diff --git a/etc/database/screen-capture-annotate/screen-capture-annotate.py b/etc/database/screen-capture-annotate/screen-capture-annotate.py index 06390961..b34b0c42 100644 --- a/etc/database/screen-capture-annotate/screen-capture-annotate.py +++ b/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 @@ -197,11 +197,42 @@ 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") @@ -209,4 +240,5 @@ def capture_analysis(self, capture): for analysis_name in rosalution_analyses: analysis = RosalutionAnalysis(analysis_name) analysis.capture_analysis(capture) + analysis.save_to_rosalution(rosalution_header)