4.1. System overview

4.1.1. Invenio v3.x

CAVEAT LECTOR

Invenio v3.0 alpha is a bleeding-edge developer preview version.

Invenio v3.0 build on top of Flask web development framework, using Jinja2 template engine, SQLAlchemy Object Relational Mapper, JSONSchema data model, PostgreSQL database for persistence, and Elasticsearch for information retrieval.

Invenio’s architecture is modular. The code base is split into more than 50 independent components that are released independently on PyPI. This ensures strict separation of components that talk among themselves over API and permits rapid development of independent components by independent teams.

Invenio compontents, named modules, can be roughly split in three categories:

  1. base modules provide interfaces to the Flask ecosystem, the Database, and other system tools and technologies that the Invenio ecosystem uses. Example: Invenio-Celery that talks to the Celery worker system.
  2. core feature modules provide most common functionality that each digital library instance is likely interested in using. Example: Invenio-Records provide record object store.
  3. additional feature modules offer additional functionality suitable for various particular use cases, such as the Integrated Library System, the Multimedia Store, or the Data Repository. Example: Invenio-Circulation offers circulation and holdings capabilities.

Here is a basic bird-eye overview of available Invenio components and their dependencies: (work in progress)

digraph invenio3 { size="20.0 20.0"; ratio="compress"; // helper floors node [shape=plaintext,style=invis]; { Floor9 -> Floor8 [style=invis]; Floor8 -> Floor7 [style=invis]; Floor7 -> Floor6 [style=invis]; Floor6 -> Floor5 [style=invis]; Floor5 -> Floor4 [style=invis]; Floor4 -> Floor3 [style=invis]; Floor3 -> Floor2 [style=invis]; Floor2 -> Floor1 [style=invis]; Floor1 -> Floor0 [style=invis]; } // invenio tools family node [shape=ellipse,style=dotted]; Elasticsearch; "JSON Schema"; MySQL; PostgreSQL; FS; Drive; Dropbox; S3; " Celery "; Flask; // invenio base plate family node [shape=box,style=filled]; Access; Admin; Assets; Base; Celery -> " Celery "; Config; DB -> MySQL; DB -> PostgreSQL; I18N; JSONSchemas -> "JSON Schema"; Logging; REST; Theme; Upgrader -> DB; // invenio search family node [shape=box,style=filled, color=green]; "Records-UI" -> Records; "Records-REST" -> Records; "Records-REST" -> PIDStore; Records -> DB; "Search-UI" -> Search; Search -> Records; "Records-REST" -> Search; PIDStore -> Records; PIDStore -> DB; node [shape=ellipse,style=filled,color=grey]; "Search-UI" -> "Query-Parser" ; "Search-UI" -> unAPI; node [shape=ellipse,style=dotted,color=black]; Search -> Elasticsearch; // invenio deposit family node [shape=box,style=filled, color=red]; "Deposit-UI" -> Deposit; "Deposit-REST" -> Deposit; Deposit -> Workflows; Deposit -> Knowledge; Deposit -> Sequencegenerator; Workflows -> Records; Workflows -> Documents; // invenio accounts family node [shape=box,style=filled, color="0.5 0.5 1.0"]; "Profiles-UI" -> Profiles; "Profiles-REST" -> Profiles; "Groups-UI" -> Groups; "Groups-REST" -> Groups; Profiles -> Access; Profiles -> Accounts; Accounts -> Access; Groups -> Accounts; // invenio helpers family node [shape=ellipse,style=filled,color=grey]; Documents; Cloudconnector; Testing; Utils; Ext; Webhooks; Redirector; // invenio OAIS family node [shape=box,style=filled,color=orange]; "OAIS-Audit-Store" -> DB; "OAIS-SIP-Store" -> DB; "OAIS-AIP-Store" -> Cloudconnector; "OAIS-DIP-Store" -> DB; Archiver; Deposit -> "OAIS-SIP-Store"; Workflows -> "OAIS-SIP-Store"; Records -> Archiver; Documents -> Archiver; Archiver -> "OAIS-AIP-Store"; Records -> "OAIS-Audit-Store"; // invenio add-ons family node [shape=box, style=filled, color=yellow]; Alerts -> Records; Annotations -> Records; Annotations -> Profiles; Classifier -> Records; Client -> "Records-REST"; Client -> "Groups-REST"; Client -> "Profiles-REST"; Client -> "Deposit-REST"; Documents -> Cloudconnector; Documents -> FS; Cloudconnector -> Dropbox; Cloudconnector -> Drive; Cloudconnector -> S3; Collections -> Records; Comments -> Records; Comments -> Profiles; Communities -> Collections; Communities -> Groups; Communities -> Profiles; Deposit -> Documents; Deposit -> Records; Deposit -> PIDStore; Documents -> Records; Formatter -> Records; Formatter -> "OAIS-DIP-Store"; Records -> JSONSchemas; News -> Theme; OAIHarvester -> DB; OAIHarvester -> Workflows; OAIHarvester -> Records; OAuthClient -> Accounts; OAuth2Server -> Accounts; Pages -> Theme; Previewer -> Records; Previewer -> "Previewer-ISPY"; Editor -> "Records-REST"; Checker -> "Records-REST"; Merger -> "Records-REST"; Statistics; Tags -> Records; Tags -> Profiles; // invenio ILS family node [shape=box, style=filled, color=purple]; "Circulation-UI" -> Circulation; "Circulation-REST" -> Circulation; "Acquisition-UI" -> Acquisition; "Acquisition-REST" -> Acquisition; Client -> "Circulation-REST"; Client -> "Acquisition-REST"; Circulation -> Records; Circulation -> Accounts; Acquisition -> Records; Acquisition -> Accounts; // invenio end user node [shape=plaintext, color=white]; Users; Users -> "Deposit-UI"; Users -> "Search-UI"; Users -> "Records-UI"; Users -> "Circulation-UI"; Users -> "Acquisition-UI"; // floor 0 { rank = same; Floor0; Elasticsearch; MySQL; PostgreSQL; " Celery "; "JSON Schema"; Flask; Drive; Dropbox; S3; FS; } // floor 1 { rank = same; Floor1; Access; Admin; Assets; Base; Celery; Config; DB; I18N; JSONSchemas; Logging; Theme; REST; Upgrader; DB; Testing; Utils; Ext; Webhooks; Redirector; } // floor 8 { rank = same; Floor8; "Records-UI"; "Records-REST"; "Deposit-UI"; "Deposit-REST"; "Search-UI"; "Profiles-UI"; "Profiles-REST"; "Groups-UI"; "Groups-REST"; "Circulation-UI"; "Circulation-REST"; "Acquisition-UI"; "Acquisition-REST"; } // floor 9 { rank = same; Floor9; Client; Users; } }

