Esempio n. 1
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 def test_constructor(self):
     params = D3RParameters()
     task = MakeBlastDBTask('/foo', params)
     self.assertEqual(task.get_name(), 'makeblastdb')
     self.assertEqual(task.get_stage(), 1)
     self.assertEqual(task.get_status(), D3RTask.UNKNOWN_STATUS)
     self.assertEqual(task.get_path(), '/foo')
     self.assertEqual(task.get_dir_name(), 'stage.1.makeblastdb')
     test_task.try_update_status_from_filesystem(self, task)
Esempio n. 2
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    def test_run_with_blast_success_useoldseq_and_postanalysis_fail(self):
        temp_dir = tempfile.mkdtemp()

        try:
            params = D3RParameters()
            params.blastnfilter = '/bin/echo'
            params.postanalysis = os.path.join(temp_dir, 'foo.py')
            params.pdbdb = '/pdbdb'
            blasttask = BlastNFilterTask(temp_dir, params)
            blasttask._can_run = True

            txt_file = os.path.join(blasttask.get_dir(), 'summary.txt')

            txt_contents = ('INPUT SUMMARY\\n' + '  sequences:  177\\n' +
                            '  complexes:  149\\n')
            # create fake blastnfilter script that makes csv files
            f = open(params.postanalysis, 'w')
            f.write('#! /usr/bin/env python\n\n')
            f.write('f = open(\'' + txt_file + '\', \'w\')\n')
            f.write('f.write(\'' + txt_contents + '\\n\')\n')
            f.write('f.flush()\nf.close()\n')
            f.flush()
            f.close()
            os.chmod(params.postanalysis, stat.S_IRWXU)

            blasttask.run()
            self.assertEqual(blasttask.get_status(), D3RTask.COMPLETE_STATUS)
            self.assertEqual(blasttask.get_error(), None)
            complete_file = os.path.join(blasttask.get_dir(),
                                         D3RTask.COMPLETE_FILE)

            self.assertEqual(os.path.isfile(complete_file), True)

            std_err_file = os.path.join(blasttask.get_dir(), 'echo.stderr')

            self.assertEqual(os.path.isfile(std_err_file), True)

            std_out_file = os.path.join(blasttask.get_dir(), 'echo.stdout')

            dataimport = DataImportTask(temp_dir, params)
            makeblast = MakeBlastDBTask(temp_dir, params)

            f = open(std_out_file, 'r')
            echo_out = f.read().replace('\n', '')
            echo_out.index('--nonpolymertsv ' +
                           os.path.join(temp_dir, dataimport.get_dir_name(),
                                        DataImportTask.NONPOLYMER_TSV))
            echo_out.index(' --sequencetsv ' +
                           os.path.join(temp_dir, dataimport.get_dir_name(),
                                        DataImportTask.OLDSEQUENCE_TSV))
            echo_out.index(' --pdbblastdb ' +
                           os.path.join(temp_dir, makeblast.get_dir_name()))
            echo_out.index(' --compinchi ' +
                           os.path.join(temp_dir, dataimport.get_dir_name(),
                                        DataImportTask.COMPINCHI_ICH))
            echo_out.index(' --outdir ' +
                           os.path.join(temp_dir, blasttask.get_dir_name()))
            echo_out.index(' --crystalpH ' +
                           os.path.join(temp_dir, dataimport.get_dir_name(),
                                        DataImportTask.CRYSTALPH_TSV))
            echo_out.index(' --pdbdb /pdbdb ')
            f.close()

            self.assertEqual(os.path.isfile(std_out_file), True)
            self.assertEquals(blasttask.get_status(), D3RTask.COMPLETE_STATUS)
            self.assertEquals(
                os.path.exists(
                    os.path.join(blasttask.get_dir(), 'foo.py.stderr')), True)
            self.assertEquals(
                os.path.exists(
                    os.path.join(blasttask.get_dir(), 'foo.py.stdout')), True)
            res = blasttask.get_email_log().rstrip('\n')
            res.index('/bin/echo')
            res.index('# txt files found: 0')
            res.index('Output from summary.txt')
            res.index('  sequences:  177')
            res.index('  complexes:  149')
            res.index(dataimport.get_sequence_tsv() +
                      ' file not found falling back to ' +
                      dataimport.get_oldsequence_tsv())
        finally:
            shutil.rmtree(temp_dir)
Esempio n. 3
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    def test_can_run(self):
        tempDir = tempfile.mkdtemp()

        try:
            # try where makeblastdb is not complete
            params = D3RParameters()
            blastTask = BlastNFilterTask(tempDir, params)
            self.assertEqual(blastTask.can_run(), False)

