FIX: bug in backing up journal file locally.

chorus_upload/upload_ops.py

@@ -536,8 +536,9 @@ def upload_files(src_path : FileSystemHelper, dest_path : FileSystemHelper,
     # backup_journal(databasename, suffix=upload_ver_str)
     # just copy the journal file to the dated dest path as a backup, and locally sa well
     journal_path.copy_file_to(journal_fn, dated_dest_path)
-    journal_path.copy_file_to("_".join([journal_fn, upload_ver_str]), src_path)
-
+    dest_fn = src_path.root.joinpath("_".join([journal_fn, upload_ver_str]))
+    journal_path.copy_file_to(journal_fn, dest_fn)
+
     del perf
     return upload_ver_str, remaining
 

tests/test.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-rm journal.db
+rm journal_test.db
 
 # test configuration
 # phase 1:  with firstsnapshot data
@@ -45,21 +45,21 @@ container="test"
 sas=""
 
 # clean up
-az storage blob delete-batch --account-name ${account} --source ${container} --sas-token ${sas} --pattern "journal.db*"
+az storage blob delete-batch --account-name ${account} --source ${container} --sas-token ${sas} --pattern "journal_test.db*"
 az storage blob delete-batch --account-name ${account} --source ${container} --sas-token ${sas} --pattern "2024*"
 
 
 # test configuration
 echo TEST phase 1:  with firstsnapshot data
-rm journal.db
+rm journal_test.db
 config=tests/configlocal.toml
 azcli=TestData/azcli1.sh
 azcli2=TestData/azcli2.sh
 
 echo TEST update journal
 echo python chorus_upload -v -c ${config} journal update --modalities OMOP,Waveforms
 python chorus_upload -v -c ${config} journal update --modalities OMOP,Waveforms
-cp journal.db TestData/journal1.1.db
+cp journal_test.db TestData/journal1.1.db
 
 echo TEST generate file list
 echo python chorus_upload -v -c ${config} file list --modalities OMOP,Waveforms --output-file ${azcli} --output-type azcli --max-num-files 15
@@ -73,11 +73,11 @@ eval ${azcli}
 
 # database should have partially uploaded data.
 # wait for user input
-cp journal.db TestData/journal1.2.db
+cp journal_test.db TestData/journal1.2.db
 
 echo python chorus_upload -v -c ${config} journal update --modalities Images
 python chorus_upload -v -c ${config} journal update --modalities Images
-cp journal.db TestData/journal1.3.db
+cp journal_test.db TestData/journal1.3.db
 
 
 echo TEST generate file list again 
@@ -89,24 +89,24 @@ echo TEST with local journal and upload to central azcli - AMENDING
 chmod a+x ${azcli2}
 # run the azcli script
 eval ${azcli2}
-cp journal.db TestData/journal1.4.db
+cp journal_test.db TestData/journal1.4.db
 
 echo TEST with local journal and upload to central built in - AMENDING
 echo python chorus_upload -v -c ${config} file upload --modalities OMOP,Waveforms  --max-num-files 15
 python chorus_upload -v -c ${config} file upload --modalities OMOP,Waveforms --max-num-files 15
-cp journal.db TestData/journal1.5.db
+cp journal_test.db TestData/journal1.5.db
 
 
 echo TEST update journal with second snapshot data
 echo python chorus_upload -v -c ${config} journal update --modalities Images
 python chorus_upload -v -c ${config} journal update --modalities Images
-cp journal.db TestData/journal1.6.db
+cp journal_test.db TestData/journal1.6.db
 
 
 echo TEST with local journal and upload to central using built in
 echo python chorus_upload -v -c ${config} file upload --modalities Images
 python chorus_upload -v -c ${config} file upload --modalities Images
-cp journal.db TestData/journal1.7.db
+cp journal_test.db TestData/journal1.7.db
 
 
 echo TEST verify the version
@@ -115,8 +115,8 @@ python chorus_upload -v -c ${config} file verify --modalities OMOP
 
 # ========================
 echo TEST phase 2:  cloud journal with firstsnapshot data
-rm journal.db
-az storage blob delete-batch --account-name ${account} --source ${container} --sas-token ${sas} --pattern "journal.db*"
+rm journal_test.db
+az storage blob delete-batch --account-name ${account} --source ${container} --sas-token ${sas} --pattern "journal_test.db*"
 config=tests/config.toml
 azcli=TestData/azcli3.sh
 azcli2=TestData/azcli4.sh
@@ -125,7 +125,7 @@ azcli2=TestData/azcli4.sh
 echo TEST update journal
 echo python chorus_upload -v -c ${config} journal update --modalities OMOP,Waveforms
 python chorus_upload -v -c ${config} journal update --modalities OMOP,Waveforms
-cp journal.db TestData/journal2.1.db
+cp journal_test.db TestData/journal2.1.db
 
 echo TEST generate file list
 echo python chorus_upload -v -c ${config} file list --modalities OMOP,Waveforms --output-file ${azcli} --output-type azcli --max-num-files 15
@@ -136,11 +136,11 @@ echo TEST with cloud journal and upload to central azcli
 chmod a+x ${azcli}
 # run the azcli script
 eval ${azcli}
-cp journal.db TestData/journal2.2.db
+cp journal_test.db TestData/journal2.2.db
 