For further information, see Module anatomy and Modules sections.

4.1.2. Invenio v2.x

Invenio v2.x was a transitional release series combining legacy code base (Invenio v1.x) with new technology (Flask etc as used in Invenio v3.x).

4.1.3. Invenio v1.x

Invenio consists of several more or less independent modules with precisely defined functionality. The general criterion for module names is to use the “Bib” prefix to denote modules that work more with the bibliographic data, and the “Web” prefix to denote modules that work more with the Web interface. (The difference is of course blurred in some cases, as in the case of search engine that has got a web interface but searches bibliographic data.)

../_images/modules-overview-diagram.jpeg

Follows a brief description of what each module does.

  • BibCheck permits administrators and library cataloguers to automate various kind of tests on the metadata to see whether the metadata comply with quality standards. For example, that certain metadata fields are of a certain length, that they have numeric content, that they must not be present when other field exists, that their content is governed by an authority base depending on values of other fields, etc. The module can report its findings or can even automatically correct some kind of errors.
  • BibClassify allows automatic extraction of keywords from fulltext documents, based on the frequency of specific terms, taken from a controlled vocabulary. Controlled vocabularies can be expressed as simple text thesauri or as structured, RDF-compliant, taxonomies, to allow a semantic classification.
  • BibConvert allows metadata conversion from any structured or semi-structured proprietary format into any other format, typically the MARC XML that is natively used in Invenio. Nevertheless the input and output formats are fully configurable and have been tested on data importations from more than one hundred data sources. The power of this utility lies in the fact that no structural attributes of data source are presumed, but they are defined in an extensive data source configuration. Inevitably, this leads to a high complexity of the BibConvert configuration language. Most frequent configurations are provided with the Invenio distribution, such as a sample configuration from Qualified Dublin Core into the MARCXML. In general the BibConvert configuration consists from the source data descriptions and target data descriptions. The processor then analyzes and parses the input data and creates the resulting data structure, similarly as the XSLT processor would do. Typically the BibConvert is aimed at usage for input data that do not dispose of an XML representation. The source data is required to be structured or semi-structured, (i.e. not expressed in natural language that is a subject of information extraction task) and its processing involves several steps including record separation and field extraction upto transformation of source field values and their formatting.
  • BibEdit permits one to edit the metadata via a Web interface.
  • BibFormat is in charge of formatting the bibliographic metadata in numerous ways. This truly enables the separation of data content administration and formatting layout. BibFormat can act in the background and format the records when needed, or can preformat records for some often used outputs, such as the brief format used when displaying search results. The BibFormat settings can be administered either through a user-friendly web interface, or directly by editing human-readable configuration files.
  • OAIHarvest represents the OAi-PMH compatible harvester allowing the repository to gather metadata from fellow OAi-compliant repositories and the OAi-PMH repository management. Repository is built directly on top of the database and disposes of an OAi repository manager that allows to perform the administrative tasks on the repository aside from the principal generic data administration module. The database can be partially or completely open for harvesting in the scope of the OAi-PMH protocol. In this case, all data is provided in raw form, where the semantics of individual tags is indicated uniquely by the MARC21 naming convention. This is particularly interesting for institutes that are specialized in cross-archive and cross-disciplinary services provision, as for example the ARC service provider.
  • BibIndex module takes care of the indexation of metadata, references and full text files. Two kinds of indexes – word and phrase index – are being maintained. The user can define several logical indexes (e.g. author index, title index, etc.) and the correspondence of which physical MARC21 metadata tag goes into which logical field index. An index consists of two parts: (i) a forward index listing various words (or phrases) found in the given field, with the set of record identifiers where the given word can be found; and (ii) a reverse index listing record identifiers, with the set of words of the given record that go to the forward index. Such a two-part indexing technique allows one to rapidly update only those words that have changed in the input metadata record. The indexes were designed with the aim to provide fast user-response search times and are faster than native MySQL (full text) indexes.
  • BibMatch permits to filter input XML files against the database content, attempting to match records via certain criteria, for example to avoid doubly-inputted records.
