Merge the docs in the main repository

.docs/.swagger/api-analyse.yaml

+{"definitions":{},"externalDocs":{"description":"Sourcecode Documentation","url":"https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services"},"info":{"contact":{"email":"andreas.rauber@tuwien.ac.at","name":"Prof. Andreas Rauber"},"description":"Service that analyses data structures","license":{"name":"Apache 2.0","url":"https://www.apache.org/licenses/LICENSE-2.0"},"title":"Database Repository Analyse Service API","version":"1.2.0"},"openapi":"3.0.0","paths":{"/api/analyse/determinedt":{"post":{"consumes":["application/json"],"description":"This is a simple API which returns the datatypes of a (path) csv file","parameters":[{"description":"to-do description","in":"body","name":"body","required":true,"schema":{"properties":{"enum":{"example":true,"type":"boolean"},"enum_tol":{"example":0.1},"filepath":{"example":"/data/testdt08.csv","type":"string"},"separator":{"example":",","type":"string"}},"type":"object"}}],"produces":["application/json"],"responses":{"200":{"description":"OK"},"405":{"description":"Invalid input"}},"summary":"Determine datatypes"}},"/api/analyse/determinepk":{"post":{"consumes":["application/json"],"description":"This is a simple API which returns the primary keys + ranking of a (path) csv file","parameters":[{"description":"to-do description","in":"body","name":"body","required":true,"schema":{"properties":{"filepath":{"example":"/data/testdt08.csv","type":"string"},"seperator":{"example":",","type":"string"}},"type":"object"}}],"produces":["application/json"],"responses":{"200":{"description":"OK"},"405":{"description":"Invalid input"}},"summary":"Determine primary keys"}}},"servers":[{"description":"Generated server url","url":"http://localhost:5000"},{"description":"Sandbox","url":"https://dbrepo2.tuwien.ac.at"}]}

.docs/.swagger/api-metadata.yaml

+openapi: 3.0.1
+info:
+  title: Database Repository Metadata Service API
+  description: Service that manages the metadata
+  contact:
+    name: Prof. Andreas Rauber
+    email: andreas.rauber@tuwien.ac.at
+  license:
+    name: Apache 2.0
+    url: https://www.apache.org/licenses/LICENSE-2.0
+  version: 1.2.0
+externalDocs:
+  description: Sourcecode Documentation
+  url: https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services
+servers:
+- url: http://localhost:9099
+  description: Generated server url
+- url: https://dbrepo2.tuwien.ac.at
+  description: Sandbox
+paths:
+  /api/oai:
+    get:
+      tags:
+      - metadata-endpoint
+      summary: Get the record
+      operationId: identify_1_1_1_1
+      parameters:
+      - name: verb
+        in: query
+      - name: parameters
+        in: query
+        required: true
+        schema:
+          $ref: '#/components/schemas/OaiListIdentifiersParameters'
+      responses:
+        "200":
+          description: List containers
+          content:
+            text/xml: {}
+components:
+  schemas:
+    OaiListIdentifiersParameters:
+      type: object
+      properties:
+        metadataPrefix:
+          type: string
+        from:
+          type: string
+        until:
+          type: string
+        set:
+          type: string
+        resumptionToken:
+          type: string
+        fromDate:
+          type: string
+          format: date-time
+        untilDate:
+          type: string
+          format: date-time
+        parametersString:
+          type: string

