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authorBryan Newbold <bnewbold@robocracy.org>2018-09-20 12:40:12 -0700
committerBryan Newbold <bnewbold@robocracy.org>2018-09-20 12:40:20 -0700
commitf10bcb49d17234dc52c8b67a7b7fd1796ab6f435 (patch)
tree070ef3376b67798b9c81c78c940a09ead51dcf49 /guide
parent90f059d1ad87a068b0dce92a965175c6ed158ba1 (diff)
downloadfatcat-f10bcb49d17234dc52c8b67a7b7fd1796ab6f435.tar.gz
fatcat-f10bcb49d17234dc52c8b67a7b7fd1796ab6f435.zip
work in progress on guide (mdbook)
Diffstat (limited to 'guide')
-rw-r--r--guide/.gitignore1
-rw-r--r--guide/README.md8
-rw-r--r--guide/book.toml5
-rwxr-xr-xguide/push_qa.sh3
-rw-r--r--guide/src/SUMMARY.md14
-rw-r--r--guide/src/bulk_exports.md1
-rw-r--r--guide/src/cookbook.md37
-rw-r--r--guide/src/data_model.md1
-rw-r--r--guide/src/entity_fields.md1
-rw-r--r--guide/src/http_api.md56
-rw-r--r--guide/src/implementation.md1
-rw-r--r--guide/src/overview.md3
-rw-r--r--guide/src/policies.md102
l---------guide/src/rfc.md1
-rw-r--r--guide/src/sources.md1
-rw-r--r--guide/src/style_guide.md109
-rw-r--r--guide/src/sw_contribute.md14
17 files changed, 358 insertions, 0 deletions
diff --git a/guide/.gitignore b/guide/.gitignore
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+book
diff --git a/guide/README.md b/guide/README.md
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+
+This is an [mdBook](https://rust-lang-nursery.github.io/mdBook/index.html),
+containing documentation for the fatcat bibliographic catalog, including:
+
+- contributor style guide (for bibliographic metadata)
+- developer (API) documentation
+- etc.
+
diff --git a/guide/book.toml b/guide/book.toml
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+[book]
+title = "Fatcat: The Guide"
+authors = ["Fatcat Documentation Contributors"]
+multilingual = false
+src = "src"
diff --git a/guide/push_qa.sh b/guide/push_qa.sh
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+++ b/guide/push_qa.sh
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+#!/bin/bash
+
+rsync -arv book/ fatcat-vm:/srv/fatcat/guide
diff --git a/guide/src/SUMMARY.md b/guide/src/SUMMARY.md
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+# Outline
+
+- [Fatcat Overview](./overview.md)
+ - [Data Model](./data_model.md)
+ - [Sources](./sources.md)
+ - [Implementation](./implementation.md)
+ - [Original Design Document](./rfc.md)
+- [Cataloging Style Guide](./style_guide.md)
+ - [Entity Field Reference](./entity_fields.md)
+- [Public API](./http_api.md)
+ - [Bulk Exports](./bulk_exports.md)
+ - [Cookbook](./cookbook.md)
+- [Software Contributions](./sw_contribute.md)
+- [Policies](./policies.md)
diff --git a/guide/src/bulk_exports.md b/guide/src/bulk_exports.md
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+# Bulk Exports
diff --git a/guide/src/cookbook.md b/guide/src/cookbook.md
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+# Cookbook
+
+### Updating an Existing Entity
+
+1. Fetch (GET) the existing entity
+2. Create (POST) a new editgroup
+3. Update (PUT) the entity, with the current revision number in the `prev` edit
+ field, and the editgroup id set
+4. Submit (POST? TBD) the editgroup for review
+
+### Merging Duplicate Entities
+
+1. Fetch (GET) both entities
+2. Decide which will be the "primary" entity (the other will redirect to it)
+3. Create (POST) a new editgroup
+4. Update (PUT) the "primary" entity with any updated metadata merged from the
+ other entity (optional), and the editgroup id set
+5. Update (PUT) the "other" entity with the redirect flag set to the primary's
+ identifier, with the current revision id (of the "other" entity) in the
+ `prev` field, and the editgroup id set
+4. Submit (POST? TBD) the editgroup for review
+
+### Lookup Fulltext URLs by DOI
+
+1. Use release lookup endpoint (GET) with the DOI a query parameter, with
+ `expand=files`
+2. If a release hit is found, iterate over the linked `file` entities, and
+ create a ranked list of URLs based on mimetype, URL "rel" type, file size,
+ or host domain.
