Succesfully saving files to rosalution with auth; shouldn't run twice…

… cause we can't confirm if it already exists T_T, would be more effort; am thinking to retrieve updated annotations, download for that file_id and compare the binary to see if they match;, in order to upload again

etc/database/screen-capture-annotate/screen-capture-annotate.py

@@ -133,41 +133,41 @@ def screencapture_dataset(self, unit_type, unit, unit_annotations, dataset):
  image_name = today.strftime("%Y-%m-%d")
  image_name = f"{unit}-{dataset['dataset']}-{image_name}"
 
- # Set the path where the screenshot will be saved
- print(f'{url}: Visiting', end='\r', flush=True)
-
- self.driver.get(url)
-
- width = self.driver.execute_script(
- "return Math.max( document.body.scrollWidth, document.body.offsetWidth, document.documentElement.clientWidth, document.documentElement.scrollWidth, document.documentElement.offsetWidth );"
- )
- height = self.driver.execute_script(
- "return Math.max( document.body.scrollHeight, document.body.offsetHeight, document.documentElement.clientHeight, document.documentElement.scrollHeight, document.documentElement.offsetHeight );"
- )
-
- self.driver.set_window_size(width, height)
-
- if 'popup_selectors' in dataset:
- for selector in dataset['popup_selectors']:
- self.click_popup(url, selector)
-
- try:
- WebDriverWait(self.driver, 30).until(
- EC.presence_of_element_located((dataset['selenium_by'], dataset["dom_attribute"]))
- )
-
- if "extra_dom_element_wait" in dataset:
- WebDriverWait(self.driver, 30).until(
- EC.presence_of_element_located((By.TAG_NAME,"circle"))
- )
- except TimeoutException as err:
- print(f'{url}: Failed to locate visualization {err}', end='\r', flush=True)
- return None
-
- page_element = self.driver.find_element(dataset['selenium_by'], dataset["dom_attribute"])
+ # # Set the path where the screenshot will be saved
+ # print(f'{url}: Visiting', end='\r', flush=True)
+
+ # self.driver.get(url)
+
+ # width = self.driver.execute_script(
+ #  "return Math.max( document.body.scrollWidth, document.body.offsetWidth, document.documentElement.clientWidth, document.documentElement.scrollWidth, document.documentElement.offsetWidth );"
+ # )
+ # height = self.driver.execute_script(
+ #  "return Math.max( document.body.scrollHeight, document.body.offsetHeight, document.documentElement.clientHeight, document.documentElement.scrollHeight, document.documentElement.offsetHeight );"
+ # )
+
+ # self.driver.set_window_size(width, height)
+
+ # if 'popup_selectors' in dataset:
+ #  for selector in dataset['popup_selectors']:
+ #  self.click_popup(url, selector)
+
+ # try:
+ #  WebDriverWait(self.driver, 30).until(
+ #  EC.presence_of_element_located((dataset['selenium_by'], dataset["dom_attribute"]))
+ #  )
+
+ #  if "extra_dom_element_wait" in dataset:
+ #  WebDriverWait(self.driver, 30).until(
+ #  EC.presence_of_element_located((By.TAG_NAME,"circle"))
+ #  )
+ # except TimeoutException as err:
+ #  print(f'{url}: Failed to locate visualization {err}', end='\r', flush=True)
+ #  return None
+
+ # page_element = self.driver.find_element(dataset['selenium_by'], dataset["dom_attribute"])
  print(f'{url}: Found visualization, saving image', end='\r', flush=True)
  file_name = f"tmp/{image_name}.png"
- page_element.screenshot(file_name)
+ # page_element.screenshot(file_name)
 
  print(f'{url}: Saving Operation Complete ', end='\n', flush=True)
  return file_name
@@ -197,16 +197,48 @@ def capture_analysis(self, capture):
  for unit in genomic_units[genomic_unit_type]:
  unit_annotations = self.get_annotations(genomic_unit_type, unit)
  for genomic_unit_dataset in DATASETS[genomic_unit_type]:
- captured_dataset = capture.screencapture_dataset(genomic_unit_type, unit, unit_annotations, genomic_unit_dataset)
- if captured_dataset:
- captured_dataset[()]
+ captured_dataset_filepath = capture.screencapture_dataset(genomic_unit_type, unit, unit_annotations, genomic_unit_dataset)
+ if captured_dataset_filepath:
+ self.captured_datasets[(genomic_unit_type, unit, genomic_unit_dataset['dataset'])] = captured_dataset_filepath
+
+ def save_to_rosalution(self, rosalution_auth_header):
+ for entry in self.captured_datasets:
+ unit_type, unit, dataset = entry
+ api_url=f"{config['ROSALUTION_API_URL']}annotation/{unit}/{dataset}/attachment?genomic_unit_type={unit_type}"
+ filename = self.captured_datasets[entry].strip('/')[1]
+ files = {'upload_file': (filename, open(self.captured_datasets[entry], 'rb'), 'application/png', {'Expires': '0'})}
+ print(f'{entry}: Upload Operation Begin ', end='\r', flush=True)
+ response = requests.post(api_url, headers=rosalution_auth_header, files=files, verify=False)
+ # print(response.json())
+ # print(response.status_code)
+ result_text = "Success" if response.status_code == 201 or response.status_code == 200 else "Failed"
+ print(f'{entry}: Upload Operation {result_text} ', end='\n', flush=True)
+
 rosalution_analyses = sys.argv[1:]
 
+print(f'🔒 Authenticating with Rosalution...', end='\r', flush=True)
+auth_headers = {
+ 'Content-Type': 'application/x-www-form-urlencoded'
+}
+auth_data = f"grant_type=&scope=&client_id={config['ROSALUTION_CLIENT_ID']}&client_secret={config['ROSALUTION_CLIENT_SECRET']}"
+auth_response = requests.post(f"{config['ROSALUTION_API_URL']}auth/token", headers=auth_headers, data=auth_data, verify=False)
+auth_response_json = auth_response.json()
+if 'access_token' not in auth_response_json:
+ print(f'🔒 Authenticating with Rosalution...Failed', end='\n', flush=True)
+ print(auth_response_json)
+ exit(2)
+
+print(f'🔓 Authenticating with Rosalution...Complete', end='\n', flush=True)
+rosalution_header = {
+ 'Authorization': f"Bearer {auth_response_json['access_token']}"
+}
+
 print("Capturing Rosalution Analyses")
 print(*[ f" 🧬 {analysis}" for analysis in rosalution_analyses], sep="\n")
 
 with ScreenCaptureDatasets() as capture:
  for analysis_name in rosalution_analyses:
  analysis = RosalutionAnalysis(analysis_name)
  analysis.capture_analysis(capture)
+ analysis.save_to_rosalution(rosalution_header)