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Add diagrams for missing functions (#117)
* doc: flowchart documentation * doc: flowchart biotools * doc: upd flowchart citation * doc: flowchart name * doc: flowchart name opposite * doc: flowchart version * chore: remove todos
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‎docs/source/api_reference/_process_diagrams/bt2gh/citation.mmd‎

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@@ -48,15 +48,16 @@ flowchart LR
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subgraph loop through bio.tools publications
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loop --> composing[["REF composing<br/>fetch publication metadata (EuropePMCIngestor) and transform (EuropePMCTransformer) to Publication"]]:::ref
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composing --> compose_ok{is composing successful?}
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compose_ok -->|no| loop
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compose_ok -->|no| check_done_loop{checked all bio.tools publications?}
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compose_ok -->|yes| is_preferred{is the bio.tools publication Primary?}
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is_preferred -->|no| add[append extracted publication to the publications list]
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add --> loop
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add --> check_done_loop
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check_done_loop -->|no| loop
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is_preferred -->|yes| add_preferred[append extracted publication to the primary publications list]
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add_preferred --> add
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end
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loop --> combine[["combine and deduplicate the list of (extracted) bio.tools publications and the list of GitHub publications from cff"]]
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check_done_loop -->|yes| combine[["combine and deduplicate the list of (extracted) bio.tools publications and the list of GitHub publications from cff"]]
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combine --> compose_base[["compose base top-level cff content from basic bio.tools metadata"]]
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compose_base --> keep_existing["keep existing non-empty values from cff"]

‎docs/source/api_reference/_process_diagrams/bt2gh/name.mmd‎

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---
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config:
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theme: base
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look: neo
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layout: elk
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elk:
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nodePlacementStrategy: NETWORK_SIMPLEX
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themeVariables:
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darkMode: true
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background: "#121212"
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primaryColor: "#005a7a"
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primaryBorderColor: "#121212"
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secondaryBorderColor: "#121212"
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edgeLabelBackground: transparent
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labelTextColor: "#5DD3FC"
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clusterBkg: transparent
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clusterBorder: "#5DD3FC"
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noteBkgColor: "#F47D22"
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noteBorderColor: "#F47D22"
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noteTextColor: "#fff"
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---
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flowchart LR
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classDef ref fill:#F47D22
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classDef notestyle fill:#F47D22
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classDef notestyle stroke:#F47D22
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classDef terminal fill:#1099c9
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classDef terminal stroke:#1099c9
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classDef success fill:#299967
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classDef success stroke:#299967
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start([start]):::terminal
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nochange([no issue, exit]):::terminal
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subgraph GitHub entry
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gh_name[/GitHub name/]
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end
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subgraph bio.tools entry
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bt_name[/bio.tools name/]
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bt_id[/bio.tools ID/]
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end
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start --> gh_name & bt_name & bt_id
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gh_name & bt_name & bt_id --> check_bt{is bio.tools entry None?}
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check_bt -->|yes| nochange
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check_bt -->|no| policy[["REF Policy: bio.tools ID over GitHub name but check equality by seeing if one string is a substring of another for GitHub name and bio.tools ID, for GitHub name and bio.tools name)"]]:::ref
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policy --> policy_check{does the policy decide to create an issue?}
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policy_check -->|no| nochange
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policy_check -->|yes| issue[create issue info: suggesting to update repository name from bio.tools metadata]
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issue --> return([return issue info]):::success

‎docs/source/api_reference/_process_diagrams/bt2gh/version.mmd‎

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---
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config:
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theme: base
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look: neo
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layout: elk
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elk:
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nodePlacementStrategy: NETWORK_SIMPLEX
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themeVariables:
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darkMode: true
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background: "#121212"
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primaryColor: "#005a7a"
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primaryBorderColor: "#121212"
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secondaryBorderColor: "#121212"
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edgeLabelBackground: transparent
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labelTextColor: "#5DD3FC"
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clusterBkg: transparent
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clusterBorder: "#5DD3FC"
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noteBkgColor: "#F47D22"
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noteBorderColor: "#F47D22"
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noteTextColor: "#fff"
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---
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flowchart LR
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classDef ref fill:#F47D22
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classDef notestyle fill:#F47D22
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classDef notestyle stroke:#F47D22
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classDef terminal fill:#1099c9
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classDef terminal stroke:#1099c9
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classDef success fill:#299967
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classDef success stroke:#299967
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start([start]):::terminal
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nochange([no issue, exit]):::terminal
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subgraph GitHub entry
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gh_version[/GitHub latest version tag/]
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end
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subgraph bio.tools entry
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bt_versions[/bio.tools versions/]
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end
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conflict_newer@{ shape: braces, label: "log conflict" }
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conflict_exist@{ shape: braces, label: "log conflict" }
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style conflict_newer fill:#F47D22,stroke:#F47D22
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style conflict_exist fill:#F47D22,stroke:#F47D22
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start --> gh_version & bt_versions
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gh_version & bt_versions --> check_bt{is bio.tools versions empty or None?}
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check_bt -->|yes| nochange
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check_bt -->|no| find_latest_bt[[find the latest bio.tools version]]
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find_latest_bt --> check_latest_bt{is the latest bio.tools version None?}
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check_latest_bt -->|yes| nochange
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check_latest_bt -->|no| check_latest_gh{is GitHub latest version tag None?}
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check_latest_gh -->|yes| conflict_exist
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conflict_exist --> issue_no_rel["create issue info: suggesting to create a first release to match bio.tools (latest) release"]
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issue_no_rel --> return([return issue info]):::success
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check_latest_gh -->|no| check_newer{are any of the bio.tools versions newer than GitHub latest version?}
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check_newer -->|no| nochange
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check_newer -->|yes| conflict_newer
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conflict_newer --> issue_newer["create issue info: suggesting to create a new release to match bio.tools (latest) release"]
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issue_newer --> return