 echo python chorus_upload -v -c ${config} journal update --modalities Images
 python chorus_upload -v -c ${config} journal update --modalities Images
-cp journal.db TestData/journal2.3.db
+cp journal_test.db TestData/journal2.3.db
 
 
 echo TEST generate file list again
@@ -152,24 +152,24 @@ echo TEST with cloud journal and upload to central azcli - AMENDING
 chmod a+x ${azcli2}
 # run the azcli script
 eval ${azcli2}
-cp journal.db TestData/journal2.4.db
+cp journal_test.db TestData/journal2.4.db
 
 echo TEST with cloud journal and upload to central built in - AMENDING
 echo python chorus_upload -v -c ${config} file upload --modalities OMOP,Waveforms  --max-num-files 15
 python chorus_upload -v -c ${config} file upload --modalities OMOP,Waveforms  --max-num-files 15
-cp journal.db TestData/journal2.5.db
+cp journal_test.db TestData/journal2.5.db
 
 
 echo TEST update journal with second snapshot data
 echo python chorus_upload -v -c ${config} journal update --modalities Images
 python chorus_upload -v -c ${config} journal update --modalities Images
-cp journal.db TestData/journal2.6.db
+cp journal_test.db TestData/journal2.6.db
 
 
 echo TEST with cloud journal and upload to central using builcloud
 echo python chorus_upload -v -c ${config} file upload --modalities Images
 python chorus_upload -v -c ${config} file upload --modalities Images
-cp journal.db TestData/journal2.7.db
+cp journal_test.db TestData/journal2.7.db
 
 echo TEST verify the version
 echo python chorus_upload -v -c ${config} file verify --modalities OMOP
@@ -178,30 +178,30 @@ python chorus_upload -v -c ${config} file verify --modalities OMOP
 
 # ========================
 echo TEST phase 3: mixture of local and cloud
-rm journal.db
-az storage blob delete-batch --account-name ${account} --source ${container} --sas-token ${sas} --pattern "journal.db*"
+rm journal_test.db
+az storage blob delete-batch --account-name ${account} --source ${container} --sas-token ${sas} --pattern "journal_test.db*"
 config=tests/config.toml
 configlocal=tests/configlocal.toml  # this should reference localjournal
 azcli=TestData/azcli5.sh
 azcli2=TestData/azcli6.sh
-localjournal=journal.db
+localjournal=journal_test.db
 
 echo TEST checkout cloud journal, update, then check in.
 echo python chorus_upload -v -c ${config} journal checkout --local-journal ${localjournal}
 python chorus_upload -v -c ${config} journal checkout --local-journal ${localjournal}
-cp journal.db TestData/journal3.1.db
+cp journal_test.db TestData/journal3.1.db
 
 echo python chorus_upload -v -c ${configlocal} journal update --modalities OMOP,Waveforms
 python chorus_upload -v -c ${configlocal} journal update --modalities OMOP,Waveforms
-cp journal.db TestData/journal3.2.db
+cp journal_test.db TestData/journal3.2.db
 
 echo python chorus_upload -v -c ${config} journal checkin --local-journal ${localjournal}
 python chorus_upload -v -c ${config} journal checkin --local-journal ${localjournal}
 
 echo TEST checkout cloud journal 
 echo python chorus_upload -v -c ${config} journal checkout --local-journal ${localjournal}
 python chorus_upload -v -c ${config} journal checkout --local-journal ${localjournal}
-cp journal.db TestData/journal3.3.db
+cp journal_test.db TestData/journal3.3.db
 
 
 echo TEST generate file list
@@ -213,7 +213,7 @@ echo TEST with local journal and upload to central azcli
 chmod a+x ${azcli}
 # run the azcli script
 eval ${azcli}
-cp journal.db TestData/journal3.4.db
+cp journal_test.db TestData/journal3.4.db
 
 
 echo TEST generate file list
@@ -225,7 +225,7 @@ echo TEST with local journal and upload to central azcli - AMENDING
 chmod a+x ${azcli2}
 # run the azcli script
 eval ${azcli2}
-cp journal.db TestData/journal3.5.db
+cp journal_test.db TestData/journal3.5.db
 
 
 echo TEST checkin journal
@@ -242,13 +242,13 @@ echo TEST with central journal and upload to central azcli - AMENDING
 chmod a+x ${azcli}
 # run the azcli script
 eval ${azcli}
-cp journal.db TestData/journal3.6.db
+cp journal_test.db TestData/journal3.6.db
 
 
 echo TEST with cloud journal upload to central built in - AMENDING
 echo python chorus_upload -v -c ${config} file upload --modalities OMOP,Waveforms
 python chorus_upload -v -c ${config} file upload --modalities OMOP,Waveforms 
-cp journal.db TestData/journal3.7.db
+cp journal_test.db TestData/journal3.7.db
 
 echo TEST verify the version
 echo python chorus_upload -v -c ${config} file verify --modalities OMOP