.docs/.swagger/api-semantics.yaml

+openapi: 3.0.1
+info:
+  title: Database Repository Semantic Service API
+  description: Service that manages the tables
+  contact:
+    name: Prof. Andreas Rauber
+    email: andreas.rauber@tuwien.ac.at
+  license:
+    name: Apache 2.0
+    url: https://www.apache.org/licenses/LICENSE-2.0
+  version: 1.2.0
+externalDocs:
+  description: Sourcecode Documentation
+  url: https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services
+servers:
+- url: http://localhost:9097
+  description: Generated server url
+- url: https://dbrepo2.tuwien.ac.at
+  description: Sandbox
+paths:
+  /api/semantic/ontology/{id}:
+    get:
+      tags:
+      - ontology-endpoint
+      summary: Find one ontology
+      operationId: find
+      parameters:
+      - name: id
+        in: path
+        required: true
+        schema:
+          type: integer
+          format: int64
+      responses:
+        "200":
+          description: Find one ontology
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/OntologyDto'
+        "404":
+          description: Could not find ontology
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ApiErrorDto'
+    put:
+      tags:
+      - ontology-endpoint
+      summary: Update an ontology
+      operationId: update
+      parameters:
+      - name: id
+        in: path
+        required: true
+        schema:
+          type: integer
+          format: int64
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/OntologyModifyDto'
+        required: true
+      responses:
+        "202":
+          description: Updated ontology successfully
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/OntologyDto'
+        "404":
+          description: Could not find ontology
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ApiErrorDto'
+      security:
+      - bearerAuth: []
+    delete:
+      tags:
+      - ontology-endpoint
+      summary: Delete an ontology
+      operationId: delete
+      parameters:
+      - name: id
+        in: path
+        required: true
+        schema:
+          type: integer
+          format: int64
+      responses:
+        "202":
+          description: Deleted ontology successfully
+          content:
+            application/json: {}
+        "404":
+          description: Could not find ontology
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ApiErrorDto'
+      security:
+      - bearerAuth: []
+  /api/semantic/unit:
+    get:
+      tags:
+      - semantics-endpoint
+      summary: List semantic units
+      operationId: findAllUnits
+      responses:
+        "200":
+          description: Find all semantic units
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/UnitDto'
+    post:
+      tags:
+      - semantics-endpoint
+      summary: Save a semantic unit
+      operationId: saveUnit
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/UnitSaveDto'
+        required: true
+      responses:
+        "202":
+          description: Saved a semantic unit
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/UnitDto'
+      security:
+      - bearerAuth: []
+  /api/semantic/ontology:
+    get:
+      tags:
+      - ontology-endpoint
+      summary: List all ontologies
+      operationId: findAll
+      responses:
+        "200":
+          description: List all ontologies
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/OntologyDto'
+    post:
+      tags:
+      - ontology-endpoint
+      summary: Register a new ontology
+      operationId: create
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/OntologyCreateDto'
+        required: true
+      responses:
+        "201":
+          description: Registered ontology successfully
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/OntologyDto'
+      security:
+      - bearerAuth: []
+  /api/semantic/concept:
+    get:
+      tags:
+      - semantics-endpoint
+      summary: List semantic concepts
+      operationId: findAllConcepts
+      responses:
+        "200":
+          description: Find all semantic concepts
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/ConceptDto'
+    post:
+      tags:
+      - semantics-endpoint
+      summary: Create or update a semantic concept
+      operationId: saveUnit_1
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/ConceptSaveDto'
+        required: true
+      responses:
+        "202":
+          description: Saved a semantic concept
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ConceptDto'
+      security:
+      - bearerAuth: []
+  /api/semantic/ontology/{id}/entity:
+    get:
+      tags:
+      - query-endpoint
+      summary: Find entities
+      operationId: find_1
+      parameters:
+      - name: id
+        in: path
+        required: true
+        schema:
+          type: integer
+          format: int64
+      - name: label
+        in: query
+        required: false
+        schema:
+          type: string
+      - name: uri
+        in: query
+        required: false
+        schema:
+          type: string
+      responses:
+        "200":
+          description: Found entities
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/EntityDto'
+        "417":
+          description: Generated query or uri is malformed
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ApiErrorDto'
