Merge branch 'py-scripts' into 'master'

Py scripts

See merge request !1

.gitignore

+_site
+.sass-cache
+.jekyll-metadata
+.idea
+.cache
+builds
+test
+Gemfile.lock
+.DS_Store

Python/create_accounts/1_create_accounts.py

+##################################################
+## MINERVA API version: 14.0
+## Script purpose: An example of MINERVA API calls adding curators form the file users.txt
+## Date: 23/03/2020
+## Author: Piort Gawron (piotr.gawron@uni.lu)
+## MANUAL: https://minerva.pages.uni.lu/doc/api/14.0/users/
+##################################################
+
+### A convenience function to handle the text files and the server repsonses
+import csv
+import requests
+
+session = requests.Session()
+
+### INPUT YOUR CREDENTIALS TO LOGIN to PD map instance
+login = "  "
+password = "  "
+api_url = "https://pdmap.uni.lu/minerva/api/"
+
+
+# LOGIN to PD map instance with your credentials
+login_request = session.post(api_url+"/doLogin", data = {'login': login, 'password': password})
+
+print(login_request.text)
+print(session.cookies.get_dict())
+
+
+# READ USER LIST from the users.txt
+with open("users.txt") as tsv:
+  for line in csv.reader(tsv, delimiter="\t"):
+    user_email = line[0]
+    user_name = line[1]
+    user_surname = line[2]
+    user_login = line[3]
+    user_password = line[4]
+    print ("User: ",user_login)
+    # GET USER DETAILS (check if user_login already exists in MINERVA)
+    user_request = session.get(api_url+"/users/"+user_login)
+
+    if user_request.status_code != 200:  # if user does not exist
+      print("Creating")
+      # CREATE NEW USER with details provided in the file users.txt
+      create_user_request = session.post(api_url+"/users/"+user_login,
+                                         data = {'name':user_name, 'surname': user_surname, 'email':user_email, 'password':user_password})
+      print(create_user_request.status_code)
+
+    else:
+      print("User Exists")
+      # GET existing USER details
+      specific_user_data = session.get(api_url+"/users/"+user_login)
+      print(specific_user_data.text)
+
+      # UPDATE USER user_login details as per the file users.txt
+      update_user_request = session.patch(api_url+"/users/"+user_login,
+                                          data = '{"user":{"name":"'+user_name+'", "surname": "'+user_surname+'", "email":"'+user_email+
+                                                 '", "password":"'+user_password+'"}}')
+      print(update_user_request.status_code)
+
+    # MODIFY USER PRIVILEGES from 'user' onto 'curator'
+    update_privileges_request = session.patch(api_url+"/users/"+user_login+
+                                              ":updatePrivileges", data = '{"privileges":{"IS_CURATOR":true, "IS_ADMIN":false}}')
+    print(update_privileges_request.status_code)
+

Python/create_accounts/users.txt

+curator-anna@dot.com	Anna	Kate	anna.kate3	test1
+curator-mike@dot.com	Mike	John	mike.john3	test2

