From 44d83d699665ffc7b07c9fefefa81b3ae8baa475 Mon Sep 17 00:00:00 2001
From: Christopher Kittel <web@christopherkittel.eu>
Date: Sat, 23 Mar 2024 01:40:44 +0100
Subject: [PATCH 01/20] Update getChartSVG.js

---
 server/services/getChartSVG.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/server/services/getChartSVG.js b/server/services/getChartSVG.js
index dea2fe48b..7fff158c5 100644
--- a/server/services/getChartSVG.js
+++ b/server/services/getChartSVG.js
@@ -10,8 +10,8 @@ function timeout(ms) {
     const page = await browser.newPage();
     await page.setViewport({width: 1920, height: 1080})
     await page.goto(process.argv[2], {waitUntil: 'networkidle2'});
-    await timeout(3000)
+    await timeout(1000)
     await page.screenshot({path: process.argv[3], clip: { x: 0, y: 0, width: 1150, height: 1080 }});
     browser.close();
 
-})();
\ No newline at end of file
+})();

From fa92d2a91e596c029e020888286b8aff87efa388 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Sun, 28 Apr 2024 20:44:33 +0200
Subject: [PATCH 02/20] generalize dateparsing

---
 server/workers/base/requirements.txt | 1 +
 server/workers/base/src/base.py      | 4 +++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/server/workers/base/requirements.txt b/server/workers/base/requirements.txt
index 614689b2a..9d94e576a 100644
--- a/server/workers/base/requirements.txt
+++ b/server/workers/base/requirements.txt
@@ -1,6 +1,7 @@
 asn1crypto==0.24.0
 async-timeout==4.0.2
 cryptography==2.1.4
+dateparser==1.1.3
 idna==2.6
 importlib-metadata==4.8.3
 keyring==10.6.0
diff --git a/server/workers/base/src/base.py b/server/workers/base/src/base.py
index ca29ac6a2..d08b8f31d 100644
--- a/server/workers/base/src/base.py
+++ b/server/workers/base/src/base.py
@@ -12,6 +12,7 @@
 from parsers import improved_df_parsing
 
 from datetime import datetime
+import dateparser
 import sys
 
 formatter = logging.Formatter(fmt='%(asctime)s %(levelname)-8s %(message)s',
@@ -382,7 +383,8 @@ def sanitize_year(year_str):
 
     for fmt in date_formats:
         try:
-            date_time_obj = datetime.strptime(year_str, fmt)
+            #date_time_obj = datetime.strptime(year_str, fmt)
+            dateparser.parse(year_str)
             sanitized_year = year_str  # here we keep the original string
             break
         except ValueError:

From c14c0e8311d2776eaac19edf857343e78118f88a Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Sun, 3 Nov 2024 14:01:42 +0100
Subject: [PATCH 03/20] temporary logging statements

---
 .gitignore                                    |  1 +
 docker-compose.yml                            |  2 --
 local_dev/proxy/docker-compose.yml            |  2 --
 .../classes/headstart/library/APIClient.php   |  3 +++
 .../persistence/PostgresPersistence.php       |  7 ++++++-
 server/services/getLastVersion.php            |  1 +
 server/services/search.php                    |  7 ++++++-
 server/workers/persistence/src/app.py         |  2 ++
 server/workers/persistence/src/persistence.py | 19 +++++++++++++++++++
 9 files changed, 38 insertions(+), 6 deletions(-)

diff --git a/.gitignore b/.gitignore
index d70ade073..abc908e04 100644
--- a/.gitignore
+++ b/.gitignore
@@ -30,6 +30,7 @@ server/workers/tests/*.csv
 server/workers/tests/*.txt
 server/workers/tests/testutils/
 local_dev/renv/*
+local_dev/dev.env
 
 # php files
 /server/classes/headstart/vendor
diff --git a/docker-compose.yml b/docker-compose.yml
index c7c721434..0a40186f7 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,5 +1,3 @@
-version: '3.7'
-
 services:
 
   db:
diff --git a/local_dev/proxy/docker-compose.yml b/local_dev/proxy/docker-compose.yml
index aeb843da2..95bbf6f28 100644
--- a/local_dev/proxy/docker-compose.yml
+++ b/local_dev/proxy/docker-compose.yml
@@ -1,5 +1,3 @@
-version: '3.7'
-
 services:
 
   proxy:
diff --git a/server/classes/headstart/library/APIClient.php b/server/classes/headstart/library/APIClient.php
index bac1a0482..e5d9d0612 100644
--- a/server/classes/headstart/library/APIClient.php
+++ b/server/classes/headstart/library/APIClient.php
@@ -32,6 +32,7 @@ public function call_api($endpoint, $payload) {
             return $res;
         }
         catch (Exception $e) {
+            error_log("Error in APIClient: " . $e);
             $res = array("status"=>"error",
                          "httpcode"=>500,
                          "reason"=>array("unexpected data processing error"));
@@ -67,6 +68,7 @@ public function handle_api_errors($res) {
         //         $res = array("status"=>"error", reason=>array());
         //     }
         // }
+        error_log(("Trying to handle API errors: " . print_r($res, true)));
         $res["status"] = "error";
         if ($res["httpcode"] == 503) {
             $res["reason"] = array();
@@ -77,6 +79,7 @@ public function handle_api_errors($res) {
         if (count($res["reason"])==0) {
             array_push($res["reason"], "unexpected data processing error");
         }
+        error_log(("Trying to handle API errors: " . print_r($res, true)));
         return $res;
     }
 
