fix pipeline

Dockerfile

@@ -30,7 +30,7 @@ RUN tar -xzf "pyflow-${PYFLOW_VERSION}.tar.gz" \
 
 ENV SPACY_VERSION=2.2.4
 ENV SPACY_MODELS_VERSION=2.2.5
-RUN pip3 install "spacy==${SPACY_VERSION}" \
+RUN pip3 install setuptools wheel && pip3 install "spacy==${SPACY_VERSION}" \
  && python3 -m spacy download "de_core_news_sm-${SPACY_MODELS_VERSION}" --direct \
  && python3 -m spacy download "el_core_news_sm-${SPACY_MODELS_VERSION}" --direct \
  && python3 -m spacy download "en_core_web_sm-${SPACY_MODELS_VERSION}" --direct \

nlp

@@ -28,16 +28,21 @@ SPACY_MODELS = {'de': 'de_core_news_sm',
 
 def parse_args():
     parser = ArgumentParser(description='NLP Pipeline utilizing spaCy.')
-    parser.add_argument('i')
+    parser.add_argument('-i', '--input-directory',
-    parser.add_argument('o')
+                        help='Input directory (only txt files get processed)',
+                        required=True)
+    parser.add_argument('-o', '--output-directory',
+                        help='Output directory',
+                        required=True)
     parser.add_argument('-l', '--language', choices=SPACY_MODELS.keys(),
                         required=True)
+    parser.add_argument('--check-encoding', action='store_true')
+    parser.add_argument('--log-dir')
     parser.add_argument('--n-cores',
                         default=min(4, multiprocessing.cpu_count()),
                         help='total number of cores available', type=int)
-    parser.add_argument('--check-encoding', action='store_true')
+    parser.add_argument('--zip',
-    parser.add_argument('--log-dir')
+                        help='Zips everything into one archive.')
-    parser.add_argument('--zip')
     return parser.parse_args()
 
 
@@ -63,41 +68,47 @@ class NLPPipeline(WorkflowRunner):
 
         '''
         ' ##################################################
-        ' # mkdir_jobs                                     #
+        ' # setup output directory                         #
         ' ##################################################
         '''
-        mkdir_jobs = []
+        setup_output_directory_jobs = []
         for i, job in enumerate(self.jobs):
             cmd = 'mkdir'
             cmd += ' -p'
             cmd += ' "{}"'.format(job.output_dir)
-            lbl = 'mkdir_job_-_{}'.format(i)
+            lbl = 'setup_output_directory_-_{}'.format(i)
-            mkdir_jobs.append(self.addTask(command=cmd, label=lbl))
+            setup_output_directory_jobs.append(self.addTask(command=cmd,
+                                                            label=lbl))
 
         '''
         ' ##################################################
-        ' # spacy_nlp_jobs                                 #
+        ' # nlp                                 #
         ' ##################################################
         '''
-        spacy_nlp_jobs = []
+        nlp_jobs = []
         n_cores = min(self.n_cores, max(1, int(self.n_cores / len(self.jobs))))
         for i, job in enumerate(self.jobs):
             output_file = os.path.join(job.output_dir,
                                        '{}.vrt'.format(job.name))
-            cmd = 'spacy-nlp "{}" "{}"'.format(job.file, output_file)
+            cmd = 'spacy-nlp'
+            cmd += ' -i "{}"'.format(job.file)
             cmd += ' -l "{}"'.format(self.lang)
-            cmd += ' --check-encoding' if self.check_encoding else ''
+            cmd += ' -o "{}"'.format(output_file)
-            deps = 'mkdir_job_-_{}'.format(i)
+            if self.check_encoding:
-            lbl = 'spacy_nlp_job_-_{}'.format(i)
+                cmd += ' --check-encoding'
-            spacy_nlp_jobs.append(self.addTask(command=cmd, dependencies=deps,
+            deps = 'setup_output_directory_-_{}'.format(i)
-                                               label=lbl, nCores=n_cores))
+            lbl = 'nlp_-_{}'.format(i)
+            nlp_jobs.append(self.addTask(command=cmd,
+                                         dependencies=deps,
+                                         label=lbl,
+                                         nCores=n_cores))
 
         '''
         ' ##################################################
-        ' # zip_jobs                                       #
+        ' # zip creation                                   #
         ' ##################################################
         '''
-        zip_jobs = []
+        zip_creation_jobs = []
         if self.zip is not None:
             # Remove .zip file extension if provided
             if self.zip.endswith('.zip'):
@@ -112,9 +123,10 @@ class NLPPipeline(WorkflowRunner):
             cmd += ' -i "*.vrt"'
             cmd += ' && '
             cmd += 'cd -'
-            deps = spacy_nlp_jobs
+            deps = nlp_jobs
-            lbl = 'zip_job'
+            lbl = 'zip_creation'
-            zip_jobs.append(self.addTask(command=cmd, dependencies=deps,
+            zip_creation_jobs.append(self.addTask(command=cmd,
+                                                  dependencies=deps,
                                                   label=lbl))
 
 
@@ -132,11 +144,13 @@ def collect_jobs(input_dir, output_dir):
 
 def main():
     args = parse_args()
-    jobs = collect_jobs(args.i, args.o)
+    jobs = collect_jobs(args.input_directory, args.output_directory)
     nlp_pipeline = NLPPipeline(args.check_encoding, jobs, args.language,
-                               args.n_cores, args.o, args.zip)
+                               args.n_cores, args.output_directory, args.zip)
-    retval = nlp_pipeline.run(dataDirRoot=(args.log_dir or args.o),
+    retval = nlp_pipeline.run(
-                              nCores=args.n_cores)
+        dataDirRoot=(args.log_dir or args.output_directory),
+        nCores=args.n_cores
+    )
     sys.exit(retval)
 
 

spacy-nlp

@@ -22,9 +22,10 @@ SPACY_MODELS = {'de': 'de_core_news_sm',
 # Parse the given arguments
 parser = ArgumentParser(description=('Tag a text file with spaCy and save it '
                                      'as a verticalized text file.'))
-parser.add_argument('i', metavar='txt-sourcefile')
+parser.add_argument('-i', '--input', metavar='txt-sourcefile', required=True)
-parser.add_argument('o', metavar='vrt-destfile')
+parser.add_argument('-o', '--output', metavar='vrt-destfile', required=True)
-parser.add_argument('-l', '--language', choices=SPACY_MODELS.keys(),
+parser.add_argument('-l', '--language',
+                    choices=SPACY_MODELS.keys(),
                     required=True)
 parser.add_argument('--check-encoding', action='store_true')
 args = parser.parse_args()
@@ -33,7 +34,7 @@ args = parser.parse_args()
 # If requested: Check the encoding of the text contents from the input file
 # Else: Use utf-8
 if args.check_encoding:
-    with open(args.i, "rb") as input_file:
+    with open(args.input, "rb") as input_file:
         bytes = input_file.read()
         encoding = chardet.detect(bytes)['encoding']
 else:
@@ -41,14 +42,14 @@ else:
 
 
 # hashing in chunks to avoid full RAM with huge files.
-with open(args.i, 'rb') as input_file:
+with open(args.input, 'rb') as input_file:
     md5_hash = hashlib.md5()
     for chunk in iter(lambda: input_file.read(128 * md5_hash.block_size), b''):
         md5_hash.update(chunk)
     md5_hash = md5_hash.hexdigest()
 
 # Load the text contents from the input file
-with open(args.i, encoding=encoding) as input_file:
+with open(args.input, encoding=encoding) as input_file:
     text = input_file.read()
     # spaCys NLP is limited to strings with maximum 1 million characters at
     # once. So we split it into suitable chunks.
@@ -64,8 +65,8 @@ nlp = spacy.load(SPACY_MODELS[args.language])
 
 # Create the output file in verticalized text format
 # See: http://cwb.sourceforge.net/files/CWB_Encoding_Tutorial/node3.html
-output_file_original_filename = args.o
+output_file_original_filename = args.output
-output_file_stand_off_filename = args.o.replace('.vrt', '.stand-off.vrt')
+output_file_stand_off_filename = args.output.replace('.vrt', '.stand-off.vrt')
 common_xml = ('<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n'
               + '<corpus>\n'
               + '<text>\n'

wrapper/nlp

@@ -12,17 +12,21 @@ UID = str(os.getuid())
 GID = str(os.getgid())
 
 parser = ArgumentParser(add_help=False)
-parser.add_argument('-i')
+parser.add_argument('-i', '--input-directory')
-parser.add_argument('-o')
+parser.add_argument('-o', '--output-directory')
 args, remaining_args = parser.parse_known_args()
 
 cmd = ['docker', 'run', '--rm', '-it', '-u', '{}:{}'.format(UID, GID)]
-if args.o is not None:
+if args.output_directory is not None:
-    cmd += ['-v', '{}:{}'.format(os.path.abspath(args.o), CONTAINER_OUTPUT_DIR)]
+    cmd += ['-v', '{}:{}'.format(os.path.abspath(args.output_directory),
+                                 CONTAINER_OUTPUT_DIR)]
     remaining_args.insert(0, CONTAINER_OUTPUT_DIR)
-if args.i is not None:
+    remaining_args.insert(0, '-o')
-    cmd += ['-v', '{}:{}'.format(os.path.abspath(args.i), CONTAINER_INPUT_DIR)]
+if args.input_directory is not None:
+    cmd += ['-v', '{}:{}'.format(os.path.abspath(args.input_directory),
+                                 CONTAINER_INPUT_DIR)]
     remaining_args.insert(0, CONTAINER_INPUT_DIR)
+    remaining_args.insert(0, '-i')
 cmd.append(CONTAINER_IMAGE)
 cmd += remaining_args