diff --git a/.eslintrc.js b/.eslintrc.js index 6a426ec1b..c3f71924d 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -5,12 +5,11 @@ module.exports = { 'eslint:recommended', 'plugin:unicorn/recommended', 'plugin:cypress/recommended', - 'plugin:import/recommended', 'plugin:import/typescript', 'plugin:@typescript-eslint/strict-type-checked', 'plugin:@typescript-eslint/stylistic-type-checked', ], - plugins: ['tsdoc', 'sort-destructure-keys'], + plugins: ['import', 'tsdoc', 'sort-destructure-keys'], parser: '@typescript-eslint/parser', parserOptions: { project: true, @@ -71,8 +70,11 @@ module.exports = { { allowNumber: true }, ], '@typescript-eslint/return-await': 'error', - // eslint-plugin-import rules (override recommended) + // eslint-plugin-import rules + 'import/export': 'error', + 'import/no-duplicates': 'warn', 'import/no-extraneous-dependencies': 'error', + 'import/no-named-as-default': 'warn', // eslint-plugin-sort-destructure-keys rules 'sort-destructure-keys/sort-destructure-keys': 'warn', // eslint-plugin-tsdoc rules diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml new file mode 100644 index 000000000..c363fefce --- /dev/null +++ b/.github/workflows/website.yml @@ -0,0 +1,34 @@ +name: Deploy Docusaurus to website + +on: + workflow_call: + workflow_dispatch: + +jobs: + reload: + name: Deploy Docusaurus to website + runs-on: ubuntu-latest + steps: + - name: Check out + uses: actions/checkout@v4 + - name: Use Node.js 18.x + uses: actions/setup-node@v4 + with: + node-version: 18 + cache: yarn + - name: Install + run: yarn --immutable + - name: Build website + working-directory: packages/website + run: yarn build + - name: Configure AWS credentials + uses: aws-actions/configure-aws-credentials@v4 + with: + aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} + aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + aws-region: us-east-1 + - name: Upload + working-directory: packages/website + run: | + aws s3 sync --delete build/ s3://jbrowse.org/jb2/ + aws cloudfront create-invalidation --distribution-id EL84YTOVCGNJZ --paths '/*' diff --git a/.husky/pre-commit.js b/.husky/pre-commit.js index b176b199d..895ebd950 100644 --- a/.husky/pre-commit.js +++ b/.husky/pre-commit.js @@ -29,13 +29,30 @@ function main() { spawn.sync( 'yarn', ['workspace', '@apollo-annotation/cli', 'oclif', 'readme'], - { - stdio: 'inherit', - }, + { stdio: 'inherit' }, + ) + spawn.sync( + 'yarn', + [ + 'workspace', + '@apollo-annotation/cli', + 'oclif', + 'readme', + '--multi', + '--dir', + '../website/docs/cli/', + ], + { stdio: 'inherit' }, + ) + spawn.sync( + 'git', + [ + 'add', + 'packages/apollo-cli/README.md', + 'packages/website/docs/cli/*.md', + ], + { stdio: 'inherit' }, ) - spawn.sync('git', ['add', 'packages/apollo-cli/README.md'], { - stdio: 'inherit', - }) } } diff --git a/packages/apollo-cli/README.md b/packages/apollo-cli/README.md index 7768c3b24..a879780a6 100644 --- a/packages/apollo-cli/README.md +++ b/packages/apollo-cli/README.md @@ -5,6 +5,7 @@ - [Table of contents](#table-of-contents) - [Usage](#usage) - [Commands](#commands) +- [Command Topics](#command-topics) # Usage @@ -29,933 +30,22 @@ USAGE -- [`apollo assembly add-fasta`](#apollo-assembly-add-fasta) -- [`apollo assembly add-gff`](#apollo-assembly-add-gff) -- [`apollo assembly check`](#apollo-assembly-check) -- [`apollo assembly delete`](#apollo-assembly-delete) -- [`apollo assembly get`](#apollo-assembly-get) -- [`apollo assembly sequence`](#apollo-assembly-sequence) -- [`apollo change get`](#apollo-change-get) -- [`apollo config [KEY] [VALUE]`](#apollo-config-key-value) -- [`apollo feature add-child`](#apollo-feature-add-child) -- [`apollo feature check`](#apollo-feature-check) -- [`apollo feature copy`](#apollo-feature-copy) -- [`apollo feature delete`](#apollo-feature-delete) -- [`apollo feature edit`](#apollo-feature-edit) -- [`apollo feature edit-attribute`](#apollo-feature-edit-attribute) -- [`apollo feature edit-coords`](#apollo-feature-edit-coords) -- [`apollo feature edit-type`](#apollo-feature-edit-type) -- [`apollo feature get`](#apollo-feature-get) -- [`apollo feature get-id`](#apollo-feature-get-id) -- [`apollo feature import`](#apollo-feature-import) -- [`apollo feature search`](#apollo-feature-search) -- [`apollo help [COMMANDS]`](#apollo-help-commands) -- [`apollo login`](#apollo-login) -- [`apollo logout`](#apollo-logout) -- [`apollo refseq add-alias`](#apollo-refseq-add-alias) -- [`apollo refseq get`](#apollo-refseq-get) -- [`apollo status`](#apollo-status) -- [`apollo user get`](#apollo-user-get) - -## `apollo assembly add-fasta` - -Add new assembly from local or external fasta file - -``` -USAGE - $ apollo assembly add-fasta -i [--profile ] [--config-file ] [-a ] [-x ] [-f] - -FLAGS - -a, --assembly= Name for this assembly. Use the file name if omitted - -f, --force Delete existing assembly, if it exists - -i, --input-file= (required) Input fasta file - -x, --index= URL of the index. Required if input is an external source and ignored if input is a local - file - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add new assembly from local or external fasta file - -EXAMPLES - From local file: - - $ apollo assembly add-fasta -i genome.fa -a myAssembly - - From external source we also need the URL of the index: - - $ apollo assembly add-fasta -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly -``` - -_See code: -[src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_ - -## `apollo assembly add-gff` - -Add new assembly from gff or gft file - -``` -USAGE - $ apollo assembly add-gff -i [--profile ] [--config-file ] [-a ] [-o] [-f] - -FLAGS - -a, --assembly= Name for this assembly. Use the file name if omitted - -f, --force Delete existing assembly, if it exists - -i, --input-file= (required) Input gff or gtf file - -o, --omit-features Do not import features, only upload the sequences - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add new assembly from gff or gft file - - The gff file is expected to contain sequences as per gff specifications. - Features are also imported by default. - -EXAMPLES - Import sequences and features: - - $ apollo assembly add-gff -i genome.gff -a myAssembly - - Import sequences only: - - $ apollo assembly add-gff -i genome.gff -a myAssembly -o -``` - -_See code: -[src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-gff.ts)_ - -## `apollo assembly check` - -Add, view, or delete checks to assembly - -``` -USAGE - $ apollo assembly check [--profile ] [--config-file ] [-a ] [-c ] [-d] - -FLAGS - -a, --assembly= Manage checks in this assembly - -c, --check=... Add these check names or IDs. If unset, print the checks set for assembly - -d, --delete Delete (instead of adding) checks - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add, view, or delete checks to assembly - - Manage checks, i.e. the rules ensuring features in an assembly are plausible. - This command only sets the checks to apply, to retrieve features flagged by - these checks use `apollo feature check`. - -EXAMPLES - View available check types: - - $ apollo assembly check - - View checks set for assembly hg19: - - $ apollo assembly check -a hg19 - - Add checks to assembly: - - $ apollo assembly check -a hg19 -c CDSCheck - - Delete checks from assembly: - - $ apollo assembly check -a hg19 -c CDSCheck --delete -``` - -_See code: -[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/check.ts)_ - -## `apollo assembly delete` - -Delete assemblies - -``` -USAGE - $ apollo assembly delete -a [--profile ] [--config-file ] [-v] - -FLAGS - -a, --assembly=... (required) Assembly names or IDs to delete - -v, --verbose Print to stdout the array of assemblies deleted - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Delete assemblies - - Assemblies to delete may be names or IDs - -EXAMPLES - Delete multiple assemblies using name or ID: - - $ apollo assembly delete -a mouse 6605826fbd0eee691f83e73f -``` - -_See code: -[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/delete.ts)_ - -## `apollo assembly get` - -Get available assemblies - -``` -USAGE - $ apollo assembly get [--profile ] [--config-file ] [-a ] - -FLAGS - -a, --assembly=... Get assemblies in this list of names or IDs - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get available assemblies - - Print to stdout the list of assemblies in json format -``` - -_See code: -[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/get.ts)_ - -## `apollo assembly sequence` - -Get reference sequence in fasta format - -``` -USAGE - $ apollo assembly sequence [--profile ] [--config-file ] [-a ] [-r ] [-s ] [-e - ] - -FLAGS - -a, --assembly= Find input reference sequence in this assembly - -e, --end= End coordinate - -r, --refseq= Reference sequence. If unset, get all sequences - -s, --start= [default: 1] Start coordinate (1-based) - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get reference sequence in fasta format - - Return the reference sequence for a given assembly and coordinates - -EXAMPLES - Get all sequences in myAssembly: - - $ apollo assembly sequence -a myAssembly - - Get sequence in coordinates chr1:1..1000: - - $ apollo assembly sequence -a myAssembly -r chr1 -s 1 -e 1000 -``` - -_See code: -[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/sequence.ts)_ - -## `apollo change get` - -Get list of changes - -``` -USAGE - $ apollo change get [--profile ] [--config-file ] [-a ] - -FLAGS - -a, --assembly=... Get changes only for these assembly names or IDs (but see description) - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get list of changes - - Return the change log in json format. Note that when an assembly is deleted the - link between common name and ID is lost (it can still be recovered by inspecting - the change log but at present this task is left to the user). In such cases you - need to use the assembly ID. -``` - -_See code: -[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/change/get.ts)_ - -## `apollo config [KEY] [VALUE]` - -Get or set apollo configuration options - -``` -USAGE - $ apollo config [KEY] [VALUE] [--profile ] [---file ] [--get-config-file] - -ARGUMENTS - KEY Name of configuration parameter - VALUE Parameter value - -FLAGS - --config-file= Use this config file (mostly for testing) - --get-config-file Return the path to the config file and exit (this file may not exist yet) - --profile= Profile to create or edit - -DESCRIPTION - Get or set apollo configuration options - - Use this command to create or edit a user profile with credentials to access - Apollo. Configuration options are: - - - address: - Address and port e.g http://localhost:3999 - - - accessType: - How to access Apollo. accessType is typically one of: google, microsoft, guest, - root. Allowed types depend on your Apollo setup - - - accessToken: - Access token. Usually inserted by `apollo login` - - - rootCredentials.username: - Username of root account. Only set this for "root" access type - - - rootCredentials.password: - Password for root account. Only set this for "root" access type - -EXAMPLES - Interactive setup: - - $ apollo config - - Setup with key/value pairs: - - $ apollo config --profile admin address http://localhost:3999 - - Get current address for default profile: - - $ apollo config address -``` - -_See code: -[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/config.ts)_ - -## `apollo feature add-child` - -Add a child feature (e.g. add an exon to an mRNA) - -``` -USAGE - $ apollo feature add-child -s -e -t [--profile ] [--config-file ] [-i ] - -FLAGS - -e, --end= (required) End coordinate of the child feature (1-based) - -i, --feature-id= [default: -] Add a child to this feature ID; use - to read it from stdin - -s, --start= (required) Start coordinate of the child feature (1-based) - -t, --type= (required) Type of child feature - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add a child feature (e.g. add an exon to an mRNA) - - See the other commands under `apollo feature` to retrive the parent ID of - interest and to populate the child feature with attributes. - -EXAMPLES - Add an exon at genomic coordinates 10..20 to this feature ID: - - $ apollo feature add-child -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20 -``` - -_See code: -[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/add-child.ts)_ - -## `apollo feature check` - -Get check results - -``` -USAGE - $ apollo feature check [--profile ] [--config-file ] [-i ] [-a ] - -FLAGS - -a, --assembly= Get checks for this assembly - -i, --feature-id=... Get checks for these feature identifiers - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get check results - - Use this command to view which features fail checks along with the reason for - failing. Use `apollo assembly check` for managing which