            # try where makeblastdb failed
            blastDb = MakeBlastDBTask(tempDir, params)
            blastDb.create_dir()
            errorFile = os.path.join(blastDb.get_path(),
                                     blastDb.get_dir_name(),
                                     D3RTask.ERROR_FILE)
            open(errorFile, 'a').close()
            self.assertEqual(blastTask.can_run(), False)
            self.assertEqual(blastTask.get_error(),
                             'makeblastdb task has error status')

            # try where data import is not complete
            completeFile = os.path.join(blastDb.get_path(),
                                        blastDb.get_dir_name(),
                                        D3RTask.COMPLETE_FILE)
            open(completeFile, 'a').close()
            self.assertEqual(blastTask.can_run(), False)
            self.assertEqual(blastTask.get_error(),
                             'dataimport task has ' + 'notfound status')

            # try where data import failed
            dataImport = DataImportTask(tempDir, params)
            dataImport.create_dir()
            errorFile = os.path.join(dataImport.get_path(),
                                     dataImport.get_dir_name(),
                                     D3RTask.ERROR_FILE)
            open(errorFile, 'a').close()
            self.assertEqual(blastTask.can_run(), False)
            self.assertEqual(blastTask.get_error(),
                             'dataimport task has error status')

            # try where blast can run
            os.remove(errorFile)
            completeFile = os.path.join(dataImport.get_dir(),
                                        D3RTask.COMPLETE_FILE)
            open(completeFile, 'a').close()
            self.assertEqual(blastTask.can_run(), True)
            self.assertEqual(blastTask.get_error(), None)

            # try where blast exists
            blastTask.create_dir()
            self.assertEqual(blastTask.can_run(), False)
            self.assertEqual(
                blastTask.get_error(),
                blastTask.get_dir_name() + ' already exists and' +
                ' status is unknown')

            # try where blast is complete
            completeFile = os.path.join(blastTask.get_path(),
                                        blastTask.get_dir_name(),
                                        D3RTask.COMPLETE_FILE)
            open(completeFile, 'a').close()
            self.assertEqual(blastTask.can_run(), False)
            self.assertEqual(blastTask.get_error(), None)

        finally:
            shutil.rmtree(tempDir)
Esempio n. 4
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def main():
    blasttask = BlastNFilterTask('', p)
    dataimport = DataImportTask('', p)
    challenge = ChallengeDataTask('', p)
    glide = GlideTask('', p)
    makedb = MakeBlastDBTask('', p)
    prot = ProteinLigPrepTask('', p)
    vina = AutoDockVinaTask('', p)
    chimeraprep = ChimeraProteinLigPrepTask('', p)
    desc = """
              Version {version}

              Runs the 9 stages (makedb, import, blast, challengedata,
              proteinligprep, {chimeraprep}, extsubmission, glide, vina, &
              evaluation) of CELPP processing pipeline
              (http://www.drugdesigndata.org)

              CELPP processing pipeline relies on a set of directories
              with specific structure. The pipeline runs a set of stages
              Each stage has a numerical value and a name. The numerical
              value denotes order and the stage name identifies separate
              tasks to run in the stage.

              The filesystem structure of the stage is:

              stage.<stage number>.<task name>

              The stage(s) run are defined via the required --stage flag.

              To run multiple stages serially just pass a comma delimited
              list to the --stage flag. Example: --stage import,blast

              NOTE:  When running multiple stages serially the program will
                     not run subsequent stages if a task in a stage fails.
                     Also note order matters, ie putting blast,import will
                     cause celpprunner.py to run blast stage first.

