From 3353c08405d970f2d052a38b94a387c41a29a78a Mon Sep 17 00:00:00 2001 From: Andrea Mannocci Date: Wed, 16 Feb 2022 15:29:05 +0100 Subject: [PATCH] restructuring the project --- deduplication/datasources/._SUCCESS.crc | Bin 8 -> 0 bytes deduplication/datasources/.part-00000.crc | Bin 1820 -> 0 bytes deduplication/datasources/.part-00001.crc | Bin 1660 -> 0 bytes deduplication/datasources/.part-00002.crc | Bin 4988 -> 0 bytes deduplication/datasources/.part-00003.crc | Bin 5768 -> 0 bytes deduplication/datasources/.part-00004.crc | Bin 3240 -> 0 bytes deduplication/datasources/.part-00005.crc | Bin 3408 -> 0 bytes deduplication/datasources/.part-00006.crc | Bin 4468 -> 0 bytes deduplication/datasources/.part-00007.crc | Bin 4360 -> 0 bytes deduplication/datasources/_SUCCESS | 0 deduplication/datasources/part-00000 | 960 ---- deduplication/datasources/part-00001 | 893 ---- deduplication/datasources/part-00002 | 2846 ---------- deduplication/datasources/part-00003 | 2965 ----------- deduplication/datasources/part-00004 | 1328 ----- deduplication/datasources/part-00005 | 1465 ----- deduplication/datasources/part-00006 | 2805 ---------- deduplication/datasources/part-00007 | 2755 ---------- deduplication/ds.tree.conf.json | 67 - .../ds_dedup_2022-02-16_13.03.17.csv | 4713 ----------------- deduplication/ds_to_json.py | 76 - ...-9fd1-cc65b62afe2b-c000.snappy.parquet.crc | Bin 116 -> 0 bytes ...-9fd1-cc65b62afe2b-c000.snappy.parquet.crc | Bin 128 -> 0 bytes ...-9fd1-cc65b62afe2b-c000.snappy.parquet.crc | Bin 132 -> 0 bytes ...-9fd1-cc65b62afe2b-c000.snappy.parquet.crc | Bin 140 -> 0 bytes ...-9fd1-cc65b62afe2b-c000.snappy.parquet.crc | Bin 120 -> 0 bytes ...-9fd1-cc65b62afe2b-c000.snappy.parquet.crc | Bin 128 -> 0 bytes ...-9fd1-cc65b62afe2b-c000.snappy.parquet.crc | Bin 128 -> 0 bytes ...-9fd1-cc65b62afe2b-c000.snappy.parquet.crc | Bin 140 -> 0 bytes deduplication/mergerels/_SUCCESS | 0 ...4581-9fd1-cc65b62afe2b-c000.snappy.parquet | Bin 13327 -> 0 bytes ...4581-9fd1-cc65b62afe2b-c000.snappy.parquet | Bin 14969 -> 0 bytes ...4581-9fd1-cc65b62afe2b-c000.snappy.parquet | Bin 15740 -> 0 bytes ...4581-9fd1-cc65b62afe2b-c000.snappy.parquet | Bin 16505 -> 0 bytes ...4581-9fd1-cc65b62afe2b-c000.snappy.parquet | Bin 13837 -> 0 bytes ...4581-9fd1-cc65b62afe2b-c000.snappy.parquet | Bin 15141 -> 0 bytes ...4581-9fd1-cc65b62afe2b-c000.snappy.parquet | Bin 15266 -> 0 bytes ...4581-9fd1-cc65b62afe2b-c000.snappy.parquet | Bin 16709 -> 0 bytes deduplication/mergerels_to_csv.py | 52 - docs/Makefile | 153 - docs/commands.rst | 10 - docs/conf.py | 244 - docs/getting-started.rst | 6 - docs/index.rst | 24 - docs/make.bat | 190 - models/.gitkeep | 0 references/.gitkeep | 0 reports/.gitkeep | 0 reports/figures/.gitkeep | 0 49 files changed, 21552 deletions(-) delete mode 100644 deduplication/datasources/._SUCCESS.crc delete mode 100644 deduplication/datasources/.part-00000.crc delete mode 100644 deduplication/datasources/.part-00001.crc delete mode 100644 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-dedup::fd7bdd79a0bfaff29a52bdc0d14c31b5;opendoar::1140;1140;"brandeis university digital collections";OpenDOAR -dedup::fdc74eb6544b2533f3f9fa8e8c7c34d7;opendoar::4470;4470;"igu institutional open access repository";OpenDOAR -dedup::fdc74eb6544b2533f3f9fa8e8c7c34d7;roar::14676;14676;"IGU Institutional Open Access Repository";roar -dedup::fddb2b9f38ec47b6debfdcac82b6a6b0;opendoar::2180;2180;"repositorio digital puce";OpenDOAR -dedup::fddb2b9f38ec47b6debfdcac82b6a6b0;roar::3951;3951;"Repositorio Digital PUCE";roar -dedup::fe173cd995e699fe3b6aa437d88913cd;roar::13329;13329;"St Paul's University Institutional Repository";roar -dedup::fe173cd995e699fe3b6aa437d88913cd;opendoar::3917;3917;"st. pauls university institutional repository";OpenDOAR -dedup::fe66a9a531633c2350b09f04cd9d5d6f;opendoar::4801;4801;"repositorio institucional unitru";OpenDOAR -dedup::fe66a9a531633c2350b09f04cd9d5d6f;roar::15176;15176;"Repositorio Institucional UNITRU";roar 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-dedup::ffbb6800107747f9224cdde0df95da7c;opendoar::3122;3122;"istanbul bilgi university library open access";OpenDOAR -dedup::ffbb6800107747f9224cdde0df95da7c;roar::13646;13646;"Istanbul Bilgi University Library Open Access";roar diff --git a/deduplication/ds_to_json.py b/deduplication/ds_to_json.py deleted file mode 100644 index 5c925b4..0000000 --- a/deduplication/ds_to_json.py +++ /dev/null @@ -1,76 +0,0 @@ -# coding=utf-8 -from pyspark import SparkContext -from pyspark import SparkConf -from pyspark.sql import SparkSession -import json -#!