Update neuromorpholib

.gitignore

@@ -0,0 +1,233 @@
+
+# Created by https://www.gitignore.io/api/node,code,macos,python
+
+### Code ###
+# Visual Studio Code - https://code.visualstudio.com/
+.settings/
+.vscode/
+tsconfig.json
+jsconfig.json
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Node ###
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+
+# nyc test coverage
+.nyc_output
+
+# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (https://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# TypeScript v1 declaration files
+typings/
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+# dotenv environment variables file
+.env
+
+# parcel-bundler cache (https://parceljs.org/)
+.cache
+
+# next.js build output
+.next
+
+# nuxt.js build output
+.nuxt
+
+# vuepress build output
+.vuepress/dist
+
+# Serverless directories
+.serverless
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+### Python Patch ###
+.venv/
+
+### Python.VirtualEnv Stack ###
+# Virtualenv
+# http://iamzed.com/2009/05/07/a-primer-on-virtualenv/
+[Bb]in
+[Ii]nclude
+[Ll]ib
+[Ll]ib64
+[Ll]ocal
+[Ss]cripts
+pyvenv.cfg
+pip-selfcheck.json
+
+
+# End of https://www.gitignore.io/api/node,code,macos,python

README.md

@@ -1 +1,24 @@
 # neuromorpholib
+
+
+## Usage
+A simple download of known dataset and name:
+```python
+from neuromorpholib import neuromorpho
+
+nmo = neuromorpho.NeuroMorpho()
+acc1 = nmo.download_swc("martone", "ACC1")
+```
+
+A query for all species=mouse neurons:
+```python
+mouse_neurons = nmo.search({"species": "mouse"})
+```
+
+Download a SWC for a mouse neuron:
+```python
+swc_demo = nmo.download_swc(
+    mouse_neurons[0]['archive'],
+    mouse_neurons[0]['neuron_name']
+)
+```

neuromorpholib/__init__.py

@@ -0,0 +1,8 @@
+"""
+Neuromorpholib is a python package for manipulation neuron morphology.
+"""
+
+from . import swc
+from . import neuromorpho
+
+__version__ = "0.0.1"

neuromorpholib/neuromorpho/__init__.py

@@ -0,0 +1,70 @@
+#!/usr/bin/enb python3
+import requests
+import glob
+
+from .. import swc
+
+
+class NeuroMorpho:
+
+    def __init__(self, cache_location="~/.neuromorphocache/"):
+        self.cache = {}
+        self.cache_location = cache_location
+        self.base_url = "http://neuromorpho.org/"
+        self._permitted_fields = self.get_json("api/neuron/fields")['Neuron Fields']
+
+    def url(self, ext=""):
+        ext = ext.lstrip("/")
+        return self.base_url + ext
+
+    def get_json(self, ext):
+        res = requests.get(self.url(ext))
+        return res.json()
+
+    def search(self, query, page=0, limit=None):
+        for k, _ in query.items():
+            if k not in self._permitted_fields:
+                raise ValueError(
+                    "Key {} is not a valid search parameter!\n".format(k) +
+                    "Must be one of:\n{}".format(self._permitted_fields)
+                )
+        query_string = "&".join([
+            "fq={}:{}".format(k, v) for k, v in query.items()
+        ])
+
+        listing = self.get_json("api/neuron/select/?" + query_string[1:] + "&page={}".format(page))
+        try:
+            results = listing["_embedded"]["neuronResources"]
+            print("Downloading page {} for {} neurons, ending in {}".format(page, len(results), results[-1]['neuron_name']))
+            neuron_listing = results
+        except KeyError:
+            return []
+
+        if (
+            "page" in listing and
+            "totalPages" in listing["page"] and
+            listing['page']['totalPages'] >= page
+        ):
+            if limit is None or len(neuron_listing) < limit:
+                if limit is None:
+                    neuron_listing += self.search(query, page=page+1)
+                else:
+                    neuron_listing += self.search(query, page=page+1, limit=limit-50)
+            else:
+                return neuron_listing
+
+        return neuron_listing
+
+    def download_swc(self, archive, neuron_name, text_only=False):
+        ext = "dableFiles/{}/CNG%20version/{}.CNG.swc".format(
+            archive.lower(),
+            neuron_name
+        )
+        res = requests.get(self.url(ext))
+        if ("<html>" in res):
+            raise ValueError("Failed to fetch from {}.".format(ext))
+
+        if text_only:
+            return res.text
+
+        return swc.read_swc(res.text)