asyml · Piyush13y · Feb 23, 2022 · Feb 19, 2022 · Feb 19, 2022 · Feb 23, 2022
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,225 @@
+# Created by https://www.gitignore.io/api/python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
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diff --git a/examples/mimic_iii/.DS_Store b/examples/mimic_iii/.DS_Store
diff --git a/examples/mimic_iii/__pycache__/mimic3_note_reader.cpython-39.pyc b/examples/mimic_iii/__pycache__/mimic3_note_reader.cpython-39.pyc
diff --git a/examples/mimic_iii/demo/.generated b/examples/mimic_iii/demo/.generated
diff --git a/examples/mimic_iii/demo/__pycache__/__init__.cpython-39.pyc b/examples/mimic_iii/demo/__pycache__/__init__.cpython-39.pyc
diff --git a/examples/mimic_iii/demo/__pycache__/clinical.cpython-39.pyc b/examples/mimic_iii/demo/__pycache__/clinical.cpython-39.pyc
diff --git a/examples/mimic_iii/demo/clinical.py b/examples/mimic_iii/demo/clinical.py
diff --git a/examples/mimic_iii/medical_pipeline.py b/examples/mimic_iii/medical_pipeline.py
@@ -5,7 +5,7 @@
 from forte.data.readers import StringReader
 from forte.pipeline import Pipeline
 from forte.processors.writers import PackIdJsonPackWriter
-from ftx.medical import MedicalEntityMention
+from ftx.medical.clinical import MedicalEntityMention
 
 from ft.onto.base_ontology import (
     Token,

diff --git a/forte_medical/ontology_specs/clinical_onto.json b/forte_medical/ontology_specs/clinical_onto.json
@@ -1,24 +1,24 @@
 {
   "name": "clinical",
-  "additional_prefixes": [
-    "demo.clinical"
-  ],
   "imports": [
     "base_ontology.json"
   ],
+  "additional_prefixes": [
+    "ftx.medical"
+  ],
   "definitions": [
     {
-      "entry_name": "demo.clinical.ClinicalEntityMention",
+      "entry_name": "ftx.medical.clinical.ClinicalEntityMention",
       "parent_entry": "ft.onto.base_ontology.EntityMention",
       "description": "A span based annotation `ClinicalEntityMention`, normally used to represent an Entity Mention in a piece of clinical text."
     },
     {
-      "entry_name": "demo.clinical.Description",
+      "entry_name": "ftx.medical.clinical.Description",
       "parent_entry": "forte.data.ontology.top.Annotation",
       "description": "A span based annotation `Description`, used to represent the description in a piece of clinical note."
     },
     {
-      "entry_name": "demo.clinical.Body",
+      "entry_name": "ftx.medical.clinical.Body",
       "parent_entry": "forte.data.ontology.top.Annotation",
       "description": "A span based annotation `Body`, used to represent the actual content in a piece of clinical note."
     }

diff --git a/forte_medical/ontology_specs/demo/.generated b/forte_medical/ontology_specs/demo/.generated
diff --git a/forte_medical/ontology_specs/demo/__init__.py b/forte_medical/ontology_specs/demo/__init__.py
diff --git a/forte_medical/ontology_specs/demo/__pycache__/__init__.cpython-39.pyc b/forte_medical/ontology_specs/demo/__pycache__/__init__.cpython-39.pyc
diff --git a/forte_medical/ontology_specs/demo/__pycache__/clinical.cpython-39.pyc b/forte_medical/ontology_specs/demo/__pycache__/clinical.cpython-39.pyc
diff --git a/forte_medical/readers/__pycache__/mimic3_note_reader.cpython-39.pyc b/forte_medical/readers/__pycache__/mimic3_note_reader.cpython-39.pyc
diff --git a/forte_medical/readers/mimic3_note_reader.py b/forte_medical/readers/mimic3_note_reader.py
@@ -21,7 +21,7 @@
 
 from forte.data.data_pack import DataPack
 from forte.data.base_reader import PackReader
-from forte_medical.ontology_specs.demo.clinical import Description, Body
+from ftx.medical.clinical import Description, Body
 
 
 class Mimic3DischargeNoteReader(PackReader):

diff --git a/examples/mimic_iii/demo/__init__.py → ftx/medical/__init__.py b/examples/mimic_iii/demo/__init__.py → ftx/medical/__init__.py
diff --git a/...e_medical/ontology_specs/demo/clinical.py → ftx/medical/clinical.py b/...e_medical/ontology_specs/demo/clinical.py → ftx/medical/clinical.py
diff --git a/setup.py b/setup.py
@@ -16,7 +16,8 @@
     long_description=long_description,
     long_description_content_type="text/markdown",
     license='',
-    packages=setuptools.find_packages(
+    packages=setuptools.find_namespace_packages(
+        include=['ftx.*'],
         exclude=["scripts*", "examples*", "tests*"]
     ),
     install_requires=[