+        "404":
+          description: Could not find ontology
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ApiErrorDto'
+        "400":
+          description: Filter params are invalid
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ApiErrorDto'
+      security:
+      - bearerAuth: []
+  /api/semantic/database/{databaseId}/table/{tableId}:
+    get:
+      tags:
+      - table-endpoint
+      summary: Suggest table semantics
+      operationId: analyseTable
+      parameters:
+      - name: databaseId
+        in: path
+        required: true
+        schema:
+          type: integer
+          format: int64
+      - name: tableId
+        in: path
+        required: true
+        schema:
+          type: integer
+          format: int64
+      responses:
+        "417":
+          description: Generated query is malformed
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ApiErrorDto'
+        "404":
+          description: Could not find the table
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ApiErrorDto'
+        "200":
+          description: Suggested table semantics successfully
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/TableColumnEntityDto'
+      security:
+      - bearerAuth: []
+  /api/semantic/database/{databaseId}/table/{tableId}/column/{columnId}:
+    get:
+      tags:
+      - table-endpoint
+      summary: Suggest table column semantics
+      operationId: analyseTableColumn
+      parameters:
+      - name: databaseId
+        in: path
+        required: true
+        schema:
+          type: integer
+          format: int64
+      - name: tableId
+        in: path
+        required: true
+        schema:
+          type: integer
+          format: int64
+      - name: columnId
+        in: path
+        required: true
+        schema:
+          type: integer
+          format: int64
+      responses:
+        "417":
+          description: Generated query is malformed
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ApiErrorDto'
+        "200":
+          description: Suggested table column semantics successfully
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/TableColumnEntityDto'
+        "404":
+          description: Could not find the table column
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ApiErrorDto'
+      security:
+      - bearerAuth: []
+components:
+  schemas:
+    OntologyModifyDto:
+      required:
+      - prefix
+      - uri
+      type: object
+      properties:
+        uri:
+          type: string
+          example: Ontology URI
+        prefix:
+          type: string
+          example: Ontology prefix
+        sparql_endpoint:
+          type: string
+          example: Ontology SPARQL endpoint
+    OntologyDto:
+      required:
+      - created
+      - id
+      - prefix
+      - rdf
+      - sparql
+      - uri
+      type: object
+      properties:
+        id:
+          type: integer
+          format: int64
+        uri:
+          type: string
+          example: Ontology URI
+        prefix:
+          type: string
+          example: Ontology prefix
+        sparql:
+          type: boolean
+          example: true
+        rdf:
+          type: boolean
+          example: true
+        creator:
+          $ref: '#/components/schemas/UserBriefDto'
+        created:
+          type: string
+          format: date-time
+          example: 2021-03-12T15:26:21.678396092Z
+        sparql_endpoint:
+          type: string
+          example: Ontology SPARQL endpoint
+    UserBriefDto:
+      required:
+      - id
+      - username
+      type: object
+      properties:
+        id:
+          type: string
+          format: uuid
+          example: 1ffc7b0e-9aeb-4e8b-b8f1-68f3936155b4
+        username:
+          type: string
+          description: Only contains lowercase characters
+          example: jcarberry
+        name:
+          type: string
+          example: Josiah Carberry
+        orcid:
+          type: string
+          example: 0000-0002-1825-0097
+        given_name:
+          type: string
+          example: Josiah
+        family_name:
+          type: string
+          example: Carberry
+        email_verified:
+          type: boolean
+          example: true
+    ApiErrorDto:
+      required:
+      - code
+      - message
+      - status
+      type: object
+      properties:
+        status:
+          type: string
+          example: STATUS
+          enum:
+          - 100 CONTINUE
+          - 101 SWITCHING_PROTOCOLS
+          - 102 PROCESSING
+          - 103 EARLY_HINTS
+          - 103 CHECKPOINT
+          - 200 OK
+          - 201 CREATED
+          - 202 ACCEPTED
+          - 203 NON_AUTHORITATIVE_INFORMATION
+          - 204 NO_CONTENT
+          - 205 RESET_CONTENT
+          - 206 PARTIAL_CONTENT
+          - 207 MULTI_STATUS
+          - 208 ALREADY_REPORTED
+          - 226 IM_USED
+          - 300 MULTIPLE_CHOICES
+          - 301 MOVED_PERMANENTLY
+          - 302 FOUND
+          - 302 MOVED_TEMPORARILY
+          - 303 SEE_OTHER
+          - 304 NOT_MODIFIED
+          - 305 USE_PROXY
+          - 307 TEMPORARY_REDIRECT
+          - 308 PERMANENT_REDIRECT
+          - 400 BAD_REQUEST
+          - 401 UNAUTHORIZED
+          - 402 PAYMENT_REQUIRED
+          - 403 FORBIDDEN