diff --git a/server/classes/headstart/persistence/PostgresPersistence.php b/server/classes/headstart/persistence/PostgresPersistence.php
index 0f247be2d..3dacc5b23 100644
--- a/server/classes/headstart/persistence/PostgresPersistence.php
+++ b/server/classes/headstart/persistence/PostgresPersistence.php
@@ -64,14 +64,19 @@ public function getLastVersion($vis_id, $details, $context): array|bool
             "details" => $details,
             "context" => $context));
         $res = $this->api_client->call_persistence("getLastVersion", $payload);
+        error_log(message: "raw result: " . print_r($res, true));
+        error_log(message: "result http code: " . $res["httpcode"]);
         if ($res["httpcode"] != 200) {
-            $data = $res;
+            $data = $res;            
           } else {
             $data = json_decode($res["result"], true);
           }
         if ($data != "null") {
             $data = array($data);
         }
+        //hypothesis: does not return a response that search.php can recognize as failed search/request
+        error_log("raw data: " . print_r($data, true));
+        error_log("data: " . json_encode($data));
         return $data;
     }
 
diff --git a/server/services/getLastVersion.php b/server/services/getLastVersion.php
index c18be5762..314e0c76e 100644
--- a/server/services/getLastVersion.php
+++ b/server/services/getLastVersion.php
@@ -24,6 +24,7 @@
 
 
 if ($last_version != null && $last_version != "null" && $last_version != false) {
+    //this logic no longer works with the new postgres database
     echo json_encode(array("status" => "success", "last_version" => $last_version));
 } else {
     echo json_encode(array("status" => "error"));
diff --git a/server/services/search.php b/server/services/search.php
index 23808a5d3..05bbe3f5b 100644
--- a/server/services/search.php
+++ b/server/services/search.php
@@ -107,12 +107,17 @@ function search($service, $dirty_query
       $repo_name = $res["repo_name"];
       $post_params["repo_name"] = $repo_name;
       $param_types[] = "repo_name";
-      // this is not duplicate code, the $params_json needs to be updated with the addition metadata
+      // this is not duplicate code, the $params_json needs to be updated with the additional metadata
       $params_json = packParamsJSON($param_types, $post_params);
     }
 
     if($retrieve_cached_map) {
       $last_version = $persistence->getLastVersion($unique_id, false, false);
+      //todo: log output of $last_version
+      // log to docker logs
+      error_log(message: "type of last_version: " . gettype($last_version));
+      error_log(message: "raw array of last_version: " . print_r($last_version, true));
+      error_log("last_version: " . json_encode($last_version));
       if ($last_version != null && $last_version != "null" && $last_version != false) {
           echo json_encode(array("query" => $query, "id" => $unique_id, "status" => "success"));
           return;
diff --git a/server/workers/persistence/src/app.py b/server/workers/persistence/src/app.py
index 48aafba9a..ddd5c4fb5 100644
--- a/server/workers/persistence/src/app.py
+++ b/server/workers/persistence/src/app.py
@@ -55,6 +55,8 @@ def api_patches(app):
 
 
 app = Flask('v1', instance_relative_config=True)
+# add logging to docker logs
+app.logger.setLevel(logging.DEBUG)
 handler = logging.StreamHandler(sys.stdout)
 handler.setLevel(app.logger.level)
 app.wsgi_app = ProxyFix(app.wsgi_app, x_proto=1, x_port=1, x_for=1, x_host=1, x_prefix=1)
diff --git a/server/workers/persistence/src/persistence.py b/server/workers/persistence/src/persistence.py
index 8d22fb0f1..9a495a79a 100644
--- a/server/workers/persistence/src/persistence.py
+++ b/server/workers/persistence/src/persistence.py
@@ -8,6 +8,7 @@
 
 from models import Revisions, Visualizations
 from database import Session
+from sqlalchemy.exc import OperationalError
 
 
 persistence_ns = Namespace("persistence", description="OKMAps persistence operations")
@@ -252,7 +253,17 @@ def post(self, database):
             return make_response(jsonify(result),
                                  200,
                                  headers)
+        # catch database connection error
+        except OperationalError as e:
+            # also log the stack trace
+            persistence_ns.logger.error("getLastVersion: %s" % str(e), exc_info=True)
+            result = {'success': False, 'reason': ["database connection error"]}
+            headers = {'ContentType': 'application/json'}
+            return make_response(jsonify(result),
+                                 500,
+                                 headers)
         except Exception as e:
+            persistence_ns.logger.error("getLastVersion: %s" % str(e), exc_info=True)
             result = {'success': False, 'reason': [str(e)]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
@@ -290,7 +301,15 @@ def post(self, database):
             return make_response(jsonify(result),
                                  200,
                                  headers)
+        except OperationalError as e:
+            persistence_ns.logger.error("getContext: %s" % str(e), exc_info=True)
+            result = {'success': False, 'reason': ["database connection error"]}
+            headers = {'ContentType': 'application/json'}
+            return make_response(jsonify(result),
+                                 500,
+                                 headers)
         except Exception as e:
+            persistence_ns.logger.error("getContext: %s" % str(e), exc_info=True)
             result = {'success': False, 'reason': [str(e)]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),

From c688a0b07387ff05d8478a2f5fe26a4bf2e522d8 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Wed, 11 Dec 2024 20:56:10 +0100
Subject: [PATCH 04/20] logging and error handling wip

---
 server/services/search.php                    | 16 ++++++++++++----
 server/workers/api/Dockerfile                 |  1 -
 server/workers/persistence/src/persistence.py | 15 +++++++++------
 3 files changed, 21 insertions(+), 11 deletions(-)

diff --git a/server/services/search.php b/server/services/search.php
index 05bbe3f5b..8d41ac4d8 100644
--- a/server/services/search.php
+++ b/server/services/search.php
@@ -112,12 +112,20 @@ function search($service, $dirty_query
     }
 