checks should be applied - to an assembly - -EXAMPLES - Get all check results in the database: - - $ apollo feature check - - Get check results for assembly hg19: - - $ apollo feature check -a hg19 -``` - -_See code: -[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/check.ts)_ - -## `apollo feature copy` - -Copy a feature to another location - -``` -USAGE - $ apollo feature copy -r -s [--profile ] [--config-file ] [-i ] [-a ] - -FLAGS - -a, --assembly= Name or ID of target assembly. Not required if refseq is unique in the database - -i, --feature-id= [default: -] Feature ID to copy to; use - to read it from stdin - -r, --refseq= (required) Name or ID of target reference sequence - -s, --start= (required) Start position in target reference sequence - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Copy a feature to another location - - The feature may be copied to the same or to a different assembly. he destination - reference sequence may be selected by name only if unique in the database or by - name and assembly or by identifier. - -EXAMPLES - Copy this feature ID to chr1:100 in assembly hg38: - - $ apollo feature copy -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38 -``` - -_See code: -[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/copy.ts)_ - -## `apollo feature delete` - -Delete one or more features by ID - -``` -USAGE - $ apollo feature delete [--profile ] [--config-file ] [-i ] [-f] [-n] - -FLAGS - -f, --force Ignore non-existing features - -i, --feature-id=... [default: -] Feature IDs to delete - -n, --dry-run Only show what would be delete - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Delete one or more features by ID - - Note that deleting a child feature after deleting its parent will result in an - error unless you set -f/--force. -``` - -_See code: -[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/delete.ts)_ - -## `apollo feature edit` - -Edit features using an appropiate json input - -``` -USAGE - $ apollo feature edit [--profile ] [--config-file ] [-j ] - -FLAGS - -j, --json-input= [default: -] Json string or json file or "-" to read json from stdin - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Edit features using an appropiate json input - - Edit a feature by submitting a json input with all the required attributes for - Apollo to process it. This is a very low level command which most users probably - do not need. - - Input may be a json string or a json file and it may be an array of changes. - This is an example input for editing feature type: - - { - "typeName": "TypeChange", - "changedIds": [ - "6613f7d22c957525d631b1cc" - ], - "assembly": "6613f7d1360321540a11e5ed", - "featureId": "6613f7d22c957525d631b1cc", - "oldType": "BAC", - "newType": "G_quartet" - } - -EXAMPLES - Editing by passing a json to stdin: - - echo '{"typeName": ... "newType": "G_quartet"}' | apollo feature edit -j - -``` - -_See code: -[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit.ts)_ - -## `apollo feature edit-attribute` - -Add, edit, or view a feature attribute - -``` -USAGE - $ apollo feature edit-attribute -a [--profile ] [--config-file ] [-i ] [-v ] [-d] - -FLAGS - -a, --attribute= (required) Attribute key to add or edit - -d, --delete Delete this attribute - -i, --feature-id= [default: -] Feature ID to edit or "-" to read it from stdin - -v, --value=... New attribute value. Separated mutliple values by space to them as a list. If unset return - current value - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add, edit, or view a feature attribute - - Be aware that there is no checking whether attributes names and values are - valid. For example, you can create non-unique ID attributes or you can set gene - ontology terms to non-existing terms - -EXAMPLES - Add attribute "domains" with a list of values: - - $ apollo feature edit-attribute -i 66...3f -a domains -v ABC PLD - - Print values in "domains" as json array: - - $ apollo feature edit-attribute -i 66...3f -a domains - - Delete attribute "domains" - - $ apollo feature edit-attribute -i 66...3f -a domains -d -``` - -_See code: -[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_ - -## `apollo feature edit-coords` - -Edit feature start and/or end coordinates - -``` -USAGE - $ apollo feature edit-coords [--profile ] [--config-file ] [-i ] [-s ] [-e ] - -FLAGS - -e, --end= New end coordinate (1-based) - -i, --feature-id= [default: -] Feature ID to edit or "-" to read it from stdin - -s, --start= New start coordinate (1-based) - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Edit feature start and/or end coordinates - - If editing a child feature that new coordinates must be within the parent's - coordinates. To get the identifier of the feature to edit consider using `apollo - feature get` or `apollo feature search` - -EXAMPLES - Edit start and end: - - $ apollo feature edit-coords -i abc...xyz -s 10 -e 1000 - - Edit end and leave start as it is: - - $ apollo feature edit-coords -i abc...xyz -e 2000 -``` - -_See code: -[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-coords.ts)_ - -## `apollo feature edit-type` - -Edit or view feature type - -``` -USAGE - $ apollo feature edit-type [--profile ] [--config-file ] [-i ] [-t ] - -FLAGS - -i, --feature-id= [default: -] Feature ID to edit or "-" to read it from stdin - -t, --type= Assign feature to this type. If unset return the current type - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Edit or view feature type - - Feature type is column 3 in gff format. It must be a valid sequence ontology - term although but the valifdity of the new term is not checked. -``` - -_See code: -[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-type.ts)_ - -## `apollo feature get` - -Get features in assembly, reference sequence or genomic window - -``` -USAGE - $ apollo feature get [--profile ] [--config-file ] [-a ] [-r ] [-s ] [-e - ] - -FLAGS - -a, --assembly= Find input reference sequence in this assembly - -e, --end= End coordinate - -r, --refseq= Reference sequence. If unset, query all sequences - -s, --start= [default: 1] Start coordinate (1-based) - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get features in assembly, reference sequence or genomic window - -EXAMPLES - Get all features in myAssembly: - - $ apollo feature get -a myAssembly - - Get features intersecting chr1:1..1000. You can omit the assembly name if there - are no other reference sequences named chr1: - - $ apollo feature get -a myAssembly -r chr1 -s 1 -e 1000 -``` - -_See code: -[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/get.ts)_ - -## `apollo feature get-id` - -Get features given their identifiers - -``` -USAGE - $ apollo feature get-id [--profile ] [--config-file ] [-i ] - -FLAGS - -i, --feature-id=... [default: -] Retrieves feature with these IDs. Use - "-" to read IDs from stdin (one per - line) - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get features given their identifiers - - Invalid identifiers or identifiers not found in the database will be silently - ignored - -EXAMPLES - Get features for these identifiers: - - $ apollo feature get-id -i abc...zyz def...foo -``` - -_See code: -[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/get-id.ts)_ - -## `apollo feature import` - -Import features from local gff file - -``` -USAGE - $ apollo feature import -i -a [--profile ] [--config-file ] [-d] - -FLAGS - -a, --assembly= (required) Import into this assembly name or assembly ID - -d, --delete-existing Delete existing features before importing - -i, --input-file= (required) Input gff or gtf file - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Import features from local gff file - - By default, features are added to the existing ones. - -EXAMPLES - Delete features in myAssembly and then import features.gff3: - - $ apollo feature import -d -i features.gff3 -a myAssembly -``` - -_See code: -[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/import.ts)_ - -## `apollo feature search` - -Free text search for feature in one or more assemblies - -``` -USAGE - $ apollo feature search -t [--profile ] [--config-file ] [-a ] - -FLAGS - -a, --assembly=... Assembly names or IDs to search; use "-" to read it from stdin. If omitted - search all assemblies - -t, --text= (required) Search for this text query - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Free text search for feature in one or more assemblies - - Return features matching a query string. This command searches only in: - - - Attribute *values* (not attribute names) - - Source field (which in fact is stored as an attribute) - - Feature type - - The search mode is: - - - Case insensitive - - Match only full words, but not necessarily the full value - - Common words are ignored. E.g. "the", "with" - - For example, given this feature: - - chr1 example SNP 10 30 0.987 . . "someKey=Fingerprint BAC with reads" - - Queries "bac" or "mRNA" return the feature. Instead these queries will NOT - match: - - - "someKey" - - "with" - - "Finger" - - "chr1" - - "0.987" - -EXAMPLES - Search "bac" in these assemblies: - - $ apollo feature search -a mm9 mm10 -t bac -``` - -_See code: -[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/search.ts)_ - -## `apollo help [COMMANDS]` - -Display help for apollo. - -``` -USAGE - $ apollo help [COMMANDS] [-n] - -ARGUMENTS - COMMANDS Command to show help for. - -FLAGS - -n, --nested-commands Include all nested commands in the output. - -DESCRIPTION - Display help for apollo. -``` - -_See code: -[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_ - -## `apollo login` - -Login to Apollo - -``` -USAGE - $ apollo login [--profile ] [--config-file ] [-a ] [-u ] [-p ] [-f] - [--port ] - -FLAGS - -a, --address= Address of Apollo server - -f, --force Force re-authentication even if user is already logged in - -p, --password= Password for - -u, --username= Username for root login - --config-file= Use this config file (mostly for testing) - --port= [default: 3000] Get token by listening to this port number (usually this is >= 1024 and < - 65536) - --profile= Use credentials from this profile - -DESCRIPTION - Login to Apollo - - Use the provided credentials to obtain and save the token to access Apollo. Once - the token for the given profile has been saved in the configuration file, users - do not normally need to execute this command again unless the token has expired. - To setup a new profile use "apollo config" - -EXAMPLES - The most basic and probably most typical usage is to login using the default - profile in configuration file: - - $ apollo login - - Login with a different profile: - - $ apollo login --profile my-profile -``` - -_See code: -[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/login.ts)_ - -## `apollo logout` - -Logout of Apollo - -``` -USAGE - $ apollo logout [--profile ] [--config-file ] - -FLAGS - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Logout of Apollo - - Logout by removing the access token from the selected profile - -EXAMPLES - Logout default profile: - - $ apollo logout - - Logout selected profile - - $ apollo logout --profile my-profile -``` - -_See code: -[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/logout.ts)_ - -## `apollo refseq add-alias` - -Add reference name aliases from a file - -``` -USAGE - $ apollo refseq add-alias -i -a [--profile ] [--config-file ] - -FLAGS - -a, --assembly= (required) Name for this assembly. - -i, --input-file= (required) Input refname alias file - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add reference name aliases from a file - - Reference name aliasing is a process to make chromosomes that are named slightly - differently but which refer to the same thing render properly. This command - reads a file with reference name aliases and adds them to the database. - -EXAMPLES - Add reference name aliases: - - $ apollo refseq add-alias -i alias.txt -a myAssembly -``` - -_See code: -[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/add-alias.ts)_ - -## `apollo refseq get` - -Get reference sequences - -``` -USAGE - $ apollo refseq get [--profile ] [--config-file ] [-a ] - -FLAGS - -a, --assembly=... Get reference sequences for these assembly names or IDs; use - to read it from stdin - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get reference sequences - - Output the reference sequences in one or more assemblies in json format. This - command returns the sequence characteristics (e.g., name, ID, etc), not the DNA - sequences. Use `assembly sequence` for that. - -EXAMPLES - All sequences in the database: - - $ apollo refseq get - - Only sequences for these assemblies: - - $ apollo refseq get -a mm9 mm10 -``` - -_See code: -[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/get.ts)_ - -## `apollo status` - -View