Devon dev

.gitignore

@@ -13,37 +13,37 @@
 
 # End of https://www.gitignore.io/api/visualstudiocode
 personal-config.ini
-environment_setup.py
-clinical/src/full_trial_data/
-clinical/src/chromedriver
-clinical/src/ctgov_nctids.json
-clinical/src/ctgov_webscraped_names.csv
-clinical/src/all_queries/
-clinical/src/metamap_cond.txt
-clinical/src/metamap_gard.txt
-clinical/src/metamap_cond_out.json
-pubmed/src/
-gard/src/*.csv
-gard/src/*.json
-gard/src/*.txt
+
+RDAS_CTKG/src/full_trial_data/
+RDAS_CTKG/src/chromedriver
+RDAS_CTKG/src/ctgov_nctids.json
+RDAS_CTKG/src/ctgov_webscraped_names.csv
+RDAS_CTKG/src/all_queries/
+RDAS_CTKG/src/metamap_cond.txt
+RDAS_CTKG/src/metamap_gard.txt
+RDAS_CTKG/src/metamap_cond_out.json
+RDAS_PAKG/src/
+RDAS_CTKG/src/*.csv
+RDAS_CTKG/src/*.json
+RDAS_CTKG/src/*.txt
 __pycache__/
-clinical/__pycache__/
-grant/__pycache__/
-pubmed/__pycache__/
-pubmed/init_new.py
-pubmed/methods_new.py
-pubmed/archive/
-grant/archive/
-gard/__pycache__/
+RDAS_CTKG/__pycache__/
+RDAS_GFKG/__pycache__/
+RDAS_PAKG/__pycache__/
+RDAS_PAKG/init_new.py
+RDAS_PAKG/methods_new.py
+RDAS_PAKG/archive/
+RDAS_GFKG/archive/
+RDAS_CTKG/__pycache__/
 email/__pycache__/
 transfer/*.dump
 transfer/*.dump
 backup/*/*.dump
 migrated/*.dump
 approved/*.dump
-grant/src/**/**/*.csv
-grant/src/**/**/*.json
-grant/src/**/**/*.zip
+RDAS_GFKG/src/**/**/*.csv
+RDAS_GFKG/src/**/**/*.json
+RDAS_GFKG/src/**/**/*.zip
 grant_2024/src/**/**/*.csv
 grant_2024/src/**/**/*.json
 crt/*.json
@@ -76,10 +76,36 @@ add_participant.txt
 epifix.py
 grant_pipeline.txt
 result.json
-pubmed/test_affiliation.py
-pubmed/test_genereview.py
+RDAS_PAKG/test_affiliation.py
+RDAS_PAKG/test_genereview.py
 test_affiliation.txt
 logs/
 terms_mapped.csv
 terms_unmapped.csv
 test_term_map.py
+RDAS_CTKG/src/ids_to_add.csv
+RDAS_CTKG/src/ids_to_update.csv
+RDAS_CTKG/src/ids_to_update_confirmed.csv
+GARD_disease_classification.csv
+gather_grant_funding_remove.py
+grant_funding_rdas.csv
+fixyear.py
+fixpubmedapi.py
+config.ini
+Cluster 7.csv
+codecamp.py
+cluster_trials.csv
+fixpubmedapi.py
+gather_grant_funding_remove.py
+grant_funding_rdas.csv
+thingforyanji.py
+deliverablesyanji
+NCATS COLLABORATION
+allennlp
+meta_annotate.py
+genereviews_epi.csv
+genereviews_epi_processed.csv
+fix_pubtator_type.py
+etc
+RDAS_GFKG/src/FineTunned_Bert_2.pt
+RDAS_GFKG/src/Finetunned_Bert_2.pt

.gitmodules

@@ -1,6 +1,6 @@
-[submodule "/home/leadmandj/RDAS/pubmed/NaturalHistory4GARD"]
-	path = pubmed/NaturalHistory4GARD
+[submodule "RDAS_PAKG/epi4GARD"]
+	path = RDAS_PAKG/epi4GARD
+	url = [email protected]:ncats/epi4GARD.git
+[submodule "RDAS_PAKG/NaturalHistory4GARD"]
+	path = RDAS_PAKG/NaturalHistory4GARD
 	url = [email protected]:ncats/NaturalHistory4GARD.git
-[submodule "pubmed/epi4GARD"]
-	path = pubmed/epi4GARD
-	url = https://github.com/ncats/epi4GARD.git