‎docs/source/api_reference/_process_diagrams/gh2bt/biotools_id.mmd‎

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---
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config:
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theme: base
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look: neo
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layout: elk
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elk:
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nodePlacementStrategy: NETWORK_SIMPLEX
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themeVariables:
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darkMode: true
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background: "#121212"
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primaryColor: "#005a7a"
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primaryBorderColor: "#121212"
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secondaryBorderColor: "#121212"
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edgeLabelBackground: transparent
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labelTextColor: "#5DD3FC"
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clusterBkg: transparent
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clusterBorder: "#5DD3FC"
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noteBkgColor: "#F47D22"
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noteBorderColor: "#F47D22"
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noteTextColor: "#fff"
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---
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flowchart LR
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classDef ref fill:#F47D22
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classDef notestyle fill:#F47D22
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classDef notestyle stroke:#F47D22
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classDef terminal fill:#1099c9
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classDef terminal stroke:#1099c9
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classDef success fill:#299967
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classDef success stroke:#299967
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start([start]):::terminal
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nochange([no change, exit]):::terminal
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subgraph GitHub entry
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gh_name[/GitHub repo name/]
35+
end
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subgraph bio.tools entry
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bt_id[/bio.tools ID/]
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end
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conflict_name@{ shape: braces, label: "log conflict" }
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conflict_exist@{ shape: braces, label: "log conflict" }
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style conflict_name fill:#F47D22,stroke:#F47D22
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style conflict_exist fill:#F47D22,stroke:#F47D22
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start --> gh_name & bt_id
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gh_name & bt_id --> gh_check{is GitHub repo name None?}
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gh_check -->|yes| nochange
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gh_check -->|no| bt_contain_check{"is bio.tools ID NOT None AND bio.tools ID and GitHub name contain each other (one is a substring on another)?"}
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bt_contain_check -->|yes| nochange
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bt_contain_check -->|no| bt_not_contain_check{"is bio.tools ID NOT None AND bio.tools ID and GitHub name do NOT contain each other?"}
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bt_not_contain_check -->|yes| confliconflict_namect
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bt_not_contain_check -->|no| check_gh_in_bt[["check if the GitHub repo name already taken as a bio.tools ID (check bio.tools for existence)"]]
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conflict_name --> check_gh_in_bt
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check_gh_in_bt --> check_gh_taken{is GitHub repo name taken?}
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check_gh_taken -->|no| return_gh([return GitHub repo name]):::success
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check_gh_taken -->|yes| conflict_exist
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conflict_exist --> loop["for each number (suffix) from 1 to 99"]
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subgraph generate unique ID
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loop --> new_candidate["create a new cadidate ID by adding suffix to the GitHub name"]
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new_candidate --> check_candidaate_in_bt[["check if the candidate ID already taken as a bio.tools ID"]]
60+
check_candidaate_in_bt -->|yes| check_candidate_taken{is candidate ID taken?}
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check_candidate_taken -->|yes| check_all_nr{checked all suffixes?}
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check_all_nr -->|no| loop
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end
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check_all_nr -->|yes| return_candidate([return candidate ID]):::success
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check_candidate_taken -->|no| nochange