authentication status - -``` -USAGE - $ apollo status [--profile ] [--config-file ] - -FLAGS - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - View authentication status - - This command returns ": Logged in" if the selected profile has an - access token and ": Logged out" otherwise. Note that this command does - not check the validity of the access token. -``` - -_See code: -[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/status.ts)_ - -## `apollo user get` - -Get list of users - -``` -USAGE - $ apollo user get [--profile ] [--config-file ] [-u ] [-r ] - -FLAGS - -r, --role= Get users with this role - -u, --username= Find this username - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get list of users - - If set, filters username and role must be both satisfied to return an entry - -EXAMPLES - By username: - - $ apollo user get -u Guest - - By role: - - $ apollo user get -r admin - - Use jq for more control: - - $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")' -``` - -_See code: -[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/user/get.ts)_ +# Command Topics + +- [`apollo assembly`](../website/docs/cli//assembly.md) - Commands to handle + assemblies +- [`apollo change`](../website/docs/cli//change.md) - Commands to handle the log + of changes made to the database +- [`apollo config`](../website/docs/cli//config.md) - Get or set apollo + configuration options +- [`apollo feature`](../website/docs/cli//feature.md) - Commands to handle + features +- [`apollo help`](../website/docs/cli//help.md) - Display help for apollo. +- [`apollo login`](../website/docs/cli//login.md) - Login to Apollo +- [`apollo logout`](../website/docs/cli//logout.md) - Logout of Apollo +- [`apollo refseq`](../website/docs/cli//refseq.md) - Commands to handle + reference sequences +- [`apollo status`](../website/docs/cli//status.md) - View authentication status +- [`apollo user`](../website/docs/cli//user.md) - Commands to handle users diff --git a/packages/apollo-cli/package.json b/packages/apollo-cli/package.json index 5fc1f1cde..f80f39389 100644 --- a/packages/apollo-cli/package.json +++ b/packages/apollo-cli/package.json @@ -29,7 +29,7 @@ "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'", "posttest": "yarn lint", "test:ci": "nyc mocha 'src/**/*.test.ts'", - "version": "oclif readme && git add README.md" + "version": "oclif readme --multi --dir ../website/docs/cli/ && oclif readme && git add README.md" }, "oclif": { "bin": "apollo", diff --git a/packages/apollo-collaboration-server/package.json b/packages/apollo-collaboration-server/package.json index fd7bc225d..e0bc85ee1 100644 --- a/packages/apollo-collaboration-server/package.json +++ b/packages/apollo-collaboration-server/package.json @@ -105,7 +105,7 @@ "@types/passport-jwt": "^3.0.6", "@types/passport-local": "^1.0.34", "@types/passport-microsoft": "^0.0.0", - "@types/react": "^17.0.34", + "@types/react": "^18.3.4", "@types/supertest": "^2.0.11", "jest": "^29.6.2", "mongodb": "^4.7.0", diff --git a/packages/jbrowse-plugin-apollo/package.json b/packages/jbrowse-plugin-apollo/package.json index 9007996cb..5af63233f 100644 --- a/packages/jbrowse-plugin-apollo/package.json +++ b/packages/jbrowse-plugin-apollo/package.json @@ -82,7 +82,7 @@ "@types/file-saver": "^2", "@types/node": "^18.14.2", "@types/prop-types": "^15", - "@types/react": "^17.0.34", + "@types/react": "^18.3.4", "@types/react-dom": "^18", "cypress": "12.17.3", "cypress-mongodb": "^6.2.0", diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts index 2ccddae6d..0f5500c58 100644 --- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts +++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts @@ -1,6 +1,5 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ /* eslint-disable @typescript-eslint/no-unsafe-return */ -/* eslint-disable import/no-named-as-default-member */ // jsonpath triggers this rule for some reason. import { query } from 'jsonpath' does not work import { checkAbortSignal } from '@jbrowse/core/util' diff --git a/packages/website/.gitignore b/packages/website/.gitignore new file mode 100644 index 000000000..40e457891 --- /dev/null +++ b/packages/website/.gitignore @@ -0,0 +1,6 @@ +# Production +/build + +# Generated files +.docusaurus +.cache-loader diff --git a/packages/website/.yarnrc.yml b/packages/website/.yarnrc.yml new file mode 100644 index 000000000..e69de29bb diff --git a/packages/website/README.md b/packages/website/README.md new file mode 100755 index 000000000..c53f9e792 --- /dev/null +++ b/packages/website/README.md @@ -0,0 +1,45 @@ +# Website + +This website is built using [Docusaurus](https://docusaurus.io/), a modern +static website generator. + +### Installation + +``` +$ yarn +``` + +### Local Development + +``` +$ yarn start +``` + +This command starts a local development server and opens up a browser window. +Most changes are reflected live without having to restart the server. + +### Build + +``` +$ yarn build +``` + +This command generates static content into the `build` directory and can be +served using any static contents hosting service. + +### Deployment + +Using SSH: + +``` +$ USE_SSH=true yarn deploy +``` + +Not using SSH: + +``` +$ GIT_USER= yarn deploy +``` + +If you are using GitHub pages for hosting, this command is a convenient way to +build the website and push to the `gh-pages` branch. diff --git a/packages/website/babel.config.js b/packages/website/babel.config.js new file mode 100755 index 000000000..bbfa5de3c --- /dev/null +++ b/packages/website/babel.config.js @@ -0,0 +1,4 @@ +/* eslint-disable no-undef */ +module.exports = { + presets: [require.resolve('@docusaurus/core/lib/babel/preset')], +} diff --git a/packages/website/docs/cli/_category_.json b/packages/website/docs/cli/_category_.json new file mode 100644 index 000000000..4d51bba61 --- /dev/null +++ b/packages/website/docs/cli/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "CLI", + "position": 3, + "link": { + "type": "generated-index", + "description": "Apollo 3 Command Line Interface (CLI)" + } +} diff --git a/packages/website/docs/cli/assembly.md b/packages/website/docs/cli/assembly.md new file mode 100644 index 000000000..03941b3ec --- /dev/null +++ b/packages/website/docs/cli/assembly.md @@ -0,0 +1,206 @@ +# `apollo assembly` + +Commands to handle assemblies + +- [`apollo assembly add-fasta`](#apollo-assembly-add-fasta) +- [`apollo assembly add-gff`](#apollo-assembly-add-gff) +- [`apollo assembly check`](#apollo-assembly-check) +- [`apollo assembly delete`](#apollo-assembly-delete) +- [`apollo assembly get`](#apollo-assembly-get) +- [`apollo assembly sequence`](#apollo-assembly-sequence) + +## `apollo assembly add-fasta` + +Add new assembly from local or external fasta file + +``` +USAGE + $ apollo assembly add-fasta -i [--profile ] [--config-file ] [-a ] [-x ] [-f] + +FLAGS + -a, --assembly= Name for this assembly. Use the file name if omitted + -f, --force Delete existing assembly, if it exists + -i, --input-file= (required) Input fasta file + -x, --index= URL of the index. Required if input is an external source and ignored if input is a local + file + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Add new assembly from local or external fasta file + +EXAMPLES + From local file: + + $ apollo assembly add-fasta -i genome.fa -a myAssembly + + From external source we also need the URL of the index: + + $ apollo assembly add-fasta -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly +``` + +_See code: +[src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_ + +## `apollo assembly add-gff` + +Add new assembly from gff or gft file + +``` +USAGE + $ apollo assembly add-gff -i [--profile ] [--config-file ] [-a ] [-o] [-f] + +FLAGS + -a, --assembly= Name for this assembly. Use the file name if omitted + -f, --force Delete existing assembly, if it exists + -i, --input-file= (required) Input gff or gtf file + -o, --omit-features Do not import features, only upload the sequences + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Add new assembly from gff or gft file + + The gff file is expected to contain sequences as per gff specifications. + Features are also imported by default. + +EXAMPLES + Import sequences and features: + + $ apollo assembly add-gff -i genome.gff -a myAssembly + + Import sequences only: + + $ apollo assembly add-gff -i genome.gff -a myAssembly -o +``` + +_See code: +[src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-gff.ts)_ + +## `apollo assembly check` + +Add, view, or delete checks to assembly + +``` +USAGE + $ apollo assembly check [--profile ] [--config-file ] [-a ] [-c ] [-d] + +FLAGS + -a, --assembly= Manage checks in this assembly + -c, --check=... Add these check names or IDs. If unset, print the checks set for assembly + -d, --delete Delete (instead of adding) checks + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Add, view, or delete checks to assembly + + Manage checks, i.e. the rules ensuring features in an assembly are plausible. + This command only sets the checks to apply, to retrieve features flagged by + these checks use `apollo feature check`. + +EXAMPLES + View available check types: + + $ apollo assembly check + + View checks set for assembly hg19: + + $ apollo assembly check -a hg19 + + Add checks to assembly: + + $ apollo assembly check -a hg19 -c CDSCheck + + Delete checks from assembly: + + $ apollo assembly check -a hg19 -c CDSCheck --delete +``` + +_See code: +[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/check.ts)_ + +## `apollo assembly delete` + +Delete assemblies + +``` +USAGE + $ apollo assembly delete -a [--profile ] [--config-file ] [-v] + +FLAGS + -a, --assembly=... (required) Assembly names or IDs to delete + -v, --verbose Print to stdout the array of assemblies deleted + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Delete assemblies + + Assemblies to delete may be names or IDs + +EXAMPLES + Delete multiple assemblies using name or ID: + + $ apollo assembly delete -a mouse 6605826fbd0eee691f83e73f +``` + +_See code: +[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/delete.ts)_ + +## `apollo assembly get` + +Get available assemblies + +``` +USAGE + $ apollo assembly get [--profile ] [--config-file ] [-a ] + +FLAGS + -a, --assembly=... Get assemblies in this list of names or IDs + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get available assemblies + + Print to stdout the list of assemblies in json format +``` + +_See code: +[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/get.ts)_ + +## `apollo assembly sequence` + +Get reference sequence in fasta format + +``` +USAGE + $ apollo assembly sequence [--profile ] [--config-file ] [-a ] [-r ] [-s ] [-e + ] + +FLAGS + -a, --assembly= Find input reference sequence in this assembly + -e, --end= End coordinate + -r, --refseq= Reference sequence. If unset, get all sequences + -s, --start= [default: 1] Start coordinate (1-based) + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get reference sequence in fasta format + + Return the reference sequence for a given assembly and coordinates + +EXAMPLES + Get all sequences in myAssembly: + + $ apollo assembly sequence -a myAssembly + + Get sequence in coordinates chr1:1..1000: + + $ apollo assembly sequence -a myAssembly -r chr1 -s 1 -e 1000 +``` + +_See code: +[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/sequence.ts)_ diff --git a/packages/website/docs/cli/change.md b/packages/website/docs/cli/change.md new file mode 100644 index 000000000..bba0acf24 --- /dev/null +++ b/packages/website/docs/cli/change.md @@ -0,0 +1,30 @@ +# `apollo change` + +Commands to handle the log of changes made to the database + +- [`apollo change get`](#apollo-change-get) + +## `apollo change get` + +Get list of changes + +``` +USAGE + $ apollo change get [--profile ] [--config-file ] [-a ] + +FLAGS + -a, --assembly=... Get changes only for these assembly names or IDs (but see description) + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get list of changes + + Return the change log in json format. Note that when an assembly is deleted the + link between common name and ID is lost (it can still be recovered by inspecting + the change log but at present this task is left to the user). In such cases you + need to use the assembly ID. +``` + +_See code: +[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/change/get.ts)_ diff --git a/packages/website/docs/cli/config.md b/packages/website/docs/cli/config.md new file mode 100644 index 000000000..a40f58810 --- /dev/null +++ b/packages/website/docs/cli/config.md @@ -0,0 +1,61 @@ +# `apollo config` + +Get or set apollo configuration options + +- [`apollo config [KEY] [VALUE]`](#apollo-config-key-value) + +## `apollo config [KEY] [VALUE]` + +Get or set apollo