Merge branch 'master' of https://intra.acdp.at/gogs/tanja/cdplib

.gitignore

@@ -0,0 +1,738 @@
+# Created by https://www.gitignore.io/api/latex,python,visualstudio
+
+# database data
+/mongo-data/*
+/mariadb-data/*
+
+### NOT_IN_USE ###
+
+/NOT_IN_USE/*
+
+### config file, env file ###
+.env
+
+### logs ###
+*.log
+/logs/*
+/logs-docker/*
+
+#### models ###
+*.pickle
+
+### Data ###
+/data/*
+/data-test/*
+
+### Documentation folder ###
+/documentation/*.xlsx
+/Server Results/*
+### LaTeX ###
+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+
+## Intermediate documents:
+*.dvi
+*.xdv
+*-converted-to.*
+# these rules might exclude image files for figures etc.
+# *.ps
+# *.eps
+# *.pdf
+
+## Generated if empty string is given at "Please type another file name for output:"
+.pdf
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex
+*.synctex(busy)
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+
+## Build tool directories for auxiliary files
+# latexrun
+latex.out/
+
+## Auxiliary and intermediate files from other packages:
+# algorithms
+*.alg
+*.loa
+
+# achemso
+acs-*.bib
+
+# amsthm
+*.thm
+
+# beamer
+*.nav
+*.pre
+*.snm
+*.vrb
+
+# changes
+*.soc
+
+# cprotect
+*.cpt
+
+# elsarticle (documentclass of Elsevier journals)
+*.spl
+
+# endnotes
+*.ent
+
+# fixme
+*.lox
+
+# feynmf/feynmp
+*.mf
+*.mp
+*.t[1-9]
+*.t[1-9][0-9]
+*.tfm
+
+#(r)(e)ledmac/(r)(e)ledpar
+*.end
+*.?end
+*.[1-9]
+*.[1-9][0-9]
+*.[1-9][0-9][0-9]
+*.[1-9]R
+*.[1-9][0-9]R
+*.[1-9][0-9][0-9]R
+*.eledsec[1-9]
+*.eledsec[1-9]R
+*.eledsec[1-9][0-9]
+*.eledsec[1-9][0-9]R
+*.eledsec[1-9][0-9][0-9]
+*.eledsec[1-9][0-9][0-9]R
+
+# glossaries
+*.acn
+*.acr
+*.glg
+*.glo
+*.gls
+*.glsdefs
+
+# gnuplottex
+*-gnuplottex-*
+
+# gregoriotex
+*.gaux
+*.gtex
+
+# htlatex
+*.4ct
+*.4tc
+*.idv
+*.lg
+*.trc
+*.xref
+
+# hyperref
+*.brf
+
+# knitr
+*-concordance.tex
+# TODO Comment the next line if you want to keep your tikz graphics files
+*.tikz
+*-tikzDictionary
+
+# listings
+*.lol
+
+# makeidx
+*.idx
+*.ilg
+*.ind
+*.ist
+
+# minitoc
+*.maf
+*.mlf
+*.mlt
+*.mtc[0-9]*
+*.slf[0-9]*
+*.slt[0-9]*
+*.stc[0-9]*
+
+# minted
+_minted*
+*.pyg
+
+# morewrites
+*.mw
+
+# nomencl
+*.nlg
+*.nlo
+*.nls
+
+# pax
+*.pax
+
+# pdfpcnotes
+*.pdfpc
+
+# sagetex
+*.sagetex.sage
+*.sagetex.py
+*.sagetex.scmd
+
+# scrwfile
+*.wrt
+
+# sympy
+*.sout
+*.sympy
+sympy-plots-for-*.tex/
+
+# pdfcomment
+*.upa
+*.upb
+
+# pythontex
+*.pytxcode
+pythontex-files-*/
+
+# thmtools
+*.loe
+
+# TikZ & PGF
+*.dpth
+*.md5
+*.auxlock
+
+# todonotes
+*.tdo
+
+# easy-todo
+*.lod
+
+# xmpincl
+*.xmpi
+
+# xindy
+*.xdy
+
+# xypic precompiled matrices
+*.xyc
+
+# endfloat
+*.ttt
+*.fff
+
+# Latexian
+TSWLatexianTemp*
+
+## Editors:
+# WinEdt
+*.bak
+*.sav
+
+# Texpad
+.texpadtmp
+
+# LyX
+*.lyx~
+
+# Kile
+*.backup
+
+# KBibTeX
+*~[0-9]*
+
+# auto folder when using emacs and auctex
+./auto/*
+*.el
+
+# expex forward references with \gathertags
+*-tags.tex
+
+# standalone packages
+*.sta
+
+### LaTeX Patch ###
+# glossaries
+*.glstex
+
+### 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
+.directory
+
+# 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.*
+.cache
+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
+.env
+.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
+
+### VisualStudio ###
+## Ignore Visual Studio temporary files, build results, and
+## files generated by popular Visual Studio add-ons.
+##
+## Get latest from https://github.com/github/gitignore/blob/master/VisualStudio.gitignore
+
+# User-specific files
+*.suo
+*.user
+*.userosscache
+*.sln.docstates
+
+# User-specific files (MonoDevelop/Xamarin Studio)
+*.userprefs
+
+# Build results
+[Dd]ebug/
+[Dd]ebugPublic/
+[Rr]elease/
+[Rr]eleases/
+x64/
+x86/
+bld/
+[Bb]in/
+[Oo]bj/
+[Ll]og/
+
+# Visual Studio 2015/2017 cache/options directory
+.vs/
+# Uncomment if you have tasks that create the project's static files in wwwroot
+#wwwroot/
+
+# Visual Studio 2017 auto generated files
+Generated\ Files/
+
+# MSTest test Results
+[Tt]est[Rr]esult*/
+[Bb]uild[Ll]og.*
+
+# NUNIT
+*.VisualState.xml
+TestResult.xml
+
+# Build Results of an ATL Project
+[Dd]ebugPS/
+[Rr]eleasePS/
+dlldata.c
+
+# Benchmark Results
+BenchmarkDotNet.Artifacts/
+
+# .NET Core
+project.lock.json
+project.fragment.lock.json
+artifacts/
+
+# StyleCop
+StyleCopReport.xml
+
+# Files built by Visual Studio
+*_i.c
+*_p.c
+*_i.h
+*.ilk
+*.meta
+*.obj
+*.iobj
+*.pch
+*.pdb
+*.ipdb
+*.pgc
+*.pgd
+*.rsp
+*.sbr
+*.tlb
+*.tli
+*.tlh
+*.tmp
+*.tmp_proj
+*.vspscc
+*.vssscc
+.builds
+*.pidb
+*.svclog
+*.scc
+
+# Chutzpah Test files
+_Chutzpah*
+
+# Visual C++ cache files
+ipch/
+*.aps
+*.ncb
+*.opendb
+*.opensdf
+*.sdf
+*.cachefile