‎docs/source/api_reference/_process_diagrams/gh2bt/documentation.mmd‎

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---
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config:
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theme: base
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look: neo
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layout: elk
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elk:
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nodePlacementStrategy: NETWORK_SIMPLEX
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themeVariables:
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darkMode: true
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background: "#121212"
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primaryColor: "#005a7a"
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primaryBorderColor: "#121212"
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secondaryBorderColor: "#121212"
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edgeLabelBackground: transparent
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labelTextColor: "#5DD3FC"
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clusterBkg: transparent
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clusterBorder: "#5DD3FC"
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noteBkgColor: "#F47D22"
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noteBorderColor: "#F47D22"
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noteTextColor: "#fff"
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---
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flowchart LR
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classDef ref fill:#F47D22
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classDef notestyle fill:#F47D22
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classDef notestyle stroke:#F47D22
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classDef terminal fill:#1099c9
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classDef terminal stroke:#1099c9
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classDef success fill:#299967
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classDef success stroke:#299967
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start([start]):::terminal
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nochange([no change, exit]):::terminal
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subgraph GitHub entry
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gh_url[/GitHub html url/]
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gh_has_wiki[/GitHub has wiki enabled/]
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gh_coc[/GitHub code of conduct/]
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gh_pages[/GitHub pages/]
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end
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subgraph bio.tools entry
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bt_docs[/bio.tools documentations/]
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end
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start --> gh_url & gh_has_wiki & gh_coc & gh_pages & bt_docs
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gh_url & gh_has_wiki & gh_coc & gh_pages & bt_docs --> check_gh_entry{is GitHub entry None?}
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check_gh_entry -->|yes| nochange
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check_gh_entry -->|no| check_wiki_exists[[check the existense of GitHub wiki repository and build its URL]]
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subgraph map wiki
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check_wiki_exists --> check_wiki{is wiki enabled on GitHub AND does wiki repo exist?}
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check_wiki -->|yes| check_wiki_in_bt{is wiki URL already included in bio.tools documentations?}
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check_wiki_in_bt -->|no| add_wiki[add wiki URL to the bio.tools documentations, assign type General]:::success
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end
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add_wiki --> coc_check{is code of conduct configured on GitHub and has a URL?}
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check_wiki_in_bt -->|yes| coc_check
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check_wiki -->|no| coc_check
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subgraph map code of conduct
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coc_check -->|yes| check_coc_in_bt{is code of conduct URL already included in bio.tools documentations?}
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check_coc_in_bt --> |no| add_coc[add code of conduct URL to the bio.tools documentations, assign type Code of conduct]:::success
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end
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add_coc --> pages_check{is cGitHub pages configured on GitHub and has a URL?}
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check_coc_in_bt --> |yes| pages_check
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coc_check -->|no| pages_check
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subgraph map GitHub pages
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pages_check -->|yes| check_pages_in_bt{is GitHub pages URL already included in bio.tools documentations?}
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check_pages_in_bt -->|no| add_pages[add GitHub pages URL to the bio.tools documentations, assign type General]:::success
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end
67+
add_pages --> return([return updated bio.tools documentations]):::success
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check_pages_in_bt -->|yes| return
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pages_check -->|no| return

‎docs/source/api_reference/_process_diagrams/gh2bt/name.mmd‎

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---
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config:
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theme: base
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look: neo
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layout: elk
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elk:
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nodePlacementStrategy: NETWORK_SIMPLEX
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themeVariables:
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darkMode: true
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background: "#121212"
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primaryColor: "#005a7a"
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primaryBorderColor: "#121212"
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secondaryBorderColor: "#121212"
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edgeLabelBackground: transparent
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labelTextColor: "#5DD3FC"
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clusterBkg: transparent
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clusterBorder: "#5DD3FC"
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noteBkgColor: "#F47D22"
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noteBorderColor: "#F47D22"
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noteTextColor: "#fff"
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---
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flowchart LR
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classDef ref fill:#F47D22
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classDef notestyle fill:#F47D22
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classDef notestyle stroke:#F47D22
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classDef terminal fill:#1099c9
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classDef terminal stroke:#1099c9
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classDef success fill:#299967
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classDef success stroke:#299967
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start([start]):::terminal
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nochange([no change, exit]):::terminal
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subgraph GitHub entry
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gh_name[/GitHub name/]
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end
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subgraph bio.tools entry
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bt_name[/bio.tools name/]
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end
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start --> gh_name & bt_name
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gh_name & bt_name --> check_gh{is GitHub name None?}
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check_gh -->|yes| nochange
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check_gh -->|no| policy[["REF Policy: GitHub name over bio.tools name (but check equality by seeing if one string is a substring of another)"]]:::ref
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policy --> return_resolved([return resolved]):::success

‎docs/source/api_reference/diagrams.rst‎

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@@ -57,17 +57,17 @@ Map publications
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Map documentation
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~~~~~~~~~~~~~~~~~~~~
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TODO: add diagram here.
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.. mermaid:: _process_diagrams/gh2bt/documentation.mmd
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Map biotools ID
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~~~~~~~~~~~~~~~~~~
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TODO: add diagram here.
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.. mermaid:: _process_diagrams/gh2bt/biotools_id.mmd
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Map name
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~~~~~~~~~~
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TODO: add diagram here.
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.. mermaid:: _process_diagrams/gh2bt/name.mmd
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Map homepage
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~~~~~~~~~~~~~~
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Map version
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~~~~~~~~~~~~~~
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TODO: add diagram here.
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.. mermaid:: _process_diagrams/bt2gh/version.mmd
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bio.tools → GitHub mapping for pull requests
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Map name
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~~~~~~~~~~
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TODO: add diagram here.
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.. mermaid:: _process_diagrams/bt2gh/name.mmd
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Map license
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~~~~~~~~~~~~~~~~

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