feat(#605): add easy migrations

anni/migration/.gitignore

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+*.json
+*.base64

anni/migration/migrate.py

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+import json
+import os
+import sys
+
+def get_input_file_path():
+    argument_error_text = 'Please provide an existing file path as argument.'
+    if len(sys.argv) != 2:
+        raise Exception(argument_error_text)
+    input_file_path = sys.argv[1]
+    if not os.path.isfile(input_file_path):
+        raise Exception(argument_error_text)
+    return input_file_path
+
+with open(get_input_file_path(), 'r') as input_file:
+    # Data is a Base64-encoded ZIP (#599)
+    # TODO: if base64, decode and unzip; test that the result is json
+    data = json.load(input_file)
+
+# Rename `cpicData` in guidelines to `externalData` (#582)
+# Add `source` field to `externalData` with value 'CPIC' (#582)
+def rename_external_data(guideline):
+    old_key = 'cpicData'
+    new_key = 'externalData'
+    if old_key in guideline:
+        guideline[new_key] = guideline.pop(old_key)
+        guideline[new_key]['source'] = 'CPIC'
+    return guideline
+
+# Change `externalData` to array (#597)
+def enlist_external_data(guideline):
+    if type(guideline['externalData']) is not list:
+        guideline['externalData'] = [guideline['externalData']]
+    return guideline
+
+# Add phenotypes for guideline (#602)
+def add_phenotypes(guideline):
+    # TODO: get phenotypes from CPIC API based on lookupkey
+    return guideline
+
+def migrate_guideline(guideline):
+    return add_phenotypes(
+        enlist_external_data(
+            rename_external_data(guideline)))
+
+for table_name in data.keys():
+    table_content = data[table_name]
+    if table_name.startswith('AppData'):
+        for row in table_content:
+            drugs = row['drugs']
+            for drug in drugs:
+                guidelines = drug['guidelines']
+                for guideline in guidelines:
+                    guideline = migrate_guideline(guideline)
+    if table_name.startswith('Guideline'):
+        for guideline in table_content:
+            guideline = migrate_guideline(guideline)
+
+# TODO: save as json in zip in base64