     if($retrieve_cached_map) {
-      $last_version = $persistence->getLastVersion($unique_id, false, false);
+      $last_version = $persistence->getLastVersion($unique_id, false, false)[0];
       //todo: log output of $last_version
       // log to docker logs
-      error_log(message: "type of last_version: " . gettype($last_version));
-      error_log(message: "raw array of last_version: " . print_r($last_version, true));
-      error_log("last_version: " . json_encode($last_version));
+
+      error_log(message: "search.php: type of last_version: " . gettype($last_version));
+      error_log(message: "search.php: keys of last_version: " . print_r(array_keys($last_version), true));
+      error_log(message: "search.php: raw array of last_version: " . print_r($last_version, true));
+      error_log(message: "search.php: raw array of last_version: " . print_r($last_version["result"], true));
+      error_log("search.php: last_version: " . json_decode($last_version["result"], true));
+      // check if success-status of last_version call is false
+      if ($last_version["httpcode"] != 200) {
+        return json_encode($last_version["result"]);
+      }
+
       if ($last_version != null && $last_version != "null" && $last_version != false) {
           echo json_encode(array("query" => $query, "id" => $unique_id, "status" => "success"));
           return;
diff --git a/server/workers/api/Dockerfile b/server/workers/api/Dockerfile
index 01418d71f..d2ab2f09f 100644
--- a/server/workers/api/Dockerfile
+++ b/server/workers/api/Dockerfile
@@ -8,7 +8,6 @@ RUN apt-get install -y gcc git libpq-dev
 WORKDIR /api
 COPY workers/api/requirements.txt .
 RUN pip install --no-cache-dir -r requirements.txt
-RUN pip install git+https://github.com/python-restx/flask-restx
 COPY workers/api/src/ ./
 
 
diff --git a/server/workers/persistence/src/persistence.py b/server/workers/persistence/src/persistence.py
index 9a495a79a..14cef7bd9 100644
--- a/server/workers/persistence/src/persistence.py
+++ b/server/workers/persistence/src/persistence.py
@@ -156,6 +156,9 @@ def get_context(database, vis_id, revision_context=False):
     except TypeError:
         persistence_ns.logger.debug("get_context: Vis ID not found: %s in database %s" % (vis_id, database))
         res = [False]
+    except OperationalError as e:
+        persistence_ns.logger.error("get_context: %s" % str(e), exc_info=True)
+        res = {"status": "error", 'reason': ["database connection error"]}
     session.close()
     return res
 
@@ -197,13 +200,13 @@ def post(self, database):
             create_visualization(database,
                                  vis_id, vis_title, data,
                                  vis_clean_query, vis_query, vis_params)
-            result = {'success': True}
+            result = {'status': "success"}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
                                  200,
                                  headers)
         except Exception as e:
-            result = {'success': False, 'reason': [str(e)]}
+            result = {'status': "error", 'reason': [str(e)]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
                                  500,
@@ -222,11 +225,11 @@ def post(self, database):
             data = payload.get("data")
             # persistence_ns.logger.debug(data)
             write_revision(database, vis_id, data)
-            result = {'success': True}
+            result = {'status': "success"}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result), 200, headers)
         except Exception as e:
-            result = {'success': False, 'reason': [str(e)]}
+            result = {'status': "error", 'reason': [str(e)]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result), 500, headers)
 
@@ -257,14 +260,14 @@ def post(self, database):
         except OperationalError as e:
             # also log the stack trace
             persistence_ns.logger.error("getLastVersion: %s" % str(e), exc_info=True)
-            result = {'success': False, 'reason': ["database connection error"]}
+            result = {'status': "error", 'reason': ["database connection error"]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
                                  500,
                                  headers)
         except Exception as e:
             persistence_ns.logger.error("getLastVersion: %s" % str(e), exc_info=True)
-            result = {'success': False, 'reason': [str(e)]}
+            result = {'status': "error", 'reason': [str(e)]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
                                  500,

From e57f9f818d9f38f82504c249211e6003768c9a99 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Sun, 15 Dec 2024 20:35:25 +0100
Subject: [PATCH 05/20] database error handling bugfixes and logging

---
 .../headstart/persistence/PostgresPersistence.php    | 12 ++++++++----
 server/services/search.php                           | 12 +++++-------
 server/workers/persistence/src/persistence.py        | 10 +++++-----
 3 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/server/classes/headstart/persistence/PostgresPersistence.php b/server/classes/headstart/persistence/PostgresPersistence.php
index 3dacc5b23..dff00ac42 100644
--- a/server/classes/headstart/persistence/PostgresPersistence.php
+++ b/server/classes/headstart/persistence/PostgresPersistence.php
@@ -64,19 +64,23 @@ public function getLastVersion($vis_id, $details, $context): array|bool
             "details" => $details,
             "context" => $context));
         $res = $this->api_client->call_persistence("getLastVersion", $payload);
-        error_log(message: "raw result: " . print_r($res, true));
-        error_log(message: "result http code: " . $res["httpcode"]);
+        error_log(message: "PostgresPersistence.php: raw result: " . print_r($res, true));
+        // this sometimes looks like array("result" => "null", "httpcode" => 200)
+        error_log(message: "PostgresPersistence.php: result http code: " . $res["httpcode"]);
         if ($res["httpcode"] != 200) {
+            // we could throw here and then handle the error in the calling function, e.g. getLastVersion.php
             $data = $res;            
           } else {
+            // in case of an error with misleading http code, the result is unpacked and returned
             $data = json_decode($res["result"], true);
           }
         if ($data != "null") {
+            // this is a workaround for the case that the result is not an array
             $data = array($data);
         }
         //hypothesis: does not return a response that search.php can recognize as failed search/request
-        error_log("raw data: " . print_r($data, true));
-        error_log("data: " . json_encode($data));
+        error_log("PostgresPersistence.php: raw data: " . print_r($data, true));
+        error_log("PostgresPersistence.php: data: " . json_encode($data));
         return $data;
     }
 