+*.VC.db
+*.VC.VC.opendb
+
+# Visual Studio profiler
+*.psess
+*.vsp
+*.vspx
+*.sap
+
+# Visual Studio Trace Files
+*.e2e
+
+# TFS 2012 Local Workspace
+$tf/
+
+# Guidance Automation Toolkit
+*.gpState
+
+# ReSharper is a .NET coding add-in
+_ReSharper*/
+*.[Rr]e[Ss]harper
+*.DotSettings.user
+
+# JustCode is a .NET coding add-in
+.JustCode
+
+# TeamCity is a build add-in
+_TeamCity*
+
+# DotCover is a Code Coverage Tool
+*.dotCover
+
+# AxoCover is a Code Coverage Tool
+.axoCover/*
+!.axoCover/settings.json
+
+# Visual Studio code coverage results
+*.coverage
+*.coveragexml
+
+# NCrunch
+_NCrunch_*
+.*crunch*.local.xml
+nCrunchTemp_*
+
+# MightyMoose
+*.mm.*
+AutoTest.Net/
+
+# Web workbench (sass)
+.sass-cache/
+
+# Installshield output folder
+[Ee]xpress/
+
+# DocProject is a documentation generator add-in
+DocProject/buildhelp/
+DocProject/Help/*.HxT
+DocProject/Help/*.HxC
+DocProject/Help/*.hhc
+DocProject/Help/*.hhk
+DocProject/Help/*.hhp
+DocProject/Help/Html2
+DocProject/Help/html
+
+# Click-Once directory
+publish/
+
+# Publish Web Output
+*.[Pp]ublish.xml
+*.azurePubxml
+# Note: Comment the next line if you want to checkin your web deploy settings,
+# but database connection strings (with potential passwords) will be unencrypted
+*.pubxml
+*.publishproj
+
+# Microsoft Azure Web App publish settings. Comment the next line if you want to
+# checkin your Azure Web App publish settings, but sensitive information contained
+# in these scripts will be unencrypted
+PublishScripts/
+
+# NuGet Packages
+*.nupkg
+# The packages folder can be ignored because of Package Restore
+**/[Pp]ackages/*
+# except build/, which is used as an MSBuild target.
+!**/[Pp]ackages/build/
+# Uncomment if necessary however generally it will be regenerated when needed
+#!**/[Pp]ackages/repositories.config
+# NuGet v3's project.json files produces more ignorable files
+*.nuget.props
+*.nuget.targets
+
+# Microsoft Azure Build Output
+csx/
+*.build.csdef
+
+# Microsoft Azure Emulator
+ecf/
+rcf/
+
+# Windows Store app package directories and files
+AppPackages/
+BundleArtifacts/
+Package.StoreAssociation.xml
+_pkginfo.txt
+*.appx
+
+# Visual Studio cache files
+# files ending in .cache can be ignored
+*.[Cc]ache
+# but keep track of directories ending in .cache
+!*.[Cc]ache/
+
+# Others
+ClientBin/
+~$*
+*~
+*.dbmdl
+*.dbproj.schemaview
+*.jfm
+*.pfx
+*.publishsettings
+orleans.codegen.cs
+
+# Including strong name files can present a security risk
+# (https://github.com/github/gitignore/pull/2483#issue-259490424)
+#*.snk
+
+# Since there are multiple workflows, uncomment next line to ignore bower_components
+# (https://github.com/github/gitignore/pull/1529#issuecomment-104372622)
+#bower_components/
+
+# RIA/Silverlight projects
+Generated_Code/
+
+# Backup & report files from converting an old project file
+# to a newer Visual Studio version. Backup files are not needed,
+# because we have git ;-)
+_UpgradeReport_Files/
+Backup*/
+UpgradeLog*.XML
+UpgradeLog*.htm
+ServiceFabricBackup/
+*.rptproj.bak
+
+# SQL Server files
+*.mdf
+*.ldf
+*.ndf
+
+# Business Intelligence projects
+*.rdl.data
+*.bim.layout
+*.bim_*.settings
+*.rptproj.rsuser
+
+# Microsoft Fakes
+FakesAssemblies/
+
+# GhostDoc plugin setting file
+*.GhostDoc.xml
+
+# Node.js Tools for Visual Studio
+.ntvs_analysis.dat
+node_modules/
+
+# Visual Studio 6 build log
+*.plg
+
+# Visual Studio 6 workspace options file
+*.opt
+
+# Visual Studio 6 auto-generated workspace file (contains which files were open etc.)
+*.vbw
+
+# Visual Studio LightSwitch build output
+**/*.HTMLClient/GeneratedArtifacts
+**/*.DesktopClient/GeneratedArtifacts
+**/*.DesktopClient/ModelManifest.xml
+**/*.Server/GeneratedArtifacts
+**/*.Server/ModelManifest.xml
+_Pvt_Extensions
+
+# Visual Studio Code
+*.vscode
+
+# Paket dependency manager
+.paket/paket.exe
+paket-files/
+
+# FAKE - F# Make
+.fake/
+
+# JetBrains Rider
+.idea/
+*.sln.iml
+
+# CodeRush
+.cr/
+
+# Python Tools for Visual Studio (PTVS)
+*.pyc
+
+# Cake - Uncomment if you are using it
+# tools/**
+# !tools/packages.config
+
+# Tabs Studio
+*.tss
+
+# Telerik's JustMock configuration file
+*.jmconfig
+
+# BizTalk build output
+*.btp.cs
+*.btm.cs
+*.odx.cs
+*.xsd.cs
+
+# OpenCover UI analysis results
+OpenCover/
+
+# Azure Stream Analytics local run output
+ASALocalRun/
+
+# MSBuild Binary and Structured Log
+*.binlog
+
+# NVidia Nsight GPU debugger configuration file
+*.nvuser
+
+# MFractors (Xamarin productivity tool) working folder
+.mfractor/
+
+# Local History for Visual Studio
+.localhistory/
+
+
+# End of https://www.gitignore.io/api/latex,python,visualstudio

Pipfile

@@ -6,7 +6,7 @@ verify_ssl = true
 [dev-packages]
 
