start testing yml

Author: miloswrath

.github/workflows/main.yml

@@ -0,0 +1,57 @@
+name: act-workflow
+on:
+  push:
+    branches:
+      - main
+      - dev
+  schedule:
+    - cron: "0 0 * * *"
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  packages: write
+  issues: write
+  id-token: write
+  pages: write
+
+jobs:
+  install-reqs-n-run-scripts:
+    name: install-py-reqs
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout code
+        uses: actions/checkout@v4
+
+      - name: set up python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+
+      - name: install pyreqs
+        run: pip install -r requirements.txt
+
+    name: install-r-reqs
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: set up R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: install rreqs
+        run: Rscript ./R_requirements.R
+
+
+  name: run orchestrator
+  runs-on: ubuntu-latest
+
+  steps:
+      - name: run orchestrator
+        run: current_date=$(date +"%Y-%m-%d")\
+          python3 ./code/orchestrate.py -i '/Volumes/VossLab/Repositories/Accelerometer_Data/' -token 'DE4E2DB72778DACA9B8848574107D2F5P' | tee > ./out/log-{}.txt'
+
+      - name: checkout code
+        uses: actions/checkout@v4
+
+

README.md

@@ -14,4 +14,7 @@ This repo contains a minimal amount of hard-coding to allow for reproducibility
     - [x] GGIR is formatted as GGIR-#.# with no more version numbers after the second. Full version number should be put into the readme
  - [x] Finish adding all required code to move to linux
  - [x] move to linux?
-- [ ] Test on linux and prepare prelims
+ - [ ] screw linux let's move to github actions
+    - [x] complete yml files
+    - [ ] test yml 
+ 

R_requirements.R

@@ -0,0 +1,2 @@
+install.packages("GGIR", dependenceies = TRUE)
+library(GGIR)

code/orchestrate.py

@@ -38,6 +38,11 @@ def init_servers():
     except Exception as e:
         print(f'An error occured trying to connect to RDSS: {e}')
         sys.exit(1)
+
+    print("""
+          Server check passed -> checking rdss files
+          *----------------------------* 
+          """)
     return None
 
 def check_files():
@@ -47,6 +52,7 @@ def check_files():
 
     if len(rdss_files) == 0:
         print("error: RDSS files were not grabbed - find out why")
+        sys.exit(1)
 
     need = compare(rdss_files, TXT)
 
@@ -62,7 +68,10 @@ def create_comparable_dataframe(need):
     from src.match import parse_files
 
     if type(need) != list:
-        print("need is not a list... you need to figure out why")
+        print("""
+             need is not a list... you need to figure out why
+             *----------------------------* 
+              """)
         exit()
 
     lab_id_file = parse_files(need)
@@ -81,7 +90,10 @@ def create_comparable_dataframe(need):
                 print(error)
             sys.exit(1)
         else:
-            print("All rows are valid")
+            print("""
+                  All rows are valid
+                  *----------------------------*
+                  """)
 
     return lab_id_file
 
@@ -111,6 +123,7 @@ def GGIR(outs):
     #this is where we run GGIR using the GGIR function in matched
     from src.match import GGIR
     GGIR(outs)
+    print("GGIR completed -> moving to validation")
     return None
 
 
@@ -131,7 +144,7 @@ def main():
 
     return None
 
-if __name__ == 'main':
+if __name__ == '__main__':
     main()
 
 

code/src/accel.R

@@ -411,4 +411,4 @@ re_run_intensity_gradient <- function(r, project_dir, project_deriv_dir, verbose
 }
 
 # Run the main function
-main(opt)
+main(opt)

code/src/clean_gg_outs.py

@@ -43,7 +43,7 @@ def rename_dirs(list, dir):
                     # Rename the directory
                     print('Renaming', os.path.join(dir, d), final)
                     os.rename(os.path.join(dir, d), final)
-    
+
     return renamed_dirs
 
 def structure_dirs(list, dir):
@@ -61,14 +61,14 @@ def structure_dirs(list, dir):
         # move the renamed directory to the new subject directory
         print('Moving', d, new_sub)
         shutil.move(d, new_sub)
-
+    return None
 
 
 
 def main():
     arg = args()
     dirs = gather_dirs(arg.dir)
     structure_dirs(rename_dirs(dirs, arg.dir), arg.dir)
-    
+
 if __name__ == '__main__':
-    main()
+    main()

code/src/match.py

@@ -91,7 +91,7 @@ def compare_ids(files, list):
         how='inner',
         validate='many_to_one'
     )
-    
+
     # Rename columns to match the desired output
     matched = matched[['lab_id', 'file', 'boost_id']].rename(columns={'file': 'raw_file', 'boost_id': 'subject_id'})
 
@@ -194,7 +194,9 @@ def save_n_rename_files(matched, dir):
         src = os.path.join(dir, row['raw_file'])
         dest = os.path.join(output_dir, f"sub-{row['subject_id']}_{row['session']}.csv")
 
-        print('source: ',  src, ' ', 'destination: ', dest)
+
+
+print('source: ',  src, ' ', 'destination: ', dest)
 
         # Copy the file to the destination
         #shutil.copy(src, dest)

code/src/val-run.py

@@ -0,0 +1,40 @@
+import os
+import sys
+import requests
+
+
+OUTDIR = '/Volumes/vosslabhpc/Projects/Boost/path/to/out'
+
+
+def parse_args():
+    from argparse import ArgumentParser
+    args = ArgumentParser(description='validates a run from an input text output')
+    args.add_argument('-i', type=str, required=True, help='input txt file from most recent GGIR pipeline out')
+
+
+    return args.parse_args()
+
+def create_obj(filepath):
+    # creates a parseable text object from a text file -> used to validate run of pipeline post-compute
+    dic = {}
+    with open(filepath, 'r') as f:
+        for line in f:
+
+    return None
+
+
+def main():
+    args = parse_args()
+    in = args.i
+
+
+
+    return None
+
+
+
+
+
+
+if __name__ == '__main__':
+    main()

dockerfile

@@ -24,7 +24,7 @@ RUN pip install --no-cache-dir -r requirements.txt
 COPY R_requirements.R /app/
 
 # Install R dependencies
-RUN python3 code/orchestrate.py -token {INSERT TOKEN HERE}
+RUN python3 code/orchestrate.py -i = -token {INSERT TOKEN HERE}
 # Copy the rest of the application code into the image
 COPY . /app/