+          - 404 NOT_FOUND
+          - 405 METHOD_NOT_ALLOWED
+          - 406 NOT_ACCEPTABLE
+          - 407 PROXY_AUTHENTICATION_REQUIRED
+          - 408 REQUEST_TIMEOUT
+          - 409 CONFLICT
+          - 410 GONE
+          - 411 LENGTH_REQUIRED
+          - 412 PRECONDITION_FAILED
+          - 413 PAYLOAD_TOO_LARGE
+          - 413 REQUEST_ENTITY_TOO_LARGE
+          - 414 URI_TOO_LONG
+          - 414 REQUEST_URI_TOO_LONG
+          - 415 UNSUPPORTED_MEDIA_TYPE
+          - 416 REQUESTED_RANGE_NOT_SATISFIABLE
+          - 417 EXPECTATION_FAILED
+          - 418 I_AM_A_TEAPOT
+          - 419 INSUFFICIENT_SPACE_ON_RESOURCE
+          - 420 METHOD_FAILURE
+          - 421 DESTINATION_LOCKED
+          - 422 UNPROCESSABLE_ENTITY
+          - 423 LOCKED
+          - 424 FAILED_DEPENDENCY
+          - 425 TOO_EARLY
+          - 426 UPGRADE_REQUIRED
+          - 428 PRECONDITION_REQUIRED
+          - 429 TOO_MANY_REQUESTS
+          - 431 REQUEST_HEADER_FIELDS_TOO_LARGE
+          - 451 UNAVAILABLE_FOR_LEGAL_REASONS
+          - 500 INTERNAL_SERVER_ERROR
+          - 501 NOT_IMPLEMENTED
+          - 502 BAD_GATEWAY
+          - 503 SERVICE_UNAVAILABLE
+          - 504 GATEWAY_TIMEOUT
+          - 505 HTTP_VERSION_NOT_SUPPORTED
+          - 506 VARIANT_ALSO_NEGOTIATES
+          - 507 INSUFFICIENT_STORAGE
+          - 508 LOOP_DETECTED
+          - 509 BANDWIDTH_LIMIT_EXCEEDED
+          - 510 NOT_EXTENDED
+          - 511 NETWORK_AUTHENTICATION_REQUIRED
+        message:
+          type: string
+          example: Error message
+        code:
+          type: string
+          example: error.service.code
+    UnitSaveDto:
+      required:
+      - description
+      - name
+      - uri
+      type: object
+      properties:
+        uri:
+          type: string
+        name:
+          type: string
+        description:
+          type: string
+    ColumnBriefDto:
+      required:
+      - column_type
+      - database_id
+      - id
+      - internal_name
+      - name
+      - table_id
+      type: object
+      properties:
+        id:
+          type: integer
+          format: int64
+        name:
+          type: string
+          example: date
+        database_id:
+          type: integer
+          format: int64
+        table_id:
+          type: integer
+          format: int64
+        internal_name:
+          type: string
+          example: mdb_date
+        column_type:
+          type: string
+          example: date
+          enum:
+          - enum
+          - number
+          - decimal
+          - string
+          - text
+          - boolean
+          - date
+          - timestamp
+          - blob
+    UnitDto:
+      required:
+      - columns
+      - created
+      - uri
+      type: object
+      properties:
+        uri:
+          type: string
+        name:
+          type: string
+        description:
+          type: string
+        created:
+          type: string
+          format: date-time
+        columns:
+          type: array
+          items:
+            $ref: '#/components/schemas/ColumnBriefDto'
+    OntologyCreateDto:
+      required:
+      - prefix
+      - uri
+      type: object
+      properties:
+        uri:
+          type: string
+          example: Ontology URI
+        prefix:
+          type: string
+          example: Ontology prefix
+        sparql_endpoint:
+          type: string
+          example: Ontology SPARQL endpoint
+    ConceptSaveDto:
+      required:
+      - description
+      - name
+      - uri
+      type: object
+      properties:
+        uri:
+          type: string
+        name:
+          type: string
+        description:
+          type: string
+    ConceptDto:
+      required:
+      - columns
+      - created
+      - uri
+      type: object
+      properties:
+        uri:
+          type: string
+        name:
+          type: string
+        description:
+          type: string
+        created:
+          type: string
+          format: date-time
+        columns:
+          type: array
+          items:
+            $ref: '#/components/schemas/ColumnBriefDto'
+    EntityDto:
+      required:
+      - label
+      - uri
+      type: object
+      properties:
+        uri:
+          type: string
+          example: https://www.wikidata.org/entity/Q1686799
+        label:
+          type: string
+          example: Apache Jena
+        description:
+          type: string
+          example: open source semantic web framework for Java
+    TableColumnEntityDto:
+      required:
+      - columnId
+      - databaseId
+      - tableId
+      - uri
+      type: object
+      properties:
+        databaseId:
+          type: integer
+          format: int64
+          example: 1
+        tableId:
+          type: integer
+          format: int64
+          example: 1
+        columnId:
+          type: integer
+          format: int64
+          example: 1
+        uri:
+          type: string
+          example: https://www.wikidata.org/entity/Q1686799
+        label:
+          type: string
+          example: Apache Jena
+        description:
+          type: string
+          example: open source semantic web framework for Java
+  securitySchemes:
+    bearerAuth:
+      type: http
+      scheme: bearer
+      bearerFormat: JWT

