From 8aa690b50fab22e1d12f331624077a397adc1863 Mon Sep 17 00:00:00 2001
From: crudnicky <crudnicky@abscibio.com>
Date: Thu, 4 Feb 2021 16:35:45 -0800
Subject: [PATCH 1/4] Add url kwarg to ptdb request file and updated readme.

---
 README.md           | 14 ++++++++++++++
 lib/ptdb_request.py |  5 +++--
 target_uploader.py  |  2 +-
 3 files changed, 18 insertions(+), 3 deletions(-)
 create mode 100644 README.md

diff --git a/README.md b/README.md
new file mode 100644
index 0000000..6f8bbc3
--- /dev/null
+++ b/README.md
@@ -0,0 +1,14 @@
+# CD19 MicAbody Target Uploader
+
+This program was written to upload 45 unique targets with different combinations of light and heavy chain subunits. There are several variables that must be given to the program via the CLI in order for it to work:
+
+`--excel_file_location`: This flag is used to determine the location of an Excel file that contains data used to create each "target".  
+`--fasata_location`: This flag is used to determine the location of the directory that holds the amino acid and dna sequences fasta files.  
+`--API_URL`: This is the URL of the PTDB.  
+`--token`: This is the API token necessary to make HTTP requests to the PTDB.
+
+Use the following command (replacing the value of `API_URL` and `token` with the appropriate values) to run the program.
+
+`python3 target_uploader.py --fasta_location=./assets/CD19_MicAbody_Xolo_FASTA_Files/ --excel_file_location=./assets/XOLO_PTDB_Nomenclature.xlsx --API_URL=https://localhost8000/api/v1/absci-targets/target-registration --token=like-id-show-you`
+
+
diff --git a/lib/ptdb_request.py b/lib/ptdb_request.py
index 6177db7..2321a8d 100644
--- a/lib/ptdb_request.py
+++ b/lib/ptdb_request.py
@@ -3,12 +3,13 @@
 
 URL = "http://localhost:8000/api/v1/absci-targets/target-registration/"
 class PTDBRequest():
-  def __init__(self, new_target):
+  def __init__(self, new_target, user_input):
     self.target = json.dumps(new_target)
+    self.url = user_input['API_URL']
 
   def post_target(self):
     headers = self.get_headers()
-    # request = requests.post(URL, data=self.target, headers=headers)
+    # request = requests.post(self.url, data=self.target, headers=headers)
     
   def get_headers(self):
     return {
diff --git a/target_uploader.py b/target_uploader.py
index 417ed8e..e3e70d1 100644
--- a/target_uploader.py
+++ b/target_uploader.py
@@ -5,7 +5,7 @@
 
 def upload_targets(user_input):    
     for target in TargetCreator(user_input).targets:
-        PTDBRequest(target).post_target()
+        PTDBRequest(target, user_input).post_target()
         
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="""This program was written to upload 45 

From b986e861a5474732cbea0352485a7e45fe8f4260 Mon Sep 17 00:00:00 2001
From: crudnicky <crudnicky@abscibio.com>
Date: Sat, 6 Feb 2021 15:54:16 -0800
Subject: [PATCH 2/4] Add tests section to readme.

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 6f8bbc3..34d2cee 100644
--- a/README.md
+++ b/README.md
@@ -11,4 +11,8 @@ Use the following command (replacing the value of `API_URL` and `token` with the
 
 `python3 target_uploader.py --fasta_location=./assets/CD19_MicAbody_Xolo_FASTA_Files/ --excel_file_location=./assets/XOLO_PTDB_Nomenclature.xlsx --API_URL=https://localhost8000/api/v1/absci-targets/target-registration --token=like-id-show-you`
 
+## Testing
 
+Unit tests are run to ensure that the program creates the correct target object. To run unit tests issue the following command:
+
+`python3 -m unittest tests/test_target_creator.py`
\ No newline at end of file

From 330dc94c9f5d37964eb0ce6bc5c645f344ce7aa7 Mon Sep 17 00:00:00 2001
From: crudnicky <crudnicky@abscibio.com>
Date: Thu, 11 Feb 2021 11:35:42 -0800
Subject: [PATCH 3/4] WIP