/usr/bin/python -import os -import sys -import shutil - -def deleteDir(x): - try: - shutil.rmtree(x) - except OSError as e: - print("Error: %s - %s." % (e.filename, e.strerror)) - -def stringToArray(x): - try: - return eval(x) - except: - return [] - -def testValidJSON(x): - try: - json.loads(x) - return True - except: - return False - -conf = SparkConf().setAppName('fairshare').setMaster('local[*]') -sc = SparkContext(conf=conf) -spark = SparkSession.builder.config(conf=conf).getOrCreate() - -deleteDir("datasources") - -fairsharing_path = "../data/raw/fairsharing_dump_api_02_2022.json" -opendoar_path = "../data/raw/openDoar.tsv" -re3data_path = "../data/raw/re3data.tsv" -roar_path = "../data/raw/export_roar_CSV.csv" - -# #FAIRSHARING V1.0 -# #FILE STRUCTURE: Full name of record | Short name | FAIRsharing URL | Homepage URL of the resource | Country Field | Subjects -# fairsharing = sc.textFile("/Users/miconis/Desktop/Fairsharing dedup/registries_analysis/data/raw/FAIRsharingDBrec_summary20210304.csv") -# fairsharing = fairsharing.filter(lambda x: " FAIRsharing URL " not in x.split("|")).map(lambda x: dict(fullname=x.split("|")[0], shortname=x.split("|")[1], fairshare_url=x.split("|")[2], homepage_url=x.split("|")[3], country=x.split("|")[4], subjects=x.split("|")[5])) -# fairsharing = fairsharing.map(lambda x: dict(id=x['fairshare_url'], originalId=x['fairshare_url'], websiteurl=x['homepage_url'], name=x['fullname'], alternativeNames=[x['shortname']], collectedfrom="FAIRsharing")) -# -# print "FAIRSHARING:" + str(fairsharing.count()) - -#FAIRSHARING (file structure: ) -fairsharing = sc.textFile(fairsharing_path).filter(testValidJSON).map(json.loads) -fairsharing = fairsharing.map(lambda x: dict(id=x['attributes']['url'], originalId=x['id'], websiteurl=x['attributes']['metadata']['homepage'], name=x['attributes']['metadata']['name'], alternativeNames=[x['attributes']['abbreviation']], collectedfrom="FAIRsharing")) -print("FAIRSHARING DS", fairsharing.count()) - -#OPENDOAR (file structure: OpenAIREID orgIdentifier repositoryName alternativeNames repositoryURL description type updateDate startDate subject contentType institution metadataPolicy dataPolicy submissionPolicy contentPolicy software api) -opendoar = sc.textFile(opendoar_path) -opendoar = opendoar.filter(lambda x: "system_metadata.id" not in x.split("\t")).map(lambda x: dict(fullname=x.split("\t")[1], shortname=x.split("\t")[1], alternativeNames=x.split("\t")[2], opendoar_id=x.split("\t")[0], homepage_url=x.split("\t")[3], subjects=x.split("\t")[9], openaire_id="opendoar::"+x.split("\t")[0])) -opendoar = opendoar.map(lambda x: dict(id=x['openaire_id'], originalId=x['opendoar_id'], websiteurl=x['homepage_url'], name=json.loads(x['fullname'])['name'], alternativeNames=x['alternativeNames'], collectedfrom="OpenDOAR")) -print("OPENDOAR DS", opendoar.count()) - -#RE3DATA (file structure: openaire_id re3data_id repository_name additional_name repository_url repository_id description type size update_date start_date end_date subject mission_statement content_type provider_type keyword institution policy database_access database_license data_access data_license data_upload data_upload_license software versioning api pid_system citation_guideline_url aid_system enhanced_publication quality_management certificate metadata_standard syndication remarks entry_date last_update) -re3data = sc.textFile(re3data_path) -re3data = re3data.filter(lambda x: "repositoryName.language" not in x.split("\t")).map(lambda x: dict(fullname=x.split("\t")[1], shortname=x.split("\t")[3], re3data_id=x.split("\t")[0], homepage_url=x.split("\t")[4], subjects=x.split("\t")[14], openaire_id="re3data::"+x.split("\t")[0])) -re3data = re3data.map(lambda x: dict(id=x['openaire_id'], originalId=x['re3data_id'], websiteurl=x['homepage_url'], name=x['fullname'], alternativeNames=stringToArray(x['shortname']), collectedfrom="re3data")) -print("RE3DATA", re3data.count()) - -#ROAR (file structure: "eprintid","rev_number","eprint_status","userid","importid","source","dir","datestamp","lastmod","status_changed","type","succeeds","commentary","metadata_visibility","latitude","longitude","relation_type","relation_uri","item_issues_id","item_issues_type","item_issues_description","item_issues_timestamp","item_issues_status","item_issues_reported_by","item_issues_resolved_by","item_issues_comment","item_issues_count","sword_depositor","sword_slug","exemplar","home_page","title","oai_pmh","sword_endpoint","rss_feed","twitter_feed","description","fulltext","open_access","mandate","organisation_title","organisation_home_page","location_country","location_city","location_latitude","location_longitude","software","geoname","version","subjects","date","note","suggestions","activity_low","activity_medium","activity_high","recordcount","recordhistory","fulltexts_total","fulltexts_docs","fulltexts_rtotal","fulltexts_rdocs","registry_name","registry_id","submit_to","submitted_to_name","submitted_to_done","webometrics_rank","webometrics_size","webometrics_visibility","webometrics_rich_files","webometrics_scholar","monthly_deposits","total_deposits","association") -roar = sc.textFile(roar_path) -roar = roar.filter(lambda x: "\"eprintid\"" not in x.split(",")).filter(lambda x: len(x.split(","))>31).map(lambda x: dict(id=x.split(",")[0], homepage_url=x.split(",")[30], title=x.split(",")[31])).filter(lambda x: x['title'] != "" and x['homepage_url'] != "") -roar = roar.map(lambda x: dict(id="roar::"+x['id'].replace("\"",""), originalId=x['id'].replace("\"",""), websiteurl=x['homepage_url'].replace("\"",""), name=x['title'].replace("\"", ""), alternativeNames=[], collectedfrom="roar")) -roar = roar.filter(lambda x: x['id'] != "" and x['name'] != "") -roar = roar.map(lambda x: (x['id'], x)).reduceByKey(lambda x, y: x).map(lambda x: x[1]) -print "ROAR:" + str(roar.count()) - -all_ds = fairsharing.union(opendoar).union(re3data).union(roar) - -all_ds.map(json.dumps).saveAsTextFile("datasources") \ No newline at end of file diff --git a/deduplication/mergerels/.part-00000-d08d9845-18fb-4581-9fd1-cc65b62afe2b-c000.snappy.parquet.crc 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one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to 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The HTML pages are in $(BUILDDIR)/html." - -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in $(BUILDDIR)/htmlhelp." - -qthelp: - $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp - @echo - @echo "Build finished; now you can run "qcollectiongenerator" with the" \ - ".qhcp project file in $(BUILDDIR)/qthelp, like this:" - @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/data-registries.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/data-registries.qhc" - -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/data-registries" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/data-registries" - @echo "# devhelp" - -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. The epub file is in $(BUILDDIR)/epub." - -latex: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo - @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." - @echo "Run \`make' in that directory to run these through (pdf)latex" \ - "(use \`make latexpdf' here to do that automatically)." - -latexpdf: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through pdflatex..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -text: - $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text - @echo - @echo "Build finished. The text files are in $(BUILDDIR)/text." - -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -texinfo: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo - @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." - @echo "Run \`make' in that directory to run these through makeinfo" \ - "(use \`make info' here to do that automatically)." - -info: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo "Running Texinfo files through makeinfo..." - make -C $(BUILDDIR)/texinfo info - @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." - -gettext: - $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale - @echo - @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." - -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." - -linkcheck: - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in $(BUILDDIR)/linkcheck/output.txt." - -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." diff --git a/docs/commands.rst b/docs/commands.rst deleted file mode 100644 index 2d162f3..0000000 --- a/docs/commands.rst +++ /dev/null @@ -1,10 +0,0 @@ -Commands -======== - -The Makefile contains the central entry points for common tasks related to this project. - -Syncing data to S3 -^^^^^^^^^^^^^^^^^^ - -* `make sync_data_to_s3` will use `aws s3 sync` to recursively sync files in `data/` up to `s3://[OPTIONAL] your-bucket-for-syncing-data (do not include 's3://')/data/`. -* `make sync_data_from_s3` will use `aws s3 sync` to recursively sync files from `s3://[OPTIONAL] your-bucket-for-syncing-data (do not include 's3://')/data/` to `data/`. diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 317865d..0000000 --- a/docs/conf.py +++ /dev/null @@ -1,244 +0,0 @@ -# -*- coding: utf-8 -*- -# -# data-registries documentation build configuration file, created by -# sphinx-quickstart. -# -# This file is execfile()d with the current directory set to its containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -import os -import sys - -# 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. -# sys.path.insert(0, os.path.abspath('.')) - -# -- General