import constants from relna, not nalaf -- Rostlab/nalaf#155

relna.py

@@ -4,7 +4,7 @@
 
 import pkg_resources
 
-from nalaf.utils import PRO_CLASS_ID, MUT_CLASS_ID, PRO_REL_MUT_CLASS_ID
+from relna.utils import PRO_CLASS_ID, MUT_CLASS_ID, PRO_REL_MUT_CLASS_ID
 from nalaf.utils.readers import TextFilesReader, PMIDReader
 from nalaf.utils.readers import StringReader
 from nalaf.utils.writers import TagTogFormat, PubTatorFormat

relna/learning/svmlight.py

@@ -2,10 +2,7 @@
 import sys
 import subprocess
 import pkg_resources
-
-from nalaf.structures.data import Label
-from nalaf.utils import MUT_CLASS_ID
-from random import random, seed
+from random import random
 
 
 class SVMLightTreeKernels:

relna/learning/taggers.py

@@ -6,7 +6,7 @@
 from relna.utils.swissprot_utils import Swissprot
 from relna.utils.go_utils import GOTerms
 from nalaf.structures.data import Entity, Relation
-from nalaf.utils import MUT_CLASS_ID, PRO_CLASS_ID, PRO_REL_MUT_CLASS_ID, ENTREZ_GENE_ID, UNIPROT_ID
+from relna.utils import MUT_CLASS_ID, PRO_CLASS_ID, ENTREZ_GENE_ID, UNIPROT_ID
 from nalaf.learning.taggers import Tagger
 
 

relna/utils/__init__.py

@@ -0,0 +1,12 @@
+THRESHOLD_VALUE = 1
+
+# TODO The constants should be renamed. Do not make sense in relna.
+# Copied from nalaf directly for historical reasons.
+
+PRO_CLASS_ID = 'e_1'
+MUT_CLASS_ID = 'e_2'
+ORG_CLASS_ID = 'e_3'
+PRO_REL_MUT_CLASS_ID = 'r_4'  # e_1/e_2
+PRO_REL_ORG_CLASS_ID = 'r_5'  # e_1/e_3
+ENTREZ_GENE_ID = 'n_4'
+UNIPROT_ID = 'n_5'

relna/utils/writers.py

@@ -1,7 +1,7 @@
 from itertools import chain
 import sys
 import os
-from nalaf.utils import MUT_CLASS_ID, PRO_CLASS_ID
+from relna.utils import MUT_CLASS_ID, PRO_CLASS_ID
 
 
 class RelnaConsoleWriter: