From 0e26499c6048ef76e67f61eb6632d0e297b3a3a3 Mon Sep 17 00:00:00 2001
From: Tamara Slosarek <tamara.slosarek@hpi.de>
Date: Thu, 6 Jun 2024 14:23:38 +0200
Subject: [PATCH] feat(scripts): add script to unstage all data

---
 pharme.code-workspace       |  2 ++
 scripts/README.md           |  8 ++++++++
 scripts/common/constants.py |  1 +
 scripts/reset.py            | 11 -----------
 scripts/unstage.py          | 14 ++++++++++++++
 5 files changed, 25 insertions(+), 11 deletions(-)
 create mode 100644 scripts/unstage.py

diff --git a/pharme.code-workspace b/pharme.code-workspace
index a801571c..e19a5fdb 100644
--- a/pharme.code-workspace
+++ b/pharme.code-workspace
@@ -77,6 +77,8 @@
       "tacrolimus",
       "tramadol",
       "unscrollable",
+      "unstage",
+      "unstaged",
       "userdata",
       "voriconazole"
     ]
diff --git a/scripts/README.md b/scripts/README.md
index 361b9d70..7fc36147 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -38,6 +38,14 @@ by deleting the history data and published data.
 Run `python reset.py <PATH_TO_BACKUP>.base64` to receive
 `<PATH_TO_BACKUP>_reset_<TIMESTAMP>.base64`.
 
+## Unstage data
+
+This is probably a use case only relevant once, we want to unstage all data and
+do a second review.
+
+Run `python unstage.py <PATH_TO_BACKUP>.base64` to receive
+`<PATH_TO_BACKUP>_reset_<TIMESTAMP>.base64`.
+
 ## Migrate data
 
 Run `pyhthon migrate.py <PATH_TO_BACKUP>[.json|.base64]` to receive
diff --git a/scripts/common/constants.py b/scripts/common/constants.py
index e5844644..d98f9e77 100644
--- a/scripts/common/constants.py
+++ b/scripts/common/constants.py
@@ -12,6 +12,7 @@
     'encode': '_encoded',
     'correct': '_corrected',
     'reset': '_reset',
+    'unstage': '_unstaged',
 }
 
 DRUG_COLLECTION_NAME = 'Drug'
diff --git a/scripts/reset.py b/scripts/reset.py
index 6b637fe2..f48d384b 100644
--- a/scripts/reset.py
+++ b/scripts/reset.py
@@ -1,18 +1,7 @@
-import copy
-
 from common.get_data import get_data
-from common.get_data import get_information_key
-from common.get_data import get_guidelines_by_ids
-from common.get_data import get_phenotype_value_lengths
-from common.get_data import get_phenotype_value
-from common.get_data import get_phenotype_key
 from common.write_data import write_data
-from common.constants import DRUG_COLLECTION_NAME
-from common.constants import GUIDELINE_COLLECTION_NAME
 from common.constants import SCRIPT_POSTFIXES
-from common.cpic_data import get_phenotype_map
 from common.remove_history import remove_history
-from common.mongo import get_object_id
 
 # Migrate data
 def reset_data():
diff --git a/scripts/unstage.py b/scripts/unstage.py
new file mode 100644
index 00000000..1f1b1eab
--- /dev/null
+++ b/scripts/unstage.py
@@ -0,0 +1,14 @@
+from common.get_data import get_data
+from common.write_data import write_data
+from common.constants import SCRIPT_POSTFIXES
+
+def unstage_data():
+    data = get_data()
+    for table_name in data.keys():
+        for item in data[table_name]:
+            if 'isStaged' in item.keys():
+                item['isStaged'] = False
+    write_data(data, postfix=SCRIPT_POSTFIXES['unstage'])
+
+if __name__ == '__main__':
+    unstage_data()
\ No newline at end of file