fhirsmith 0.18.1 → 1.0.0

package/publisher/publisher.js

@@ -14,6 +14,7 @@ const folders = require('../library/folder-setup');
 const escape = require('escape-html');
 const { requireSameOrigin } = require('../library/same-origin');
 const {Utilities} = require("../library/utilities");
+const { guarded } = require('../library/sqlite-utilities');
 
 // GitHub refuses any file larger than this at the pre-receive hook, and the rejection takes down
 // the whole push rather than just the offending file.
@@ -206,19 +207,19 @@ class PublisherModule {
 
     for (const sql of tables) {
       await new Promise((resolve, reject) => {
-        this.db.run(sql, (err) => {
+        this.db.run(sql, guarded(reject, (err) => {
           if (err) {
             this.logger.error('Failed to create table:', err);
             reject(err);
           } else {
             resolve();
           }
-        });
+        }));
       });
     }
 
-    // Create default admin user if none exists
-    await this.createDefaultAdmin();
+    // the administrator, with the configured password (or a random one)
+    await this.ensureAdmin();
 
     // Schema migrations for existing databases
     await this.runMigrations();
@@ -227,100 +228,110 @@ class PublisherModule {
   async runMigrations() {
     // Add announcement column if it doesn't exist (added after initial schema)
     const columns = await new Promise((resolve, reject) => {
-      this.db.all("PRAGMA table_info(tasks)", (err, rows) => {
+      this.db.all("PRAGMA table_info(tasks)", guarded(reject, (err, rows) => {
         if (err) reject(err);
         else resolve(rows || []);
-      });
+      }));
     });
     const columnNames = columns.map(c => c.name);
     if (!columnNames.includes('announcement')) {
       await new Promise((resolve, reject) => {
-        this.db.run('ALTER TABLE tasks ADD COLUMN announcement TEXT', (err) => {
+        this.db.run('ALTER TABLE tasks ADD COLUMN announcement TEXT', guarded(reject, (err) => {
           if (err) reject(err);
           else {
             this.logger.info('Migration: added announcement column to tasks table');
             resolve();
           }
-        });
+        }));
       });
     }
     if (!columnNames.includes('publisher_version')) {
       await new Promise((resolve, reject) => {
-        this.db.run('ALTER TABLE tasks ADD COLUMN publisher_version TEXT', (err) => {
+        this.db.run('ALTER TABLE tasks ADD COLUMN publisher_version TEXT', guarded(reject, (err) => {
           if (err) reject(err);
           else {
             this.logger.info('Migration: added publisher_version column to tasks table');
             resolve();
           }
-        });
+        }));
       });
     }
     if (!columnNames.includes('release_url')) {
       await new Promise((resolve, reject) => {
-        this.db.run('ALTER TABLE tasks ADD COLUMN release_url TEXT', (err) => {
+        this.db.run('ALTER TABLE tasks ADD COLUMN release_url TEXT', guarded(reject, (err) => {
           if (err) reject(err);
           else {
             this.logger.info('Migration: added release_url column to tasks table');
             resolve();
           }
-        });
+        }));
       });
     }
     const websiteColumns = await new Promise((resolve, reject) => {
-      this.db.all("PRAGMA table_info(websites)", (err, rows) => {
+      this.db.all("PRAGMA table_info(websites)", guarded(reject, (err, rows) => {
         if (err) reject(err);
         else resolve(rows || []);
-      });
+      }));
     });
     const websiteColumnNames = websiteColumns.map(c => c.name);
     if (!websiteColumnNames.includes('git_root')) {
       await new Promise((resolve, reject) => {
-        this.db.run('ALTER TABLE websites ADD COLUMN git_root TEXT', (err) => {
+        this.db.run('ALTER TABLE websites ADD COLUMN git_root TEXT', guarded(reject, (err) => {
           if (err) reject(err);
           else {
             this.logger.info('Migration: added git_root column to websites table');
             resolve();
           }
-        });
+        }));
       });
     }
   }
 
