Minghui dev #55
Minghui dev #55
Conversation
* test pull (#48) * remove test file * modify the email module to use the rdas system to send email, move the initiation firebase admin to the star_dev, replaced ses_firebase.py codes by test_ses_firebase.py * remove test emails and remove '/' from file_paths in the sysvars.py --------- Co-authored-by: devonleadman <shanmardev@hotmail.com>
…ses alerts into one email.
sysvars.py
Outdated
| @@ -16,11 +16,12 @@ | |||
| firebase_key_path = '{base_path}crt/ncats-summer-interns-firebase-adminsdk-9g7zz-a4e783d24c.json'.format(base_path=base_path) # May have to set this in new enviroment | |||
|
|
|||
| # if you are not using minghui's test dataset, make db_prefix="" | |||
| db_prefix="minghui." | |||
| db_prefix="minghui.rdas." | |||
There was a problem hiding this comment.
Change this back to "" before commiting
sysvars.py
Outdated
| @@ -5,7 +5,7 @@ | |||
| # Basic user information | |||
| current_user = 'aom2' | |||
| base_directory_name = 'RDAS' | |||
| base_path = '/home/{current_user}/{base_directory_name}/'.format(current_user=current_user, base_directory_name=base_directory_name) | |||
| base_path = '/home/{current_user}/RDAS_master/{base_directory_name}/'.format(current_user=current_user, base_directory_name=base_directory_name) | |||
There was a problem hiding this comment.
Change this back to '/home/{current_user}/{base_directory_name}/'
start_dev.py
Outdated
|
|
||
| print(f'Update of {full_db_name} Database Complete...') | ||
| if True in has_updates.values(): | ||
| ses_firebase.trigger_email(firestore_db,has_updates, date_start='03/23/22',date_end='03/30/24') |
There was a problem hiding this comment.
Hard coded dates, i think these should be some sort of variable
start_dev.py
Outdated
| for k,v in current_updates.items(): | ||
| print("updates:::",k,v) | ||
| if v == True: | ||
| full_db_name = sysvars.db_abbrevs[k] | ||
| print(f'{full_db_name} Update Initiated') | ||
| has_updates[full_db_name]=True | ||
| # p = Popen(['python3', 'driver_manual.py', '-db', f'{k}', '-m', 'update'], encoding='utf8') |
There was a problem hiding this comment.
Make sure to un-comment the lines of codes 91 - 119
start_dev.py
Outdated
| @@ -38,7 +41,8 @@ def check_update(db_type): | |||
| # Get the current date and time | |||
| today = datetime.now() | |||
|
|
|||
| config_selection = {'ct':['clinical_update', 'ct_interval'], 'pm':['pubmed_update', 'pm_interval'], 'gnt':['grant_update', 'gnt_interval']} | |||
| # config_selection = {'ct':['clinical_update', 'ct_interval'], 'pm':['pubmed_update', 'pm_interval'], 'gnt':['grant_update', 'gnt_interval']} | |||
There was a problem hiding this comment.
I think this line needs to be uncommented and the below line commented out, that or use the variable in sysvars.py to make this generalizable
emails/ses_firebase.py
Outdated
| cred = credentials.Certificate(sysvars.firebase_key_path) | ||
| firebase_admin.initialize_app(cred) | ||
| firestore_db = firestore.client() | ||
| convert = {prefix+'ctkg':['ClinicalTrial','GARD','GardId'], prefix+'pakg':['Article','GARD','GardId'], prefix+'gfkg':['Project','GARD','GardId']} |
There was a problem hiding this comment.
manually doing "prefix+'ctkg'" seems unnecessary as in sysvars.py we already build out the DB name we are using. Example: the variable ct_db in sysvars.py
There was a problem hiding this comment.
We can just set the prefix ="". by keeping the prefix it will be easier for the development because it unifies the settings according to our needs. so next time if we need to make any improvement, we don't need to change all the parameters over and over again.
emails/ses_firebase.py
Outdated
| firebase_admin.initialize_app(cred) | ||
| firestore_db = firestore.client() | ||
| convert = {prefix+'ctkg':['ClinicalTrial','GARD','GardId'], prefix+'pakg':['Article','GARD','GardId'], prefix+'gfkg':['Project','GARD','GardId']} | ||
| connect_to_gard = {prefix+'ctkg':'--(:Condition)--(:Annotation)--',prefix+'pakg':'--',prefix+'gfkg':'--'} |
There was a problem hiding this comment.
same as my above comment
emails/ses_firebase.py
Outdated
| def trigger_email(firestore_db,has_updates,date_start=datetime.today().strftime('%m/%d/%y'), date_end=datetime.today().strftime('%m/%d/%y')): | ||
| print("start_date",date_start, " end date:: ",date_end) | ||
| #obtain users contact information | ||
| txt_tabs_1 = {'trials':prefix +'ctkg', 'grants':prefix +'gfkg', 'articles':prefix +'pakg'} |
There was a problem hiding this comment.
same as above for lines 71-72
There was a problem hiding this comment.
same as my above comment
| date_list = pd.date_range(date_start_obj, date_end_obj, freq='D').strftime('%m/%d/%y').to_list() | ||
|
|
||
| print(f'Searching for nodes created between {date_start_string} and {date_end_string}') | ||
| prefix = sysvars.db_prefix # you can set the db_prefix in sysvars.py |
There was a problem hiding this comment.
you can probably remove this with the fixes below this
config.ini
Outdated
| minghui.grant_update = 11/30/22 | ||
| minghui.pubmed_update = 10/30/22 | ||
| minghui.gard_update = 11/30/23 | ||
| ; minghui.clinical_update = 01/08/24 |
There was a problem hiding this comment.
confused on what these lines are with the ; symbol
There was a problem hiding this comment.
the ; symbol means these lines are commented out
updated start_dev.py and modified email models to merge clinical trail, grants and publications into one email alert.