Merge pull request #17 from PRIDE-Archive/ascpS3AndGlobus

Ascp s3 and globus
PRIDE-Archive · Sep 26, 2024 · 7a6ab64 · 7a6ab64
2 parents a361024 + e027199
commit 7a6ab64
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diff --git a/.github/workflows/conda-build.yml b/.github/workflows/conda-build.yml
@@ -0,0 +1,64 @@
+name: Conda Build and Test
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: 3.8
+        channels: conda-forge,defaults,bioconda
+
+    - name: Create conda environment
+      run: conda env create -f environment.yml
+
+    - name: Install mamba, boa and conda-build
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate pridepy
+        conda install conda-forge::mamba
+        conda install conda-forge::boa
+        mamba install conda-build anaconda-client
+      shell: bash -l {0}
+
+    - name: Activate conda environment and build package
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate pridepy
+        conda mambabuild recipe
+      shell: bash -l {0}
+
+    - name: Install the built package
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate pridepy
+        mamba install --use-local pridepy
+      shell: bash -l {0}
+
+    - name: Output package info
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate pridepy
+        conda list
+      shell: bash -l {0}
+
+    - name: Test the installed package
+      run: |
+        conda activate pridepy
+        pridepy --help
+
+      shell: bash -l {0}
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 [![PyPI version](https://badge.fury.io/py/pridepy.svg)](https://badge.fury.io/py/pridepy)
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/pridepy)
 
-Python Client library for PRIDE Rest API 
+Python Client library for PRIDE Rest API
 
 # Installation
 To install, simply use `pip`:
@@ -13,21 +13,28 @@ To install, simply use `pip`:
 $ pip install --upgrade pridepy
 ```
 
-# Examples 
+# Examples
 
-Download all the raw files from a dataset(eg: PXD012353). 
+Download all the raw files from a dataset(eg: PXD012353).
 Warning: Raw files are generally large in size, so it may take some time to download depending on the number of files and file sizes.
+-p in download specifies protocol , Available protocols nows are ftp, aspera, s3 and globus. Default is ftp.
 
 ```python
-$ pridepy download-all-raw-files -a PXD012353 -o /Users/yourname/Downloads/foldername/
+$ pridepy download-all-raw-files -a PXD012353 -o /Users/yourname/Downloads/foldername/ -p aspera
 ```
 
 Download single file by name
 
 ```python
-$ pridepy download-files-by-name -a PXD022105 -o /Users/yourname/Downloads/foldername/ -f checksum.txt
+$ pridepy download-files-by-name -a PXD022105 -o /Users/yourname/Downloads/foldername/ -f checksum.txt -p s3
 ```
 
+```python
+$ pridepy download-files-by-name -a PXD022105 -o /Users/yourname/Downloads/foldername/ -f checksum.txt -p globus
+```
+
+Please note : Currently we use globus urls ( when -p globus is used) via https not globus protocol.
+
 Search projects with keywords and filters
 
