From df4e1bc8d788d1372961ead1efd6b1954a657f56 Mon Sep 17 00:00:00 2001 From: Tim-Oliver Husser Date: Wed, 19 Jan 2022 12:09:20 +0100 Subject: [PATCH] added docs and pyproject.toml --- docs/Makefile | 31 + docs/make.bat | 36 + docs/source/_static/pyobs.gif | Bin 0 -> 1794 bytes docs/source/conf.py | 121 +++ docs/source/index.rst | 241 ++++++ poetry.lock | 1432 +++++++++++++++++++++++++++++++++ pyproject.toml | 35 + 7 files changed, 1896 insertions(+) create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/_static/pyobs.gif create mode 100644 docs/source/conf.py create mode 100644 docs/source/index.rst create mode 100644 poetry.lock create mode 100644 pyproject.toml diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..58a3aeb --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,31 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +SPHINXPROJ = pyobs +SOURCEDIR = source +BUILDDIR = ../.doc-build + +#.EXPORT_ALL_VARIABLES: + +#PYTHONPATH:=../pyobs-core/:../pyobs-sbig/:../pyobs-fli:../pyobs-weather:../pyobs-archive:${PYTHONPATH} + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +html: + @$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) + +livehtml: + sphinx-autobuild -b html --watch ../pyobs_sbig $(ALLSPHINXOPTS) "$(SOURCEDIR)/" "$(BUILDDIR)/html/" + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..10520da --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,36 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build +set SPHINXPROJ=pyobs + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% + +:end +popd diff --git a/docs/source/_static/pyobs.gif b/docs/source/_static/pyobs.gif new file mode 100644 index 0000000000000000000000000000000000000000..08d4b66a8e6a0ef6f2f7d9055bca10fa6bec2adb GIT binary patch literal 1794 zcmV+d2mSa*Nk%w1VJ8870HFZ@000000RI30{{R60A^s6Va%Ew3Wn>_CX>@2HM@dak z03rDV0SW*D04x9i001WeeE4~F7Mmgb43>dLn63&(6g z*R+i1`i|QEZ{rDv#G(U;^ck1TW-JK}IH%NVD4Mitx7-L8*$s=kU*PzRZkB)PwtKf$ zzUTC3xsK1fp!&Ywl=UY#$Pq|*h$vy0$k>Rm=opCzDOvePX_<+KsoCkq=@~i(Dq6Zl zYMMHQs@iJA>Ke-fD_bi=Yn$7GtJ~WH<{NwqEL^-xY@GaSR>gO8(*YnoJxxJs0SEC>o5ib7S-u(^_FFy}Hfi9K7YY+vJzfM5FdiDS`D0puH!f*r^ zQhNY!AU<;p0B(rLMxaFg1`Z7-=*aLR$ZQ8kKCFl_BLz|^p;>5&MM6geCPN;md6FYe zkLqBm^g>aiPnU{@(wb>tXTqdP8-na{fY+4d$f~-`ZQ6+m7 zVw`^YWOjWk?d#614j-Y_x**Wqv{PBFaSJ!D&Vmn?M)L+?ZC=F<_Wo^5E^*8Y04iI) zj5+gVz?wA|?hFF7T7MHK_qBNX3*@p``6=uSn=)+7+C+1(z1lU~$WR#rRlPWjU}ni(hjU6DZ&1URpQkp#fEDDKgV#%IS`&hV>~skCrIuq^8<98fy`~pedWHx~W`}f7*p*jKq-o zAzm%5kp63TztR+Eam&JL;tAvsI}Rp8osjH_ugcXbt8YRXt+a+v+n;bom5{Br-+H?) zyMYQCE+FI5S}TB2jgW4FyT0};v)hte>^cBfK;^l7Hmhv6{3`5dyP(D@>#+2~8!wO; zG0O0!2s72M00<9UE~3HSIq0>zZmciL`!?Jw#YD*~@yMb=4DPAwwv6t|3p?y@#xHtE zkcinQ24RzT0X1%SmzhWIW+0i!s_2YuO z{;Ut;cPo84%X#y?H|5L395>x2mR)n@+NF*6=B|Q?wVX5u9rfhZ0z>Q5hs%cg&h2Uq z?aP4U>9ya`(97WMaOSRd&wZC}`tPF#A0{)zldgQ`xVK(C&e*&D_djP+PoebSKkU1O ziCb>H=6Un}GvS5LI)2px*B*bH8gHLH+wAvV{+Lrj-@f_9FM$2i+w#zNK)dw{f7~k| z$p(_BsRhn`!n+#s%(p-FZB2FIlbz#y7r_VeC4?R9o&nRRKosgOP#Gkk14UOcOuem8 zjVqpfQr9_8-4KQ^d>=)uHbWXdjYQkwAO>5gIQWRrggyk33};8CC(4hBtJ~rJ@sxBbiji_X{Ei*Fb;ukdP=(AZ*&zK`sWQ4`H5MBBLojCynk8_j1&N2*bfUi73WB|=GY#nP4*RHdkjsZ2vkQ0#SVxr>j=ArZ$x-G!?m3 zmkx8OW>Xy&!&=d?Ms`UBCe9HtYt5Y+01HI00jU5J5rWxRR910 literal 0 HcmV?d00001 diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..8b2fdc1 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,121 @@ +# -*- coding: utf-8 -*- +# +# Configuration file for the Sphinx documentation builder. +# +# This file does only contain a selection of the most common options. For a +# full list see the documentation: +# http://www.sphinx-doc.org/en/stable/config + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +import os +import sys + +sys.path.insert(0, os.path.abspath("../../")) + +# -- Django -------------------- +import os +import sys +import django +sys.path.insert(0, os.path.abspath('..')) +os.environ['DJANGO_SETTINGS_MODULE'] = 'pyobs_archive.settings' +django.setup() + +# -- Project information ----------------------------------------------------- + +project = "pyobs-archive" +copyright = "2022, Tim-Oliver Husser" +author = "Tim-Oliver Husser" + +# The short X.Y version +# version = "0.16" +# The full version, including alpha/beta/rc tags +# release = "0.16.0" + + +# -- General configuration --------------------------------------------------- + +add_module_names = False + +# If your documentation needs a minimal Sphinx version, state it here. +# +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.githubpages", + "sphinx.ext.napoleon", + "sphinx.ext.viewcode", + "sphinx.ext.autosectionlabel", + #'sphinx_autodoc_typehints' +] + +intersphinx_mapping = {"http://docs.python.org/3": None} + +# napoleon settings +napoleon_google_docstring = True +napoleon_numpy_docstring = False +napoleon_use_param = False +napoleon_use_ivar = True + +# typehints +# set_type_checking_flag = True +# autodoc_typehints = "description" + +# show c'tor parameters in class only +autoclass_content = "both" + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +source_suffix = ".rst" + +# The master toctree document. +master_doc = "index" + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = "en" + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path . +exclude_patterns = [] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = "sphinx" + +# Be a little nitpicky +nitpicky = True +nitpick_ignore = [] + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = "sphinx_rtd_theme" +html_theme_options = { + "collapse_navigation": False, + "sticky_navigation": True, + "navigation_depth": 4, + "display_version": False, + "logo_only": False, + "prev_next_buttons_location": "bottom", + "titles_only": False, + "style_nav_header_background": "#cccccc", +} +html_logo = "_static/pyobs.gif" diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..3c53360 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,241 @@ +pyobs-archive +============= + +*pyobs-archive* is a stand-alone archive for FITS images. It provides a general look&feel and an REST API similar +to the one used by the `LCO archive `_. + + +.. _archive Installation: +Installation +------------ + +While it is definitely possible to run *pyobs-weather* without Docker, we highly recommend it for its simplicity. + +First, build the image:: + + cd https://github.com/pyobs/pyobs-archive.git + cd pyobs-archive + docker build . -t pyobs-archive + +*pyobs-archive* requires a database for storing its data and nginx for serving static files. Easiest way to deploy +everything is using docker-compose. + +A typical docker-compose.yml looks like this:: + + version: '3' + + services: + db: + image: postgres:11 + volumes: + - pgdata:/var/lib/postgresql/data + restart: always + + archive: + image: pyobs-archive + volumes: + - /local_data/:/data/ + - ./local_settings.py:/archive/pyobs_archive/local_settings.py + - static:/archive/static + depends_on: + - db + restart: always + command: bash -c "python manage.py collectstatic --no-input && python manage.py makemigrations && python manage.py migrate && gunicorn --workers=3 pyobs_archive.wsgi -b 0.0.0.0:8000" + + nginx: + image: nginx + volumes: + - ./nginx.conf:/etc/nginx/conf.d/default.conf + - static:/static/static + ports: + - 8001:80 + restart: always + + volumes: + pgdata: + static: + +The configuration for the "archive" container contains a volume that points to the local directory /local_data/. This +will be the directory where the archive stores its files. Please adjust as necessary. + +In this example, nginx needs a configuration file nginx.conf in the same directory, which might look like this:: + + server { + listen 80; + server_name 127.0.0.1; + client_max_body_size 50M; + + location / { + proxy_set_header X-Real-IP $remote_addr; + proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; + proxy_set_header Host $host; + proxy_redirect off; + if (!