 [packages]
-# cdplib = {editable = true,git = "https://readonly:readonly@intra.acdp.at/gogs/tanja/cdplib.git"}
+cdplib = {editable = true,git = "https://readonly:readonly@intra.acdp.at/gogs/tanja/cdplib.git"}
 pycodestyle = "*"
 ipykernel = "*"
 spyder-kernels = "==0.*"
@@ -33,6 +33,7 @@ xeger = "*"
 simplejson = "*"
 mysql = "*"
 sqlalchemy-utils = "*"
+apyori==1.1.1
 
 [requires]
 python_version = "3"

Pipfile.lock

@@ -0,0 +1,840 @@
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+                "sha256:79b129fe65fdf3765440f7a73edaffc89ae9e7885d4e2adafe6aa37913a00fbb",
+                "sha256:b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5",
+                "sha256:c206f47cbf9f32b573c9885f0ec813d2622976cf5effcf7e472344bc2e020ac1",
+                "sha256:d8e238f20bcf70063ee8691d4a72162bcec1f4c38f83c93e6851e72ad545dabb",
+                "sha256:ee9625fc8ee164902dfbb0ff932b26df112da9f871c32f0f9c1bcf20c350fe2a",
+                "sha256:fb2530b53c28f0d4d84990e945c2ebb470edb469d63e389bf02ff409012fe7c5",
+                "sha256:feadb95170e45f439455354904768608e356c5b174ca30b3d11b0e3f24b5c0df"
+            ],
+            "index": "pypi",
+            "version": "==3.16.0"
+        },
+        "six": {
+            "hashes": [
+                "sha256:3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c",
+                "sha256:d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73"
+            ],
+            "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+            "version": "==1.12.0"
+        },
+        "sortedcontainers": {
+            "hashes": [
+                "sha256:974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a",
+                "sha256:d9e96492dd51fae31e60837736b38fe42a187b5404c16606ff7ee7cd582d4c60"
+            ],
+            "version": "==2.1.0"
+        },
+        "spyder-kernels": {
+            "hashes": [
+                "sha256:01354b7fa180a87212cc005553b31a7300159b108d36828e301d3782291323f7",
+                "sha256:77c419daa2f5fde3259bc4d79d1c7c417e40302366187f0fac64ee1cb34b7e59"
+            ],
+            "index": "pypi",
+            "version": "==0.*"
+        },
+        "sqlalchemy": {
+            "hashes": [
+                "sha256:0f0768b5db594517e1f5e1572c73d14cf295140756431270d89496dc13d5e46c"
+            ],
+            "index": "pypi",
+            "version": "==1.3.10"
+        },
+        "sqlalchemy-utils": {
+            "hashes": [
+                "sha256:01f0f0ebed696386bc7bf9231cd6894087baba374dd60f40eb1b07512d6b1a5e"
+            ],
+            "index": "pypi",
+            "version": "==0.35.0"
+        },
+        "sqlparse": {
+            "hashes": [
+                "sha256:40afe6b8d4b1117e7dff5504d7a8ce07d9a1b15aeeade8a2d10f130a834f8177",
+                "sha256:7c3dca29c022744e95b547e867cee89f4fce4373f3549ccd8797d8eb52cdb873"
+            ],
+            "index": "pypi",
+            "version": "==0.3.0"
+        },
+        "statsmodels": {
+            "hashes": [
+                "sha256:0013c9c5c8ff1cfad519da1284e34297b9882d9708c768b23f3cf49d40657fa0",
+                "sha256:13970b517e3b6a7b22c4ccb0f8df040952904a8a5e27186843a05720b999d759",
+                "sha256:248a3b2e3774fda04f40e533da1a5e96d97c153df78c757e4468ccdac5f56256",
+                "sha256:249ddab20cc0a4497151b3343cf849809712e62ba495a889c861bdcdb038e795",
+                "sha256:320659a80f916c2edf9dfbe83512d9004bb562b72eedb7d9374562038697fa10",
+                "sha256:3b2a411a92ad7382901744e69fb4a61fd9053a13a267175674eb2112cda143e0",
+                "sha256:509b5ad86361024a7b9a084f4f9b435dc240d68801c128938abd6128c7360500",
+                "sha256:53e1bb1671b9f93e706d007bb97cc63e3d0c59954e08cb35a62d7b6f7405ee29",
+                "sha256:671e5917241edc9c69b08157e6b258105a611541482a41ebab88bcb646526465",
+                "sha256:8741ae7d1c5a7abd96a9cc1840d02a938745dabf38edc645d388cf3fc0f2c0d5",
+                "sha256:b81b8c08b884d8029e14156aa836d878cf528bef6111d421db82eaa33dbe6559",
+                "sha256:ba4554bc43c23700734f970d09f45d9fccd2fc97441d0ce1a448bae35d56c29e",
+                "sha256:bc0a836185caee3f532ea1fc41fe3792289241f268d70c6e978343d061bceede",
+                "sha256:cb9ae882becae277e28a5e683582725aedc01a41fb36ed9eee0bb90bcfd1a457",
+                "sha256:df122a07c65a92ba9087af9626ddd44c8de0236ecfd7e42bf6a71f186c888f4b",
+                "sha256:e061aa63412d4051ce69c37381848d259a15c15cb8bace4d3727bf9b7fbafb0c",
+                "sha256:edb9f2d4bb23b83af6c31cddb3a50e800dad07f3fb33e44f876139e6c32b23fa",
+                "sha256:ef1b80d0f82f69bef8d1e766112af3827c1d4b09f4c146ecdf5901d0d2dc6986",
+                "sha256:efb250efe8d1cddf1fd5118de2a5e40523711b9b4c5b816a072635f07e20ab00",
+                "sha256:f1ba91668eb673dfb97b9a04420dad386a80acc93d8dde0b0884c127be530024"
+            ],
+            "version": "==0.10.1"
+        },
+        "tblib": {
+            "hashes": [
+                "sha256:1735ff8fd6217446384b5afabead3b142cf1a52d242cfe6cab4240029d6d131a",
+                "sha256:c1c8f4edf820a8703d64838804ed3bb37ee35722231c26760cef292ec9d154e4"
+            ],
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+            "version": "==1.5.0"
+        },
+        "text-unidecode": {
+            "hashes": [
+                "sha256:1311f10e8b895935241623731c2ba64f4c455287888b18189350b67134a822e8",
+                "sha256:bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93"
+            ],
+            "version": "==1.3"
+        },
+        "toolz": {
+            "hashes": [
+                "sha256:08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560"
+            ],
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+            "version": "==0.10.0"
+        },
+        "tornado": {
+            "hashes": [
+                "sha256:349884248c36801afa19e342a77cc4458caca694b0eda633f5878e458a44cb2c",
+                "sha256:398e0d35e086ba38a0427c3b37f4337327231942e731edaa6e9fd1865bbd6f60",
+                "sha256:4e73ef678b1a859f0cb29e1d895526a20ea64b5ffd510a2307b5998c7df24281",
+                "sha256:559bce3d31484b665259f50cd94c5c28b961b09315ccd838f284687245f416e5",
+                "sha256:abbe53a39734ef4aba061fca54e30c6b4639d3e1f59653f0da37a0003de148c7",
+                "sha256:c845db36ba616912074c5b1ee897f8e0124df269468f25e4fe21fe72f6edd7a9",
+                "sha256:c9399267c926a4e7c418baa5cbe91c7d1cf362d505a1ef898fde44a07c9dd8a5"
+            ],
+            "markers": "python_version >= '3.5'",
+            "version": "==6.0.3"
+        },
+        "tqdm": {
+            "hashes": [
+                "sha256:94d2a64582150f503a294b3b8889413e7e56d6043473d6a5672d46185b043902",
+                "sha256:fca09992116d6dc3ad9789cf601a254081eb40d5c14c1863ab6cd10e15c2cb26"
+            ],
+            "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+            "version": "==4.37.0"
+        },
+        "traitlets": {
+            "hashes": [
+                "sha256:70b4c6a1d9019d7b4f6846832288f86998aa3b9207c6821f3578a6a6a467fe44",
+                "sha256:d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7"
+            ],
+            "version": "==4.3.3"
+        },
+        "tsfresh": {
+            "hashes": [
+                "sha256:070becc4fdcd173ccae068774c1420d304c99964dbc73bc6f7d6290cfb4ae38d",
+                "sha256:f9c5f43252100cf37fc23cc70164b46293bde1a883f2e74eac5bd5e98640e801"
+            ],
+            "index": "pypi",
+            "version": "==0.12.0"
+        },
+        "urllib3": {
+            "hashes": [
+                "sha256:3de946ffbed6e6746608990594d08faac602528ac7015ac28d33cee6a45b7398",
+                "sha256:9a107b99a5393caf59c7aa3c1249c16e6879447533d0887f4336dde834c7be86"
+            ],
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' and python_version < '4'",
+            "version": "==1.25.6"
+        },
+        "wcwidth": {
+            "hashes": [
+                "sha256:3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e",
+                "sha256:f4ebe71925af7b40a864553f761ed559b43544f8f71746c2d756c7fe788ade7c"
+            ],
+            "version": "==0.1.7"
+        },
+        "xeger": {
+            "hashes": [
+                "sha256:2a91341fc2c814b27917b8bd24e8d212c8a3b904d98e9a6703d27484c2cb0f82"
+            ],
+            "index": "pypi",
+            "version": "==0.3.5"
+        },
+        "xgboost": {
+            "hashes": [
+                "sha256:5ec073f6d68348784e9afdb831371fefb89de896d8eb58e79244ad05177c5753",
+                "sha256:898f26bb66589c644d17deff1b03961504f7ad79296ed434d0d7a5e9cb4deae6",
+                "sha256:d69f90d61a63e8889fd39a31ad00c629bac1ca627f8406b9b6d4594c9e29ab84"
+            ],
+            "index": "pypi",
+            "version": "==0.90"
+        },
+        "xlrd": {
+            "hashes": [
+                "sha256:546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2",
+                "sha256:e551fb498759fa3a5384a94ccd4c3c02eb7c00ea424426e212ac0c57be9dfbde"
+            ],
+            "index": "pypi",
+            "version": "==1.2.0"
+        },
+        "xmltodict": {
+            "hashes": [
+                "sha256:50d8c638ed7ecb88d90561beedbf720c9b4e851a9fa6c47ebd64e99d166d8a21",
+                "sha256:8bbcb45cc982f48b2ca8fe7e7827c5d792f217ecf1792626f808bf41c3b86051"
+            ],
+            "index": "pypi",
+            "version": "==0.12.0"
+        },
+        "zict": {
+            "hashes": [
+                "sha256:be8c7a24e3e78f871b72bfff16245105d1f0448606b1decdae054a14bfdf5996",
+                "sha256:e34dd25ea97def518fb4c77f2c27078f3a7d6c965b0a3ac8fe5bdb0a8011a310"
+            ],
+            "version": "==1.0.0"
+        }
+    },
+    "develop": {}
+}

README.md

@@ -17,3 +17,7 @@ How to set up a new Package:
 
 `from cdplib.db_migration import DataFrameToCollection`
 
+### Update lib locally or in Docker
+
+* If changes are made run `pipenv update` in the wokring directory
+

cdplib/FlattenData.py

@@ -14,13 +14,12 @@ import pandas as pd
 import copy
 sys.path.append(os.getcwd())
 from cdplib.log import Log
-log = Log("Flatten data")
 
 class FlattenData():
 
     def __init__(self):
-        log.info('Flatten Data Initialized')
-
+        self._log = Log("Flatten data")
+    
     def flatten(self, data):
         '''
         :parm data: data given in either dictionary, list or dataframe format.
@@ -32,7 +31,7 @@ class FlattenData():
         start = time.time()
         if type(data) is pd.DataFrame:
             return_data = self.flatten_dataframe(data)
-            print(('Data has been flattened in {} seconds').format(time.time()-start))
+            self._log.info(('Data has been flattened, created {} columns in {} seconds').format(len(return_data.columns)- len(data.columns), time.time()-start))
             return return_data
         if type(data) is dict:
             return self.flatten_dict(data)
@@ -129,13 +128,14 @@ class FlattenData():
                         key = incoming_key + '_' + str(data_list[iteration]['stationsnummer']) + '_' + str(data_list[iteration]['stage'])
                 else:
                     key = incoming_key + '_' + str(iteration)
+            else:
+                key = str(iteration)
             if type(temp_dataframe) == list:
                 temp_result = self.flatten_list(temp_dataframe, key)
-                result_dict = self.append_to_dict(result_dict, temp_result)
 
             elif type(temp_dataframe) == dict:
                 temp_result = self.flatten_dict(temp_dataframe, key)
-                result_dict = self.append_to_dict(result_dict, temp_result)
+
             else:
                 result_dict[key] = temp_dataframe
 

cdplib/db_handlers/MongodbHandler.py

@@ -9,20 +9,19 @@ Created on Mon Sep 16 13:27:44 2019
 """
 