 ```python
@@ -67,7 +74,6 @@ $ python3 pridepy.py --help
   search-peptide-evidences        
   search-projects-by-keywords-and-filters
   search-protein-evidences       
-  search-spectra-evidences        
   update-metadata                 
 
 ```

diff --git a/aspera/etc/aspera-license b/aspera/etc/aspera-license
@@ -0,0 +1,27 @@
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+VFhDZ3A1Z3RWDQp6RlhxUEJLbTFUQUZ3MHpBc3ZsMEVma0VmK0lzYXE4bFVx
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+U3FvazljQThIcURoN1NXVnBkKzBHOGNsVk8wY29IYWNwYnVKejQ4VXEvbg0K
+UmhVY20zTVEwMFN3YUJnSk1JdGF1c3Y5UWl4MWJtRmtHQU4xNGJGdGt3PT0N
+Cg==
diff --git a/aspera/etc/aspera.conf b/aspera/etc/aspera.conf
@@ -0,0 +1,15 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<CONF version="2">
+
+  <central_server>
+    <port>40001</port>
+    <address>127.0.0.1</address>
+  </central_server>
+
+  <default>
+  </default>
+
+  <aaa>
+  </aaa>
+
+</CONF>
diff --git a/aspera/key/asperaweb_id_dsa.openssh b/aspera/key/asperaweb_id_dsa.openssh
@@ -0,0 +1,12 @@
+-----BEGIN DSA PRIVATE KEY-----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+-----END DSA PRIVATE KEY-----
diff --git a/aspera/linux-32/ascmd b/aspera/linux-32/ascmd
diff --git a/aspera/linux-32/ascp b/aspera/linux-32/ascp
diff --git a/aspera/linux-32/ascp4 b/aspera/linux-32/ascp4
diff --git a/aspera/linux-32/aspshell b/aspera/linux-32/aspshell
diff --git a/aspera/linux-32/astokengen b/aspera/linux-32/astokengen
diff --git a/aspera/linux-32/faspstream b/aspera/linux-32/faspstream
diff --git a/aspera/linux-64/ascmd b/aspera/linux-64/ascmd
diff --git a/aspera/linux-64/ascp b/aspera/linux-64/ascp
diff --git a/aspera/linux-64/ascp4 b/aspera/linux-64/ascp4
diff --git a/aspera/linux-64/aspshell b/aspera/linux-64/aspshell
diff --git a/aspera/linux-64/astokengen b/aspera/linux-64/astokengen
diff --git a/aspera/linux-64/faspstream b/aspera/linux-64/faspstream
diff --git a/aspera/mac-intel/ascmd b/aspera/mac-intel/ascmd
diff --git a/aspera/mac-intel/ascp b/aspera/mac-intel/ascp
diff --git a/aspera/mac-intel/aspshell b/aspera/mac-intel/aspshell
diff --git a/aspera/mac-intel/astokengen b/aspera/mac-intel/astokengen
diff --git a/aspera/windows-32/ascmd.exe b/aspera/windows-32/ascmd.exe
diff --git a/aspera/windows-32/ascp.exe b/aspera/windows-32/ascp.exe
diff --git a/aspera/windows-32/ascp4.exe b/aspera/windows-32/ascp4.exe
diff --git a/aspera/windows-32/aspshell.exe b/aspera/windows-32/aspshell.exe
diff --git a/aspera/windows-32/astokengen.exe b/aspera/windows-32/astokengen.exe
diff --git a/aspera/windows-32/fasp3.dll b/aspera/windows-32/fasp3.dll
diff --git a/aspera/windows-32/faspstream.exe b/aspera/windows-32/faspstream.exe
diff --git a/aspera/windows-32/libeay32.dll b/aspera/windows-32/libeay32.dll
diff --git a/aspera/windows-32/msvcp100.dll b/aspera/windows-32/msvcp100.dll
diff --git a/aspera/windows-32/msvcr100.dll b/aspera/windows-32/msvcr100.dll
diff --git a/aspera/windows-32/ssleay32.dll b/aspera/windows-32/ssleay32.dll
diff --git a/aspera/windows-64/ascp.exe b/aspera/windows-64/ascp.exe
diff --git a/aspera/windows-64/ascp4.exe b/aspera/windows-64/ascp4.exe
diff --git a/aspera/windows-64/fasp3.dll b/aspera/windows-64/fasp3.dll
diff --git a/aspera/windows-64/faspstream.exe b/aspera/windows-64/faspstream.exe
diff --git a/aspera/windows-64/libeay32.dll b/aspera/windows-64/libeay32.dll
diff --git a/aspera/windows-64/msvcp100.dll b/aspera/windows-64/msvcp100.dll
diff --git a/aspera/windows-64/msvcr100.dll b/aspera/windows-64/msvcr100.dll
diff --git a/aspera/windows-64/ssleay32.dll b/aspera/windows-64/ssleay32.dll
diff --git a/authentication/authentication.py b/authentication/authentication.py
@@ -25,8 +25,14 @@ def get_token(self, username, password):
 
         # get token to access the api
         url = self.base_url + "getAAPToken"
-        headers = {'Content-type': 'application/json', 'Accept': 'text/plain'}
-        credentials = "{\"Credentials\":{\"username\":\"" + username + "\", \"password\":\"" + password + "\"}}"
+        headers = {"Content-type": "application/json", "Accept": "text/plain"}
+        credentials = (
+            '{"Credentials":{"username":"'
+            + username
+            + '", "password":"'
+            + password
+            + '"}}'
+        )
 
         response = requests.post(url, data=credentials, headers=headers)
 
@@ -44,8 +50,12 @@ def validate_token(self, token):
         :return: Return True if the token is valid and not expired: Otherwise returns False
         """
         url = self.base_url + "token-validation"
-        headers = {'Authorization': 'Bearer ' + token}
+        headers = {"Authorization": "Bearer " + token}
 
         response = requests.post(url, headers=headers)
 
-        return response.ok and response.status_code == 200 and response.text == 'Token Valid'
+        return (
+            response.ok
+            and response.status_code == 200
+            and response.text == "Token Valid"
+        )
diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,15 @@
+# environment.yml
+name: pridepy
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - requests~=2.31.0
+  - ratelimit~=2.2.1
+  - click~=8.1.7
+  - pytest~=8.0.2
+  - setuptools
+  - plotly~=5.22.0
+  - boto3~=1.34.61
+  - botocore~=1.34.74
+  - tqdm