-  async createDefaultAdmin() {
-    return new Promise((resolve, reject) => {
-      this.db.get('SELECT COUNT(*) as count FROM users WHERE is_admin = 1', (err, row) => {
-        if (err) {
-          reject(err);
-          return;
-        }
-
-        if (row.count === 0) {
-          const defaultPassword = 'admin123'; // Change this!
-          bcrypt.hash(defaultPassword, 10, (err, hash) => {
-            if (err) {
-              reject(err);
-              return;
-            }
+  /**
+   * The administrator, login 'admin'. Its password is the config's adminPassword, set (or reset)
+   * at every start, so changing the config changes it. With no adminPassword, an 'admin' that
+   * doesn't exist yet (and no other administrator) - or that still has the old fixed default
+   * password, admin123 - gets a random password (a UUID), which is logged: set adminPassword to
+   * choose it. There is no page to change a password
+   */
+  async ensureAdmin() {
+    const get = (sql, params = []) => new Promise((resolve, reject) =>
+      this.db.get(sql, params, guarded(reject, (err, row) => err ? reject(err) : resolve(row))));
+    const run = (sql, params = []) => new Promise((resolve, reject) =>
+      this.db.run(sql, params, guarded(reject, (err) => err ? reject(err) : resolve())));
+    const setPassword = async (admin, password) => {
+      const hash = await bcrypt.hash(password, 10);
+      if (admin) {
+        await run('UPDATE users SET password_hash = ?, is_admin = 1 WHERE id = ?', [hash, admin.id]);
+      } else {
+        await run('INSERT INTO users (name, login, password_hash, is_admin) VALUES (?, ?, ?, ?)',
+          ['Administrator', 'admin', hash, 1]);
+      }
+    };
 
-            this.db.run(
-                'INSERT INTO users (name, login, password_hash, is_admin) VALUES (?, ?, ?, ?)',
-                ['Administrator', 'admin', hash, 1],
-                (err) => {
-                  if (err) {
-                    this.logger.error('Failed to create default admin:', err);
-                    reject(err);
-                  } else {
-                    this.logger.warn('Created default admin user - login: admin, password: admin123 - CHANGE THIS!');
-                    resolve();
-                  }
-                }
-            );
-          });
-        } else {
-          resolve();
-        }
-      });
-    });
+    const configured = typeof this.config.adminPassword === 'string' && this.config.adminPassword.trim() !== ''
+      ? this.config.adminPassword : null;
+    const admin = await get("SELECT id, password_hash FROM users WHERE login = 'admin'");
+    if (configured) {
+      if (!admin || !(await bcrypt.compare(configured, admin.password_hash))) {
+        await setPassword(admin, configured);
+        this.logger.info(`Administrator 'admin': password ${admin ? 'changed to' : 'set from'} the configured adminPassword`);
+      }
+      return;
+    }
+    if (!admin) {
+      const others = await get('SELECT COUNT(*) as count FROM users WHERE is_admin = 1');
+      if (others.count > 0) {
+        return;
+      }
+      const password = crypto.randomUUID();
+      await setPassword(null, password);
+      this.logger.warn(`Created administrator - login: admin, password: ${password}. Set adminPassword in the publisher config to choose the password`);
+    } else if (await bcrypt.compare('admin123', admin.password_hash)) {
+      const password = crypto.randomUUID();
+      await setPassword(admin, password);
+      this.logger.warn(`Administrator 'admin' had the old default password (admin123); it is now ${password}. Set adminPassword in the publisher config to choose the password`);
+    }
   }
 
   setupRoutes() {
@@ -485,10 +496,10 @@ class PublisherModule {
       this.db.get(
           'SELECT * FROM tasks WHERE status = ? ORDER BY queued_at ASC LIMIT 1',
           ['queued'],
-          (err, row) => {
+          guarded(reject, (err, row) => {
             if (err) reject(err);
             else resolve(row);
-          }
+          })
       );
     });
   }
@@ -498,10 +509,10 @@ class PublisherModule {
       this.db.get(
           'SELECT * FROM tasks WHERE status = ? ORDER BY publishing_at ASC LIMIT 1',
           ['publishing'],
-          (err, row) => {
+          guarded(reject, (err, row) => {
             if (err) reject(err);
             else resolve(row);
-          }
+          })
       );
     });
   }
@@ -536,10 +547,10 @@ class PublisherModule {
       this.db.run(
           'UPDATE tasks SET ' + fields.join(', ') + ' WHERE id = ?',
           values,
-          (err) => {
+          guarded(reject, (err) => {
             if (err) reject(err);
             else resolve();
-          }
+          })
       );
     });
   }
@@ -558,20 +569,20 @@ class PublisherModule {
       this.db.run(
           'UPDATE tasks SET ' + assignments.join(', ') + ' WHERE id = ?',
           values,
-          (err) => {
+          guarded(reject, (err) => {
             if (err) reject(err);
             else resolve();
-          }
+          })
       );
     });
   }
 