+
+### Batch Insert New Entities (Bootstrapping)
+
+When bootstrapping a blank catalog, we need to insert 10s or 100s of millions
+of entities as fast as possible.
+
+1. Create (POST) a new editgroup, with progeny information included
+2. Batch create (POST) entities
diff --git a/guide/src/data_model.md b/guide/src/data_model.md
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+# Data Model
diff --git a/guide/src/entity_fields.md b/guide/src/entity_fields.md
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+# Entity Field Reference
diff --git a/guide/src/http_api.md b/guide/src/http_api.md
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+# REST API
+
+The fatcat HTTP API is mostly a classic REST CRUD (Create, Read, Update,
+Delete) API, with a few twists.
+
+A declarative specification of all API endpoints, JSON data models, and
+response types is available in OpenAPI 2.0 format. Code generation tools are
+used to generate both server-side type-safe endpoint routes and client-side
+libraries. Auto-generated reference documentation is, for now, available at
+<https://api.qa.fatcat.wiki>.
+
+All API traffic is over HTTPS; there is no insecure HTTP endpoint, even for
+read-only operations. To start, all endpoints accept and return only JSON
+serialized content.
+
+## Editgroups
+
+All mutating entity operations (create, update, delete) accept an
+`editgroup_id` query parameter. If the parameter isn't set, the editor's
+"currently active" editgroup will be used, or a new editgroup will be created
+from scratch. It's generally preferable to manually create an editgroup and use
+the `id` in edit requests; the allows appropriate metadata to be set. The
+"currently active" editgroup behavior may be removed in the future.
+
+## Sub-Entity Expansion
+
+To reduce the need for multiple GET queries when looking for common related
+metadata, it is possible to include linked entities in responses using the
+`expand` query parameter. For example, by default the `release` model only
+includes an optional `container_id` field which points to a container entity.
+If the `expand` parameter is set:
+
+ https://api.qa.fatcat.wiki/v0/release/aaaaaaaaaaaaarceaaaaaaaaam?expand=container
+
+Then the full container model will be included under the `container` field.
+Multiple expand parameters can be passed, comma-separated.
+
+## Authentication and Authorization
+
+There are two editor types: bots and humans. Additionally, either type of
+editor may have additional privileges which allow them to, eg, directly accept
+editgroups (as opposed to submitting edits for review).
+
+All mutating API calls (POST, PUT, DELETE HTTP verbs) require token-based
+authentication using an HTTP Bearer token. If you can't generate such a token
+from the web interface (because that feature hasn't been implemented), look for
+a public demo token for experimentation, or ask an administrator for a token.
+
+## QA Instance
+
+The intent is to run a public "sandbox" QA instance of the catalog, using a
+subset of the full catalog, running the most recent development branch of the
+API specification. This instance can be used by developers for prototyping and
+experimentation, though note that all data is periodically wiped, and this
+endpoint is more likely to have bugs or be offline.
+
diff --git a/guide/src/implementation.md b/guide/src/implementation.md
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+# Implementation
diff --git a/guide/src/overview.md b/guide/src/overview.md
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+# Fatcat Overview
+
+For now, see the [RFC](https://fatcat.wiki).
diff --git a/guide/src/policies.md b/guide/src/policies.md
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+# Norms and Policies
+
+These social norms are explicitly expected to evolve and mature if the number
+of contributors to the project grows. It is important to have some policies as
+a starting point, but also important not to set these policies in stone until
+they have been reviewed.
+
+## Social Norms and Conduct
+
+Contributors (editors and software developers) are expected to treat each other
+excellently, to assume good intentions, and to participate constructively.
+
+## Metadata Licensing
+
+The Fatcat catalog content license is the Creative Commons Zero ("CC-0")
+license, which is effectively a public domain grant. This applies to the
+catalog metadata itself (titles, entity relationships, citation metadata, URLs,
+hashes, identifiers), as well as "meta-meta-data" provided by editors (edit
+descriptions, progeny metadata, etc).
+
+The core catalog is designed to contain only factual information: "this work,
+known by this title and with these third-party identifiers, is believed to be
+represented by these files and published under such-and-such venue". As a norm,
+sourcing metadata (for attribution and progeny) is retained for each edit made
+to the catalog.