configuration options + +``` +USAGE + $ apollo config [KEY] [VALUE] [--profile ] [---file ] [--get-config-file] + +ARGUMENTS + KEY Name of configuration parameter + VALUE Parameter value + +FLAGS + --config-file= Use this config file (mostly for testing) + --get-config-file Return the path to the config file and exit (this file may not exist yet) + --profile= Profile to create or edit + +DESCRIPTION + Get or set apollo configuration options + + Use this command to create or edit a user profile with credentials to access + Apollo. Configuration options are: + + - address: + Address and port e.g http://localhost:3999 + + - accessType: + How to access Apollo. accessType is typically one of: google, microsoft, guest, + root. Allowed types depend on your Apollo setup + + - accessToken: + Access token. Usually inserted by `apollo login` + + - rootCredentials.username: + Username of root account. Only set this for "root" access type + + - rootCredentials.password: + Password for root account. Only set this for "root" access type + +EXAMPLES + Interactive setup: + + $ apollo config + + Setup with key/value pairs: + + $ apollo config --profile admin address http://localhost:3999 + + Get current address for default profile: + + $ apollo config address +``` + +_See code: +[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/config.ts)_ diff --git a/packages/website/docs/cli/feature.md b/packages/website/docs/cli/feature.md new file mode 100644 index 000000000..d4f3a3608 --- /dev/null +++ b/packages/website/docs/cli/feature.md @@ -0,0 +1,426 @@ +# `apollo feature` + +Commands to handle features + +- [`apollo feature add-child`](#apollo-feature-add-child) +- [`apollo feature check`](#apollo-feature-check) +- [`apollo feature copy`](#apollo-feature-copy) +- [`apollo feature delete`](#apollo-feature-delete) +- [`apollo feature edit`](#apollo-feature-edit) +- [`apollo feature edit-attribute`](#apollo-feature-edit-attribute) +- [`apollo feature edit-coords`](#apollo-feature-edit-coords) +- [`apollo feature edit-type`](#apollo-feature-edit-type) +- [`apollo feature get`](#apollo-feature-get) +- [`apollo feature get-id`](#apollo-feature-get-id) +- [`apollo feature import`](#apollo-feature-import) +- [`apollo feature search`](#apollo-feature-search) + +## `apollo feature add-child` + +Add a child feature (e.g. add an exon to an mRNA) + +``` +USAGE + $ apollo feature add-child -s -e -t [--profile ] [--config-file ] [-i ] + +FLAGS + -e, --end= (required) End coordinate of the child feature (1-based) + -i, --feature-id= [default: -] Add a child to this feature ID; use - to read it from stdin + -s, --start= (required) Start coordinate of the child feature (1-based) + -t, --type= (required) Type of child feature + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Add a child feature (e.g. add an exon to an mRNA) + + See the other commands under `apollo feature` to retrive the parent ID of + interest and to populate the child feature with attributes. + +EXAMPLES + Add an exon at genomic coordinates 10..20 to this feature ID: + + $ apollo feature add-child -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20 +``` + +_See code: +[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/add-child.ts)_ + +## `apollo feature check` + +Get check results + +``` +USAGE + $ apollo feature check [--profile ] [--config-file ] [-i ] [-a ] + +FLAGS + -a, --assembly= Get checks for this assembly + -i, --feature-id=... Get checks for these feature identifiers + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get check results + + Use this command to view which features fail checks along with the reason for + failing. Use `apollo assembly check` for managing which checks should be applied + to an assembly + +EXAMPLES + Get all check results in the database: + + $ apollo feature check + + Get check results for assembly hg19: + + $ apollo feature check -a hg19 +``` + +_See code: +[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/check.ts)_ + +## `apollo feature copy` + +Copy a feature to another location + +``` +USAGE + $ apollo feature copy -r -s [--profile ] [--config-file ] [-i ] [-a ] + +FLAGS + -a, --assembly= Name or ID of target assembly. Not required if refseq is unique in the database + -i, --feature-id= [default: -] Feature ID to copy to; use - to read it from stdin + -r, --refseq= (required) Name or ID of target reference sequence + -s, --start= (required) Start position in target reference sequence + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Copy a feature to another location + + The feature may be copied to the same or to a different assembly. he destination + reference sequence may be selected by name only if unique in the database or by + name and assembly or by identifier. + +EXAMPLES + Copy this feature ID to chr1:100 in assembly hg38: + + $ apollo feature copy -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38 +``` + +_See code: +[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/copy.ts)_ + +## `apollo feature delete` + +Delete one or more features by ID + +``` +USAGE + $ apollo feature delete [--profile ] [--config-file ] [-i ] [-f] [-n] + +FLAGS + -f, --force Ignore non-existing features + -i, --feature-id=... [default: -] Feature IDs to delete + -n, --dry-run Only show what would be delete + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Delete one or more features by ID + + Note that deleting a child feature after deleting its parent will result in an + error unless you set -f/--force. +``` + +_See code: +[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/delete.ts)_ + +## `apollo feature edit` + +Edit features using an appropiate json input + +``` +USAGE + $ apollo feature edit [--profile ] [--config-file ] [-j ] + +FLAGS + -j, --json-input= [default: -] Json string or json file or "-" to read json from stdin + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Edit features using an appropiate json input + + Edit a feature by submitting a json input with all the required attributes for + Apollo to process it. This is a very low level command which most users probably + do not need. + + Input may be a json string or a json file and it may be an array of changes. + This is an example input for editing feature type: + + { + "typeName": "TypeChange", + "changedIds": [ + "6613f7d22c957525d631b1cc" + ], + "assembly": "6613f7d1360321540a11e5ed", + "featureId": "6613f7d22c957525d631b1cc", + "oldType": "BAC", + "newType": "G_quartet" + } + +EXAMPLES + Editing by passing a json to stdin: + + echo '{"typeName": ... "newType": "G_quartet"}' | apollo feature edit -j - +``` + +_See code: +[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit.ts)_ + +## `apollo feature edit-attribute` + +Add, edit, or view a feature attribute + +``` +USAGE + $ apollo feature edit-attribute -a [--profile ] [--config-file ] [-i ] [-v ] [-d] + +FLAGS + -a, --attribute= (required) Attribute key to add or edit + -d, --delete Delete this attribute + -i, --feature-id= [default: -] Feature ID to edit or "-" to read it from stdin + -v, --value=... New attribute value. Separated mutliple values by space to them as a list. If unset return + current value + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Add, edit, or view a feature attribute + + Be aware that there is no checking whether attributes names and values are + valid. For example, you can create non-unique ID attributes or you can set gene + ontology terms to non-existing terms + +EXAMPLES + Add attribute "domains" with a list of values: + + $ apollo feature edit-attribute -i 66...3f -a domains -v ABC PLD + + Print values in "domains" as json array: + + $ apollo feature edit-attribute -i 66...3f -a domains + + Delete attribute "domains" + + $ apollo feature edit-attribute -i 66...3f -a domains -d +``` + +_See code: +[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_ + +## `apollo feature edit-coords` + +Edit feature start and/or end coordinates + +``` +USAGE + $ apollo feature edit-coords [--profile ] [--config-file ] [-i ] [-s ] [-e ] + +FLAGS + -e, --end= New end coordinate (1-based) + -i, --feature-id= [default: -] Feature ID to edit or "-" to read it from stdin + -s, --start= New start coordinate (1-based) + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Edit feature start and/or end coordinates + + If editing a child feature that new coordinates must be within the parent's + coordinates. To get the identifier of the feature to edit consider using `apollo + feature get` or `apollo feature search` + +EXAMPLES + Edit start and end: + + $ apollo feature edit-coords -i abc...xyz -s 10 -e 1000 + + Edit end and leave start as it is: + + $ apollo feature edit-coords -i abc...xyz -e 2000 +``` + +_See code: +[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-coords.ts)_ + +## `apollo feature edit-type` + +Edit or view feature type + +``` +USAGE + $ apollo feature edit-type [--profile ] [--config-file ] [-i ] [-t ] + +FLAGS + -i, --feature-id= [default: -] Feature ID to edit or "-" to read it from stdin + -t, --type= Assign feature to this type. If unset return the current type + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Edit or view feature type + + Feature type is column 3 in gff format. It must be a valid sequence ontology + term although but the valifdity of the new term is not checked. +``` + +_See code: +[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-type.ts)_ + +## `apollo feature get` + +Get features in assembly, reference sequence or genomic window + +``` +USAGE + $ apollo feature get [--profile ] [--config-file ] [-a ] [-r ] [-s ] [-e + ] + +FLAGS + -a, --assembly= Find input reference sequence in this assembly + -e, --end= End coordinate + -r, --refseq= Reference sequence. If unset, query all sequences + -s, --start= [default: 1] Start coordinate (1-based) + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get features in assembly, reference sequence or genomic window + +EXAMPLES + Get all features in myAssembly: + + $ apollo feature get -a myAssembly + + Get features intersecting chr1:1..1000. You can omit the assembly name if there + are no other reference sequences named chr1: + + $ apollo feature get -a myAssembly -r chr1 -s 1 -e 1000 +``` + +_See code: +[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/get.ts)_ + +## `apollo feature get-id` + +Get features given their identifiers + +``` +USAGE + $ apollo feature get-id [--profile ] [--config-file ] [-i ] + +FLAGS + -i, --feature-id=... [default: -] Retrieves feature with these IDs. Use + "-" to read IDs from stdin (one per + line) + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get features given their identifiers + + Invalid identifiers or identifiers not found in the database will be silently + ignored + +EXAMPLES + Get features for these identifiers: + + $ apollo feature get-id -i abc...zyz def...foo +``` + +_See code: +[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/get-id.ts)_ + +## `apollo feature import` + +Import features from local gff file + +``` +USAGE + $ apollo feature import -i -a [--profile ] [--config-file ] [-d] + +FLAGS + -a, --assembly= (required) Import into this assembly name or assembly ID + -d, --delete-existing Delete existing features before importing + -i, --input-file= (required) Input gff or gtf file + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Import features from local gff file + + By default, features are added to the existing ones. + +EXAMPLES + Delete features in myAssembly and then import features.gff3: + + $ apollo feature import -d -i features.gff3 -a myAssembly +``` + +_See code: +[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/import.ts)_ + +## `apollo feature search` + +Free text search for feature in one or more assemblies + +``` +USAGE + $ apollo feature search -t [--profile ] [--config-file ] [-a ] + +FLAGS + -a, --assembly=... Assembly names or IDs to search; use "-" to read it from stdin. If omitted + search all assemblies + -t, --text= (required) Search for this text query + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Free text search for feature in one or more assemblies + + Return features matching a query string. This command searches only in: + + - Attribute *values* (not attribute names) + - Source field (which in fact is stored as an attribute) + - Feature type + + The search mode is: + + - Case insensitive + - Match only full words, but not necessarily the full value + - Common words are ignored. E.g. "the", "with" + + For example, given this feature: + + chr1 example SNP 10 30 0.987 . . "someKey=Fingerprint BAC with reads" + + Queries "bac" or "mRNA" return the feature. Instead these queries will NOT + match: + + - "someKey" + - "with" + - "Finger" + - "chr1" + - "0.987" + +EXAMPLES + Search "bac" in these assemblies: + + $ apollo feature search -a mm9 mm10 -t bac +``` + +_See code: +[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/search.ts)_ diff --git a/packages/website/docs/cli/help.md b/packages/website/docs/cli/help.md new file mode 100644 index 000000000..1041c5c49 --- /dev/null +++ b/packages/website/docs/cli/help.md @@ -0,0 +1,26 @@ +# `apollo help` + +Display help for apollo. + +- [`apollo help [COMMANDS]`](#apollo-help-commands) + +## `apollo help [COMMANDS]` + +Display help for apollo. + +``` +USAGE + $ apollo help [COMMANDS] [-n] + +ARGUMENTS + COMMANDS Command to show help for. + +FLAGS + -n, --nested-commands Include all nested commands in the output. + +DESCRIPTION + Display help for apollo. +``` + +_See code: +[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_ diff --git a/packages/website/docs/cli/login.md b/packages/website/docs/cli/login.md new file mode 100644 index 000000000..a6aa8a623 --- /dev/null +++ b/packages/website/docs/cli/login.md @@ -0,0 +1,46 @@ +# `apollo login` + +Login to Apollo + +- [`apollo login`](#apollo-login) + +## `apollo login` + +Login to Apollo + +``` +USAGE + $ apollo login [--profile ] [--config-file ] [-a ] [-u ] [-p ] [-f] + [--port ] + +FLAGS + -a, --address= Address of Apollo server + -f, --force Force re-authentication even if user is already logged in + -p, --password= Password for + -u, --username= Username for root login + --config-file= Use this config file (mostly for testing) + --port= [default: 3000] Get token by listening to this port number (usually this is >= 1024 and < + 65536) + --profile= Use credentials from this profile + +DESCRIPTION + Login to Apollo + + Use the provided credentials to obtain and save the token to access Apollo. Once + the token for the given profile has been saved in the configuration file, users + do not normally need to execute this command again unless the token has expired. + To setup a new profile use "apollo config" + +EXAMPLES + The most basic and probably most typical usage is to login using the default + profile in configuration file: + + $ apollo login + + Login with a different profile: + + $ apollo login --profile my-profile +``` + +_See code: +[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/login.ts)_ diff --git a/packages/website/docs/cli/logout.md b/packages/website/docs/cli/logout.md new file mode 100644 index 000000000..5eabbaa4e --- /dev/null +++ b/packages/website/docs/cli/logout.md @@ -0,0 +1,35 @@ +# `apollo logout` + +Logout of Apollo + +- [`apollo logout`](#apollo-logout) + +## `apollo logout` + +Logout of Apollo + +``` +USAGE + $ apollo logout [--profile ] [--config-file ] + +FLAGS + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Logout of Apollo + + Logout by removing the access token from the selected profile + +EXAMPLES + Logout default profile: + + $ apollo logout + + Logout selected profile + + $ apollo logout --profile my-profile +``` + +_See code: +[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/logout.ts)_ diff --git a/packages/website/docs/cli/refseq.md b/packages/website/docs/cli/refseq.md new file mode 100644 index 000000000..170e97244 --- /dev/null +++ b/packages/website/docs/cli/refseq.md @@ -0,0 +1,69 @@ +# `apollo refseq` + +Commands to handle reference sequences + +- [`apollo refseq add-alias`](#apollo-refseq-add-alias) +- [`apollo refseq get`](#apollo-refseq-get) + +## `apollo refseq add-alias` + +Add reference name aliases from a file + +``` +USAGE + $ apollo refseq add-alias -i -a [--profile ] [--config-file ] + +FLAGS + -a, --assembly= (required) Name for this assembly. + -i, --input-file= (required) Input refname alias file + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Add reference name aliases from a file + + Reference name aliasing is a process to make chromosomes that are named slightly + differently but which refer to the same thing render properly. This command + reads a file with reference name aliases and adds them to the database. + +EXAMPLES + Add reference name aliases: + + $ apollo refseq add-alias -i alias.txt -a myAssembly +``` + +_See code: +[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/add-alias.ts)_ + +## `apollo refseq get` + +Get reference sequences + +``` +USAGE + $ apollo refseq get [--profile ] [--config-file ] [-a ] + +FLAGS + -a, --assembly=... Get reference sequences for these assembly names or IDs; use - to read it from stdin + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get reference sequences + + Output the reference sequences in one or more assemblies in json format. This + command returns the sequence characteristics (e.g., name, ID, etc), not the DNA + sequences. Use `assembly sequence` for that. + +EXAMPLES + All sequences in the database: + + $ apollo refseq get + + Only sequences for these assemblies: + + $ apollo refseq get -a mm9 mm10 +``` + +_See code: +[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/get.ts)_ diff --git a/packages/website/docs/cli/status.md b/packages/website/docs/cli/status.md new file mode 100644 index 000000000..db616f284 --- /dev/null +++ b/packages/website/docs/cli/status.md @@ -0,0 +1,28 @@ +# `apollo status` + +View authentication status + +- [`apollo status`](#apollo-status) + +## `apollo status` + +View authentication status + +``` +USAGE + $ apollo status [--profile ] [--config-file ] + +FLAGS + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + View authentication status + + This command returns ": Logged in" if the selected profile has an + access token and ": Logged out" otherwise. Note that this command does + not check the validity of the access token. +``` + +_See code: +[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/status.ts)_ diff --git a/packages/website/docs/cli/user.md b/packages/website/docs/cli/user.md new file mode 100644 index 000000000..b8568b628 --- /dev/null +++ b/packages/website/docs/cli/user.md @@ -0,0 +1,41 @@ +# `apollo user` + +Commands to handle users + +- [`apollo user get`](#apollo-user-get) + +## `apollo user get` + +Get list of users + +``` +USAGE + $ apollo user get [--profile ] [--config-file ] [-u ] [-r ] + +FLAGS + -r, --role= Get users with this role + -u, --username= Find this username + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get list of users + + If set, filters username and role must be both satisfied to return an entry + +EXAMPLES + By username: + + $ apollo user get -u Guest + + By role: + + $ apollo user get -r admin + + Use jq for more control: + + $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")' +``` + +_See code: +[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/user/get.ts)_ diff --git a/packages/website/docs/installation.md b/packages/website/docs/installation.md new file mode 100755 index 000000000..c55c18349 --- /dev/null +++ b/packages/website/docs/installation.md @@ -0,0 +1,597 @@ +--- +sidebar_position: 1 +--- + +# Installation + +## Getting Started + +This guide will help you get up and running quickly with the Apollo3 using +Docker Compose. + +### Prerequisites + +- You have [Docker](https://docs.docker.com/install/) and + [Docker Compose version 2.0 or higher](https://docs.docker.com/compose/install/) + working on your machine. + +## Full deployment with collaboration server + +Apollo can be used in some cases on local files with no need to set up a server, +but this guide will focus on deploying Apollo with all the components needed for +a hosted server that allows collaborative annotation. + +### Basic components + +
+
JBrowse
+
+ The Apollo user interface is a JBrowse plugin, so a server hosting the + JBrowse code is needed. +
+
+ Since JBrowse is a client-side app, the requirements for serving it are low. + All you need is a simple static file server. For example, JBrowse can be + served by uploading the app's files into an Amazon S3 bucket and then making + them publicly available. +
+
+ For most Apollo installations, though, it's easier to serve JBrowse with a + static file server on the same machine that is running the Apollo + Collaboration Server. +
+
Apollo JBrowse Plugin
+
+ The code for the JBrowse plugin that adds Apollo functionality also needs to + be hosted by a server somewhere. This is a single file that has the same + hosting requirements as the JBrowse app. It's usually easiest to copy this + code to the same place the JBrowse code is hosted and use its same file + server. +
+
Apollo Collaboration Server
+
+ This server is what the Apollo JBrowse plugin connects to in order to + retrieve data as well as send requests to modify data. +
+
+ The server requires Node.js 18 or higher to run as well as at least two CPU + cores and 2GB Memory for basic usage. More memory may be needed for larger + assemblies or several concurrent users. The server also needs access to a + location on its file system to save uploaded files. The size of hard drive + it needs is dependant on how many files will need to be uploaded. +
+
MongoDB Database
+
+ The Apollo Collaboration Server stores its data in a MongoDB database. Since + the server uses some specialized MongoDB functionality, the database needs + to be in a replica set configuration. The database can be on the same + machine as the collaboration server, or it can be external. +
+
+ +### Deploying with Docker + +One possible deployment strategy, which we use internally to deploy the Apollo +demo website, is to use Docker as a deployment strategy. That way the only thing +the host machine needs to have installed on it is Docker, and the rest of the +packages and configurations can be taken care of using Docker. This guide will +cover some of the basics of Docker as part of describing the deployment, but if +you are unfamiliar with Docker it might be useful to see an overview of what it +does [here](https://docs.docker.com/get-started/overview/). + +Docker Compose is especially useful for this type of deployment, since it allows +us to use multiple Docker containers, each with its own specialized role, and +coordinate them with a `compose.yml` file. + +
+ compose.yml + +``` + name: apollo-demo-site + + services: + apollo-collaboration-server: + image: ghcr.io/gmod/apollo-collaboration-server:development + depends_on: + mongo-node-1: + condition: service_healthy + env_file: .env + environment: + MONGODB_URI: mongodb://mongo-node-1:27017,mongo-node-2:27018/apolloDb?replicaSet=rs0 + FILE_UPLOAD_FOLDER: /data/uploads + ALLOW_GUEST_USER: true + URL: http://my-apollo-site.org + JWT_SECRET: change_this_value + SESSION_SECRET: change_this_value + ports: + - 3999:3999 + volumes: + - uploaded-files-volume:/data/uploads + + client: + build: + args: + APOLLO_VERSION: 0.1.0 + JBROWSE_VERSION: 2.10.3 + FORWARD_HOSTNAME: apollo-collaboration-server + FORWARD_PORT: 3999 + context: . + depends_on: + - apollo-collaboration-server + ports: + - '80:80' + + mongo-node-1: + image: mongo:7 + command: + - '--replSet' + - rs0 + - '--bind_ip_all' + - '--port' + - '27017' + healthcheck: + interval: 30s + retries: 3 + start_interval: 5s + start_period: 2m + test: | + mongosh --port 27017 --quiet --eval " + try { + rs.status() + console.log('replica set ok') + } catch { + rs.initiate({ + _id: 'rs0', + members: [ + { _id: 0, host: 'mongo-node-1:27017', priority: 1 }, + { _id: 1, host: 'mongo-node-2:27018', priority: 0.5 }, + ], + }) + console.log('replica set initiated') + } + " + timeout: 10s + ports: + - '27017:27017' + volumes: + - mongo-node-1_data:/data/db + - mongo-node-1_config:/data/configdb + + mongo-node-2: + image: mongo:7 + command: + - '--replSet' + - rs0 + - '--bind_ip_all' + - '--port' + - '27018' + ports: + - '27018:27018' + volumes: + - mongo-node-2_data:/data/db + - mongo-node-2_config:/data/configdb + + volumes: + mongo-node-1_config: null + mongo-node-1_data: null + mongo-node-2_config: null + mongo-node-2_data: null + uploaded-files-volume: null +``` + +