  • BibRank permits to set up various ranking criteria that will be used later by the search engine. For example, ranking by the word frequency, or by some metadata tag value such as journal name by means of the journal impact factor knowledge base, or even by the number of downloads of a particular paper. Note that BibRank is independent of BibIndex.
  • BibSched The bibliographic task scheduler is central unit of the system that allows all other modules to access the bibliographic database in a controlled manner, preventing sharing violation threats and assuring the coherent execution of the database update tasks. The module comes with an administrative interface that allows to monitor the task queue including various possibilities of a manual intervention, for example to re-schedule queued tasks, change the task order, etc.
  • BibUpload allows to load the new bibliographic data into the database. To effectuate this task the data must be a well-formed XML file that complies with the current metadata tag selection schema. Usually, the properly structured input files of BibUpload come from the BibConvert utility.
  • ElmSubmit is an email submission gateway that permits for automatic document uploads from trusted sources via email. (Usually web submission or harvesting is preferred.)
  • MiscUtil is a collection of miscellaneous utilities that other modules are using, like the international messages, etc.
  • WebAccess module is responsible for granting access to users for performing various actions within the system. A Role-Based Access Control (RBAC) technique is used, where users belong to several groups according to their role in the system. Each user group can be granted to perform certain actions depending on possible one more action arguments. WebAccess is presently used mainly for the administrative interface. There are basically two kinds of actions: (i) configuration of administrative modules and (ii) running administrative tasks.
  • WebAlert module allows the end user to be alerted whenever a new document matching her personal criteria is inserted into the database. The criteria correspond to a typical user query as if it would be done via the search interface. For example, a user may want to get notified whenever a new document containing certain words, or of a certain subject, is inserted. A user may create several alerts with a daily, weekly, or a monthly frequency. The results of alert searches are either sent back to the user by email or can also be stored into her baskets.
  • WebBasket module enables the end user of the system to store the documents she is interested in in a personal basket or a personal shelf. The concept is similar to popular shopping carts. One user may own several baskets. A basket can be either private or public, allowing a simple document sharing mechanism within a group.
  • WebComment provides a community-oriented tool to rank documents by the readers or to share comments on the documents by the readers. Integrated with the group-aware WebBasket, WebGroup, WebMessage tools, WebComment is at the heart of the social network features of the Invenio software.
  • WebHelp presents some global user-level, admin-level, and hacker-level documenation on Invenio. The module-specific documentation is included within each particular module.
  • WebMessage permits the communication between (possibly anonymous) end users via web message boards, to invite readers to join the groups, etc.
  • WebSearch module handles user requests to search for a certain words or phrases in the database. Two types of searching can be performed: a word search or a phrase search. The system allows for complex boolean queries, regular expression searching, or a combined metadata, references and full text file searching in one go. Users have a possibility to browse for present index terms. If no direct match could have been found with the user-typed query pattern, the system proposes alternative matches as a search guidance. The search indexes were designed to provide fast response times for middle-sized data collections of up to 106 records. The metadata corpus is organized into metadata collections that are directly accessible through the browse function, similarly to the popular concept of Web Directories. Orthogonal views on the document corpus are enabled in the search interface via a concept of virtual collections: for example, a document may be classified both according to its type (e.g. preprint, book) and according to its Dewey decimal classification number. Such a flexible organization views allows for the creation of easy navigation schemata to the end users.
  • WebSession is a session and user management module that permits to differentiate between users. Useful for personalization of the interface and services like personal baskets and alerts.
  • WebStat is a configurable system that permits to gather statistics about the health of the server, the usage of the system, as well as about some particular system features.
  • WebStyle is a library of design-related modules that defines look and feel of Invenio pages.
  • WebSubmit is a comprehensive submission system allowing authorized individuals (authors, secretaries and repository maintenance staff) to submit individual documents into the system. The submission system disposes of a flow-control mechanism that assures the data approval by authorized units. In total there are several different exploitable submission schemas at a disposal, including an automated full text document conversion from various textual and image formats. This module also disposes of information extraction functionality, focusing on bibliographic entities such as references, authors, keywords or other implicit metadata.