   async logTaskMessage(taskId, level, message) {
-    return new Promise((resolve) => {
+    return new Promise((resolve, reject) => {
       this.db.run(
           'INSERT INTO task_logs (task_id, level, message) VALUES (?, ?, ?)',
           [taskId.toString(), level, message],
-          () => resolve() // Don't fail if logging fails
+          guarded(reject, () => resolve()) // Don't fail if logging fails
       );
     });
   }
@@ -1629,10 +1640,10 @@ class PublisherModule {
           this.db.get(
               'SELECT * FROM users WHERE login = ?',
               [login],
-              (err, row) => {
+              guarded(reject, (err, row) => {
                 if (err) reject(err);
                 else resolve(row);
-              }
+              })
           );
         });
 
@@ -1874,10 +1885,10 @@ class PublisherModule {
           this.db.run(
               'INSERT INTO tasks (user_id, website_id, github_org, github_repo, git_branch, npm_package_id, version) VALUES (?, ?, ?, ?, ?, ?, ?)',
               [req.session.userId, website_id, github_org, github_repo, git_branch, npm_package_id, version],
-              function (err) {
+              guarded(reject, function (err) {
                 if (err) reject(err);
                 else resolve(this.lastID);
-              }
+              })
           );
         });
 
@@ -1924,10 +1935,10 @@ class PublisherModule {
           this.db.run(
               'UPDATE tasks SET status = ?, approved_by = ?, publishing_at = CURRENT_TIMESTAMP WHERE id = ?',
               ['publishing', req.session.userId, taskId],
-              (err) => {
+              guarded(reject, (err) => {
                 if (err) reject(err);
                 else resolve();
-              }
+              })
           );
         });
 
@@ -1985,18 +1996,18 @@ class PublisherModule {
 
         // Delete task logs
         await new Promise((resolve, reject) => {
-          this.db.run('DELETE FROM task_logs WHERE task_id = ?', [taskId.toString()], (err) => {
+          this.db.run('DELETE FROM task_logs WHERE task_id = ?', [taskId.toString()], guarded(reject, (err) => {
             if (err) reject(err);
             else resolve();
-          });
+          }));
         });
 
         // Delete task record
         await new Promise((resolve, reject) => {
-          this.db.run('DELETE FROM tasks WHERE id = ?', [taskId], (err) => {
+          this.db.run('DELETE FROM tasks WHERE id = ?', [taskId], guarded(reject, (err) => {
             if (err) reject(err);
             else resolve();
-          });
+          }));
         });
 
         this.logUserAction(req.session.userId, 'delete_task', taskId, req.ip);
@@ -2027,7 +2038,7 @@ class PublisherModule {
           this.db.run(
               'INSERT INTO tasks (user_id, website_id, github_org, github_repo, git_branch, npm_package_id, version) VALUES (?, ?, ?, ?, ?, ?, ?)',
               [req.session.userId, task.website_id, task.github_org, task.github_repo, task.git_branch, task.npm_package_id, task.version],
-              function (err) { if (err) reject(err); else resolve(this.lastID); }
+              guarded(reject, function (err) { if (err) reject(err); else resolve(this.lastID); })
           );
         });
         this.logUserAction(req.session.userId, 'retry_task', newTaskId.toString(), req.ip);
@@ -2451,7 +2462,7 @@ class PublisherModule {
         this.db.run(
             'UPDATE websites SET name=?, local_folder=?,  git_root = ?, history_templates=?, web_templates=?, server_update_script=?, is_active=? WHERE id=?',
             [name, local_folder,  git_root, history_templates, web_templates, server_update_script, is_active === '1' ? 1 : 0, websiteId],
-            (err) => err ? reject(err) : resolve()
+            guarded(reject, (err) => err ? reject(err) : resolve())
         );
       });
 
