From 338fcc9d355f42a116d514e6516d014d096b302a Mon Sep 17 00:00:00 2001
From: Juan Miguel Cejuela <i@juanmi.rocks>
Date: Fri, 24 Jun 2016 11:27:57 +0200
Subject: [PATCH] import constants from relna, not nalaf --
 https://github.com/Rostlab/nalaf/issues/155

---
 relna.py                   |  2 +-
 relna/learning/svmlight.py |  5 +----
 relna/learning/taggers.py  |  2 +-
 relna/utils/__init__.py    | 12 ++++++++++++
 relna/utils/writers.py     |  2 +-
 5 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/relna.py b/relna.py
index 1720b07..89154f1 100644
--- a/relna.py
+++ b/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
diff --git a/relna/learning/svmlight.py b/relna/learning/svmlight.py
index 7223c28..dc9b37d 100644
--- a/relna/learning/svmlight.py
+++ b/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:
diff --git a/relna/learning/taggers.py b/relna/learning/taggers.py
index 76e1857..58e1fba 100644
--- a/relna/learning/taggers.py
+++ b/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
 
 
diff --git a/relna/utils/__init__.py b/relna/utils/__init__.py
index e69de29..88de072 100644
--- a/relna/utils/__init__.py
+++ b/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'
diff --git a/relna/utils/writers.py b/relna/utils/writers.py
index 803ed63..5ca0ea0 100644
--- a/relna/utils/writers.py
+++ b/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: