edited import for all python templates

tiagofilipe12 · tiagofilipe12 · commit 0491b288c4cf · 2018-11-05T13:25:17.000Z
diff --git a/flowcraft/templates/assembly_report.py b/flowcraft/templates/assembly_report.py
@@ -43,7 +43,11 @@
 from collections import OrderedDict
 from subprocess import PIPE
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/downsample_fastq.py b/flowcraft/templates/downsample_fastq.py
@@ -47,7 +47,11 @@
 
 from os.path import basename
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/fastqc.py b/flowcraft/templates/fastqc.py
@@ -42,7 +42,11 @@
 from subprocess import PIPE
 from os.path import exists, join
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/fastqc_report.py b/flowcraft/templates/fastqc_report.py
@@ -58,7 +58,11 @@
 
 from collections import OrderedDict
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/integrity_coverage.py b/flowcraft/templates/integrity_coverage.py
@@ -86,7 +86,11 @@
 
 from itertools import chain
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/megahit.py b/flowcraft/templates/megahit.py
@@ -47,7 +47,11 @@
 
 from subprocess import PIPE
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/metaspades.py b/flowcraft/templates/metaspades.py
@@ -45,7 +45,11 @@
 
 from subprocess import PIPE
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/pipeline_status.py b/flowcraft/templates/pipeline_status.py
@@ -29,7 +29,11 @@
 
 from os.path import join
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/process_abricate.py b/flowcraft/templates/process_abricate.py
@@ -39,7 +39,11 @@
 
 from subprocess import PIPE
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/process_assembly.py b/flowcraft/templates/process_assembly.py
@@ -53,7 +53,11 @@
 import json
 import operator
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/process_assembly_mapping.py b/flowcraft/templates/process_assembly_mapping.py
@@ -59,7 +59,11 @@
 from subprocess import PIPE
 from collections import OrderedDict
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/process_mapping.py b/flowcraft/templates/process_mapping.py
@@ -1,13 +1,5 @@
 #!/usr/bin/env python3
 
-import re
-import os
-import json
-
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
-
-
-
 """
 Purpose
 -------
@@ -36,6 +28,16 @@
 
 """
 
+import re
+import os
+import json
+
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
+
 __version__ = "1.0.1"
 __build__ = "10.09.2018"
 __template__ = "remove_host-nf"
diff --git a/flowcraft/templates/process_newick.py b/flowcraft/templates/process_newick.py
@@ -1,22 +1,14 @@
 #!/usr/bin/env python3
 
-import os
-import json
-import dendropy
-
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
-
-
-
 """
 Purpose
 -------
 
 This module is intended to process the newick generated by
- a proces to generate a report. The newick tree will be 
- rooted (midpoint). 
- 
- 
+ a proces to generate a report. The newick tree will be
+ rooted (midpoint).
+
+
 Expected input
 --------------
 
@@ -34,6 +26,16 @@
 
 """
 
+import os
+import json
+import dendropy
+
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
+
 __version__ = "1.0.1"
 __build__ = "20.09.2018"
 __template__ = "raxml-nf"
diff --git a/flowcraft/templates/process_viral_assembly.py b/flowcraft/templates/process_viral_assembly.py
@@ -1,14 +1,5 @@
 #!/usr/bin/env python3
 
-import os
-import json
-import operator
-from itertools import groupby
-
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
-
-
-
 """
 Purpose
 -------
@@ -38,6 +29,17 @@
 
 """
 
+import os
+import json
+import operator
+from itertools import groupby
+
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
+
 __version__ = "1.0.1"
 __build__ = "11.09.2018"
 __template__ = "viral_assembly-nf"
diff --git a/flowcraft/templates/skesa.py b/flowcraft/templates/skesa.py
@@ -42,7 +42,11 @@
 
 from subprocess import PIPE
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/spades.py b/flowcraft/templates/spades.py
@@ -54,7 +54,11 @@
 
 from subprocess import PIPE
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/split_fasta.py b/flowcraft/templates/split_fasta.py
@@ -32,7 +32,11 @@
 import os
 from itertools import groupby
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
@@ -86,4 +90,4 @@ def main(sample_id, assembly, min_size):
 
 if __name__ == '__main__':
 
-    main(SAMPLE_ID, ASSEMBLY, MIN_SIZE)
+    main(SAMPLE_ID, ASSEMBLY, MIN_SIZE)
diff --git a/flowcraft/templates/trimmomatic.py b/flowcraft/templates/trimmomatic.py
@@ -61,7 +61,11 @@
 from subprocess import PIPE
 from collections import OrderedDict
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
diff --git a/flowcraft/templates/trimmomatic_report.py b/flowcraft/templates/trimmomatic_report.py
@@ -36,8 +36,12 @@
 
 from collections import OrderedDict
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
-
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
+    
 logger = get_logger(__file__)
 
 
