if resp_code == requests.codes.ok:\n resp_content = str(req.content);\n # convert out to json\n@@ -42,7 +50,6 @@\n task_processed = False;\n # results json content\n json_status_content = None;\n- task_status = None;\n while task_processed is False:\n # create a new session\n session = requests.Session();\n@@ -50,7 +57,7 @@\n status_query_url = STATUS_URL.replace("<task_id>", task_id);\n status_req = session.get(status_query_url);\n status_resp_content = str(status_req.content);\n- print(status_resp_content+"\\n\\n");\n+ #print(status_resp_content+"\\n\\n");\n # convert out to json\n json_status_content = json.loads(status_resp_content);\n # take a look at the state\n@@ -59,16 +66,11 @@\n task_processed = True;\n break;\n elif json_status_content[\'state\'] in [\'FAILURE\', \'REVOKED\']:\n- return "Task status: "+str(json_status_content[\'state\']);\n+ return raiseException( 1, "Task ID: "+str(task_id)+"\\nTask status: "+str(json_status_content[\'state\']), str(options.errorfile) );\n else:\n time.sleep(QUERY_DELAY); # in seconds\n \n- # get output dir (collection) path\n- output_dir_path = options.outputdir;\n- if not os.path.exists(output_dir_path):\n- os.makedirs(output_dir_path);\n out_file_format = "tabular";\n-\n for block in json_status_content[\'results\']:\n seq_id = block[\'sequence_id\'];\n accessions = block[\'accession_numbers\'];\n@@ -79,10 +81,12 @@\n accessions_list = accessions_list + accession_number + "\\n";\n with open(output_file_path, \'w\') as out:\n out.write(accessions_list.strip());\n+ return sys.exit(0);\n else:\n- return "Unable to query the remote server. Please try again in a while.";\n+ return raiseException( 1, "Unable to query the remote server. Please try again in a while.", str(options.errorfile) );\n \n def query( options, args ):\n+ output_dir_path = options.outputdir;\n multiple_data = {};\n comma_sep_file_paths = options.files;\n #print("files: "+str(comma_sep_file_paths)+" - "+str(type(comma_sep_file_paths)));\n@@ -106,13 +110,13 @@\n seq_id = \'\'.join(e for e in seq_id if e in VALID_CHARS)\n seq_text = line_split[1];\n if seq_id in multiple_data:\n- return "Error: the id \'"+seq_id+"\' is duplicated";\n+ return raiseException( 1, "Error: the id \'"+seq_id+"\' is duplicated", str(options.e'..b'est="outfile", help="output file");\n- \n # TEST\n- #--search \'rrr\'\n- #--sthreshold 0.5\n- #--exact 0\n- #--sequences \'id0__tc__CAATTAATGATAAATATTTTATAAGGTGCGGAAATAAAGTGAGGAATATCTTTTAAATTCAAGTTCAATTCTGAAAGC\'\n- #--outputdir \'collection_content\'\n #sequences = \'NM_001169378.2__tc__atttcggatgctttggagggaggaactctagtgctgcattgattggggcgtgtgttaatgatattcccagttcgcatggcgagcatcgattcctggtacgtatgtgggccccttgactcccacttatcgcacttgtcgttcgcaatttgcatgaattccgcttcgtctgaaacgcacttgcgccagacttctccggctggtctgatctggtctgtgatccggtctggtggggcgccagttgcgtttcgagctcatcaccagtcactccgcagtcgcattctgccagaggtctccgatcaagagcgcttctccattcgagattcaaacgcagcgcggtctgacgccgccacatcgagtgaaatccatatcgatggccacattcacacaggacgagatcgacttcctgcgcagccatggcaacgagctgtgtgccaagacctggctgggattgtgggatccgaagcgggctgtgcaccagcaggagcagcgcgaactgatgatggacaagtatgagcggaagcgatactacctggagccggccagtcctcttaagtcgctggccaatgcggtcaacctgaagtcgtctgctccggcgacgaaccacactcagaatggccaccaaaatgggtatgccagcatccatttgacgcctcctgctgcccagcggacctcggccaatggattgcagaaggtggccaactcgtcgagtaactcttctggaaagacctcatcctcgatcagtaggccacactataatcaccagaacaacagccaaaacaacaatcacgatgcctttggcctgggtggcggattgagcagcctgaacagcgccggttccacatccactggagctctttccgacaccagcagttgtgctagcaatggcttcggtgcggactgcgactttgtggctgactttggctcggccaacattttcgacgccacatcggcgcgttccacaggatcgccggcggtgtcgtccgtgtcctcagtgggttccagcaatggctacgccaaggtgcagcccatccgggcagctcatctccagcagcaacagcagttgcagcagcagctgcatcagcagcagctcctcaatggcaatggtcatcagggcactgagaactttgccgacttcgatcacgctcccatctacaatgcagtggctccaccgacttttaacgattggatcagcgactggagcaggcggggcttccacgatcccttcgacgattgcgatgactcgccaccaggtgcccgccctccagcacctgcgccagctcctgctcaagttcccgcagtatcatcaccattgccaaccgtccgagaagaaccagagcttgcgtggaatttttgggaggacgagatgcgaatagaggcgcaggaaaaggagtcccaaactaaacagccggagttgggctactccttttcgattagtactactacgcccctttccccttcgaatcccttcctgccctaccttgtcagtgaggagcagcatcgaaatcatccagagaagccctccttttcgtattcgttgttcagctccatatcaaatagttcgcaagaagatcaggcggatgatcatgagatgaatgttttaaatgccaatttccatgatttctttacgtggagtgctcccttgcagaacggccatacgaccagtccgcccaagggcggaaatgcagcgatggcgcccagtgaggatcgatatgccgctcttaaggatctcgacgagcagctgcgagaactgaaggccagcgaaagcgccacagagacgcccacgcccaccagtggcaatgttcaggccacagatgcctttggtggagccctcaacaacaatccaaatcccttcaagggccagcaacagcagcagctcagcagccatgtggtgaatccattccagcagcagcaacagcagcagcaccagcagaatctctatggccagttgacgctcataccaaatgcctacggcagcagttcccagcagcagatggggcaccatctcctccagcagcagcagcagcaacagcagagcttcttcaacttcaacaacaacgggttcgccatctcgcagggtctgcccaacggctgcggcttcggcagcatgcaacccgctcctgtgatggccaacaatccctttgcagccagcggcgccatgaacaccaacaatccattcttatgagactcaacccgggagaatccgcctcgcgccacctggcagaggcgctgagccagcgaacaaagagcagacgcggaggaaccgaaccgaaattagtccattttactaacaatagcgttaatctatgtatacataatgcacgccggagagcactctttgtgtacatagcccaaatatgtacacccgaaaggctccacgctgacgctagtcctcgcggatggcggaggcggactggggcgttgatatattcttttacatggtaactctactctaacgtttacggatacggatatttgtatttgccgtttgccctagaactctatacttgtactaagcgcccatgaacacttcatccactaacatagctactaatcctcatcctagtggaggatgcagttggtccagacactctgttatttgttttatccatcctcgtacttgtctttgtcccatttagcactttcgttgcggataagaactttgtcagttattgattgtgtggccttaataagattataaaactaaatattataacgtacgactatacatatacggatacagatacagattcagacacagttagtacagatacagatatacatatacgcttttgtacctaatgaattgcttcttgtttccattgctaatcatctgcttttcgtgtgctaattttatacactagtacgtgcgatatcggccgtgcagatagattgctcagctcgcgagtcaagcctcttttggttgcacccacggcagacatttgtacatatactgtctgattgtaagcctcgtgtaatacctccattaacaccactcccccaccacccatccatcgaaccccgaatccatgactcaattcactgctcacatgtccatgcccatgccttaacgtgtcaaacattatcgaagccttaaagttatttaaaactacgaaatttcaataaaaacaaataagaacgctatc\';\n- #print(sequences);\n #(options, args) = parser.parse_args([\'-x\', \'rrr\', \'-t\', 0.5, \'-s\', sequences, \'-o\', \'collection_content\']);\n- \n+\n (options, args) = parser.parse_args();\n- return query( options, args );\n+ if options.version:\n+ print __version__;\n+ else:\n+ # create output dir (collection)\n+ output_dir_path = options.outputdir;\n+ if not os.path.exists(output_dir_path):\n+ os.makedirs(output_dir_path);\n+\n+ return query( options, args );\n \n if __name__ == "__main__": __main__()\n' |
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| diff -r 0d0f7080b55c -r 039e8e1e8b1f query.xml --- a/query.xml Wed Jan 31 17:29:13 2018 -0500 +++ b/query.xml Thu Feb 01 16:23:17 2018 -0500 |
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| @@ -34,17 +34,17 @@ <option value="1">By manually inserted text</option> </param> <when value="0"> - <param format="tabular" name="txtfiles" type="data" label="Select files" multiple="true" optional="true" help="Select one or more tabular files containing (ID, TRANSCRIPT) touples for each line. The content of these files will be merged and the result will represent a query to the AllSome Sequence Bloom Tree Search Engine that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." /> + <param format="tabular" name="txtfiles" type="data" label="Select files" multiple="true" optional="false" help="Select one or more tabular files containing (ID, TRANSCRIPT) couples for each line. The content of these files will be merged and the result will represent a query to the AllSome Sequence Bloom Tree Search Engine that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." /> </when> <when value="1"> - <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequences" optional="true" help="Insert a list of (ID, TRANSCRIPT) touples in a tab delimited format, one for each line. The content of this text box will represent a query to the AllSome Sequence Bloom Tree Search Engine that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." /> + <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequences" optional="false" help="Insert a list of (ID, TRANSCRIPT) couples in a tab delimited format, one for each line. The content of this text box will represent a query to the AllSome Sequence Bloom Tree Search Engine that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." /> </when> </conditional> <param name="sthreshold" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." /> </inputs> <outputs> <collection name="output_collect" type="list" label="AllSome Sequence Bloom Tree Search Collection"> - <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<ext>[^_]+)" directory="collection_content" ext="tabular" /> + <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<ext>[^_]+)" directory="collection_content" ext="auto" /> </collection> </outputs> @@ -54,9 +54,7 @@ ---- -**Example** - -The input for this tool is a list of (ID, TRANSCRIPT) touples, one for each line, +The input for this tool is a list of (ID, TRANSCRIPT) couples, one for each line, in a tab delimited format:: id0 CCAACCAAAGGGAAAACTTTTTTCCGACTTTGGCCTAAAGGGTTTAACGGCCAAGTCAGAAGGGAAAAAGTTGCGCCA |