@@ -2572,10 +2583,10 @@ class PublisherModule {
           this.db.run(
               'INSERT INTO websites (name, local_folder,  git_root, history_templates, web_templates, server_update_script) VALUES (?, ?, ?, ?, ?, ?)',
               [name, local_folder, git_root, history_templates, web_templates, server_update_script],
-              function (err) {
+              guarded(reject, function (err) {
                 if (err) reject(err);
                 else resolve();
-              }
+              })
           );
         });
 
@@ -2716,10 +2727,10 @@ class PublisherModule {
           this.db.run(
               'INSERT INTO users (name, login, password_hash, is_admin) VALUES (?, ?, ?, ?)',
               [name, login, passwordHash, is_admin ? 1 : 0],
-              function (err) {
+              guarded(reject, function (err) {
                 if (err) reject(err);
                 else resolve();
-              }
+              })
           );
         });
 
@@ -2750,10 +2761,10 @@ class PublisherModule {
 
         // Clear existing permissions
         await new Promise((resolve, reject) => {
-          this.db.run('DELETE FROM user_website_permissions WHERE user_id = ?', [user_id], (err) => {
+          this.db.run('DELETE FROM user_website_permissions WHERE user_id = ?', [user_id], guarded(reject, (err) => {
             if (err) reject(err);
             else resolve();
-          });
+          }));
         });
 
         // Add new permissions
@@ -2766,10 +2777,10 @@ class PublisherModule {
               this.db.run(
                   'INSERT INTO user_website_permissions (user_id, website_id, can_queue, can_approve) VALUES (?, ?, ?, ?)',
                   [user_id, website.id, canQueue ? 1 : 0, canApprove ? 1 : 0],
-                  (err) => {
+                  guarded(reject, (err) => {
                     if (err) reject(err);
                     else resolve();
-                  }
+                  })
               );
             });
           }
@@ -2795,10 +2806,10 @@ class PublisherModule {
         sql += ' LIMIT ' + limit;
       }
 
-      this.db.all(sql, (err, rows) => {
+      this.db.all(sql, guarded(reject, (err, rows) => {
         if (err) reject(err);
         else resolve(rows || []);
-      });
+      }));
     });
   }
 
@@ -2807,10 +2818,10 @@ class PublisherModule {
       this.db.get(
           'SELECT t.*, u.name as user_name, u.login as user_login, w.name as website_name, approver.name as approved_by_name FROM tasks t JOIN users u ON t.user_id = u.id JOIN websites w ON t.website_id = w.id LEFT JOIN users approver ON t.approved_by = approver.id WHERE t.id = ?',
           [taskId],
-          (err, row) => {
+          guarded(reject, (err, row) => {
             if (err) reject(err);
             else resolve(row);
-          }
+          })
       );
     });
   }
@@ -2820,10 +2831,10 @@ class PublisherModule {
       this.db.all(
           'SELECT * FROM task_logs WHERE task_id = ? ORDER BY timestamp ASC',
           [taskId.toString()],
-          (err, rows) => {
+          guarded(reject, (err, rows) => {
             if (err) reject(err);
             else resolve(rows || []);
-          }
+          })
       );
     });
   }
@@ -2833,10 +2844,10 @@ class PublisherModule {
       this.db.all(
           'SELECT ua.*, u.name as user_name, u.login as user_login FROM user_actions ua LEFT JOIN users u ON ua.user_id = u.id WHERE ua.target_id = ? ORDER BY ua.timestamp ASC',
           [taskId.toString()],
-          (err, rows) => {
+          guarded(reject, (err, rows) => {
             if (err) reject(err);
             else resolve(rows || []);
-          }
+          })
       );
     });
   }
@@ -2846,10 +2857,10 @@ class PublisherModule {
       this.db.all(
           'SELECT w.* FROM websites w JOIN user_website_permissions p ON w.id = p.website_id WHERE p.user_id = ? AND p.can_queue = 1 AND w.is_active = 1',
           [userId],
-          (err, rows) => {
+          guarded(reject, (err, rows) => {
             if (err) reject(err);
             else resolve(rows || []);
-          }
+          })
       );
     });
   }
@@ -2859,10 +2870,10 @@ class PublisherModule {
       this.db.get(
           'SELECT can_queue FROM user_website_permissions WHERE user_id = ? AND website_id = ?',
           [userId, websiteId],
-          (err, row) => {
+          guarded(reject, (err, row) => {
             if (err) reject(err);
             else resolve(row && row.can_queue);
-          }
+          })
       );
     });
   }
@@ -2872,10 +2883,10 @@ class PublisherModule {
       this.db.get(
           'SELECT can_approve FROM user_website_permissions WHERE user_id = ? AND website_id = ?',
           [userId, websiteId],
-          (err, row) => {
+          guarded(reject, (err, row) => {
             if (err) reject(err);
             else resolve(row && row.can_approve);
-          }
+          })
       );
     });
   }
@@ -2885,10 +2896,10 @@ class PublisherModule {
       this.db.get(
           'SELECT * FROM tasks WHERE npm_package_id = ? AND version = ? AND status NOT IN (?, ?) ORDER BY queued_at DESC LIMIT 1',
           [packageId, version, 'complete', 'failed'],
-          (err, row) => {
+          guarded(reject, (err, row) => {
             if (err) reject(err);
             else resolve(row);
-          }
+          })
       );
     });
   }
@@ -2898,29 +2909,29 @@ class PublisherModule {
       this.db.get(
           'SELECT * FROM tasks WHERE npm_package_id = ? AND version = ? ORDER BY queued_at DESC LIMIT 1',
           [packageId, version],
-          (err, row) => {
+          guarded(reject, (err, row) => {
             if (err) reject(err);
             else resolve(row);
-          }
+          })
       );
     });
   }
 