configuration ----------------------------------------------------- - -# 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 = [] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix of source filenames. -source_suffix = '.rst' - -# The encoding of source files. -# source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = u'data-registries' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = '0.1' -# The full version, including alpha/beta/rc tags. -release = '0.1' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -# today = '' -# Else, today_fmt is used as the format for a strftime call. -# today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = ['_build'] - -# The reST default role (used for this markup: `text`) to use for all documents. -# default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -# add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -# add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -# show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# A list of ignored prefixes for module index sorting. -# modindex_common_prefix = [] - - -# -- 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 = 'default' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# html_theme_options = {} - -# Add any paths that contain custom themes here, relative to this directory. -# html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -# html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -# html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -# html_logo = None - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -# html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -# html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -# html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -# html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -# html_additional_pages = {} - -# If false, no module index is generated. -# html_domain_indices = True - -# If false, no index is generated. -# html_use_index = True - -# If true, the index is split into individual pages for each letter. -# html_split_index = False - -# If true, links to the reST sources are added to the pages. -# html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -# html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -# html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -# html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -# html_file_suffix = None - -# Output file base name for HTML help builder. -htmlhelp_basename = 'data-registriesdoc' - - -# -- Options for LaTeX output -------------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # 'papersize': 'letterpaper', - - # The font size ('10pt', '11pt' or '12pt'). - # 'pointsize': '10pt', - - # Additional stuff for the LaTeX preamble. - # 'preamble': '', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass [howto/manual]). -latex_documents = [ - ('index', - 'data-registries.tex', - u'data-registries Documentation', - u"Andrea Mannocci", 'manual'), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -# latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -# latex_use_parts = False - -# If true, show page references after internal links. -# latex_show_pagerefs = False - -# If true, show URL addresses after external links. -# latex_show_urls = False - -# Documents to append as an appendix to all manuals. -# latex_appendices = [] - -# If false, no module index is generated. -# latex_domain_indices = True - - -# -- Options for manual page output -------------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'data-registries', u'data-registries Documentation', - [u"Andrea Mannocci"], 1) -] - -# If true, show URL addresses after external links. -# man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------------ - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ('index', 'data-registries', u'data-registries Documentation', - u"Andrea Mannocci", 'data-registries', - 'A short description of the project.', 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -# texinfo_appendices = [] - -# If false, no module index is generated. -# texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -# texinfo_show_urls = 'footnote' diff --git a/docs/getting-started.rst b/docs/getting-started.rst deleted file mode 100644 index b4f71c3..0000000 --- a/docs/getting-started.rst +++ /dev/null @@ -1,6 +0,0 @@ -Getting started -=============== - -This is where you describe how to get set up on a clean install, including the -commands necessary to get the raw data (using the `sync_data_from_s3` command, -for example), and then how to make the cleaned, final data sets. diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 92a1ec3..0000000 --- a/docs/index.rst +++ /dev/null @@ -1,24 +0,0 @@ -.. data-registries documentation master file, created by - sphinx-quickstart. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -data-registries documentation! -============================================== - -Contents: - -.. toctree:: - :maxdepth: 2 - - getting-started - commands - - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index 7cf5761..0000000 --- a/docs/make.bat +++ /dev/null @@ -1,190 +0,0 @@ -@ECHO OFF - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set BUILDDIR=_build -set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . -set I18NSPHINXOPTS=%SPHINXOPTS% . -if NOT "%PAPER%" == "" ( - set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% - set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% -) - -if "%1" == "" goto help - -if "%1" == "help" ( - :help - echo.Please use `make ^` where ^ is one of - echo. html to make standalone HTML files - echo. dirhtml to make HTML files named index.html in directories - echo. singlehtml to make a single large HTML file - echo. pickle to make pickle files - echo. json to make JSON files - echo. htmlhelp to make HTML files and a HTML help project - echo. qthelp to make HTML files and a qthelp project - echo. devhelp to make HTML files and a Devhelp project - echo. epub to make an epub - echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter - echo. text to make text files - echo. man to make manual pages - echo. texinfo to make Texinfo files - echo. gettext to make PO message catalogs - echo. changes to make an overview over all changed/added/deprecated items - echo. linkcheck to check all external links for integrity - echo. doctest to run all doctests embedded in the documentation if enabled - goto end -) - -if "%1" == "clean" ( - for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i - del /q /s %BUILDDIR%\* - goto end -) - -if "%1" == "html" ( - %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/html. - goto end -) - -if "%1" == "dirhtml" ( - %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. - goto end -) - -if "%1" == "singlehtml" ( - %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. - goto end -) - -if "%1" == "pickle" ( - %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the pickle files. - goto end -) - -if "%1" == "json" ( - %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the JSON files. - goto end -) - -if "%1" == "htmlhelp" ( - %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run HTML Help Workshop with the ^ -.hhp project file in %BUILDDIR%/htmlhelp. - goto end -) - -if "%1" == "qthelp" ( - %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run "qcollectiongenerator" with the ^ -.qhcp project file in %BUILDDIR%/qthelp, like this: - echo.^> qcollectiongenerator %BUILDDIR%\qthelp\data-registries.qhcp - echo.To view the help file: - echo.^> assistant -collectionFile %BUILDDIR%\qthelp\data-registries.ghc - goto end -) - -if "%1" == "devhelp" ( - %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. - goto end -) - -if "%1" == "epub" ( - %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The epub file is in %BUILDDIR%/epub. - goto end -) - -if "%1" == "latex" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "text" ( - %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The text files are in %BUILDDIR%/text. - goto end -) - -if "%1" == "man" ( - %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The manual pages are in %BUILDDIR%/man. - goto end -) - -if "%1" == "texinfo" ( - %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. - goto end -) - -if "%1" == "gettext" ( - %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The message catalogs are in %BUILDDIR%/locale. - goto end -) - -if "%1" == "changes" ( - %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes - if errorlevel 1 exit /b 1 - echo. - echo.The overview file is in %BUILDDIR%/changes. - goto end -) - -if "%1" == "linkcheck" ( - %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck - if errorlevel 1 exit /b 1 - echo. - echo.Link check complete; look for any errors in the above output ^ -or in %BUILDDIR%/linkcheck/output.txt. - goto end -) - -if "%1" == "doctest" ( - %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest - if errorlevel 1 exit /b 1 - echo. - echo.Testing of doctests in the sources finished, look at the ^ -results in %BUILDDIR%/doctest/output.txt. - goto end -) - -:end diff --git a/models/.gitkeep b/models/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/references/.gitkeep b/references/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/reports/.gitkeep b/reports/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/reports/figures/.gitkeep b/reports/figures/.gitkeep deleted file mode 100644 index e69de29..0000000