diff --git a/environment.yml b/environment.yml index 746fe16..1a1d94d 100644 --- a/environment.yml +++ b/environment.yml @@ -9,7 +9,6 @@ dependencies: - click - pytest - setuptools - - plotly - boto3 - botocore - tqdm diff --git a/pridepy/aspera/key/aspera_tokenauth_id_rsa b/pridepy/aspera/key/aspera_tokenauth_id_rsa index d5945f3..31ca55d 100644 --- a/pridepy/aspera/key/aspera_tokenauth_id_rsa +++ b/pridepy/aspera/key/aspera_tokenauth_id_rsa @@ -1,49 +1,27 @@ ------BEGIN OPENSSH PRIVATE KEY----- -b3BlbnNzaC1rZXktdjEAAAAABG5vbmUAAAAEbm9uZQAAAAAAAAABAAACFwAAAAdzc2gtcn -NhAAAAAwEAAQAAAgEA4FbWABq7/xksqaNSJWrhTIwwmsDKEUALyzu9U3OSsJawBUV5JXE0 -WdkF7Igx7LIdCk1Y5jUsuxV3HDJSQlzAE8l3kd7I2NiXXJNzVhPPShSGkqf/gOgBWL+qya -qavGsWx5gbkAOxkWzkoVrdebWdGsVgj9LEa9NvdWw6/blm4JBUtJY6+d/N/QDmfXm1nDVq -QGrwfRVOUTD8JmJtoYb4SjO0tKmqt9IDdx5qxEXDX9zHpyl0rk6eoSjtNA/KIVkuUiT7I7 -rejv2leHeui91Q+j5jfiXcVq88zVl+7Mr0Hf1u6aX8Nmf0rvMYdp1AtPRuzjd4+q5Sl+EZ -N42IDjNItcvFcAj52Nvg3UVsqsDhWZb+bZmVSGJAvFHYUbt4XSJp57g7xwy/PIPwmhM7jh -mC6DFbUR/NoGqEGOJ+48iZOIp3OHfYvCZJ5eibTj33OaXh0Zh450rqb7h2gLOGmadMGonf -xeFMiNJgnyCnvv1W8cjmZ/ZuG9/FwjKE8nxJo0u7OfUYcXyuyRHcyQtZaVg/d22fyeo8zM -wyXyaTeHAyEmPad4S30dTNbbpReOLHL+ep9/Fw8s5LY+namtT/4SToDloZ7EXvE2osHRAO -hBKh8FBKdrEpyzZ5OY30HrZ4t3r82ouC8ufAymPhN9ZeTOtPggtnTHBxCbxf+QKiZqD4zs -0AAAc45zREkec0RJEAAAAHc3NoLXJzYQAAAgEA4FbWABq7/xksqaNSJWrhTIwwmsDKEUAL -yzu9U3OSsJawBUV5JXE0WdkF7Igx7LIdCk1Y5jUsuxV3HDJSQlzAE8l3kd7I2NiXXJNzVh -PPShSGkqf/gOgBWL+qyaqavGsWx5gbkAOxkWzkoVrdebWdGsVgj9LEa9NvdWw6/blm4JBU -tJY6+d/N/QDmfXm1nDVqQGrwfRVOUTD8JmJtoYb4SjO0tKmqt9IDdx5qxEXDX9zHpyl0rk -6eoSjtNA/KIVkuUiT7I7rejv2leHeui91Q+j5jfiXcVq88zVl+7Mr0Hf1u6aX8Nmf0rvMY -dp1AtPRuzjd4+q5Sl+EZN42IDjNItcvFcAj52Nvg3UVsqsDhWZb+bZmVSGJAvFHYUbt4XS -Jp57g7xwy/PIPwmhM7jhmC6DFbUR/NoGqEGOJ+48iZOIp3OHfYvCZJ5eibTj33OaXh0Zh4 -50rqb7h2gLOGmadMGonfxeFMiNJgnyCnvv1W8cjmZ/ZuG9/FwjKE8nxJo0u7OfUYcXyuyR 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-nEzg0+YHN7JGrFpR0ZRgKUORs8ajC7OCkkeunXicGrABkWcEzfhzHJ0kIhb/jKRThMwv5g -VrDBOxh0ODDRAAAAAAEC ------END OPENSSH PRIVATE KEY----- +-----BEGIN RSA PRIVATE KEY----- +MIIEpAIBAAKCAQEA3k3TTTgZ9R9HezmJ3Q5RBdy5cJpS4jF6ULUMA228KVCa++CM +9O4b0J8QoaZBnMX4jcIRB4kd9e+PwJjUcDwHGpL+41YSl46Vnic7gOuRxLDo2nwm +8YU+zJ0Qlz0faO7AlzfyGAwSinsapCg07pnfvbQwmACLFLs3MOiKZrUZzGufTw9P +MVkClxxMUANjzdgIqvOFEENcCYtNyt1uGCvo5A1gIKiRJWtuk8WKea9zvF5EAmIw +YnEmbUELtWsnMoHDERmcsrGPlSwNxWpPQYeluy2InlNQgZyMNduAqevJDQwf2SXZ +7kzxQ/HmHzVRKWSVmE9ZQ5vzGrnOWghVdSffwQIDAQABAoIBAA7Nv3O9t+rNI7E2 +xnHAVZBun7G6MSlLcrIDsHJdASH+MmfyDujzn0oQAadGH0ntnAzynrgx/xsE0j2Y +39K+iJmSLuOcNH4/ukJvKeT+qvUec88y49QDE8jD79omcZxHA+++A8LqsORkaMSE +QewetpnXMUI6DQj7I6R/49GNn1NvuoN3mx7ID9wBOGHtvTRPgYSASXOsCaqCq7eq +mzdYD1Hg45ozZHOXVQBXbJ6cRx7EDyI2ggyQTj4C2EqHRHhViTI/U3JwGXl5skFr +M26TyUyT+i+stHwUjgkiK05nD/cWLgaE/untGHkkzSCRehxaUiYCHmWIoFlyxMMm +lbcW2g0CgYEA82JG1y01A4Sut/jmVseAI99juU2aoSH7xsvuPBYga19YIHW5hkbH 