+ +We'll break down each of the sections of the compose.yml file and what is being +done in each. In this guide we'll assume you're first creating these files on +your local computer, and then we'll discuss how to deploy them to your server. + +#### Name + +At the top of the example file is `name: apollo-demo-site`. You can rename this +or even remove it, it's mostly there as an easy-to-recognize name in various +Docker command outputs. + +#### Volumes + +Next we're going to skip to the bottom section called `volumes`. In this compose +file, we're using volumes to keep certain kinds of data around even if one of +the containers needs to be rebuild. For example, let's say you're using a +MongoDB container that uses v7.0.6 of MongoDB, but you want to upgrade to +v7.0.7. With Docker, instead of upgrading the running container, you usually +build a brand new container based on a Docker image that has the new version you +want. Volumes give Docker a place to store files outside the container, so a new +container can connect to the old volume and then all your data is still in your +database with your upgraded container. + +In the example `compose.yml`, we use simple entries like +`mongo-node-1_config: null` means that we are defining a volume with the name +"mongo-node-1_config" that we can refer to elsewhere in the compose file. + +#### Services + +Services are where most of the configuration is done in the compose file. Each +entry in the `services` section will be run as a separate Docker container, and +the service names can be used so that different services can refer to each +other. + +##### Client + +We'll start by describing the `client` service. Here is the section from the +compose file: + +```yml +client: + build: + args: + APOLLO_VERSION: 0.1.0 + JBROWSE_VERSION: 2.10.3 + FORWARD_HOSTNAME: apollo-collaboration-server + FORWARD_PORT: 3999 + context: . + depends_on: + - apollo-collaboration-server + ports: + - '80:80' +``` + +This service will be a static file server that serves the JBrowse and Apollo +JBrowse Plugin code. We're using Apache (`httpd`) in this example, but if you +know how to properly configure it, you could use NGINX as well. + +The `build` section included here means that instead of using a pre-built Docker +image, this container will use an image built from a Dockerfile. The reason we +don't publish a pre-built container for this service is that it would be +complicated to organize and publish images with every combination of Apollo and +JBrowse versions, and it's much easier to download the exact versions you +specify when deploying your app. + +
+ Dockerfile + +``` + FROM httpd:alpine + ARG JBROWSE_VERSION + ARG APOLLO_VERSION + ARG FORWARD_HOSTNAME + ARG FORWARD_PORT + COPY < + RewriteEngine on + + RewriteCond %{DOCUMENT_ROOT}/\$1 !-f + RewriteCond %{DOCUMENT_ROOT}/\$1 !-d + RewriteRule ^/(.*)$ http://${FORWARD_HOSTNAME}:${FORWARD_PORT}/\$1 [P,QSA] + ProxyPassReverse / http://${FORWARD_HOSTNAME}:${FORWARD_PORT}/ + + EOF + COPY <> /usr/local/apache2/conf/httpd.conf + wget https://github.com/GMOD/jbrowse-components/releases/download/v$JBROWSE_VERSION/jbrowse-web-v$JBROWSE_VERSION.zip + unzip -o jbrowse-web-v$JBROWSE_VERSION.zip + rm jbrowse-web-v$JBROWSE_VERSION.zip + wget --output-document=- --quiet https://registry.npmjs.org/@apollo-annotation/jbrowse-plugin-apollo/-/jbrowse-plugin-apollo-$APOLLO_VERSION.tgz | \ + tar --extract --gzip --file=- --strip=2 package/dist/jbrowse-plugin-apollo.umd.production.min.js + EOF +``` + +
+ +Docker Compose will expect this Dockerfile to be named `Dockerfile` and be +located next to the `compose.yml` in the filesystem. In the example Dockerfile +we configure the file server, download the specified versions of Apollo and +JBrowse, and add the JBrowse and Apollo configuration. The `FORWARD_HOSTNAME` +and `FORWARD_PORT` args should match the service name and port of the Apollo +Collaboration Server service (described in the next section). + +The configuration added to the `httpd.conf` file in that Dockerfile makes it so +that any request that comes to the server that doesn't match a file hosted on +the server is forwarded to the Apollo Collaboration Server. + +The `depends_on` section makes sure the collaboration server has started before +starting the client, and the `port` section makes the container's server +available outside the container on port 80. + +##### Apollo Collaboration Server + +The next service is the Apollo server component. Here is its section of the +compose file: + +```yml +apollo-collaboration-server: + image: ghcr.io/gmod/apollo-collaboration-server:development + depends_on: + mongo-node-1: + condition: service_healthy + env_file: .env + environment: + MONGODB_URI: mongodb://mongo-node-1:27017,mongo-node-2:27018/apolloDb?replicaSet=rs0 + FILE_UPLOAD_FOLDER: /data/uploads + ALLOW_GUEST_USER: true + URL: http://my-apollo-site.org + JWT_SECRET: change_this_value + SESSION_SECRET: change_this_value + ports: + - 3999:3999 + volumes: + - uploaded-files-volume:/data/uploads +``` + +This service uses a published Docker image for its container. It also uses +`depends_on` to ensure that the database is started and in a healthy state +before starting the collaboration server, and defines which port the app is +exposed on. + +The collaboration server is configured with environment variables, often in a +`.env` file. However, we use the `environment` option to set a couple variables +whose value depends on other places in the compose file, to try to keep the +related options all in one place. These two variables are `MONGODB_URI` and +`FILE_UPLOAD_FOLDER`. The example URI is +`mongodb://mongo-node-1:27017,mongo-node-2:27018/apolloDb?replicaSet=rs0`. If +you change the names of either of the MongoDB services, their ports, or add or +remove a MongoDB service, be sure to update this value. The value of +`FILE_UPLOAD_FOLDER` should match what's on the right side of the colon in the +`volumes` section (e.g. `/data/uploads`). + +There are a few other variables that need to be configured for the Apollo +Collaboration Server to work. They are `URL`, `JWT_SECRET`, and `SESSION_SECRET` +variables. `URL` is the URL of the server that's hosting Apollo. We'll discuss +this more in a later section when talking about authentication. You can think of +`JWT_SECRET` and `SESSION_SECRET` as kind of like passwords. They need to be a +random string, but should be the same each time you run the server so that user +sessions are not invalidated (unless you want to intentionally invalidate user +sessions). You can use a password generator to create them. + +You can put these variables in the `environment` section, or you can put them in +a `.env` file, which has a format that looks like this + +```env +URL=https://my-apollo-site.org +``` + +
+ .env + +``` + ############## + ## REQUIRED ## + ############## + + # URL + # URL=http://my-apollo-site.org + + # MongoDB connection + # MONGODB_URI=mongodb://127.0.0.1:27017/apolloDb + # Alternatively, can be a path to a file with the URI + # MONGODB_URI_FILE=/run/secrets/mongodb-uri + + # Output folder for uploaded files + # FILE_UPLOAD_FOLDER=./data/uploads + + # Secret used to encode JWT tokens + # JWT_SECRET= + # Alternatively, can be a path to a file with the client secret + # JWT_SECRET_FILE=/run/secrets/jwt-secret + + # Secret used to encode express sessions + # SESSION_SECRET= + # Alternatively, can be a path to a file with the session secret + # SESSION_SECRET_FILE=/run/secrets/session-secret + + ############################################################################## + ## To enable users to log in, you need either (or both) Google or Microsoft ## + ## OAuth configured. Without them, only userless guest access is possible. ## + ############################################################################## + + # Google client id and secret. + # GOOGLE_CLIENT_ID= + # Alternatively, can be a path to a file with the client ID + # GOOGLE_CLIENT_ID_FILE=/run/secrets/google-client-id + # GOOGLE_CLIENT_SECRET= + # Alternatively, can be a path to a file with the client secret + # GOOGLE_CLIENT_SECRET_FILE=/run/secrets/google-client-secret + + # Microsoft client id and secret. + # MICROSOFT_CLIENT_ID= + # Alternatively, can be a path to a file with the client ID + # MICROSOFT_CLIENT_ID_FILE=/run/secrets/microsoft-client-id + # MICROSOFT_CLIENT_SECRET= + # Alternatively, can be a path to a file with the client secret + # MICROSOFT_CLIENT_SECRET_FILE=/run/secrets/microsoft-client-secret + + ############## + ## OPTIONAL ## + ############## + + # Application port, defaults to 3999 + # PORT=3999 + + # Enable all CORS requests, defaults to false + # CORS=false + + # Comma-separated list of log levels to output + # Possible values are: error, warn, log, debug, verbose. + # Defaults to error,warn,log + # LOG_LEVELS=error,warn,log + + # Reference sequence chunk size, defaults to 262144 (256 KiB) + # CHUNK_SIZE=262144 + + # Default new user role, possible values are admin, user, readOnly, and none + # Defaults to none + # DEFAULT_NEW_USER_ROLE=none + + # Whether to broadcast users locations, defaults to true + # BROADCAST_USER_LOCATION=true + + # Whether to allow guest users who do not have to log in, defaults to false + ALLOW_GUEST_USER=true + # If guest users are allowed, what role will they have + # Possible values are admin, readOnly and user; defaults to readonly + # GUEST_USER_ROLE=readOnly + + # Whether to allow a root user. Root users cannot log in to the user interface, + # but can be used in the Apollo CLI as an account that can log in without + # needing an identity provider (such as Google). Defaults to false. + # ALLOW_ROOT_USER=false + # The username for the root user, if allowed + # ROOT_USER_NAME=root + # The password for the root user, if allowed + # ROOT_USER_PASSWORD= + # Alternatively, can be a path to a file with the root password + # ROOT_USER_PASSWORD_FILE=/run/secrets/root-user-password + + # Apollo by default uses The Sequence Ontology. You can override this by + # providing a path to an ontology file in the OBO Graphs JSON format. You can + # use `robot` to convert an OBO or OWL to OBO Graphs JSON. + # http://robot.obolibrary.org/convert + # ONTOLOGY_FILE = '/data/ontology.json' + + # Comma-separated list of Apollo plugins to use + # PLUGIN_URLS=https://example.com/apollo-plugin-example.umd.production.min.js + # Alternatively, can be a path to a file with a list of plugin URLs, one URL per + # line + # PLUGIN_URLS_FILE=/data/plugin-urls +``` + +
+ +There are several other options you can configure. You can see sample `.env` +section for a description of the other configuration options. For now, we will +set `ALLOW_GUEST_USER` to be true to simplify testing. + +##### MongoDB + +MongoDB needs to be in a replica set configuration for the Apollo Collaboration +Server to work properly. MongoDB replica sets are intended to ensure +uninterrupted connection to the database even if one database node goes down. In +our case we're running all our nodes on the same server, so some of that +protection is lost, but we still run two different node containers so if one +container goes down, the database can still be accessed. We're using two nodes, +although you can use only a single node if you like. If you need high +availability in a production environment, you might need more nodes hosted on +different servers. In that case you could delete the MongoDB sections from the +compose file and update the `MONGODB_URI` variable in the collaboration server +appropriately. + +Here is one of the MongoDB service entries: + +```yml +mongo-node-1: + image: mongo:7 + command: + - '--replSet' + - rs0 + - '--bind_ip_all' + - '--port' + - '27017' + healthcheck: + interval: 30s + retries: 3 + start_interval: 5s + start_period: 2m + test: | + mongosh --port 27017 --quiet --eval " + try { + rs.status() + console.log('replica set ok') + } catch { + rs.initiate({ + _id: 'rs0', + members: [ + { _id: 0, host: 'mongo-node-1:27017', priority: 1 }, + { _id: 1, host: 'mongo-node-2:27018', priority: 0.5 }, + ], + }) + console.log('replica set initiated') + } + " + timeout: 10s + ports: + - '27017:27017' + volumes: + - mongo-node-1_data:/data/db + - mongo-node-1_config:/data/configdb +``` + +This uses the official MongoDB image, runs on port 27017, and uses two volumes +to store data and configuration in. The second node is almost identical, with a +different and and port and without the `healthcheck` section. + +The `healthcheck` section is there to initialize the replica set the first time +the container runs, and then to provide a way for the collaboration server to +know the database is healthy and ready for requests from the app. + +### Starting everything + +Once you have your `compose.yml`, `Dockerfile`, and optionally `.env` file set +up, you can start everything up to see if it works. Do this by opening up the +terminal in the directory where your compose file is and running +`docker compose up`. You'll see a lot of log output, and after a bit you should +be able to open http://localhost/ in your browser and see the app. You can stop +the process with Ctrl + C. + +You can then try running `docker compose up -d`. This starts the containers in +the background, so you won't see the log output you saw before. You can still +access the logs, though. For example, running `docker compose logs client` will +show you the logs generated by your "client" service. + +To stop the containers after they started with the `-d` option, you can run +`docker compose down`. + +### Deploying + +There are a couple ways to deploy this app to your server. One option is to copy +all the file over and run `docker compse up -d` there. Another