-f $request_filename) { + proxy_pass http://archive:8000; + break; + } + } + + location /static/ { + root /static; + } + } + +And *pyobs-archive* itself needs a configuration file called local_settings.py. Here is the file for MONET/S as an +example:: + + # disable debug + DEBUG = False + + # we're reverse proxying, so only localhost is allowed to access + ALLOWED_HOSTS = ['localhost'] + + # settings for archive + ARCHIV_SETTINGS = { + 'HTTP_ROOT': 'https://archive.example.com/', + 'ARCHIVE_ROOT': '/data/', + 'PATH_FORMATTER': '{SITEID}/{DAY-OBS}/', + 'FILENAME_FORMATTER': None, + } + +You have to adjust the settings in ARCHIV_SETTINGS as necessary: + +- HTTP_ROOT is the URL the archive will be accessible at. +- ARCHIVE_ROOT is the internal data directory and is mapped in the docker-compose file to a local directory. Should + be left as it is. +- PATH_FORMATTER: A format for the pathes to store the image in. Uses FITS header keywords as placeholders. +- FILENAME_FORMATTER: Same as the PATH_FORMATTER, but for the filename. If None, filenames won't be changed. + +With all three files in one directory, you can easily do:: + + docker-compose up -d + +and the whole system should be up and running within a minute. + +Finally, you need to get into the container and create a superuser:: + + docker exec -it weather_weather_1 bash + ./manage.py createsuperuser + +The web frontend should now be accessible via web browser at http://localhost:8001/ and the admin panel +at http://localhost:8001/admin. + + +.. _archive API Reference: +REST API Reference +------------------ + +Authentication +^^^^^^^^^^^^^^ + +All requests to the REST API must contain a HTTP header of the form:: + + Authentication: Token + +Where is an auth token that can be obtained by calling the /api-token-auth/ endpoint with valid credentials. + +As an example, you can get a token like this:: + + http https://archive.example.com/api-token-auth/ username=husser password=topsecret + +Which might return something like this:: + + {"token":"3d46d6b98edef947402e032e73eca7b54661c968"} + +The token can now be used in other requests:: + + http https://archive.example.com/frames/ "Authorization: Token 3d46d6b98edef947402e032e73eca7b54661c968" + + +List images +^^^^^^^^^^^ + +Images in the archive can easily be listed using the /frames/ endpoint. It accepts HTTP GET parameters for filtering. +A typical example would be:: + + http https://archive.example.com/frames/?night=2020-02-01 + +for getting a list of all images taken in the night of 1 Feb, 2020. + +Other possible filter parameters are: + +- IMAGETYPE: Type of image (see :ref:`Filter options` for details). +- binning: Binning of image (see :ref:`Filter options` for details). +- SITE: Site the image was taken (see :ref:`Filter options` for details). +- TELESCOPE: Telescope the image was taken with (see :ref:`Filter options` for details). +- INSTRUMENT: Instrument the image was taken with (see :ref:`Filter options` for details). +- FILTER: Filter the image was taken with (see :ref:`Filter options` for details). +- RLEVEL: Reduction level (0=unreduced, 1=reduced). +- OBJECT: Name of observed object. +- EXPTIME: Exposure time in seconds. +- night: Night of observation in yyyy-mm-dd format. +- basename: Name of FITS file. +- REQNUM: Request number from robotic system. +- start: Limit to images taken after this, given in isot format. +- end: Limit to images taken before this, given in isot format. +- RA: If RA/DEC are given, limit search to 10' around position +- DEC: See above. +- limit: Maximum number of images to return. +- offset: Offset for list of images to return, use for pagination together with limit above. +- order: Order results using this column. +- asc: If given, order ascending instead of descending. + + +Filter options +^^^^^^^^^^^^^^ + +A call to the /frames/aggregate/ endpoint gives possible choices for some of the filter options:: + + http https://archive.example.com/frames/aggregate/ + +Might result in something like:: + + { + "binnings": ["1x1", "3x3"], + "filters": ["B", "V", "R"], + "imagetypes": ["bias", "dark", "object", "skyflat"], + "instruments": ["instr1", "instr2"], + "sites": ["Paranal", "Mauna