diff --git a/server/services/search.php b/server/services/search.php
index 8d41ac4d8..da622f395 100644
--- a/server/services/search.php
+++ b/server/services/search.php
@@ -115,18 +115,16 @@ function search($service, $dirty_query
       $last_version = $persistence->getLastVersion($unique_id, false, false)[0];
       //todo: log output of $last_version
       // log to docker logs
-
-      error_log(message: "search.php: type of last_version: " . gettype($last_version));
-      error_log(message: "search.php: keys of last_version: " . print_r(array_keys($last_version), true));
-      error_log(message: "search.php: raw array of last_version: " . print_r($last_version, true));
-      error_log(message: "search.php: raw array of last_version: " . print_r($last_version["result"], true));
-      error_log("search.php: last_version: " . json_decode($last_version["result"], true));
+     
       // check if success-status of last_version call is false
       if ($last_version["httpcode"] != 200) {
-        return json_encode($last_version["result"]);
+        error_log("search.php: last_version call failed with http code " . $last_version["httpcode"]);
+        error_log("search.php: last_version call failed with result " . $last_version["result"]);
+        return $last_version["result"];
       }
 
       if ($last_version != null && $last_version != "null" && $last_version != false) {
+          // for example, non-existant vis_id is handled here, which looks like [False]
           echo json_encode(array("query" => $query, "id" => $unique_id, "status" => "success"));
           return;
       }
diff --git a/server/workers/persistence/src/persistence.py b/server/workers/persistence/src/persistence.py
index 14cef7bd9..0708639e7 100644
--- a/server/workers/persistence/src/persistence.py
+++ b/server/workers/persistence/src/persistence.py
@@ -128,7 +128,7 @@ def get_revision(database, vis_id, rev_id, details=False, context=False):
                 res = rev.rev_data
     except TypeError:
         persistence_ns.logger.debug("get_revision: Vis ID not found: %s in database %s" % (vis_id, database))
-        res = "null"    
+        res = "null"
     session.close()
     return res
 
@@ -156,9 +156,7 @@ def get_context(database, vis_id, revision_context=False):
     except TypeError:
         persistence_ns.logger.debug("get_context: Vis ID not found: %s in database %s" % (vis_id, database))
         res = [False]
-    except OperationalError as e:
-        persistence_ns.logger.error("get_context: %s" % str(e), exc_info=True)
-        res = {"status": "error", 'reason': ["database connection error"]}
+        # 
     session.close()
     return res
 
@@ -263,7 +261,7 @@ def post(self, database):
             result = {'status': "error", 'reason': ["database connection error"]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
-                                 500,
+                                 503,
                                  headers)
         except Exception as e:
             persistence_ns.logger.error("getLastVersion: %s" % str(e), exc_info=True)
@@ -299,12 +297,14 @@ def post(self, database):
             vis_id = payload.get('vis_id')
             revision_context = payload.get('revision_context', False)
             result = get_context(database, vis_id, revision_context)
+            # when error, then result is a list [False]
             persistence_ns.logger.debug(result)
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
                                  200,
                                  headers)
         except OperationalError as e:
+            # this is not yet working, in the sense the search flow does not react to it
             persistence_ns.logger.error("getContext: %s" % str(e), exc_info=True)
             result = {'success': False, 'reason': ["database connection error"]}
             headers = {'ContentType': 'application/json'}

From 2d270f84bc28e57d6bedc7aa9f5d55348531cc52 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Mon, 16 Dec 2024 13:51:43 +0100
Subject: [PATCH 06/20] clean up problematic changes

---
 .../persistence/PostgresPersistence.php        |  8 ++++----
 server/services/search.php                     | 14 +++++++-------
 server/workers/persistence/src/persistence.py  | 18 ++++++++++++------
 3 files changed, 23 insertions(+), 17 deletions(-)

diff --git a/server/classes/headstart/persistence/PostgresPersistence.php b/server/classes/headstart/persistence/PostgresPersistence.php
index dff00ac42..7bd67438c 100644
--- a/server/classes/headstart/persistence/PostgresPersistence.php
+++ b/server/classes/headstart/persistence/PostgresPersistence.php
@@ -64,9 +64,9 @@ public function getLastVersion($vis_id, $details, $context): array|bool
             "details" => $details,
             "context" => $context));
         $res = $this->api_client->call_persistence("getLastVersion", $payload);
-        error_log(message: "PostgresPersistence.php: raw result: " . print_r($res, true));
+        // error_log(message: "PostgresPersistence.php: raw result: " . print_r($res, true));
         // this sometimes looks like array("result" => "null", "httpcode" => 200)
-        error_log(message: "PostgresPersistence.php: result http code: " . $res["httpcode"]);
+        // error_log(message: "PostgresPersistence.php: result http code: " . $res["httpcode"]);
         if ($res["httpcode"] != 200) {
             // we could throw here and then handle the error in the calling function, e.g. getLastVersion.php
             $data = $res;            
@@ -79,8 +79,8 @@ public function getLastVersion($vis_id, $details, $context): array|bool
             $data = array($data);
         }
         //hypothesis: does not return a response that search.php can recognize as failed search/request
-        error_log("PostgresPersistence.php: raw data: " . print_r($data, true));
-        error_log("PostgresPersistence.php: data: " . json_encode($data));
+        // error_log("PostgresPersistence.php: raw data: " . print_r($data, true));
+        // error_log("PostgresPersistence.php: data: " . json_encode($data));
         return $data;
     }
 
diff --git a/server/services/search.php b/server/services/search.php
index da622f395..4fc9df002 100644
--- a/server/services/search.php
+++ b/server/services/search.php
@@ -112,7 +112,13 @@ function search($service, $dirty_query
     }
 
     if($retrieve_cached_map) {
-      $last_version = $persistence->getLastVersion($unique_id, false, false)[0];
+      $last_version = $persistence->getLastVersion($unique_id, false, false);
+      if ($last_version != null && $last_version != "null" && $last_version != false) {
+          error_log("search.php: last_version call returned " . print_r($last_version, true));
+          // for example, non-existant vis_id is handled here, which looks like [False]
+          echo json_encode(array("query" => $query, "id" => $unique_id, "status" => "success"));
+          return;
+      }
       //todo: log output of $last_version
       // log to docker logs
      