 
-import json
+
 import simplejson
 import sys
 import os
-import jsonref
 
-from copy import deepcopy
+import pymongo
 from pymongo import MongoClient
 import pandas as pd
 import numpy as np
 
 sys.path.append(os.getcwd())
 from cdplib.log import Log
-from cdplib.Singleton_Threadsafe import SingletonThreadsafe
+from cdplib.db_migration.ParseJsonSchema import ParseJsonSchema
 
 
 #class MongodbHandlerPool(metaclass=SingletonThreadsafe):
@@ -85,79 +84,57 @@ class MongodbHandler:
 
         self._database_name = database_name
 
-    def set_database(self, database_name):
-        self._database = self._client[database_name]
-
-    def drop_database(self):
+    def set_database(self, database_name: str):
         '''
+        :param str database_name: Name of the database.
         '''
-        self._client.drop_database(self._database_name)
+        assert(isinstance(database_name, str)),\
+            "Parameter 'database_name' must be a string type"
 
-    def drop_collection(self, collection_name: str):
-        '''
-        '''
-        self._database[collection_name].drop()
+        if database_name not in self._client.list_database_names():
+            self._log.info(('Database: {} didnt exist, it will be created for you once a collection is created in it').format(database_name))
+        self._database = self._client[database_name]
 
-    def _read_schema(self, schema_path: str) -> dict:
+
+    def drop_database(self):
         '''
-        :param str schema_path: path to the schema file.
         '''
+        try:
+            self._client.drop_database(self._database_name)
+        except Exception as error:
+            self._log.log_and_raise_error(('Couldnt drop the database. Error: {}').format(error))
+    
 
-        assert(isinstance(schema_path, str)),\
-            "Parameter 'schema_path must be a string type"
-
-        with open(schema_path) as json_file:
-            schema = json.load(json_file)
-
-        definitions_flag = self._analyze_schema(schema)
-
-        if definitions_flag:
-            schema = self._dereference_schema(schema)
-
-        return schema
-
-    def _analyze_schema(self, schema: dict, definitions_flag: bool = False) -> dict:
-
-
-        for key in schema:
-            if key == 'definitions':
-                definitions_flag = True
-                return definitions_flag
-
-            if key == 'default' or key == 'default_values':
-                return self._remove_defaults(schema)
-
-            if type(schema[key]) == dict:
-                definitions_flag = self._analyze_schema(schema[key], definitions_flag)
-
-        return definitions_flag
-
-    def _dereference_schema(self, schema: dict) -> dict:
+    def drop_collection(self, collection_name: str):
         '''
-        :param dict schema: dictionary containing a schema which uses references.
         '''
-
-        assert(isinstance(schema, dict)),\
-            "Parameter 'schema' must be a dictionary type"
-
-        schema = jsonref.loads(str(schema).replace("'", "\""))
-        schema = deepcopy(schema)
-        schema.pop('definitions', None)
-        return schema
-
-    def _remove_defaults(self, schema: dict) -> dict:
+        try:
+            return_message = self._database.drop_collection(collection_name)
+            if 'errmsg' in return_message:
+                self._log.warning(('Couldnt drop the collection {}. Error: {}').format(collection_name, return_message['errmsg']))
+        except Exception as error:
+            self._log.log_and_raise_error(('Couldnt drop the collection {}. Error: {}').format(collection_name, error))
+    
+    def create_index(self, collection_name: str, key: str, direction: (str, int)='text'):
         '''
-        :param dict schema: dictionary containing a schema which uses references.
+        :param str collection_name: name on the collection for which the schema will be set.
+        :param str key: Which value should be used as the index.
+        :param str direction: see https://api.mongodb.com/python/current/api/pymongo/collection.html for reference.
         '''
-        if 'default' in schema:
-            del schema['default']
-        if 'default_values' in schema:
-            del schema['default_values']
-        return schema
 
+        allowed_directions = [1, -1, '2d', 'geoHaystack', '2dsphere', 'hashed', 'text']
 
-        assert(isinstance(schema, dict)),\
-            "Parameter 'schema' must be a dictionary type"
+        assert(isinstance(collection_name, str)),\
+            "Parameter 'collection_name' must be a string type"
+        assert(isinstance(key, (str, int))),\
+            "Parameter 'key' must be a string or integer type"
+        assert(direction in allowed_directions),\
+            "Parameter 'key' must be one of these values: 1, -1, '2d', 'geoHaystack', '2dsphere', 'hashed', 'text' "
+        assert(isinstance(direction, str)),\
+            "Parameter 'direction' must be a string type"
+            
+        self._database[collection_name].create_index([(key, direction)], name=key)
+        #collection.create_index([('field_i_want_to_index', pymongo.TEXT)], name='search_index', default_language='english')
 
     def set_collection_schema(self, collection_name: str, schema_path: str,
                               validation_level: str = 'moderate',validation_action: str = 'error'):
@@ -172,12 +149,13 @@ class MongodbHandler:
         assert(isinstance(schema_path, str)),\
             "Parameter 'schema_path' must be a string type"
         assert(isinstance(validation_level, str)),\
-            "Parameter 'validation_lever' must be a string type"
+            "Parameter 'validation_level' must be a string type"
         assert(isinstance(validation_action, str)),\
             "Parameter 'validation_action' must be a string type"
+            
+        parse_obj = ParseJsonSchema(schema_paths=schema_path)
 
-        schema = self._read_schema(schema_path)
-
+        schema = parse_obj.read_schema_and_parse_for_mongodb(schema_path)
         command = {
                     'collMod': collection_name,
                     'validator': {
@@ -204,13 +182,13 @@ class MongodbHandler:
         if collection_name not in self._database.list_collection_names():
             try:
                 self._log.info(("Collection '{}' has been created").format(collection_name))
-                return self._database.create_collection(collection_name)
+                self._database.create_collection(collection_name)
 
             except Exception as error:
                 self._log.log_and_raise_error(('An error occured while creating the new collection: {}. \nError: {}').format(collection_name, error))
         else:
             self._log.info(("Collection '{}' already exists").format(collection_name))
-            return self._database[collection_name]
+            self._database[collection_name]
 
     def insert_data_into_collection(self, data: (dict, list, np.ndarray, pd.DataFrame, pd.Series),
                                     collection_name: str,
@@ -268,7 +246,7 @@ class MongodbHandler:
         self.set_collection_schema(collection_name=collection_name, schema_path=schema_path)
 
     def query_data_and_generate_dataframe(self, collection_name: str, attribute: str = None,
-                                          attribute_value: str = None, comparison_operator: str = '$eq'):
+                                          attribute_value: str = None, comparison_operator: str = '$eq', index = None):
         '''
 