   async getWebsites() {
     return new Promise((resolve, reject) => {
-      this.db.all('SELECT * FROM websites ORDER BY name', (err, rows) => {
+      this.db.all('SELECT * FROM websites ORDER BY name', guarded(reject, (err, rows) => {
         if (err) reject(err);
         else resolve(rows || []);
-      });
+      }));
     });
   }
 
   async getWebsite(websiteId) {
     return new Promise((resolve, reject) => {
-      this.db.get('SELECT * FROM websites WHERE id = ?', [websiteId], (err, row) => {
+      this.db.get('SELECT * FROM websites WHERE id = ?', [websiteId], guarded(reject, (err, row) => {
         if (err) reject(err);
         else resolve(row);
-      });
+      }));
     });
   }
 
@@ -2967,10 +2978,10 @@ class PublisherModule {
 
   async getUsers() {
     return new Promise((resolve, reject) => {
-      this.db.all('SELECT id, name, login, is_admin, created_at FROM users ORDER BY name', (err, rows) => {
+      this.db.all('SELECT id, name, login, is_admin, created_at FROM users ORDER BY name', guarded(reject, (err, rows) => {
         if (err) reject(err);
         else resolve(rows || []);
-      });
+      }));
     });
   }
 
@@ -2979,10 +2990,10 @@ class PublisherModule {
       this.db.all(
           'SELECT * FROM user_website_permissions WHERE user_id = ?',
           [userId],
-          (err, rows) => {
+          guarded(reject, (err, rows) => {
             if (err) reject(err);
             else resolve(rows || []);
-          }
+          })
       );
     });
   }
@@ -2997,7 +3008,7 @@ class PublisherModule {
       return 'The database is not open.';
     }
     const get = (sql, params) => new Promise((resolve, reject) =>
-      this.db.get(sql, params, (err, row) => err ? reject(err) : resolve(row)));
+      this.db.get(sql, params, guarded(reject, (err, row) => err ? reject(err) : resolve(row))));
     // the timestamps are CURRENT_TIMESTAMP: UTC, 'YYYY-MM-DD HH:MM:SS'
     const utc = ms => new Date(ms).toISOString().replace('T', ' ').substring(0, 19);
     try {
@@ -3039,15 +3050,15 @@ class PublisherModule {
 
     // Close database
     if (this.db) {
-      return new Promise((resolve) => {
-        this.db.close((err) => {
+      return new Promise((resolve, reject) => {
+        this.db.close(guarded(reject, (err) => {
           if (err) {
             this.logger.error('Error closing database:', err);
           } else {
             this.logger.info('Database closed');
           }
           resolve();
-        });
+        }));
       });
     }
   }