@@ -122,12 +128,6 @@ function search($service, $dirty_query
         error_log("search.php: last_version call failed with result " . $last_version["result"]);
         return $last_version["result"];
       }
-
-      if ($last_version != null && $last_version != "null" && $last_version != false) {
-          // for example, non-existant vis_id is handled here, which looks like [False]
-          echo json_encode(array("query" => $query, "id" => $unique_id, "status" => "success"));
-          return;
-      }
     }
 
     $payload = json_encode($post_params);
diff --git a/server/workers/persistence/src/persistence.py b/server/workers/persistence/src/persistence.py
index 0708639e7..7017ddb69 100644
--- a/server/workers/persistence/src/persistence.py
+++ b/server/workers/persistence/src/persistence.py
@@ -156,7 +156,6 @@ def get_context(database, vis_id, revision_context=False):
     except TypeError:
         persistence_ns.logger.debug("get_context: Vis ID not found: %s in database %s" % (vis_id, database))
         res = [False]
-        # 
     session.close()
     return res
 
@@ -198,13 +197,15 @@ def post(self, database):
             create_visualization(database,
                                  vis_id, vis_title, data,
                                  vis_clean_query, vis_query, vis_params)
-            result = {'status': "success"}
+            # result = {'status': "success"}
+            result = {'success': True}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
                                  200,
                                  headers)
         except Exception as e:
-            result = {'status': "error", 'reason': [str(e)]}
+            result = {'success': False, 'reason': [str(e)]}
+            # result = {'status': "error", 'reason': [str(e)]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
                                  500,
@@ -223,11 +224,13 @@ def post(self, database):
             data = payload.get("data")
             # persistence_ns.logger.debug(data)
             write_revision(database, vis_id, data)
-            result = {'status': "success"}
+            result = {'success': True}
+            # result = {'status': "success"}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result), 200, headers)
         except Exception as e:
-            result = {'status': "error", 'reason': [str(e)]}
+            result = {'success': False, 'reason': [str(e)]}
+            # result = {'status': "error", 'reason': [str(e)]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result), 500, headers)
 
@@ -265,7 +268,10 @@ def post(self, database):
                                  headers)
         except Exception as e:
             persistence_ns.logger.error("getLastVersion: %s" % str(e), exc_info=True)
-            result = {'status': "error", 'reason': [str(e)]}
+            # it says success because function executeSearchRequest() in search.js expects it
+            # and does an output.status === "success" check against it
+            result = {'success': False, 'reason': [str(e)]}
+            # result = {'status': "error", 'reason': [str(e)]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
                                  500,

From 91eb13b0c44dda68015831a981f5388ee0a91e6c Mon Sep 17 00:00:00 2001
From: Thomas Arrow <tom@openknowledgemaps.org>
Date: Mon, 16 Dec 2024 16:19:01 +0000
Subject: [PATCH 07/20] TomChris thoughts from 2024-12-16 working session

---
 .../classes/headstart/.phpunit.result.cache   |    1 +
 server/classes/headstart/composer.lock        | 1266 +++++++----------
 .../tests/DispatchingPersistenceTest.php      |    5 +
 .../tests/PostgresPersistenceTest.php         |   60 +
 .../successfulGetContextResponse.json         |    7 +
 ...ssfulGetContextDBHostCannotBeResolved.json |    6 +
 ...cessfulgetContextResponseVisIdNotInDB.json |    3 +
 server/services/getContext.php                |   21 +-
 8 files changed, 609 insertions(+), 760 deletions(-)
 create mode 100644 server/classes/headstart/.phpunit.result.cache
 create mode 100644 server/classes/headstart/tests/PostgresPersistenceTest.php
 create mode 100644 server/classes/headstart/tests/test_data/successfulGetContextResponse.json
 create mode 100644 server/classes/headstart/tests/test_data/unsuccessfulGetContextDBHostCannotBeResolved.json
 create mode 100644 server/classes/headstart/tests/test_data/unsuccessfulgetContextResponseVisIdNotInDB.json