Kea"], + "telescopes": ["39m0","30m0"] + } + + +Image information +^^^^^^^^^^^^^^^^^ + +Information about a single image can be retrieved using the /frames/image/ endpoint, e.g.:: + + http https://archive.example.com/frames/1000/ + +More specific information can be obtaines using:: + + # for a list of related images. + http https://archive.example.com/frames/1000/related/ + + # for the FITS headers in JSON format. + http https://archive.example.com/frames/1000/headers/ + + # for a preview image. + http https://archive.example.com/frames/1000/preview/ + +A single image can be downloaded via:: + + wget https://archive.example.com/frames/1000/download/ + + +Downloading images +^^^^^^^^^^^^^^^^^^ + +A whole bunch of images can be downloaded via /zip/ and listing the frames in the body, e.g.:: + + wget https://archive.example.com/frames/zip/ --post-data="auth_token=&frame_ids[]=1000&frame_ids[]=1001" -O data.zip + +The auth token needs to go into the POST body in this case, and a list of image IDs can be added using "frame_ids[]". + +Uploading images +^^^^^^^^^^^^^^^^ + +A registered admin user may send new files to the /create/ endpoint for automatically inserting images into the archive. + + + diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..fead389 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1432 @@ +[[package]] +name = "alabaster" +version = "0.7.12" +description = "A configurable sidebar-enabled Sphinx theme" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "asgiref" +version = "3.4.1" +description = "ASGI specs, helper code, and adapters" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.extras] +tests = ["pytest", "pytest-asyncio", "mypy (>=0.800)"] + +[[package]] +name = "astropy" +version = "5.0" +description = "Astronomy and astrophysics core library" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +numpy = ">=1.18" +packaging = ">=19.0" +pyerfa = ">=2.0" +PyYAML = ">=3.13" + +[package.extras] +all = ["scipy (>=1.3)", "matplotlib (>=3.1,!=3.4.0)", "certifi", "dask", "h5py", "pyarrow (>=5.0.0)", "beautifulsoup4", "html5lib", "bleach", "pandas", "sortedcontainers", "pytz", "jplephem", "mpmath", "asdf (>=2.6)", "bottleneck", "ipython (>=4.2)", "pytest", "typing-extensions"] +docs = ["sphinx (<4)", "sphinx-astropy (>=1.6)", "pytest", "scipy (>=1.3)", "matplotlib (>=3.1,!=3.4.0)", "sphinx-changelog (>=1.1.0)"] +recommended = ["scipy (>=1.3)", "matplotlib (>=3.1,!=3.4.0)"] +test = ["pytest-astropy (>=0.9)", "pytest-xdist"] +test_all = ["pytest-astropy (>=0.9)", "pytest-xdist", "objgraph", "ipython (>=4.2)", "coverage", "skyfield (>=1.20)", "sgp4 (>=2.3)"] + +[[package]] +name = "babel" +version = "2.9.1" +description = "Internationalization utilities" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[package.dependencies] +pytz = ">=2015.7" + +[[package]] +name = "black" +version = "21.12b0" +description = "The uncompromising code formatter." +category = "dev" +optional = false +python-versions = ">=3.6.2" + +[package.dependencies] +click = ">=7.1.2" +mypy-extensions = ">=0.4.3" +pathspec = ">=0.9.0,<1" +platformdirs = ">=2" +tomli = ">=0.2.6,<2.0.0" +typing-extensions = [ + {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}, + {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""}, +] + +[package.extras] +colorama = ["colorama (>=0.4.3)"] +d = ["aiohttp (>=3.7.4)"] +jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] +python2 = ["typed-ast (>=1.4.3)"] +uvloop = ["uvloop (>=0.15.2)"] + +[[package]] +name = "certifi" +version = "2021.10.8" +description = "Python package for providing Mozilla's CA Bundle." +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "cffi" +version = "1.15.0" +description = "Foreign Function Interface for Python calling C code." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +pycparser = "*" + +[[package]] +name = "charset-normalizer" +version = "2.0.10" +description = "The Real First Universal Charset Detector. 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