         '''
@@ -281,30 +259,34 @@ class MongodbHandler:
         except Exception as error:
             self._log.log_and_raise_error(('An error occured trying to query data from {}, with query {}: {}:{}. \nError:{}').format(collection_name, attribute_value, comparison_operator, attribute_value, error))
 
-        return self.convert_mongo_data_into_dataframe(data)
+        return self.convert_mongo_data_into_dataframe(data, index, collection_name)
 
-    def aggregate_data_and_generate_dataframe(self, collection_name: str, aggregation_pipeline: list):
+    def aggregate_data_and_generate_dataframe(self, collection_name: str, aggregation_pipeline: list, index: str = None):
 
         try:
             data = self._database[collection_name].aggregate(pipeline=aggregation_pipeline, allowDiskUse=True)
-
         except Exception as error:
             self._log.log_and_raise_error(('A problem occured when aggregating the collection {} with the pipeline {}. \nError: {}').format(collection_name, aggregation_pipeline, error))
 
-        return self.convert_mongo_data_into_dataframe(data)
+        return self.convert_mongo_data_into_dataframe(data, index, collection_name)
 
-    def convert_mongo_data_into_dataframe(self, data) -> pd.DataFrame():
+    def convert_mongo_data_into_dataframe(self, data, index: str = None, collection_name: str = None) -> pd.DataFrame():
 
         data = list(data)
         try:
             if len(data)> 0:
+                if collection_name:
+                    self._log.info(('{} rows were fetched from the {} collection').format(len(data), collection_name))
+                else:
+                    self._log.info(('{} rows were fetched from the database').format(len(data)))
                 df = pd.DataFrame(data)
-                df.set_index('radsatznummer', inplace=True)
+                if index is not None:
+                    df.set_index(index, inplace=True)
                 return df
             else:
                 self._log.warning(('No data for the query was found').format())
         except Exception as error:
-            self._log.log_and_raise_error(('An error occured trying to convert mongo data into pd.Dataframe. \nError: {} ').format(errors))
+            self._log.log_and_raise_error(('An error occured trying to convert mongo data into pd.Dataframe. \nError: {} ').format(error))
 
     def update_data_in_collection(self, query_label: str, query_value: str, update_label:str, update_value: str, collection_name:str):
         self._database[collection_name].update_one({query_label:query_value}, {"$set": {update_label: update_value}})
@@ -316,7 +298,14 @@ if __name__ == "__main__":
 
     log.info('Script started')
 
-    db_handler = MongodbHandler()
+    database_url = "mongodb://{0}:{1}@{2}:{3}"\
+                           .format('root',
+                                   'oebb',
+                                   'localhost',
+                                   27017)
+    database_name = 'test_database'
+
+    db_handler = MongodbHandler(database_name=database_name, database_url=database_url)
 
     # Create a colleciton for the wheelsets and give it its schema.
     for schema_path in [
@@ -329,6 +318,8 @@ if __name__ == "__main__":
             collection_name = os.path.basename(schema_path).lstrip("_schema").split(".")[0]
 
             db_handler.create_collection_and_set_schema(collection_name, schema_path)
+        else:
+            log.log_and_raise_warning(('No file exists at path: {}').format(schema_path))
 
     log.info(("Existing databases: {}, Collection in OEBB database {}")\
              .format(db_handler._client.list_database_names(), db_handler._database.list_collection_names()))

cdplib/db_migration/DataFrameToCollection.py

@@ -10,7 +10,6 @@ Created on Mon Jul 22 11:05:47 2019
 """
 
 import pandas as pd
-import numpy as np
 import os
 import sys
 
@@ -78,7 +77,7 @@ class DataFrameToCollection():
             schema = self.schema
 
         for field in schema["properties"]:
-
+            
             if field not in self._unroll_nested_names(data.columns):
                 continue
 
@@ -112,25 +111,28 @@ class DataFrameToCollection():
             elif field_type == "object":
 
                 sub_schema = deepcopy(schema["properties"][field])
-
+            
                 # rename sub-schema properties to match with data column names
                 sub_schema["properties"] =\
                     {".".join([field, k]): v for k, v
                      in sub_schema["properties"].items()}
-
+                
                 sub_data = self.to_list_of_documents(
                             data=data,
                             schema=sub_schema,
                             grp_fields=grp_fields,
                             _final_step=False)
-
-                reshaped_field = sub_data.apply(self._make_dict, axis=1)
-                reshaped_field.name = field
-
-                reshaped_fields.append(reshaped_field)
+                
+                # Need to be checked since child elements can be empty
+                if sub_data is not None:
+                    reshaped_field = sub_data.apply(self._make_dict, axis=1)
+                    reshaped_field.name = field
+    
+                    reshaped_fields.append(reshaped_field)
 
             # if field is a list of dictionaries
             elif field_type == "array":
+             
 
                 items_type = schema["properties"][field]["items"]["bsonType"]
 
@@ -155,7 +157,7 @@ class DataFrameToCollection():
 
                         self._log.error(err)
                         raise Exception(err)
-
+                        
                     # group and reshape sub-fields with complex types
                     sub_data = self.to_list_of_documents(
                                 data=data,
@@ -303,7 +305,7 @@ class DataFrameToCollection():
 
 if __name__ == "__main__":
 
-    # Testing
+#     Testing
 
     df = pd.DataFrame({
                        "a": [1]*8 + [2]*8,
@@ -394,3 +396,11 @@ if __name__ == "__main__":
                     data=df,
                     schema=schm,
                     grp_fields=grp_fields)
+
+    
+    
+    
+    
+    
+    
+    

cdplib/db_migration/MigrationCleaning.py

@@ -562,3 +562,4 @@ if __name__ == "__main__":
         data = cleaner.filter_notallowed_values(data)
 
     print("Done!")
+    

cdplib/db_migration/ParseJsonSchema.py

@@ -10,6 +10,10 @@ import os
 import sys
 from copy import deepcopy
 import numpy as np
+import json
+
+import jsonref
+from pathlib import Path
 
 sys.path.append(os.getcwd())
 