diff --git a/server/classes/headstart/.phpunit.result.cache b/server/classes/headstart/.phpunit.result.cache
new file mode 100644
index 000000000..494fe2476
--- /dev/null
+++ b/server/classes/headstart/.phpunit.result.cache
@@ -0,0 +1 @@
+{"version":1,"defects":{"headstart\\tests\\DispatchingPersistenceTest::testCreateVisualizationDispatcherToOldPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testGetRevisionDispatchesToNewPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testWriteRevisionDispatchesToNewPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testExistsVisualizationDispatchesToNewPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testGetLastVersionDispatchesToOldPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testGetLastVersionDispatchesToNewPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testGetLatestRevisionsDispatchesToNewPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testCreateID":2,"headstart\\tests\\DispatchingPersistenceTest::testGetRevisionDispatchesToOldPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testWriteRevisionDispatchesToOldPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testExistsVisualizationDispatchesToOldPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testGetLatestRevisionsDispatchesToOldPersistence":2,"headstart\\tests\\DispatchingPersistenceTest::testGetContextDispatchesToOldPersistence":2,"headstart\\tests\\PostgresPersistenceTest::testCreateVisualizationDispatcherToOldPersistence":5,"headstart\\tests\\PostgresPersistenceTest::test":5,"headstart\\tests\\PostgresPersistenceTest::testThatInSuccesfulConditionsReturnsAResponseObjectWeCanHandle":5,"headstart\\tests\\PostgresPersistenceTest::testWhenDBMissingReturnsAResponseObjectWeCanHandle":5},"times":{"headstart\\tests\\DispatchingPersistenceTest::testCreateVisualizationDispatcherToOldPersistence":0,"headstart\\tests\\DispatchingPersistenceTest::testGetRevisionDispatchesToOldPersistence":0,"headstart\\tests\\DispatchingPersistenceTest::testGetRevisionDispatchesToNewPersistence":0.001,"headstart\\tests\\DispatchingPersistenceTest::testWriteRevisionDispatchesToOldPersistence":0,"headstart\\tests\\DispatchingPersistenceTest::testWriteRevisionDispatchesToNewPersistence":0,"headstart\\tests\\DispatchingPersistenceTest::testExistsVisualizationDispatchesToOldPersistence":0,"headstart\\tests\\DispatchingPersistenceTest::testExistsVisualizationDispatchesToNewPersistence":0,"headstart\\tests\\DispatchingPersistenceTest::testGetLastVersionDispatchesToOldPersistence":0.007,"headstart\\tests\\DispatchingPersistenceTest::testGetLastVersionDispatchesToNewPersistence":0,"headstart\\tests\\DispatchingPersistenceTest::testGetLatestRevisionsDispatchesToOldPersistence":0,"headstart\\tests\\DispatchingPersistenceTest::testGetLatestRevisionsDispatchesToNewPersistence":0,"headstart\\tests\\DispatchingPersistenceTest::testGetContextDispatchesToOldPersistence":0,"headstart\\tests\\DispatchingPersistenceTest::testCreateID":0,"headstart\\DbConnectionTest::testCreateVisualizationAndRetrieve":0.01,"headstart\\tests\\PostgresPersistenceTest::testCreateVisualizationDispatcherToOldPersistence":0,"headstart\\tests\\PostgresPersistenceTest::test":0.001,"headstart\\tests\\PostgresPersistenceTest::testThatInSuccesfulConditionsReturnsAResponseObjectWeCanHandle":0.003,"headstart\\tests\\PostgresPersistenceTest::testWhenDBMissingReturnsAResponseObjectWeCanHandle":0,"headstart\\tests\\PostgresPersistenceTest::testWhenVisIDNotInDBReturnsAResponseObjectWeCanHandle":0}}
\ No newline at end of file
diff --git a/server/classes/headstart/composer.lock b/server/classes/headstart/composer.lock
index b4e6480c2..407da8237 100644
--- a/server/classes/headstart/composer.lock
+++ b/server/classes/headstart/composer.lock
@@ -4,209 +4,153 @@
         "Read more about it at https://getcomposer.org/doc/01-basic-usage.md#installing-dependencies",
         "This file is @generated automatically"
     ],
-    "content-hash": "e771e925f84aadb6dcb911900c72ad94",
+    "content-hash": "a4b5d7f7252fe9b0f06c5b8ce897fb22",
     "packages": [],
     "packages-dev": [
         {
-            "name": "doctrine/deprecations",
-            "version": "v1.1.1",
+            "name": "myclabs/deep-copy",
+            "version": "1.12.1",
             "source": {
                 "type": "git",
-                "url": "https://github.com/doctrine/deprecations.git",
-                "reference": "612a3ee5ab0d5dd97b7cf3874a6efe24325efac3"
+                "url": "https://github.com/myclabs/DeepCopy.git",
+                "reference": "123267b2c49fbf30d78a7b2d333f6be754b94845"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/doctrine/deprecations/zipball/612a3ee5ab0d5dd97b7cf3874a6efe24325efac3",
-                "reference": "612a3ee5ab0d5dd97b7cf3874a6efe24325efac3",
+                "url": "https://api.github.com/repos/myclabs/DeepCopy/zipball/123267b2c49fbf30d78a7b2d333f6be754b94845",
+                "reference": "123267b2c49fbf30d78a7b2d333f6be754b94845",
                 "shasum": ""
             },
             "require": {
                 "php": "^7.1 || ^8.0"
             },
-            "require-dev": {
-                "doctrine/coding-standard": "^9",
-                "phpstan/phpstan": "1.4.10 || 1.10.15",
-                "phpstan/phpstan-phpunit": "^1.0",
-                "phpunit/phpunit": "^7.5 || ^8.5 || ^9.5",
-                "psalm/plugin-phpunit": "0.18.4",
-                "psr/log": "^1 || ^2 || ^3",
-                "vimeo/psalm": "4.30.0 || 5.12.0"
-            },
-            "suggest": {
-                "psr/log": "Allows logging deprecations via PSR-3 logger implementation"
-            },
-            "type": "library",
-            "autoload": {
-                "psr-4": {
-                    "Doctrine\\Deprecations\\": "lib/Doctrine/Deprecations"
-                }
-            },
-            "notification-url": "https://packagist.org/downloads/",
-            "license": [
-                "MIT"
-            ],
-            "description": "A small layer on top of trigger_error(E_USER_DEPRECATED) or PSR-3 logging with options to disable all deprecations or selectively for packages.",
-            "homepage": "https://www.doctrine-project.org/",
-            "support": {
-                "issues": "https://github.com/doctrine/deprecations/issues",
-                "source": "https://github.com/doctrine/deprecations/tree/v1.1.1"
-            },
-            "time": "2023-06-03T09:27:29+00:00"
-        },
-        {
-            "name": "doctrine/instantiator",
-            "version": "1.5.0",
-            "source": {
-                "type": "git",
-                "url": "https://github.com/doctrine/instantiator.git",
-                "reference": "0a0fa9780f5d4e507415a065172d26a98d02047b"
-            },
-            "dist": {
-                "type": "zip",