package/publisher/readme.md

@@ -0,0 +1,75 @@
+# Publisher - publishing FHIR implementation guides
+
+The `publisher` module runs IG publications for the websites it is set up for: a user asks for
+a publication of an IG (a GitHub repository, branch, package id and version), the module builds
+it with the IG Publisher, and once an approver has looked at the draft, it publishes it into the
+website's web folder and pushes it.
+
+This module exists to run the publication service at healthintersections.com.au/publisher; it
+isn't designed for anyone else to run, though nothing stops you. It needs Java, git, SUSHI (npm)
+and a checkout of each website's web folder on the server, and push access to them.
+
+## How a publication runs
+
+1. **Request**: a logged-in user who may publish to the website creates a task: the website,
+   the GitHub org, repository and branch, and the package id and version it should produce.
+   The task is `queued`.
+2. **Draft build** (`building`): the module clones the repository into a task folder under
+   `workspaceRoot`, downloads the latest IG Publisher, updates SUSHI, runs the IG Publisher,
+   and checks that the package id and version are the ones asked for. Then the task is
+   `waiting for approval`, with its output, history and QA report on the task's pages.
+3. **Approval**: a user who may approve for the website approves it (or deletes it).
+4. **Publication** (`publishing`): the module clones the supporting repositories (the history
+   and web templates, and the IG registry), pulls the web folder, runs the IG Publisher in
+   go-publish mode, checks the result is a publication build, moves files too big for GitHub
+   out of the web folder (`large-file-archive`), commits and pushes the web folder, then the
+   IG registry. With a `github-app`, it then tags the IG source repository and makes a GitHub
+   release with a zip of the source - a failure there is only a warning.
+
+A task that fails can be retried. Only one task runs at a time.
+
+## Configuration
+
+In `config.json`, under `modules`:
+
+```json
+"publisher": {
+  "enabled": true,
+  "database": "publisher.db",
+  "sessionSecret": "a-long-random-string",
+  "adminPassword": "a-good-password",
+  "workspaceRoot": "workspaces"
+}
+```
+
+| Setting | Default | Description |
+|---|---|---|
+| `enabled` | false | Run the module, at `/publisher` |
+| `database` | - | The SQLite database (users, websites, permissions, tasks). A relative path is in the data directory's `publisher` folder |
+| `sessionSecret` | random | Signs the login session cookie. Set it: without it, a random one is made at startup (with a warning), and logins don't survive a restart |
+| `adminPassword` | random | The password of the administrator, `admin` (see [Administration](#administration)) |
+| `cookieSecure` | true | The session cookie is only sent over https. Set `false` only to run over plain http. Behind a TLS proxy, the proxy must set `X-Forwarded-Proto`, or logins seem to do nothing |
+| `workspaceRoot` | - | Where task folders (`task-{id}`) are made. A relative path is in the data directory's `publisher` folder |
+| `igPublisherTimeoutMinutes` | 60 | An IG Publisher run that takes longer is stopped, and the task fails |
+| `pollInterval` | 5000 | How often (ms) the module looks for a task to run |
+| `loginAttemptsPerWindow` | 20 | Failed logins allowed per IP address per 15 minutes |
+| `taskActionsPerMinute` | 30 | Task actions (create, approve, delete, retry) per IP address per minute |
+| `taskReadsPerMinute` | 300 | Reads of task output, history and QA pages per IP address per minute |
+| `large-file-archive` | none | Where files over GitHub's 100 MB limit are moved from the web folder, for websites whose publish setup says they are on GitHub. A relative path is in the data directory's `publisher` folder. Without it they are left in place, and the push fails |
+| `ig-registry-url` | `git@github.com:FHIR/ig-registry.git` | Where the IG registry is cloned from and pushed to. Set it to an ssh_config Host alias to push with a repository deploy key |
+| `github-app` | none | `app-id`, `private-key` (a .pem file) and `installations` (GitHub org -> installation id) for the GitHub App that tags source repositories and makes releases. Without it, that step is skipped |
+
+`config-template.json` has the same settings, with more on each.
+
+## Administration
+
+The administrator's login is `admin`, and its password is `adminPassword` from the config,
+set at every start - so to change it, change the config and restart. Without `adminPassword`,
+the first start gives the administrator a random password (a UUID) and logs it; set
+`adminPassword` to choose your own. There is no page to change a password.
+
+Administrators manage (at `/publisher/admin/...`):
+
+- **Websites**: each has a name, its local web folder (a git checkout), the history and web
+  templates, and a server update script.
+- **Users**, and what each may do for each website: publish (create tasks) and approve.