Mercurial > repos > sanbi-uwc > data_manager_shapeit_reference

changeset 7:78ec8f452966 draft

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planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9772b96ea77a4daac91b5fc87643972a1d71eda-dirty
author sanbi-uwc
date Mon, 17 Sep 2018 12:56:35 -0400
parents 6b54dcb42cd5
children ec2c5e521533
files bioblend/.ipynb_checkpoints/Untitled-checkpoint.ipynb bioblend/.nbgrader.log bioblend/Untitled.ipynb tool_data_table_conf.xml.sample
diffstat 4 files changed, 229 insertions(+), 2 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bioblend/.ipynb_checkpoints/Untitled-checkpoint.ipynb	Mon Sep 17 12:56:35 2018 -0400
@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bioblend/.nbgrader.log	Mon Sep 17 12:56:35 2018 -0400
@@ -0,0 +1,25 @@
+[NotebookApp | WARNING] No nbgrader_config.py file found (rerun with --debug to see where nbgrader is looking)
+[NotebookApp | INFO] Loading the validate_assignment nbgrader serverextension
+[NotebookApp | INFO] ✓ nbpresent HTML export ENABLED
+[NotebookApp | WARNING] ✗ nbpresent PDF export DISABLED: No module named 'nbbrowserpdf'
+[NotebookApp | INFO] Serving notebooks from local directory: /home/pvh/Documents/code/SANBI/CPGR/data_managers/data_manager_shapeit_ref/bioblend
+[NotebookApp | INFO] 0 active kernels
+[NotebookApp | INFO] The Jupyter Notebook is running at:
+[NotebookApp | INFO] http://localhost:8888/?token=61e63c3509f8ac0317fda9361f366d62624139ff97fe34b1
+[NotebookApp | INFO] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
+[NotebookApp | CRITICAL] 
+    
+    Copy/paste this URL into your browser when you connect for the first time,
+    to login with a token:
+        http://localhost:8888/?token=61e63c3509f8ac0317fda9361f366d62624139ff97fe34b1
+[NotebookApp | INFO] Accepting one-time-token-authenticated connection from 127.0.0.1
+[NotebookApp | INFO] Creating new notebook in 
+[NotebookApp | INFO] Kernel started: 80389481-149c-4b52-9ae8-fa1b81e1ca1b
+[NotebookApp | INFO] Adapting to protocol v5.1 for kernel 80389481-149c-4b52-9ae8-fa1b81e1ca1b
+[NotebookApp | INFO] Saving file at /Untitled.ipynb
+[NotebookApp | INFO] Saving file at /Untitled.ipynb
+[NotebookApp | INFO] Saving file at /Untitled.ipynb
+[NotebookApp | INFO] Saving file at /Untitled.ipynb
+[NotebookApp | INFO] Saving file at /Untitled.ipynb
+[NotebookApp | INFO] Saving file at /Untitled.ipynb
+[NotebookApp | INFO] Saving file at /Untitled.ipynb
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bioblend/Untitled.ipynb	Mon Sep 17 12:56:35 2018 -0400
@@ -0,0 +1,196 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from bioblend import toolshed"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ts = toolshed.ToolShedInstance(url='https://testtoolshed.g2.bx.psu.edu', key='49ad6deed569af1c011647e3911b9ea7')\n",
+    "all_repos = ts.repositories.get_repositories()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[{'category_ids': ['83f763caf629aa54'],\n",
+       "  'deleted': False,\n",
+       "  'deprecated': False,\n",
+       "  'description': 'Add path for SHAPEIT reference data to shapeit_ref table',\n",
+       "  'homepage_url': '',\n",
+       "  'id': '59c15cd8db07b838',\n",
+       "  'model_class': 'Repository',\n",
+       "  'name': 'data_manager_shapeit_reference',\n",
+       "  'owner': 'sanbi-uwc',\n",
+       "  'private': False,\n",
+       "  'remote_repository_url': 'https://github.com/pvanheus/data_manager_shapeit_reference',\n",
+       "  'times_downloaded': 22,\n",
+       "  'type': 'unrestricted',\n",
+       "  'user_id': '25a703560f0040ae'}]"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "[ repo for repo in all_repos if repo['owner'] == 'sanbi-uwc' and repo['name'] == 'data_manager_shapeit_reference' ]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "all_revisions = ts.repositories.repository_revisions() "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[{'changeset_revision': '6b54dcb42cd5',\n",
+       "  'downloadable': False,\n",
+       "  'has_repository_dependencies': False,\n",
+       "  'id': 'c85f89a2a97b5743',\n",
+       "  'includes_datatypes': False,\n",
+       "  'includes_tool_dependencies': False,\n",
+       "  'includes_tools': False,\n",
+       "  'includes_tools_for_display_in_tool_panel': False,\n",
+       "  'includes_workflows': False,\n",
+       "  'malicious': False,\n",
+       "  'missing_test_components': False,\n",