+
+A notable exception to this policy are abstracts, for which no copyright claims
+or license is made. Abstract content is kept separate from core catalog
+metadata; downstream users need to make their own decision regarding reuse and
+distribution of this material.
+
+As a social norm, it is expected (and appreciated!) that downstream users of
+the public API and/or bulk exports provide attribution, and even transitive
+attribution (acknowledging the original source of metadata contributed to
+Fatcat). As an academic norm, researchers are encouraged to cite the corpus as
+a dataset (when this option becomes available). However, neither of these norms
+are enforced via the copyright mechanism.
+
+As a strong norm, editors should expect full access to the full corpus and edit
+history, including all of their contributions.
+
+## Immutable History
+
+All editors agree to the licensing terms, and understand that their full public
+history of contributions is made irrevokably public. Edits and contributions
+may be *reverted*, but the history (and content) of their edits are retained.
+Edit history is not removed from the corpus on the request of an editor or when
+an editor closes their account.
+
+In an emergency situation, such as non-bibliographic content getting encoded in
+the corpus by bypassing normal filters (eg, base64 encoding hate crime content
+or exploitive photos, as has happened to some blockchain projects), the
+ecosystem may decide to collectively, in a coordinated manner, expunge specific
+records from their history.
+
+## Documentation Licensing
+
+This guide ("Fatcat: The Guide") is licensed under the Creative Commons
+Attribution license.
+
+## Software Licensing
+
+The Fatcat software project licensing policy is to adopt strong copyleft
+licenses for server software (where the majority of software development takes
+place), and permissive licenses for client library and bot framework software,
+and CC-0 (public grant) licensing for declarative interface specifications
+(such as SQL schemas and REST API specifications).
+
+## Privacy Policy
+
+*It is important to note that this section is currently aspirational: the
+servers hosting early deployments of fatcat are largely in a default
+configuration and have not been audited to ensure that these guidelines are
+being followed.*
+
+It is a goal for fatcat to conduct as little surveillence of reader and editor
+bahavior and activities as possible. In pratical terms, this means minimizing
+the overall amount of logging and collection of identifying information. This
+is in contrast to *submitted edit content*, which is captured, preserved, and
+republished as widely as possible.
+
+The general intention is to:
+
+- not use third-party tracking (via extract browser-side requests or
+ javascript)
+- collect aggregate *metrics* (overall hit numbers), but not *log* individual
+ interactions ("this IP visited this page at this time")
+
+Exceptions will likely be made:
+
+- temporary caching of IP addresses may be necessary to implement rate-limiting
+ and debug traffic spikes
+- exception logging, abuse detection, and other exceptional
+
+Some uncertain areas of privacy include:
+
+- should third-party authenticion identities be linked to editor ids? what
+ about the specific case of ORCiDs if used for login?
+- what about discussion and comments on edits? should conversations be included
+ in full history dumps? should editors be allowed to update or remove
+ comments?
+
diff --git a/guide/src/rfc.md b/guide/src/rfc.md
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+../../fatcat-rfc.md \ No newline at end of file
diff --git a/guide/src/sources.md b/guide/src/sources.md
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+# Sources
diff --git a/guide/src/style_guide.md b/guide/src/style_guide.md
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+# Cataloging Style Guide
+
+## Language and Translation of Metadata
+
+The Fatcat data model does not include multiple titles or names for the same
+entity, or even a "native"/"international" representation as seems common in
+other bibliographic systems. This most notably applies to release titles, but
+also to container and publisher names, and likely other fields.
+
+For now, editors must use their own judgement over whether to use the title of
+the release listed in the work itself
+
+This is not to be confused with *translations* of entire works, which should be
+treated as an entirely separate `release`.
+
+## Work/Release Distinction
+
+## External Identifiers
+
+"Fake identifiers", which are actually registered and used in examples and
+documentation (such as DOI `10.5555/12345678`) are allowed (and the entity
+should be tagged as a fake or example). Non-registered "identifier-like
+strings", which are semantically valid but not registered, should not exist in
+fatcat metadata in an identifier column. Invalid identifier strings can be
+stored in "extra" metadata. Crossref has [blogged]() about this distinction.
+
+[blogged]: https://www.crossref.org/blog/doi-like-strings-and-fake-dois/
+
+#### DOI
+
+All DOIs stored in an entity column should be registered (aka, should be
+resolvable from `doi.org`). Invalid identifiers may be cleaned up or removed by
+bots.