---
 assets/~$XOLO_PTDB_Nomenclature.xlsx | Bin 0 -> 165 bytes
 lib/ptdb_request.py                  |  11 +++++++----
 lib/target_creator.py                |   2 +-
 3 files changed, 8 insertions(+), 5 deletions(-)
 create mode 100644 assets/~$XOLO_PTDB_Nomenclature.xlsx

diff --git a/assets/~$XOLO_PTDB_Nomenclature.xlsx b/assets/~$XOLO_PTDB_Nomenclature.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..5a932052db2a5d1e1d32a453f59be330b8becc3b
GIT binary patch
literal 165
zcmWgj%}g%JFV0UZQSeVo%S=vH2rW)6QXm9G8GIQs8Il=_81fm4fjEt!gh7G9A4sQx
R#Z!U2P@qgIP=x};5CA3W7%cz*

literal 0
HcmV?d00001

diff --git a/lib/ptdb_request.py b/lib/ptdb_request.py
index 2321a8d..e6f8a2f 100644
--- a/lib/ptdb_request.py
+++ b/lib/ptdb_request.py
@@ -1,19 +1,22 @@
 import json
 import requests
-
-URL = "http://localhost:8000/api/v1/absci-targets/target-registration/"
+from pprint import pprint
 class PTDBRequest():
   def __init__(self, new_target, user_input):
     self.target = json.dumps(new_target)
     self.url = user_input['API_URL']
+    self.token = user_input['token']
+    pprint(self.target, indent=2)
+    print(" ")
 
   def post_target(self):
     headers = self.get_headers()
-    # request = requests.post(self.url, data=self.target, headers=headers)
+    request = requests.post(self.url, data=self.target, headers=headers)
+    pprint(request.content)
     
   def get_headers(self):
     return {
-      "Authorization": f"Token {TOKEN}",
+      "Authorization": f"Token {self.token}",
       "Accept": "*/*",
       "Content-Type": "application/json"
     }
diff --git a/lib/target_creator.py b/lib/target_creator.py
index 2805f38..d9c3878 100644
--- a/lib/target_creator.py
+++ b/lib/target_creator.py
@@ -12,7 +12,7 @@ def __init__(self, user_input):
     self.excel_reader()
 
   def excel_reader(self):
-      for row in range(2, self.max_row + 1):
+      for row in range(self.max_row, self.max_row + 1):
           target = {
               "target": self.ws.cell(row, 1).value,
               "partner": "Xyphos",

From 17961af4564a70011ae40395b8687e54057f1a9b Mon Sep 17 00:00:00 2001
From: crudnicky <crudnicky@abscibio.com>
Date: Thu, 11 Feb 2021 13:01:20 -0800
Subject: [PATCH 4/4] Done.

---
 assets/XOLO_PTDB_Nomenclature.xlsx | Bin 11136 -> 11164 bytes
 lib/ptdb_request.py                |   3 +--
 lib/target_creator.py              |   2 +-
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/assets/XOLO_PTDB_Nomenclature.xlsx b/assets/XOLO_PTDB_Nomenclature.xlsx
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diff --git a/lib/ptdb_request.py b/lib/ptdb_request.py
index e6f8a2f..3e6f85d 100644
--- a/lib/ptdb_request.py
+++ b/lib/ptdb_request.py
@@ -3,11 +3,10 @@
 from pprint import pprint
 class PTDBRequest():
   def __init__(self, new_target, user_input):
+    print(new_target['target'])
     self.target = json.dumps(new_target)
     self.url = user_input['API_URL']
     self.token = user_input['token']
-    pprint(self.target, indent=2)
-    print(" ")
 
   def post_target(self):
     headers = self.get_headers()
diff --git a/lib/target_creator.py b/lib/target_creator.py
index d9c3878..2805f38 100644
--- a/lib/target_creator.py
+++ b/lib/target_creator.py
@@ -12,7 +12,7 @@ def __init__(self, user_input):
     self.excel_reader()
 
   def excel_reader(self):
-      for row in range(self.max_row, self.max_row + 1):
+      for row in range(2, self.max_row + 1):
           target = {
               "target": self.ws.cell(row, 1).value,
               "partner": "Xyphos",