is to use Docker +Contexts (see +[here](https://docs.docker.com/engine/context/working-with-contexts/)), which +allows you to run a command locally that looks like +`docker --context apollo-server compose up -d` on your local computer, and it +will remotely run the command on your server. diff --git a/packages/website/docs/user-guide/_category_.json b/packages/website/docs/user-guide/_category_.json new file mode 100644 index 000000000..368d7de35 --- /dev/null +++ b/packages/website/docs/user-guide/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "User guide", + "position": 2, + "link": { + "type": "generated-index", + "description": "Apollo3 user guide" + } +} diff --git a/packages/website/docs/user-guide/delete-assembly.md b/packages/website/docs/user-guide/delete-assembly.md new file mode 100644 index 000000000..ff5905311 --- /dev/null +++ b/packages/website/docs/user-guide/delete-assembly.md @@ -0,0 +1,20 @@ +--- +sidebar_position: 2 +--- + +# Delete assembly + +This guide will walk you through the process of deleting an assembly from +Apollo3. + +1. Navigate to the [Apollo3](https://apollo.jbrowse.org/demo) and log in to your + account. +2. Click on the `Delete assembly` button under the `Apollo` dropdown from top + navigation bar. + +![alt text](image-10.png) + +3. In the delete assembly dialog, select the assembly which you want to delete + and click on the `Delete` button. + +![alt text](image-11.png) diff --git a/packages/website/docs/user-guide/image-1.png b/packages/website/docs/user-guide/image-1.png new file mode 100644 index 000000000..90af62407 Binary files /dev/null and b/packages/website/docs/user-guide/image-1.png differ diff --git a/packages/website/docs/user-guide/image-10.png b/packages/website/docs/user-guide/image-10.png new file mode 100644 index 000000000..5cc58bab1 Binary files /dev/null and b/packages/website/docs/user-guide/image-10.png differ diff --git a/packages/website/docs/user-guide/image-11.png b/packages/website/docs/user-guide/image-11.png new file mode 100644 index 000000000..227ac8730 Binary files /dev/null and b/packages/website/docs/user-guide/image-11.png differ diff --git a/packages/website/docs/user-guide/image-2.png b/packages/website/docs/user-guide/image-2.png new file mode 100644 index 000000000..74c07d05c Binary files /dev/null and b/packages/website/docs/user-guide/image-2.png differ diff --git a/packages/website/docs/user-guide/image-3.png b/packages/website/docs/user-guide/image-3.png new file mode 100644 index 000000000..df1208d4f Binary files /dev/null and b/packages/website/docs/user-guide/image-3.png differ diff --git a/packages/website/docs/user-guide/image-4.png b/packages/website/docs/user-guide/image-4.png new file mode 100644 index 000000000..03675361a Binary files /dev/null and b/packages/website/docs/user-guide/image-4.png differ diff --git a/packages/website/docs/user-guide/image-5.png b/packages/website/docs/user-guide/image-5.png new file mode 100644 index 000000000..f3bad21d3 Binary files /dev/null and b/packages/website/docs/user-guide/image-5.png differ diff --git a/packages/website/docs/user-guide/image-6.png b/packages/website/docs/user-guide/image-6.png new file mode 100644 index 000000000..e7a9b80af Binary files /dev/null and b/packages/website/docs/user-guide/image-6.png differ diff --git a/packages/website/docs/user-guide/image-7.png b/packages/website/docs/user-guide/image-7.png new file mode 100644 index 000000000..ef1bb8fce Binary files /dev/null and b/packages/website/docs/user-guide/image-7.png differ diff --git a/packages/website/docs/user-guide/image-8.png b/packages/website/docs/user-guide/image-8.png new file mode 100644 index 000000000..81d43933f Binary files /dev/null and b/packages/website/docs/user-guide/image-8.png differ diff --git a/packages/website/docs/user-guide/image-9.png b/packages/website/docs/user-guide/image-9.png new file mode 100644 index 000000000..38fc9c964 Binary files /dev/null and b/packages/website/docs/user-guide/image-9.png differ diff --git a/packages/website/docs/user-guide/image.png b/packages/website/docs/user-guide/image.png new file mode 100644 index 000000000..d11cc9955 Binary files /dev/null and b/packages/website/docs/user-guide/image.png differ diff --git a/packages/website/docs/user-guide/import-features.md b/packages/website/docs/user-guide/import-features.md new file mode 100644 index 000000000..e11ef8a06 --- /dev/null +++ b/packages/website/docs/user-guide/import-features.md @@ -0,0 +1,45 @@ +--- +sidebar_position: 2 +--- + +# Import features + +This guide will walk you through the process of importing features/annotations +to Apollo3 using GFF3 file. + +There are two ways to import features to Apollo3: + +- Follow steps mentioned in [Upload assembly](/docs/user-guide/upload-assembly) + guide to upload the GFF3 file containing features and sequence. +- Use the `Import features` button in the `Apollo` dropdown from top navigation + bar to import features to an existing assembly. + +In the guide below, we will walk you through the process of importing features +to an existing assembly. + +1. Navigate to the [Apollo3](https://apollo.jbrowse.org/demo) and log in to your + account. +2. Click on the `Import features` button under the `Apollo` dropdown from top + navigation bar. + +![alt text](image-6.png) + +3. In the import features dialog, select the assembly to which you want to + import the features and click on the `Choose file` button to select the GFF3 + file containing features. +4. If the features were already imported to the assembly, you have option to + delete exiting features and import the new features by selecting the + `Yes, delete existing features` checkbox. + +![alt text](image-7.png) + +5. Click on the `Submit` button to start the import process. We can see the + progress of the import in the `Jobs list` widget and once the import is + complete we get a success message. + +![alt text](image-8.png) + +![alt text](image-9.png) + +Now we should be able to see the imported features in the apollo track and can +start annotating the genome. diff --git a/packages/website/docs/user-guide/upload-assembly.md b/packages/website/docs/user-guide/upload-assembly.md new file mode 100644 index 000000000..b8bcde8b8 --- /dev/null +++ b/packages/website/docs/user-guide/upload-assembly.md @@ -0,0 +1,43 @@ +--- +sidebar_position: 2 +--- + +# Upload assembly + +This guide will walk you through the process of uploading an assembly file to +Apollo3. + +1. Navigate to the [Apollo3](https://apollo.jbrowse.org/demo) and log in to your + account. +2. Click on the `Add Assembly` button under the `Apollo` dropdown from top + navigation bar. ![alt text](image.png) +3. Now we have 3 options to upload the assembly: + + - Upload fasta file containing sequence + + ![alt text](image-1.png) + + - Upload gff3 file containing annotation along with sequence. If we want to + upload annotations along with the sequence, we needc to select + `Also load features from GFF3 file`. + + ![alt text](image-2.png) + + - Instead of uploading the files, we can also provide the URL of the files + and query the data on the fly. + + ![alt text](image-3.png) + +4. After selecting appropriate option and providing the necessary files, click + on the `Submit` button. We can see the progress of the upload in the + `Jobs list` widget and once the upload is complete we get a success message. + +![alt text](image-4.png) + +5. Now click on `Launch view' button to view the uploaded assembly in Apollo3 + (If its not visible please refresh the page). + +![alt text](image-5.png) + +Now we have successfully uploaded the assembly to Apollo3 and can start +browsing/annotating the genome. diff --git a/packages/website/docusaurus.config.ts b/packages/website/docusaurus.config.ts new file mode 100755 index 000000000..46b182cad --- /dev/null +++ b/packages/website/docusaurus.config.ts @@ -0,0 +1,105 @@ +import { themes as prismThemes } from 'prism-react-renderer' +import type { Config } from '@docusaurus/types' +import type * as Preset from '@docusaurus/preset-classic' + +const config: Config = { + title: 'Apollo', + tagline: + 'Collaborative, customizable, and scalable graphical genome annotation', + favicon: 'img/favicon.ico', + + // Set the production url of your site here + url: 'https://your-docusaurus-site.example.com', + // Set the // pathname under which your site is served + // For GitHub pages deployment, it is often '//' + baseUrl: '/', + + // GitHub pages deployment config. + // If you aren't using GitHub pages, you don't need these. + organizationName: 'GMOD', // Usually your GitHub org/user name. + projectName: 'Apollo3', // Usually your repo name. + + onBrokenLinks: 'throw', + onBrokenMarkdownLinks: 'warn', + + // Even if you don't use internationalization, you can use this field to set + // useful metadata like html lang. For example, if your site is Chinese, you + // may want to replace "en" with "zh-Hans". + i18n: { + defaultLocale: 'en', + locales: ['en'], + }, + + presets: [ + [ + 'classic', + { + docs: { + sidebarPath: './sidebars.ts', + // Please change this to your repo. + // Remove this to remove the "edit this page" links. + editUrl: + 'https://github.com/facebook/docusaurus/tree/main/packages/create-docusaurus/templates/shared/', + }, + theme: { + customCss: './src/css/custom.css', + }, + } satisfies Preset.Options, + ], + ], + + themeConfig: { + // Replace with your project's social card + // image: 'img/docusaurus-social-card.jpg', + navbar: { + title: 'Apollo', + logo: { + alt: 'Apollo', + src: 'img/logo.png', + }, + items: [ + { + type: 'docSidebar', + sidebarId: 'docsSidebar', + position: 'left', + label: 'Docs', + }, + { + href: 'https://github.com/GMOD/Apollo3', + label: 'GitHub', + position: 'right', + }, + ], + }, + footer: { + style: 'dark', + links: [ + { + title: 'Docs', + items: [ + { + label: 'Docs', + to: '/docs/installation', + }, + ], + }, + { + title: 'More', + items: [ + { + label: 'GitHub', + href: 'https://github.com/GMOD/Apollo3', + }, + ], + }, + ], + copyright: `Copyright © ${new Date().getFullYear()} Evolutionary Software Foundation, Inc. Built with Docusaurus.`, + }, + prism: { + theme: prismThemes.github, + darkTheme: prismThemes.dracula, + }, + } satisfies Preset.ThemeConfig, +} + +export default config diff --git a/packages/website/package.json b/packages/website/package.json new file mode 100755 index 000000000..51a1c05a6 --- /dev/null +++ b/packages/website/package.json @@ -0,0 +1,34 @@ +{ + "name": "@apollo-annotation/website", + "version": "0.1.17", + "private": true, + "scripts": { + "start": "docusaurus start --port 3131", + "build": "docusaurus build", + "swizzle": "docusaurus swizzle", + "deploy": "docusaurus deploy", + "clear": "docusaurus clear", + "serve": "docusaurus serve", + "write-translations": "docusaurus write-translations", + "write-heading-ids": "docusaurus write-heading-ids", + "typecheck": "tsc" + }, + "dependencies": { + "@docusaurus/core": "3.5.2", + "@docusaurus/preset-classic": "3.5.2", + "@mdx-js/react": "^3.0.0", + "clsx": "^1.1.1", + "prism-react-renderer": "^2.3.0", + "react": "^18.2.0", + "react-dom": "^18.2.0" + }, + "devDependencies": { + "@docusaurus/module-type-aliases": "^3.5.2", + "@docusaurus/theme-classic": "^3.5.2", + "@docusaurus/tsconfig": "^3.5.2", + "@docusaurus/types": "^3.5.2", + "@types/node": "^18.14.2", + "@types/react": "^18.3.4", + "typescript": "^5.5.3" + } +} diff --git a/packages/website/sidebars.ts b/packages/website/sidebars.ts new file mode 100755 index 000000000..315a36be5 --- /dev/null +++ b/packages/website/sidebars.ts @@ -0,0 +1,31 @@ +import type { SidebarsConfig } from '@docusaurus/plugin-content-docs' + +/** + * Creating a sidebar enables you to: + - create an ordered group of docs + - render a sidebar for each doc of that group + - provide next/previous navigation + + The sidebars can be generated from the filesystem, or explicitly defined here. + + Create as many sidebars as you want. + */ +const sidebars: SidebarsConfig = { + // By default, Docusaurus generates a sidebar from the docs folder structure + docsSidebar: [{ type: 'autogenerated', dirName: '.' }], + + // But you can create a sidebar manually + /* + tutorialSidebar: [ + 'intro', + 'hello', + { + type: 'category', + label: 'Tutorial', + items: ['tutorial-basics/create-a-document'], + }, + ], + */ +} + +export default sidebars diff --git a/packages/website/src/components/HomepageFeatures/index.tsx b/packages/website/src/components/HomepageFeatures/index.tsx new file mode 100755 index 000000000..6b9c9c9ad --- /dev/null +++ b/packages/website/src/components/HomepageFeatures/index.tsx @@ -0,0 +1,73 @@ +import { clsx } from 'clsx' +import Heading from '@theme/Heading' +import styles from './styles.module.css' + +interface FeatureItem { + title: string + Svg: React.ComponentType> + description: JSX.Element +} + +const FeatureList: FeatureItem[] = [ + { + title: 'Easy to Use', + // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-var-requires, @typescript-eslint/no-unsafe-member-access + Svg: require('@site/static/img/undraw_docusaurus_mountain.svg').default, + description: ( + <> + Docusaurus was designed from the ground up to be easily installed and + used to get your website up and running quickly. + + ), + }, + { + title: 'Focus on What Matters', + // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-var-requires, @typescript-eslint/no-unsafe-member-access + Svg: require('@site/static/img/undraw_docusaurus_tree.svg').default, + description: ( + <> + Docusaurus lets you focus on your docs, and we'll do the chores. Go + ahead and move your docs into the docs directory. + + ), + }, + { + title: 'Powered by React', + // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-var-requires, @typescript-eslint/no-unsafe-member-access + Svg: require('@site/static/img/undraw_docusaurus_react.svg').default, + description: ( + <> + Extend or customize your website layout by reusing React. Docusaurus can + be extended while reusing the same header and footer. + + ), + }, +] + +function Feature({ Svg, description, title }: FeatureItem) { + return ( +