-                "url": "https://api.github.com/repos/doctrine/instantiator/zipball/0a0fa9780f5d4e507415a065172d26a98d02047b",
-                "reference": "0a0fa9780f5d4e507415a065172d26a98d02047b",
-                "shasum": ""
-            },
-            "require": {
-                "php": "^7.1 || ^8.0"
+            "conflict": {
+                "doctrine/collections": "<1.6.8",
+                "doctrine/common": "<2.13.3 || >=3 <3.2.2"
             },
             "require-dev": {
-                "doctrine/coding-standard": "^9 || ^11",
-                "ext-pdo": "*",
-                "ext-phar": "*",
-                "phpbench/phpbench": "^0.16 || ^1",
-                "phpstan/phpstan": "^1.4",
-                "phpstan/phpstan-phpunit": "^1",
-                "phpunit/phpunit": "^7.5 || ^8.5 || ^9.5",
-                "vimeo/psalm": "^4.30 || ^5.4"
+                "doctrine/collections": "^1.6.8",
+                "doctrine/common": "^2.13.3 || ^3.2.2",
+                "phpspec/prophecy": "^1.10",
+                "phpunit/phpunit": "^7.5.20 || ^8.5.23 || ^9.5.13"
             },
             "type": "library",
             "autoload": {
+                "files": [
+                    "src/DeepCopy/deep_copy.php"
+                ],
                 "psr-4": {
-                    "Doctrine\\Instantiator\\": "src/Doctrine/Instantiator/"
+                    "DeepCopy\\": "src/DeepCopy/"
                 }
             },
             "notification-url": "https://packagist.org/downloads/",
             "license": [
                 "MIT"
             ],
-            "authors": [
-                {
-                    "name": "Marco Pivetta",
-                    "email": "ocramius@gmail.com",
-                    "homepage": "https://ocramius.github.io/"
-                }
-            ],
-            "description": "A small, lightweight utility to instantiate objects in PHP without invoking their constructors",
-            "homepage": "https://www.doctrine-project.org/projects/instantiator.html",
+            "description": "Create deep copies (clones) of your objects",
             "keywords": [
-                "constructor",
-                "instantiate"
+                "clone",
+                "copy",
+                "duplicate",
+                "object",
+                "object graph"
             ],
             "support": {
-                "issues": "https://github.com/doctrine/instantiator/issues",
-                "source": "https://github.com/doctrine/instantiator/tree/1.5.0"
+                "issues": "https://github.com/myclabs/DeepCopy/issues",
+                "source": "https://github.com/myclabs/DeepCopy/tree/1.12.1"
             },
             "funding": [
                 {
-                    "url": "https://www.doctrine-project.org/sponsorship.html",
-                    "type": "custom"
-                },
-                {
-                    "url": "https://www.patreon.com/phpdoctrine",
-                    "type": "patreon"
-                },
-                {
-                    "url": "https://tidelift.com/funding/github/packagist/doctrine%2Finstantiator",
+                    "url": "https://tidelift.com/funding/github/packagist/myclabs/deep-copy",
                     "type": "tidelift"
                 }
             ],
-            "time": "2022-12-30T00:15:36+00:00"
+            "time": "2024-11-08T17:47:46+00:00"
         },
         {
-            "name": "myclabs/deep-copy",
-            "version": "1.11.1",
+            "name": "nikic/php-parser",
+            "version": "v5.3.1",
             "source": {
                 "type": "git",
-                "url": "https://github.com/myclabs/DeepCopy.git",
-                "reference": "7284c22080590fb39f2ffa3e9057f10a4ddd0e0c"
+                "url": "https://github.com/nikic/PHP-Parser.git",
+                "reference": "8eea230464783aa9671db8eea6f8c6ac5285794b"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/myclabs/DeepCopy/zipball/7284c22080590fb39f2ffa3e9057f10a4ddd0e0c",
-                "reference": "7284c22080590fb39f2ffa3e9057f10a4ddd0e0c",
+                "url": "https://api.github.com/repos/nikic/PHP-Parser/zipball/8eea230464783aa9671db8eea6f8c6ac5285794b",
+                "reference": "8eea230464783aa9671db8eea6f8c6ac5285794b",
                 "shasum": ""
             },
             "require": {
-                "php": "^7.1 || ^8.0"
-            },
-            "conflict": {
-                "doctrine/collections": "<1.6.8",
-                "doctrine/common": "<2.13.3 || >=3,<3.2.2"
+                "ext-ctype": "*",
+                "ext-json": "*",
+                "ext-tokenizer": "*",
+                "php": ">=7.4"
             },
             "require-dev": {
-                "doctrine/collections": "^1.6.8",
-                "doctrine/common": "^2.13.3 || ^3.2.2",
-                "phpunit/phpunit": "^7.5.20 || ^8.5.23 || ^9.5.13"
+                "ircmaxell/php-yacc": "^0.0.7",
+                "phpunit/phpunit": "^9.0"
             },
+            "bin": [
+                "bin/php-parse"
+            ],
             "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "5.0-dev"
+                }
+            },
             "autoload": {
-                "files": [
-                    "src/DeepCopy/deep_copy.php"
-                ],
                 "psr-4": {
-                    "DeepCopy\\": "src/DeepCopy/"
+                    "PhpParser\\": "lib/PhpParser"
                 }
             },
             "notification-url": "https://packagist.org/downloads/",
             "license": [
-                "MIT"
+                "BSD-3-Clause"
             ],
-            "description": "Create deep copies (clones) of your objects",
+            "authors": [
+                {
+                    "name": "Nikita Popov"
+                }
+            ],
+            "description": "A PHP parser written in PHP",
             "keywords": [
-                "clone",
-                "copy",
-                "duplicate",
-                "object",
-                "object graph"
+                "parser",
+                "php"
             ],
             "support": {
-                "issues": "https://github.com/myclabs/DeepCopy/issues",
-                "source": "https://github.com/myclabs/DeepCopy/tree/1.11.1"
+                "issues": "https://github.com/nikic/PHP-Parser/issues",
+                "source": "https://github.com/nikic/PHP-Parser/tree/v5.3.1"
             },
-            "funding": [
-                {
-                    "url": "https://tidelift.com/funding/github/packagist/myclabs/deep-copy",
-                    "type": "tidelift"
-                }
-            ],
-            "time": "2023-03-08T13:26:56+00:00"
+            "time": "2024-10-08T18:51:32+00:00"
         },
         {
             "name": "phar-io/manifest",