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+++ b/pridepy/files/files.py @@ -284,7 +284,7 @@ def download_files_from_aspera( """ ascp_path = Files.get_ascp_binary() key_full_path = importlib.resources.files("pridepy").joinpath( - "aspera/key/aspera_tokenauth_id_rsa" + "aspera/key/asperaweb_id_dsa.openssh" ) key_path = os.path.abspath(key_full_path) for file in file_list_json: diff --git a/pridepy/statistics/__init__.py b/pridepy/statistics/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/pridepy/statistics/statistics.py b/pridepy/statistics/statistics.py deleted file mode 100644 index ddd3f98..0000000 --- a/pridepy/statistics/statistics.py +++ /dev/null @@ -1,48 +0,0 @@ -import plotly -import plotly.graph_objs as go - -from pridepy.util.api_handling import Util - -base_url = "https://www.ebi.ac.uk/pride/ws/archive/v3/" - - -class Statistics: - """ - Statistics class supports to produce charts on PRIDE submission statistics. - """ - - @staticmethod - def plot_monthly_submissions(output_filename): - """ - Plot monthly submission as a bar chart and save into a file - :param output_filename: html output file - :return: - """ - - # get monthly submission data from API - request_url = base_url + "stats/submissions-monthly" - headers = {"Accept": "application/JSON"} - - response = Util.get_api_call(request_url, headers) - response_body = response.json() - - # sort data by past to present - data = [ - go.Bar( - x=[d[0] for d in response_body][::-1], - y=[d[1] for d in response_body][::-1], - ) - ] - - # plot the data in a bar chart - plotly.offline.plot(data, filename=output_filename, auto_open=True) - - @staticmethod - def plot_submissions_by_instrument(output_filename): - """ - Plot submissions by instruments to visualise the pecentage of submission from different instruments. - :param output_filename: - :return: html output file - """ - # Todo - pass diff --git a/pyproject.toml b/pyproject.toml index 870d8cb..04f5804 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "pridepy" -version = "0.0.10" +version = "0.0.12" description = "Python Client library for PRIDE Rest API" authors = [ "PRIDE Team ", @@ -48,7 +48,6 @@ python = "^3.9" requests = "^2.31.0" ratelimit = "^2.2.1" click = "^8.1.7" -plotly = "^5.18.0" tqdm = "^4.66.1" boto3 = "^1.34.0" botocore = "^1.34.0" diff --git a/recipe/meta.yaml b/recipe/meta.yaml index f4178cc..bef43a0 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -1,7 +1,7 @@ # recipe/meta.yaml package: name: pridepy - version: "0.0.8" + version: "0.0.12" source: path: ../ @@ -26,7 +26,6 @@ requirements: - click~=8.1.7 - pytest~=8.0.2 - setuptools - - plotly~=5.22.0 - boto3~=1.34.61 - botocore~=1.34.74 - tqdm diff --git a/requirements.txt b/requirements.txt index 6750e0a..3bae141 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,7 +3,6 @@ ratelimit click pytest setuptools -plotly boto3 botocore tqdm