@@ -24,7 +28,6 @@ class ParseJsonSchema(ParseDbSchema):
     def __init__(self, schema_paths: [list, str], log_file: str = None):
         '''
         '''
-        import json
         from cdplib.log import Log
 
         super().__init__(schema_paths=schema_paths, log_file=log_file)
@@ -47,6 +50,8 @@ class ParseJsonSchema(ParseDbSchema):
             try:
                 with open(schema_path, "r") as f:
                     self.schemas.append(json.load(f))
+                # Load schmea dereferenced and cleaned by default values
+                #self.schemas.append(self.read_schema_and_parse_for_mongodb(schema_path))
 
             except Exception as e:
                 err = ("Could not load json schema, "
@@ -326,13 +331,80 @@ class ParseJsonSchema(ParseDbSchema):
 
         return already_parsed
 
+    def _dereference_schema(self, schema: dict) -> dict:
+        '''
+        :param dict schema: dictionary containing a schema which uses references.
+        '''
 
-if __name__ == "__main__":
+        assert(isinstance(schema, dict)),\
+            "Parameter 'schema' must be a dictionary type"
+            
+        base_dir_url = Path(os.path.join(os.getcwd(), "mongo_schema")).as_uri() + '/'
+        schema = jsonref.loads(str(schema).replace("'", "\""), base_uri=base_dir_url)
+        schema = deepcopy(schema)
+        schema.pop('definitions', None)
+        return schema
+
+    def _remove_defaults(self, schema: dict) -> dict:
+        '''
+        :param dict schema: dictionary containing a schema which uses references.
+        '''
+        if 'default' in schema:
+            del schema['default']
+        if 'default_values' in schema:
+            del schema['default_values']
+        return schema
+    
+        assert(isinstance(schema, dict)),\
+        "Parameter 'schema' must be a dictionary type"
+    
+    # Need to parse schmema for importing to mongo db 
+    # Reason:
+    # We need to drop default values since MongoDB can't handle them
+    # We need to deference json before import to Mongo DB pymongo can't deal with references
+    def read_schema_and_parse_for_mongodb(self, schema_path: str) -> dict:
+        '''
+        :param str schema_path: path to the schema file.
+        '''
+
+        assert(isinstance(schema_path, str)),\
+            "Parameter 'schema_path must be a string type"
 
-    # Only for testing
+        with open(schema_path) as json_file:
+            schema = json.load(json_file)
+
+        definitions_flag = self._analyze_schema(schema)
+
+        if definitions_flag:
+            schema = self._dereference_schema(schema)
+
+        return schema
+           
+   
+    def _analyze_schema(self, schema: dict, definitions_flag: bool = False) -> dict:
+
+
+        for key in schema:
+            if key == '$ref':
+                definitions_flag = True
+                return definitions_flag
+
+            if key == 'default' or key == 'default_values':
+                return self._remove_defaults(schema)
+
+            if type(schema[key]) == dict:
+                definitions_flag = self._analyze_schema(schema[key], definitions_flag)
+
+        return definitions_flag
+
+
+
+if __name__ == "__main__":
 
-    schema_path = os.path.join(".", "mongo_schema", "schema_wheelsets.json")
+#     Only for testing
 
+    schema_path = os.path.join(".", "mongo_schema", "schema_components.json")
+    
     if os.path.isfile(schema_path):
 
         parse_obj = ParseJsonSchema(schema_paths=schema_path)
@@ -352,3 +424,4 @@ if __name__ == "__main__":
         allowed_values = parse_obj.get_allowed_values()
 
         descriptions = parse_obj.get_field_descriptions()
+    

cdplib/log.py

@@ -29,6 +29,7 @@ class Log():
             name = ''
 
         self._logger = logging.getLogger(name)
+        
 
         self._logger.setLevel("DEBUG")
 

cdplib/unit_tests/TestFlattenData.py

@@ -0,0 +1,44 @@
+import unittest
+import sys
+import os
+import pandas as pd
+sys.path.append(os.getcwd())
+from cdplib.log import Log
+from cdplib.FlattenData import FlattenData
+
+class TestMongodbHandler(unittest.TestCase):
+
+    def setUp(self):
+        self.flattener = FlattenData()
+
+    def test_A_flatten(self):
+        '''
+        Create some nested test data, in the formats: dict, list and dataframe
+        Flatten the test data
+        Compare the results
+        '''
+        nested_data_dict = {
+            "one_level": "test_level_1",
+            "two_levels": {
+                "one_level": "test_level_2"
+            },
+            "three_levels": {
+                "two_levels": {
+                    "one_level": "test_level_3"
+                }
+            }
+        }
+
+        nested_data_list = [nested_data_dict, nested_data_dict]
+        nested_data_df = pd.DataFrame.from_dict([nested_data_dict])
+
+        flattened_dict = self.flattener.flatten(nested_data_dict)
+        flattened_list = self.flattener.flatten(nested_data_list)
+        flattened_df = self.flattener.flatten(nested_data_df)
+
+        self.assertEqual(nested_data_dict["two_levels"]["one_level"], flattened_dict['two_levels_one_level'])
+        self.assertEqual(nested_data_dict["two_levels"]["one_level"], flattened_list['0_two_levels_one_level'])
+        self.assertEqual(nested_data_dict["two_levels"]["one_level"], flattened_df.loc[0 , 'two_levels_one_level'])
+        
+if __name__ == '__main__':
+    unittest.main()