              This program drops a pid lockfile
              (celpprunner.<stage>.lockpid) in celppdir to prevent duplicate
              invocation.

              When run, this program will examine the stage and see
              if work can be done.  If stage is complete or previous
              steps have not completed, the program will exit silently.
              If previous steps have failed or current stage already
              exists in an error or uncomplete state then program will
              report the error via email using addresses set in --email
              flag. Errors will also be reported via stderr/stdout.
              The program will also exit with nonzero exit code.

              This program utilizes simple token files to denote stage
              completion.  If within the stage directory there is a:

              '{complete}' file - then stage is done and no other
                                checking is done.

              'error' file - then stage failed.

              'start' file - then stage is running.

              Notification of stage start and end will be sent to
              addresses set via --email flag.

              Unless --customweekdir is set, this program will
              examine the 'celppdir' (last argument passed on
              commandline) to find the latest directory with this path:

              <year>/dataset.week.#

              The program will find the latest <year> and within
              that year the dataset.week.# with highest #.  The output
              directories created will be put within this directory.

              Setting --customweekdir will cause program to use 'celppdir'
              path.

              Setting the --createweekdir flag will instruct this
              program to create a new directory for the current
              celpp week/year before running any stage processing.

              NOTE: CELPP weeks start on Friday and end on Thursday
                    and week # follows ISO8601 rules so week numbers
                    at the end and start of the year are a bit
                    wonky.

              Breakdown of behavior of program is defined by
              value passed with --stage flag:

              If --stage '{createchallenge}'

              This is NOT a stage, but has the same effect as
              calling --stage makedb,import,blast,challengedata
              The four stages that need to run to generate the challenge
              data package.

              If --stage 'makedb'

              In this stage the file {pdb_seqres} is downloaded from
              an ftp site set by --pdbsequrl.
              This file is then gunzipped and NCBI makeblastdb
              (set by --makeblastdb) is run on it to create a blast
              database.  The files are stored in {makeblastdb_dirname}

              If --stage 'import'

              In this stage 4 files are downloaded from urls specified
              by --compinchi and --pdbfileurl flags on the commandline
              into {dataimport_dirname} directory.

              The tsv files are (--pdbfileurl flag sets url to
              download these files from):

              {nonpolymer_tsv}
              {sequence_tsv}
              {crystal_tsv}

              The Components ich file is (--compinchi flag sets base url to
              download this file from):

              {compinchi_ich}

              This stage will just wait and retry if any of the tsv files
              have NOT been updated since the start of the current
              celpp week as determined by a HEAD request. To bypass
              this delay add --skipimportwait flag.  --importsleep denotes
              the time to wait before re-examining the update time of the
              tsv files and --importretry sets number of times to retry
              before giving up.

              If --stage 'blast'

              Verifies {dataimport_dirname} exists and has '{complete}'
              file.  Also verifies {makeblastdb_dirname} exists and has
              '{complete}' file.  If both conditions are met then the
              'blast' stage is run which invokes script set by
              --blastnfilter flag and output stored in
              {blast_dirname}.
              Requires --pdbdb to be set to a directory with valid PDB
              database files.

              Note: --blastnfilter script is killed after time set with
              --blastnfiltertimeout flag.


              If --stage 'challengedata'

              Verifies {blast_dirname} exists and has '{complete}'
              file.  If complete, this stage runs which invokes program
              set in --genchallenge flag to create a challenge dataset
              file.  The --pdbdb flag must also be set when calling this
              stage. If --ftpconfig is set with {challengepath} field then
              this stage will also upload the challenge dataset tarfile
              to the ftp server with path set by {challengepath}.  The
              code will also upload a {latest_txt} file containing name
              of the tarfile to the same destination overwriting any
              {latest_txt} file that already exists.

              Example file for --ftpconfig:

              {host} some.ftp.com
              {user} bob
              {passn} mypass
              {path} /celpp
              {challengepath} /challenge
              {submissionpath} /submissions


              If --stage '{chimeraprep}'

              Verifies {challenge_dirname} exists and has '{complete}'
              file.  If complete, this stage runs which invokes program
              set in --chimeraprep flag to prepare pdb and inchi files
              storing output in {chimeraprep_dirname}.  --pdbdb flag
              must also be set when calling this stage.