Python/requirements.txt

+requests
\ No newline at end of file

Python/upload_advanced_model/4_upload_advanced_model.py

+##################################################
+## MINERVA API version: 14.0
+## Script purpose: An example of MINERVA API calls uploading zipped project
+## Date: 23/03/2020
+## Author: Piort Gawron (piotr.gawron@uni.lu)
+## MANUAL: https://minerva.pages.uni.lu/doc/api/14.0/projects/
+##################################################
+
+
+import requests
+import os
+import json
+
+session = requests.Session()
+
+### INPUT YOUR CREDENTIALS TO LOGIN to PD map instance
+login = "  "
+password = "  "
+api_url = "https://pdmap.uni.lu/minerva/api/"
+map_file = "example_advanced.zip"
+
+# LOGIN to PD map instance with your credentials
+login_request = session.post(api_url+"/doLogin", data = {'login': login, 'password': password})
+print(login_request.text)
+print(session.cookies.get_dict())
+
+
+# UPLOAD FILE TO THE SYSTEM
+stat_info = os.stat(map_file)
+with open(map_file, mode ="rb") as f: file_content = f.read()
+
+# Before creating a new project in MINERVA, source file 'map_file' must be uploaded to the instance (MANUAL: https://minerva.pages.uni.lu/doc/api/14.0/files/)
+# Allocate memory in the system for 'map_file', which length is 'stat_info.st_size' bytes
+create_file_request = session.post(api_url+"/files/", data = {'filename': map_file, 'length': stat_info.st_size})
+
+# Get the information about the uploaded file: the 'id' is necessary to upload the file's content.
+content  = json.loads(create_file_request.text)
+
+file_id = content["id"]
+# Upload file's content to the instance
+upload_content_request = session.post(api_url+"/files/"+str(file_id)+":uploadContent", data = file_content)
+
+
+# CREATE PROJECT FROM FILE
+project_id = "adv_"+str(file_id)
+
+# DEFINE PROJECT PARAMETERS (what is what in the zip file)
+data = [
+  ('projectId', project_id),
+  ('name', ''),
+  ('parser', 'lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser'),
+  ('file-id', str(file_id)),
+  ('auto-resize', 'true'),
+  ('cache', 'false'),
+  ('notify-email', ''),
+  ('disease', ''),
+  ('version', ''),
+  ('organism', ''),
+  ('mapCanvasType', 'OPEN_LAYERS'),
+  ('sbgn', 'false'),
+  ('semantic-zoom', 'false'),
+  ('annotate', 'false'),
+  ('verify-annotations', 'false'),
+  ('zip-entries[0][_type]', 'MAP'),
+  ('zip-entries[0][_filename]', 'example_advanced_map.xml'),
+  ('zip-entries[0][_data][root]', 'true'),
+  ('zip-entries[0][_data][name]', 'example_advanced_map'),
+  ('zip-entries[0][_data][type][id]', 'UNKNOWN'),
+  ('zip-entries[0][_data][type][name]', 'Unknown'),
+  ('zip-entries[1][_type]', 'IMAGE'),
+  ('zip-entries[1][_filename]', 'images/coords.txt'),
+  ('zip-entries[2][_type]', 'IMAGE'),
+  ('zip-entries[2][_filename]', 'images/overview_sub.png'),
+  ('zip-entries[3][_type]', 'IMAGE'),
+  ('zip-entries[3][_filename]', 'images/overview_main.png'),
+  ('zip-entries[4][_type]', 'OVERLAY'),
+  ('zip-entries[4][_filename]', 'overlays/example_upload_basic.txt'),
+  ('zip-entries[4][_data][name]', 'Advanced example'),
+  ('zip-entries[4][_data][description]', 'Advanced example of custom layout'),
+  ('zip-entries[5][_type]', 'MAP'),
+  ('zip-entries[5][_filename]', 'submaps/mapping.xml'),
+  ('zip-entries[5][_data][mapping]', 'true'),
+  ('zip-entries[5][_data][name]', 'mapping'),
+  ('zip-entries[5][_data][type][id]', 'UNKNOWN'),
+  ('zip-entries[5][_data][type][name]', 'Unknown'),
+  ('zip-entries[6][_type]', 'MAP'),
+  ('zip-entries[6][_filename]', 'submaps/example_submap.xml'),
+  ('zip-entries[6][_data][name]', 'example_submap'),
+  ('zip-entries[6][_data][type][id]', 'UNKNOWN'),
+  ('zip-entries[6][_data][type][name]', 'Unknown'),
+]
+
+# AND CREATE A PROJECT
+create_map_request = session.post(api_url+"/projects/"+project_id, data = data)
+
+print(create_map_request.text)