cdplib/unit_tests/TestMongodbHandler.py

@@ -0,0 +1,141 @@
+import unittest
+import sys
+import os
+from pymongo import MongoClient
+sys.path.append(os.getcwd())
+from cdplib.log import Log
+from cdplib.db_handlers.MongodbHandler import MongodbHandler
+
+class TestMongodbHandler(unittest.TestCase):
+
+    def setUp(self):
+        database_url = "mongodb://{0}:{1}@{2}:{3}"\
+                           .format('root',
+                                   'oebb',
+                                   'localhost',
+                                   27017)
+        self.database_name = 'test_database'
+        self.first_collection_name = 'first_test_collection'
+        self.second_collection_name = 'second_test_collection'
+        self.mongodb_handler = MongodbHandler(database_name=self.database_name, database_url=database_url)
+        self.client = MongoClient(database_url) 
+        self.database = self.client[self.database_name]
+        self.valid_schema_path = os.path.join('.', 'cdplib', 'unit_tests', "valid_test_schema.json")
+        self.invalid_schema_path = os.path.join('.', 'cdplib', 'unit_tests', "invalid_test_schema.json")
+        self.valid_input = {
+                        "test_value_string": "test_value",
+                        "test_value_double": 2.4,
+                        "test_value_double_array": [1.4, 1.6, 3.5]
+                        }
+        self.invalid_input = {
+                        "test_value_string": 1,
+                        "test_value_double": "Wrong value",
+                        "test_value_double_array": [1.4, 1.6, 3.5]
+                        }
+
+
+    def test_A_set_database(self):
+        '''
+        Checks that the database doesnt exist.
+        Creates the database.
+        Create a collection in the database.
+        Check that the database now exists.
+        Check that an assertionerror is thrown then an integer value is sent to the method.
+        '''
+        self.assertFalse(self.database_name in self.client.list_database_names())
+        #self.test_B_create_collection()
+        #self.assertTrue(self.database_name in self.client.list_database_names())
+        self.assertRaises(AssertionError, lambda:self.mongodb_handler.set_database(123))
+
+    def test_B_create_collection(self):
+        '''
+        Checks that the collection doesnt exist
+        Creates the collection
+        Checks that the collection now exists
+        Checks that an Exception is thrown when an integervalue is given to the method.
+        '''
+        self.assertFalse(self.first_collection_name in self.database.list_collection_names())
+        self.mongodb_handler.create_collection(self.first_collection_name)
+        self.mongodb_handler.create_collection(self.second_collection_name)
+        self.assertTrue(self.first_collection_name in self.database.list_collection_names())
+        self.assertRaises(Exception, lambda:self.mongodb_handler.create_collection(123))
+
+    def test_C_set_collection_schema(self):
+        '''
+        Sets a schema for the collection
+        Tries to set a schema which has syntax errors
+        '''
+        self.mongodb_handler.set_collection_schema(self.first_collection_name, self.valid_schema_path)
+        self.assertRaises(Exception, lambda:set_collection_schema(self.first_collection_name, self.invalid_schema_path))
+
+    def test_D_insert_data_into_collection(self):
+        '''
+        Inserts data into the collection
+        Tries to insert data which doesnt comform to the schema.
+        '''
+        self.mongodb_handler.insert_data_into_collection(self.valid_input, self.first_collection_name)
+        self.assertRaises(Exception, lambda:set_collection_schemaself.mongodb_handler.insert_data_into_collection(self.invalid_input, self.first_collection_name))
+        
+    def test_E_query_data_and_generate_dataframe(self):
+        '''
+        Fetch data and confirms thats it is the same as was entered into the database
+        Do the same with more specific query
+        '''
+        self.assertEqual(self.mongodb_handler.query_data_and_generate_dataframe(self.first_collection_name).to_dict()['test_value_double'][0], self.valid_input['test_value_double'])
+        self.assertEqual(self.mongodb_handler.query_data_and_generate_dataframe(self.first_collection_name, 'test_value_string', 'test_value').to_dict()['test_value_double'][0], self.valid_input['test_value_double'])
+    
+    def test_F_aggregate_data_and_generate_dataframe(self):
+        '''
+        Make an aggregation call
+        Make sure its the same data as was entered into the database
+        '''
+        aggregation_pipeline = [
+                                { '$match': {}}
+                                ]
+        self.assertEqual(self.mongodb_handler.aggregate_data_and_generate_dataframe(self.first_collection_name, aggregation_pipeline).to_dict()['test_value_double'][0], self.valid_input['test_value_double'])
+    
+    def test_G_update_data_in_collection(self):
+        '''
+        Fetch data from database
+        Make sure its the same as was entered into the database
+        Update a value in the data
+        Fetch the new data
+        Make sure that it is different from the original data.
+        '''
+        original_value = self.mongodb_handler.query_data_and_generate_dataframe(self.first_collection_name).to_dict()['test_value_string'][0]
+        self.assertEqual(original_value, self.valid_input['test_value_string'])
+        self.mongodb_handler.update_data_in_collection('test_value_string', 'test_value', 'test_value_string', 'new_test_value', self.first_collection_name)
+        new_value =  self.mongodb_handler.query_data_and_generate_dataframe(self.first_collection_name).to_dict()['test_value_string'][0]
+        self.assertNotEqual(original_value, new_value)
+
+    def test_H_create_index(self):
+        '''
+        Create a index in the collection
+        Make sure that the index exists in the collection indexes
+        '''
+        index = 'test_value_string'
+        self.mongodb_handler.create_index(self.first_collection_name, index)
+        self.assertTrue(index in list(self.database[self.first_collection_name].index_information().keys()))
+    
+    def test_Y_drop_collection(self):
+        '''
+        Checks that the collection exists
+        Drops the collection
+        Checks that the collection doesn't exist anymore
+        '''
+        self.assertTrue(self.first_collection_name in self.database.list_collection_names())
+        self.mongodb_handler.drop_collection(self.first_collection_name)
+        self.assertFalse(self.first_collection_name in self.database.list_collection_names())
+    
+    def test_Z_drop_database(self):
+        '''
+        Checks that the database exists
+        Drops the database
+        Checks that the database doesn't exist anymore
+        '''
+        self.assertTrue(self.database_name in self.client.list_database_names())
+        self.mongodb_handler.drop_database()
+        self.assertFalse(self.database_name in self.client.list_database_names())
+
+if __name__ == '__main__':
+    unittest.main()

cdplib/unit_tests/invalid_test_schema.json

@@ -0,0 +1,19 @@
+{
+    "bsonType": "object",
+    "properties": {
+
+        "test_value_string": {
+            "bsonType": "string",
+        },
+        "test_value_double": {
+            "bsonType": "double",
+        },
+        "test_value_double_array": {
+            "bsonType": "array",
+            "items": {
+                "bsonType": "double"
+            }
+        }
+    }
+}
+}

cdplib/unit_tests/valid_test_schema.json

@@ -0,0 +1,17 @@
+{
+    "bsonType": "object",
+    "properties": {
+        "test_value_string": {
+            "bsonType": "string"
+        },
+        "test_value_double": {
+            "bsonType": "double"
+        },
+        "test_value_double_array": {
+            "bsonType": "array",
+            "items": {
+                "bsonType": "double"
+            }
+        }
+    }
+}

setup.py

@@ -31,7 +31,7 @@ INSTALL_REQUIRES = [
 
 
 setup(name='cdplib',
-      version='0.3',
+      version='0.0.1',
       description='Libraries shared by cdp projects',
       url='https://intra.acdp.at/gogs/tanja/cdplib.git',
       author='Tatiana Zolotareva',