+       "  'model_class': 'RepositoryMetadata',\n",
+       "  'repository_id': '59c15cd8db07b838',\n",
+       "  'url': '/api/repository_revisions/c85f89a2a97b5743'},\n",
+       " {'changeset_revision': 'f0c7cab2f547',\n",
+       "  'downloadable': False,\n",
+       "  'has_repository_dependencies': False,\n",
+       "  'id': '35de89a3905a4173',\n",
+       "  'includes_datatypes': False,\n",
+       "  'includes_tool_dependencies': False,\n",
+       "  'includes_tools': False,\n",
+       "  'includes_tools_for_display_in_tool_panel': False,\n",
+       "  'includes_workflows': False,\n",
+       "  'malicious': False,\n",
+       "  'missing_test_components': False,\n",
+       "  'model_class': 'RepositoryMetadata',\n",
+       "  'repository_id': '59c15cd8db07b838',\n",
+       "  'url': '/api/repository_revisions/35de89a3905a4173'},\n",
+       " {'changeset_revision': '52f0767fe68d',\n",
+       "  'downloadable': True,\n",
+       "  'has_repository_dependencies': False,\n",
+       "  'id': '778b955f13aeb7f7',\n",
+       "  'includes_datatypes': False,\n",
+       "  'includes_tool_dependencies': False,\n",
+       "  'includes_tools': True,\n",
+       "  'includes_tools_for_display_in_tool_panel': False,\n",
+       "  'includes_workflows': False,\n",
+       "  'malicious': False,\n",
+       "  'missing_test_components': False,\n",
+       "  'model_class': 'RepositoryMetadata',\n",
+       "  'repository_id': '59c15cd8db07b838',\n",
+       "  'url': '/api/repository_revisions/778b955f13aeb7f7'},\n",
+       " {'changeset_revision': 'f86c65c60056',\n",
+       "  'downloadable': True,\n",
+       "  'has_repository_dependencies': False,\n",
+       "  'id': '32de50d3c34e66d3',\n",
+       "  'includes_datatypes': False,\n",
+       "  'includes_tool_dependencies': False,\n",
+       "  'includes_tools': True,\n",
+       "  'includes_tools_for_display_in_tool_panel': False,\n",
+       "  'includes_workflows': False,\n",
+       "  'malicious': False,\n",
+       "  'missing_test_components': False,\n",
+       "  'model_class': 'RepositoryMetadata',\n",
+       "  'repository_id': '59c15cd8db07b838',\n",
+       "  'url': '/api/repository_revisions/32de50d3c34e66d3'},\n",
+       " {'changeset_revision': '495439e68fca',\n",
+       "  'downloadable': True,\n",
+       "  'has_repository_dependencies': False,\n",
+       "  'id': '6ac625afb8ce0ebd',\n",
+       "  'includes_datatypes': False,\n",
+       "  'includes_tool_dependencies': False,\n",
+       "  'includes_tools': True,\n",
+       "  'includes_tools_for_display_in_tool_panel': False,\n",
+       "  'includes_workflows': False,\n",
+       "  'malicious': False,\n",
+       "  'missing_test_components': False,\n",
+       "  'model_class': 'RepositoryMetadata',\n",
+       "  'repository_id': '59c15cd8db07b838',\n",
+       "  'url': '/api/repository_revisions/6ac625afb8ce0ebd'},\n",
+       " {'changeset_revision': '203133a92000',\n",
+       "  'downloadable': True,\n",
+       "  'has_repository_dependencies': False,\n",
+       "  'id': 'eed087cca5ea50c4',\n",
+       "  'includes_datatypes': False,\n",
+       "  'includes_tool_dependencies': False,\n",
+       "  'includes_tools': True,\n",
+       "  'includes_tools_for_display_in_tool_panel': False,\n",
+       "  'includes_workflows': False,\n",
+       "  'malicious': False,\n",
+       "  'missing_test_components': False,\n",
+       "  'model_class': 'RepositoryMetadata',\n",
+       "  'repository_id': '59c15cd8db07b838',\n",
+       "  'url': '/api/repository_revisions/eed087cca5ea50c4'}]"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "[ revision for revision in all_revisions if revision['repository_id'] == '59c15cd8db07b838' ]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python [Root]",
+   "language": "python",
+   "name": "Python [Root]"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.5.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
--- a/tool_data_table_conf.xml.sample	Mon Sep 17 06:04:44 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Mon Sep 17 12:56:35 2018 -0400
@@ -1,6 +1,6 @@
 <tables>
     <table name="shapeit_ref" comment_char="#">
-        <columns>value, name, path, reference_prefix, map_prefix, sample_prefix</columns>
+        <columns>value, name, path, reference_prefix, map_prefix</columns>
         <file path="tool-data/shapeit_ref.loc" />
     </table>
-</tables>
\ No newline at end of file
+</tables>