Python/upload_data_overlay/3_upload_data_overlay.py

+##################################################
+## MINERVA API version: 14.0
+## Script purpose: An example of MINERVA API calls uploading overlays
+## Date: 23/03/2020
+## Author: Piort Gawron (piotr.gawron@uni.lu)
+## MANUAL: https://minerva.pages.uni.lu/doc/api/14.0/projects/
+##################################################
+
+
+import requests
+import os
+import json
+
+session = requests.Session()
+
+### INPUT YOUR CREDENTIALS TO LOGIN to PD map instance
+login = "  "
+password = "  "
+api_url = "https://pdmap.uni.lu/minerva/api/"
+overlay_file = "example_upload_basic.txt"
+project_id = "empty"
+
+# LOGIN to PD map instance with your credentials
+login_request = session.post(api_url+"/doLogin", data = {'login': login, 'password': password})
+print(login_request.text)
+print(session.cookies.get_dict())
+
+
+# UPLOAD OVERLAY FILE TO THE SYSYETM
+stat_info = os.stat(overlay_file)
+with open(overlay_file) as f: file_content = f.read()
+
+# Before addind an overlay in MINERVA, data overlay file must be uploaded to the instance (MANUAL: https://minerva.pages.uni.lu/doc/api/14.0/files/)
+# Allocate memory in the system for 'overlay_file', which length is 'stat_info.st_size' bytes
+create_file_request = session.post(api_url+"/files/", data = {'filename': overlay_file, 'length': stat_info.st_size})
+
+# Get the information about the uploaded file: the 'id' is necessary to upload the file's content
+content = json.loads(create_file_request.text)
+
+file_id = content["id"]
+# Upload file's content to the instance
+upload_content_request = session.post(api_url+"/files/"+str(file_id)+":uploadContent", data = file_content)
+
+
+# CREATE DATA OVERLAY FROM UPLOADED FILE
+create_overlay_request = session.post(api_url+"/projects/"+project_id+"/overlays/", data = {"fileId":file_id, "filename":overlay_file, "name":"auto-overlay-simple"+str(file_id), "description":"there is a data overlay", "googleLicenseConsent":"true"})
+
+print("Overlay Added: ", create_overlay_request.text)

Python/upload_data_overlay/example_upload_basic.txt

+NAME	VALUE
+SNCA	-0.5
+PARK2	0.75
\ No newline at end of file

Python/upload_simple/2_upload_simple.py

+##################################################
+## MINERVA API version: 14.0
+## Script purpose: An example of MINERVA API calls adding new project
+## Date: 23/03/2020
+## Author: Piort Gawron (piotr.gawron@uni.lu)
+## MANUAL: https://minerva.pages.uni.lu/doc/api/14.0/projects/
+##################################################
+
+
+import requests
+import os
+import json
+import time
+
+session = requests.Session()
+
+### INPUT YOUR CREDENTIALS TO LOGIN to PD map instance
+login = " "
+password = " "
+api_url = "https://pdmap.uni.lu/minerva/api/"
+map_file = "example_map.xml"
+
+# LOGIN to PD map instance with your credentials
+login_request = session.post(api_url+"/doLogin", data = {'login': login, 'password': password})
+print(login_request.text, "\n")
+print(session.cookies.get_dict(), "\n")
+
+
+# UPLOAD FILE TO THE SYSTEM
+stat_info = os.stat(map_file)
+with open(map_file) as f: file_content = f.read()
+
+# Before creating a new project in MINERVA, source file 'map_file' must be uploaded to the instance (MANUAL: https://minerva.pages.uni.lu/doc/api/14.0/files/)
+# Allocate memory in the system for 'map_file', which length is 'stat_info.st_size' bytes
+create_file_request = session.post(api_url+"/files/", data = {'filename': map_file, 'length': stat_info.st_size})
+
+# Get the information about the uploaded file: the 'id' is necessary to upload the file's content.
+content = json.loads(create_file_request.text)
+
+file_id = content["id"]
+# Upload file's content to the instance
+upload_content_request = session.post(api_url+"/files/"+str(file_id)+":uploadContent", data = file_content)
+
+
+# CREATE THE PROJECT
+project_id = "map_"+str(file_id)
+project_name = "An example"
+create_map_request = session.post(api_url+"/projects/"+project_id, data = {"file-id":file_id, "name": project_name , "version": "example", "mapCanvasType":"OPEN_LAYERS", "parser":"lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"})
+
+time.sleep(1)
+
+# GET LIST of all (sub)maps in the project
+get_submaps_request = session.get(api_url+"/projects/"+project_id+"/models/")
+content  = json.loads(get_submaps_request.text)
+# In this example there is only one map uploaded
+submap_id = content[0]['idObject']
+
+# PUT A COMMENT to the map pinned to the coordinates (100.00,100.00)
+create_comment_request = session.post(api_url+"/projects/"+project_id+"/comments/models/"+str(submap_id)+"/points/100.00,100.00", data = {"name":"Your Name", "email":"your_email@dot.com", "content":"automatically generated content","pinned":"true"})
+
+print("Comment details:", create_comment_request.text)
+