              If --stage 'proteinligprep'

              Verifies {challenge_dirname} exists and has '{complete}'
              file.  If complete, this stage runs which invokes program
              set in --proteinligprep flag to prepare pdb and inchi files
              storing output in {proteinligprep_dirname}.  --pdbdb flag
              must also be set when calling this stage.

              If --stage 'extsubmission'

              Connects to server specified by --ftpconfig and downloads
              external docking submissions from {submissionpath} on remote
              server.

              Submissions should be named:

              celpp_weekXX_YYYY_dockedresults_ZZZZ.tar.gz as documented here:

              https://github.com/drugdata/d3r/wiki/Proposed-challenge-docked\
              -results-file-structure

              For each submission a directory named stage.X.ZZZZ.extsubmission
              will be created and uncompressed contents of package will be
              stored in that directory.  If data does not conform properly
              'error' file will be placed in directory denoting failure

              If --stage 'glide'

              Verifies {proteinligprep_dirname} exists and has a '{complete}'
              file within it.  If complete, this stage runs which invokes
              program set in --glide flag to perform docking via glide
              storing output in {glide_dirname}

              If --stage 'vina'

              Verifies {proteinligprep_dirname} exists and has a '{complete}'
              file within it.  If complete, this stage runs which invokes
              program set in --vina flag to perform docking via AutoDock Vina
              storing output in {vina_dirname}

              If --stage 'evaluation'

              Finds all stage.{dockstage}.<algo> directories with '{complete}'
              files in them which do not end in name '{webdata}' and runs
              script set via --evaluation parameter storing the result of
              the script into stage.{evalstage}.<algo>.evaluation. --pdbdb flag
              must also be set when calling this stage.


              """.format(makeblastdb_dirname=makedb.get_dir_name(),
                         dataimport_dirname=dataimport.get_dir_name(),
                         blast_dirname=blasttask.get_dir_name(),
                         challenge_dirname=challenge.get_dir_name(),
                         createchallenge=CREATE_CHALLENGE,
                         proteinligprep_dirname=prot.get_dir_name(),
                         glide_dirname=glide.get_dir_name(),
                         vina_dirname=vina.get_dir_name(),
                         dockstage=str(glide.get_stage()),
                         evalstage=str(glide.get_stage() + 1),
                         complete=blasttask.COMPLETE_FILE,
                         chimeraprep_dirname=chimeraprep.get_dir_name(),
                         chimeraprep=CHIMERA_PREP,
                         compinchi_ich=DataImportTask.COMPINCHI_ICH,
                         pdb_seqres=MakeBlastDBTask.PDB_SEQRES_TXT_GZ,
                         nonpolymer_tsv=DataImportTask.NONPOLYMER_TSV,
                         sequence_tsv=DataImportTask.SEQUENCE_TSV,
                         crystal_tsv=DataImportTask.CRYSTALPH_TSV,
                         webdata=EvaluationTaskFactory.WEB_DATA_SUFFIX,
                         latest_txt=ChallengeDataTask.LATEST_TXT,
                         host=FtpFileTransfer.HOST,
                         user=FtpFileTransfer.USER,
                         passn=FtpFileTransfer.PASS,
                         path=FtpFileTransfer.PATH,
                         challengepath=FtpFileTransfer.CHALLENGEPATH,
                         submissionpath=FtpFileTransfer.SUBMISSIONPATH,
                         version=d3r.__version__)

    theargs = _parse_arguments(desc, sys.argv[1:])
    theargs.program = sys.argv[0]
    theargs.version = d3r.__version__

    util.setup_logging(theargs)

    try:
        run_stages(theargs)
    except Exception:
        logger.exception("Error caught exception")
        sys.exit(2)
Esempio n. 5
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 def test_get_pdbseqres_txt(self):
     params = D3RParameters()
     task = MakeBlastDBTask('/foo', params)
     self.assertEqual(
         task.get_pdb_seqres_txt(),
         os.path.join('/foo', task.get_dir_name(), 'pdb_seqres.txt'))