+
+DOIs should *always* be stored and transfered in lower-case form. Note that
+there are almost no other constraints on DOIs (and handles in general): they
+may have muliple forward slashes, whitespace, of arbitrary length, etc.
+Crossref has a [number of examples]() of such "valid" but frustratingly
+formatted strings.
+
+[number of examples]: https://www.crossref.org/blog/dois-unambiguously-and-persistently-identify-published-trustworthy-citable-online-scholarly-literature-right/
+
+In the fatcat ontology, DOIs and release entities are one-to-one.
+
+It is the intention to automatically (via bot) create a fatcat release for
+every Crossref-registered DOI from a whitelist of media types
+("journal-article" etc, but not all), and it would be desirable to auto-create
+entities for in-scope publications from all registrars. It is not the intention
+to auto-create a release for every registered DOI. In particular,
+"sub-component" DOIs (eg, for an individual figure or table from a publication)
+aren't currently auto-created, but could be stored in "extra" metadata, or on a
+case-by-case basis.
+
+## Human Names
+
+Representing names of human beings in databases is a fraught subject. For some
+background reading, see:
+
+- [Falsehoods Programmers Believe About Names](https://www.kalzumeus.com/2010/06/17/falsehoods-programmers-believe-about-names/) (blog post)
+- [Personal names around the world](https://www.w3.org/International/questions/qa-personal-names) (W3C informational)
+- [Hubert Blaine Wolfeschlegelsteinhausenbergerdorff Sr.](https://en.wikipedia.org/wiki/Hubert_Blaine_Wolfeschlegelsteinhausenbergerdorff_Sr.) (Wikipedia article)
+
+Particular difficult issues in the context of a bibliographic database include
+the non-universal concept of "family" vs. "given" names and their relationship
+to first and last names; the inclusion of honarary titles and other suffixes
+and prefixes to a name; the distinction between "prefered", "legal", and
+"bibliographic" names, or other situations where a person may not wish to be
+known under the name they are commonly refered to under; language and character
+set issues; and pseudonyms, anonymous publications, and fake personas (perhaps
+representing a group, like Bourbaki).
+
+The general guidance for Fatcat is to:
+
+- not be a "source of truth" for representing a persona or human being; ORCiD
+ and Wikidata are better suited to this task
+- represent author personas, not necessarily 1-to-1 with human beings
+- prioritize the concerns of a reader or researcher over that of the author
+- enable basic interoperability with external databases, file formats, schemas,
+ and style gudies
+- when possible, respect the wishes of individuals
+
+The data model for the `creator` entity has three name fields:
+
+- `surname` and `given_name`: needed for "aligning" with external databases,
+ and to export metadata to many standard formats
+- `display_name`: the "prefered" representation for display of the entire name,
+ in the context of international attribution of authorship of a written work
+
+Names to not necessarily need to expressed in a Latin character set, but also
+does not necessarily need to be in the native language of the creator or the
+language of their notable works
+
+Ideally all three fields are populated for all creators.
+
+It seems likely that this schema and guidance will need review. "Extra"
+metadata can be used to store aliases and alternative representations, which
+may be useful for disambiguation and automated de-duplication.
+
+## Editgroups and Meta-Meta-Data
+
+Editors are expected to group their edits in semantically meaningful editgroups
+of a reasonable size for review and acceptance. For example, merging two
+`creators` and updating related `releases` could all go in a single editgroup.
+Large refactors, conversions, and imports, which may touch thousands of
+entities, should be grouped into reasonable size editgroups; extremely large
+editgroups may cause technical issues, and make review unmanagable. 50 edits is
+a decent batch size, and 100 is a good upper limit (and may be enforced by the
+server).
+
diff --git a/guide/src/sw_contribute.md b/guide/src/sw_contribute.md
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+# Software Contributions
+
+For now, issues and patches can be filed at <https://github.com/bnewbold/fatcat>.
+
+To start, the back-end (fatcatd, in rust), web interface (fatcat-web, in
+python), bots, and this guide are all versioned in the same git repository.
+
+See the `rust/README` and `rust/HACKING` documents for some common tasks and
+gotchas when working with the rust backend.
+
+When considering making a non-trivial contribution, it can save review time and
+duplicated work to post an issue with your intentions and plan. New code and
+features will need to include unit tests before being merged, though we can
+help with writing them.