.docs/.swagger/fetch.sh

+#!/bin/bash
+# This script is executed before pushing to the pipeline for the moment.
+# @author: Martin Weise
+
+declare -A services
+services[5000]=analyse
+services[9050]=mirror
+services[9093]=data
+services[9099]=metadata
+
+function retrieve () {
+  if [[ "$2" == analyse ]]; then
+    echo "... retrieve json api from localhost:$1"
+    wget "http://localhost:$1/api-$2.json" -O "./.docs/.swagger/api-$2.yaml" -q
+  else
+    echo "... retrieve yaml api from localhost:$1"
+    wget "http://localhost:$1/v3/api-docs.yaml" -O "./.docs/.swagger/api-$2.yaml" -q
+  fi
+}
+
+for key in "${!services[@]}"; do
+  echo "Generating ${services[$key]} API"
+  retrieve "$key" "${services[$key]}"
+done
\ No newline at end of file

.docs/.swagger/generate.sh

+#!/bin/bash
+
+# clean up
+echo "clean up ./dist ./site"
+rm -rf ./dist ./site
+
+# ensure target directories are present
+echo "ensure target directory ./site are present"
+mkdir -p ./site
+
+# extract static site
+echo "extract static site .docs/.swagger/dist.tar.gz"
+tar xzf .docs/.swagger/dist.tar.gz
+for service in "analyse" "mirror" "data" "metadata" "upload"; do
+  mkdir -p ./site/$service
+  echo "extract static site ./dist -> ./site/$service"
+  cp -r ./dist/* ./site/$service
+  echo "placing .docs/.swagger/api-$service.yaml -> ./site/$service/api.yaml"
+  cp ".docs/.swagger/api-$service.yaml" "./site/$service/api.yaml"
+done

.docs/contact.md

+---
+author: Martin Weise
+hide:
+- navigation
+---
+
+# Contact
+
+## Team
+
+### Project Management
+
+Ao.univ.Prof. Dr. [Andreas Rauber](https://www.ifs.tuwien.ac.at/~andi)<br />
+Technische Universit&auml;t Wien<br />
+Research Unit Data Science<br />
+Favoritenstra&szlig;e 9-11<br />
+A-1040 Vienna, Austria
+
+### Development
+
+Projektass. Dipl.-Ing. [Martin Weise](https://ec.tuwien.ac.at/~weise/)<br />
+Technische Universit&auml;t Wien<br />
+Research Unit Data Science<br />
+Favoritenstra&szlig;e 9-11<br />
+A-1040 Vienna, Austria
+
+## Contributors (alphabetically)
+
+- Ganguly, Raman
+- Gergely, Eva
+- Grantner, Tobias
+- Karnbach, Geoffrey
+- Michlits, Cornelia
+- Rauber, Andreas
+- Staudinger, Moritz
+- Stytsenko, Kirill
+- Taha, Josef
+- Tsepelakis, Sotiris
+- Weise, Martin

.docs/customization.md

+---
+author: Martin Weise
+hide:
+- navigation
+---
+
+# Customization
+
+!!! info "Abstract"
+
+    On this page, we showcase the customization capabilities of DBRepo to e.g. whitelabel your deployment.
+
+## Custom Title
+
+The default title is "Database Repository" and can be replaced by changing the `TITLE` environment variable.
+
+## Custom Logo
+
+The default placeholder logo consists of the two universities that developed this software. You can replace it by
+mounting your own logo with a volume.
+
+```console
+docker run -v /path/to/your_logo.png:/logo.png ...
+```
+
+In case your logo is not in PNG format, you need to change the environment variable `LOGO` accordingly, e.g. for a logo
+in JPEG format, set `LOGO: "/logo.JPEG"` in the `.env` file and start the container with a volume.
+
+```console
+docker run -v /path/to/your_logo.JPEG:/logo.JPEG ...
+```
+
+<figure markdown>
+![](images/custom_logo.png)
+<figcaption>Custom logo which replaces the default placeholder logo</figcaption>
+</figure>
+
+## Custom Icon
+
+The default placeholder icon can be replaced by mounting your own icon with a volume.
+
+```console
+docker run -v /path/to/your_logo.ico:/favicon.ico ...
+```
+
+<figure markdown>
+![](images/custom_icon.png)
+<figcaption>Custom icon which replaces the default placeholder icon</figcaption>
+</figure>
+
+In case your icon is not in ICO format, you need to change the environment variable `ICON` accordingly, e.g. for an icon
+in GIF format, set `ICON: "/favicon.GIF"` in the `.env` file and start the container with a volume.
+
+```console
+docker run -v /path/to/favicon.GIF:/favicon.GIF ...
+```

.docs/docker/mweise.pub

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+role: mweise
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+-----END PUBLIC KEY-----