+
+ +
+
+ {title} +

{description}

+
+
+ ) +} + +export default function HomepageFeatures(): JSX.Element { + return ( +
+
+
+ {FeatureList.map((props, idx) => ( + + ))} +
+
+
+ ) +} diff --git a/packages/website/src/components/HomepageFeatures/styles.module.css b/packages/website/src/components/HomepageFeatures/styles.module.css new file mode 100755 index 000000000..b248eb2e5 --- /dev/null +++ b/packages/website/src/components/HomepageFeatures/styles.module.css @@ -0,0 +1,11 @@ +.features { + display: flex; + align-items: center; + padding: 2rem 0; + width: 100%; +} + +.featureSvg { + height: 200px; + width: 200px; +} diff --git a/packages/website/src/css/custom.css b/packages/website/src/css/custom.css new file mode 100755 index 000000000..2dff92c00 --- /dev/null +++ b/packages/website/src/css/custom.css @@ -0,0 +1,30 @@ +/** + * Any CSS included here will be global. The classic template + * bundles Infima by default. Infima is a CSS framework designed to + * work well for content-centric websites. + */ + +/* You can override the default Infima variables here. */ +:root { + --ifm-color-primary: #1d817b; + --ifm-color-primary-dark: #1a746f; + --ifm-color-primary-darker: #196e69; + --ifm-color-primary-darkest: #145a56; + --ifm-color-primary-light: #208e87; + --ifm-color-primary-lighter: #21948d; + --ifm-color-primary-lightest: #26a8a0; + --ifm-code-font-size: 95%; + --docusaurus-highlighted-code-line-bg: rgba(0, 0, 0, 0.1); +} + +/* For readability concerns, you should choose a lighter palette in dark mode. */ +[data-theme='dark'] { + --ifm-color-primary: #25a7a0; + --ifm-color-primary-dark: #219690; + --ifm-color-primary-darker: #1f8e88; + --ifm-color-primary-darkest: #1a7570; + --ifm-color-primary-light: #29b8b0; + --ifm-color-primary-lighter: #2bc0b8; + --ifm-color-primary-lightest: #37d3ca; + --docusaurus-highlighted-code-line-bg: rgba(0, 0, 0, 0.3); +} diff --git a/packages/website/src/pages/index.module.css b/packages/website/src/pages/index.module.css new file mode 100755 index 000000000..9f71a5da7 --- /dev/null +++ b/packages/website/src/pages/index.module.css @@ -0,0 +1,23 @@ +/** + * CSS files with the .module.css suffix will be treated as CSS modules + * and scoped locally. + */ + +.heroBanner { + padding: 4rem 0; + text-align: center; + position: relative; + overflow: hidden; +} + +@media screen and (max-width: 996px) { + .heroBanner { + padding: 2rem; + } +} + +.buttons { + display: flex; + align-items: center; + justify-content: center; +} diff --git a/packages/website/src/pages/index.tsx b/packages/website/src/pages/index.tsx new file mode 100755 index 000000000..367fdc8bd --- /dev/null +++ b/packages/website/src/pages/index.tsx @@ -0,0 +1,42 @@ +// import Link from '@docusaurus/Link' +import useDocusaurusContext from '@docusaurus/useDocusaurusContext' +// import HomepageFeatures from '@site/src/components/HomepageFeatures' +import Heading from '@theme/Heading' +import Layout from '@theme/Layout' +import { clsx } from 'clsx' + +import styles from './index.module.css' + +function HomepageHeader() { + const { siteConfig } = useDocusaurusContext() + return ( +
+
+ + {siteConfig.title} + +

{siteConfig.tagline}

+ {/*
+ + Docusaurus Tutorial - 5min ⏱️ + +
*/} +
+
+ ) +} + +export default function Home(): JSX.Element { + const { siteConfig } = useDocusaurusContext() + return ( + + + {/*
+ +
*/} + + ) +} diff --git a/packages/website/src/pages/markdown-page.md b/packages/website/src/pages/markdown-page.md new file mode 100755 index 000000000..9756c5b66 --- /dev/null +++ b/packages/website/src/pages/markdown-page.md @@ -0,0 +1,7 @@ +--- +title: Markdown page example +--- + +# Markdown page example + +You don't need React to write simple standalone pages. diff --git a/packages/website/static/.nojekyll b/packages/website/static/.nojekyll new file mode 100755 index 000000000..e69de29bb diff --git a/packages/website/static/img/docusaurus-social-card.jpg b/packages/website/static/img/docusaurus-social-card.jpg new file mode 100755 index 000000000..ffcb44821 Binary files /dev/null and b/packages/website/static/img/docusaurus-social-card.jpg differ diff --git a/packages/website/static/img/docusaurus.png b/packages/website/static/img/docusaurus.png new file mode 100755 index 000000000..f458149e3 Binary files /dev/null and b/packages/website/static/img/docusaurus.png differ diff --git a/packages/website/static/img/favicon.ico b/packages/website/static/img/favicon.ico new file mode 100644 index 000000000..26db57e06 Binary files /dev/null and b/packages/website/static/img/favicon.ico differ diff --git a/packages/website/static/img/logo.png b/packages/website/static/img/logo.png new file mode 100644 index 000000000..48e559616 Binary files /dev/null and b/packages/website/static/img/logo.png differ diff --git a/packages/website/static/img/logo.svg b/packages/website/static/img/logo.svg new file mode 100755 index 000000000..9db6d0d06 --- /dev/null +++ b/packages/website/static/img/logo.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/packages/website/static/img/undraw_docusaurus_mountain.svg b/packages/website/static/img/undraw_docusaurus_mountain.svg new file mode 100755 index 000000000..af961c49a --- /dev/null +++ b/packages/website/static/img/undraw_docusaurus_mountain.svg @@ -0,0 +1,171 @@ + + Easy to Use + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/packages/website/static/img/undraw_docusaurus_react.svg b/packages/website/static/img/undraw_docusaurus_react.svg new file mode 100755 index 000000000..94b5cf08f --- /dev/null +++ b/packages/website/static/img/undraw_docusaurus_react.svg @@ -0,0 +1,170 @@ + + Powered by React + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/packages/website/static/img/undraw_docusaurus_tree.svg b/packages/website/static/img/undraw_docusaurus_tree.svg new file mode 100755 index 000000000..d9161d339 --- /dev/null +++ b/packages/website/static/img/undraw_docusaurus_tree.svg @@ -0,0 +1,40 @@ + + Focus on What Matters + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/packages/website/tsconfig.json b/packages/website/tsconfig.json new file mode 100755 index 000000000..a88e02936 --- /dev/null +++ b/packages/website/tsconfig.json @@ -0,0 +1,8 @@ +{ + // This file is not used in compilation. It is here just for a nice editor experience. + "extends": "@docusaurus/tsconfig", + "compilerOptions": { + "baseUrl": ".", + "strictNullChecks": true, + }, +} diff --git a/yarn.lock b/yarn.lock index a269b764f..f51810c29 100644 --- a/yarn.lock +++ b/yarn.lock @@ -26,6 +26,207 @@ __metadata: languageName: node linkType: hard +"@algolia/autocomplete-core@npm:1.9.3": + version: 1.9.3 + resolution: "@algolia/autocomplete-core@npm:1.9.3" + dependencies: + "@algolia/autocomplete-plugin-algolia-insights": "npm:1.9.3" + "@algolia/autocomplete-shared": "npm:1.9.3" + checksum: 10c0/a751b20f15c9a30b8b2d5a4f1f62fb4dbd012fb7ffec1b12308d6e7388b5a4dc83af52176634f17facb57a7727204843c5aa2f6e80efafaaf244275f44af11d9 + languageName: node + linkType: hard + +"@algolia/autocomplete-plugin-algolia-insights@npm:1.9.3": + version: 1.9.3 + resolution: "@algolia/autocomplete-plugin-algolia-insights@npm:1.9.3" + dependencies: + "@algolia/autocomplete-shared": "npm:1.9.3" + peerDependencies: + search-insights: 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resolution: "@webassemblyjs/floating-point-hex-parser@npm:1.11.6" @@ -8019,9 +10630,16 @@ __metadata: languageName: node linkType: hard -"@webassemblyjs/helper-numbers@npm:1.11.6": - version: 1.11.6 - resolution: "@webassemblyjs/helper-numbers@npm:1.11.6" +"@webassemblyjs/helper-buffer@npm:1.12.1": + version: 1.12.1 + resolution: "@webassemblyjs/helper-buffer@npm:1.12.1" + checksum: 10c0/0270724afb4601237410f7fd845ab58ccda1d5456a8783aadfb16eaaf3f2c9610c28e4a5bcb6ad880cde5183c82f7f116d5ccfc2310502439d33f14b6888b48a + languageName: node + linkType: hard + +"@webassemblyjs/helper-numbers@npm:1.11.6": + version: 1.11.6 + resolution: "@webassemblyjs/helper-numbers@npm:1.11.6" dependencies: "@webassemblyjs/floating-point-hex-parser": "npm:1.11.6" "@webassemblyjs/helper-api-error": "npm:1.11.6" @@ -8049,6 +10667,18 @@ __metadata: languageName: node linkType: hard +"@webassemblyjs/helper-wasm-section@npm:1.12.1": + version: 1.12.1 + resolution: "@webassemblyjs/helper-wasm-section@npm:1.12.1" + 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resolution: "agent-base@npm:6.0.2" @@ -8298,7 +11027,7 @@ __metadata: languageName: node linkType: hard -"ajv-keywords@npm:^3.5.2": +"ajv-keywords@npm:^3.4.1, ajv-keywords@npm:^3.5.2": version: 3.5.2 resolution: "ajv-keywords@npm:3.5.2" peerDependencies: @@ -8307,6 +11036,17 @@ __metadata: languageName: node linkType: hard +"ajv-keywords@npm:^5.1.0": + version: 5.1.0 + resolution: "ajv-keywords@npm:5.1.0" + dependencies: + fast-deep-equal: "npm:^3.1.3" + peerDependencies: + ajv: ^8.8.2 + checksum: 10c0/18bec51f0171b83123ba1d8883c126e60c6f420cef885250898bf77a8d3e65e3bfb9e8564f497e30bdbe762a83e0d144a36931328616a973ee669dc74d4a9590 + languageName: node + linkType: hard + "ajv@npm:8.11.0": version: 8.11.0 resolution: "ajv@npm:8.11.0" @@ -8331,7 +11071,7 @@ __metadata: languageName: node linkType: hard -"ajv@npm:^6.12.4, ajv@npm:^6.12.5, ajv@npm:~6.12.6": +"ajv@npm:^6.12.2, ajv@npm:^6.12.4, ajv@npm:^6.12.5, ajv@npm:~6.12.6": version: 6.12.6 resolution: "ajv@npm:6.12.6" dependencies: @@ 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linkType: hard +"ansi-html-community@npm:^0.0.8": + version: 0.0.8 + resolution: "ansi-html-community@npm:0.0.8" + bin: + ansi-html: bin/ansi-html + checksum: 10c0/45d3a6f0b4f10b04fdd44bef62972e2470bfd917bf00439471fa7473d92d7cbe31369c73db863cc45dda115cb42527f39e232e9256115534b8ee5806b0caeed4 + languageName: node + linkType: hard + "ansi-regex@npm:^5.0.1": version: 5.0.1 resolution: "ansi-regex@npm:5.0.1" @@ -8563,7 +11358,7 @@ __metadata: languageName: node linkType: hard -"arg@npm:5.0.2, arg@npm:^5.0.2": +"arg@npm:5.0.2, arg@npm:^5.0.0, arg@npm:^5.0.2": version: 5.0.2 resolution: "arg@npm:5.0.2" checksum: 10c0/ccaf86f4e05d342af6666c569f844bec426595c567d32a8289715087825c2ca7edd8a3d204e4d2fb2aa4602e09a57d0c13ea8c9eea75aac3dbb4af5514e6800e @@ -8790,6 +11585,15 @@ __metadata: languageName: node linkType: hard +"astring@npm:^1.8.0": + version: 1.9.0 + resolution: "astring@npm:1.9.0" + bin: + astring: bin/astring + checksum: 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languageName: node + linkType: hard + "bcrypt-pbkdf@npm:^1.0.0": version: 1.0.2 resolution: "bcrypt-pbkdf@npm:1.0.2" @@ -9121,6 +12015,13 @@ __metadata: languageName: node linkType: hard +"big.js@npm:^5.2.2": + version: 5.2.2 + resolution: "big.js@npm:5.2.2" + checksum: 10c0/230520f1ff920b2d2ce3e372d77a33faa4fa60d802fe01ca4ffbc321ee06023fe9a741ac02793ee778040a16b7e497f7d60c504d1c402b8fdab6f03bb785a25f + languageName: node + linkType: hard + "bin-links@npm:^3.0.0": version: 3.0.3 resolution: "bin-links@npm:3.0.3" @@ -9247,6 +12148,23 @@ __metadata: languageName: node linkType: hard +"bonjour-service@npm:^1.0.11": + version: 1.2.1 + resolution: "bonjour-service@npm:1.2.1" + dependencies: + fast-deep-equal: "npm:^3.1.3" + multicast-dns: "npm:^7.2.5" + checksum: 10c0/953cbfc27fc9e36e6f988012993ab2244817d82426603e0390d4715639031396c932b6657b1aa4ec30dbb5fa903d6b2c7f1be3af7a8ba24165c93e987c849730 + languageName: node + linkType: hard + +"boolbase@npm:^1.0.0": + version: 1.0.0 + resolution: 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