-            "version": "1.0.3",
+            "version": "2.0.4",
             "source": {
                 "type": "git",
                 "url": "https://github.com/phar-io/manifest.git",
-                "reference": "7761fcacf03b4d4f16e7ccb606d4879ca431fcf4"
+                "reference": "54750ef60c58e43759730615a392c31c80e23176"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/phar-io/manifest/zipball/7761fcacf03b4d4f16e7ccb606d4879ca431fcf4",
-                "reference": "7761fcacf03b4d4f16e7ccb606d4879ca431fcf4",
+                "url": "https://api.github.com/repos/phar-io/manifest/zipball/54750ef60c58e43759730615a392c31c80e23176",
+                "reference": "54750ef60c58e43759730615a392c31c80e23176",
                 "shasum": ""
             },
             "require": {
                 "ext-dom": "*",
+                "ext-libxml": "*",
                 "ext-phar": "*",
-                "phar-io/version": "^2.0",
-                "php": "^5.6 || ^7.0"
+                "ext-xmlwriter": "*",
+                "phar-io/version": "^3.0.1",
+                "php": "^7.2 || ^8.0"
             },
             "type": "library",
             "extra": {
                 "branch-alias": {
-                    "dev-master": "1.0.x-dev"
+                    "dev-master": "2.0.x-dev"
                 }
             },
             "autoload": {
@@ -238,26 +182,32 @@
             "description": "Component for reading phar.io manifest information from a PHP Archive (PHAR)",
             "support": {
                 "issues": "https://github.com/phar-io/manifest/issues",
-                "source": "https://github.com/phar-io/manifest/tree/master"
+                "source": "https://github.com/phar-io/manifest/tree/2.0.4"
             },
-            "time": "2018-07-08T19:23:20+00:00"
+            "funding": [
+                {
+                    "url": "https://github.com/theseer",
+                    "type": "github"
+                }
+            ],
+            "time": "2024-03-03T12:33:53+00:00"
         },
         {
             "name": "phar-io/version",
-            "version": "2.0.1",
+            "version": "3.2.1",
             "source": {
                 "type": "git",
                 "url": "https://github.com/phar-io/version.git",
-                "reference": "45a2ec53a73c70ce41d55cedef9063630abaf1b6"
+                "reference": "4f7fd7836c6f332bb2933569e566a0d6c4cbed74"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/phar-io/version/zipball/45a2ec53a73c70ce41d55cedef9063630abaf1b6",
-                "reference": "45a2ec53a73c70ce41d55cedef9063630abaf1b6",
+                "url": "https://api.github.com/repos/phar-io/version/zipball/4f7fd7836c6f332bb2933569e566a0d6c4cbed74",
+                "reference": "4f7fd7836c6f332bb2933569e566a0d6c4cbed74",
                 "shasum": ""
             },
             "require": {
-                "php": "^5.6 || ^7.0"
+                "php": "^7.2 || ^8.0"
             },
             "type": "library",
             "autoload": {
@@ -288,331 +238,51 @@
             ],
             "description": "Library for handling version information and constraints",
             "support": {
-                "issues": "https://github.com/phar-io/version/issues",
-                "source": "https://github.com/phar-io/version/tree/master"
-            },
-            "time": "2018-07-08T19:19:57+00:00"
-        },
-        {
-            "name": "phpdocumentor/reflection-common",
-            "version": "2.2.0",
-            "source": {
-                "type": "git",
-                "url": "https://github.com/phpDocumentor/ReflectionCommon.git",
-                "reference": "1d01c49d4ed62f25aa84a747ad35d5a16924662b"
-            },
-            "dist": {
-                "type": "zip",
-                "url": "https://api.github.com/repos/phpDocumentor/ReflectionCommon/zipball/1d01c49d4ed62f25aa84a747ad35d5a16924662b",
-                "reference": "1d01c49d4ed62f25aa84a747ad35d5a16924662b",
-                "shasum": ""
-            },
-            "require": {
-                "php": "^7.2 || ^8.0"
-            },
-            "type": "library",
-            "extra": {
-                "branch-alias": {
-                    "dev-2.x": "2.x-dev"
-                }
-            },
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@@ -1648,13 +1448,21 @@
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+                },
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+                    "email": "whatthejeff@gmail.com"
+                },
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-            "homepage": "https://www.github.com/sebastianbergmann/resource-operations",
+            "description": "Provides functionality to recursively process PHP variables",
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-                "source": "https://github.com/sebastianbergmann/resource-operations/tree/3.0.3"
+                "issues": "https://github.com/sebastianbergmann/recursion-context/issues",
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@@ -1662,32 +1470,32 @@
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@@ -1718,29 +1526,29 @@
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@@ -1771,20 +1579,20 @@
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diff --git a/server/classes/headstart/tests/DispatchingPersistenceTest.php b/server/classes/headstart/tests/DispatchingPersistenceTest.php
index 94eb13ca0..954202bbd 100644
--- a/server/classes/headstart/tests/DispatchingPersistenceTest.php
+++ b/server/classes/headstart/tests/DispatchingPersistenceTest.php
@@ -13,6 +13,11 @@
 class DispatchingPersistenceTest extends TestCase
 {
 
+    protected function setUp(): void
+    {
+        $this->markTestIncomplete('Skipping because this is no longer used for dispatching');
+    }
+
     public function testCreateVisualizationDispatcherToOldPersistence(): void
     {
         $oldPersistence = $this->createMock(Persistence::class);
diff --git a/server/classes/headstart/tests/PostgresPersistenceTest.php b/server/classes/headstart/tests/PostgresPersistenceTest.php
new file mode 100644
index 000000000..5b345ca6a
--- /dev/null
+++ b/server/classes/headstart/tests/PostgresPersistenceTest.php
@@ -0,0 +1,60 @@
+<?php
+
+namespace headstart\tests;
+
+require_once("autoload.inc.php"); // use some autoloading script that was already present
+
+
+use headstart\persistence\Persistence;
+use headstart\persistence\PostgresPersistence;
+use headstart\library\APIClient;
+use PHPUnit\Framework\TestCase;
+
+/**
+ * @covers \headstart\persistence\PostgresPersistence
+ */
+class PostgresPersistenceTest extends TestCase
+{
+    public function testThatInSuccesfulConditionsReturnsAResponseObjectWeCanHandle(): void {
+        $apiclient = $this->createMock(APIClient::class);
+        $jsonFilePath = __DIR__ . "/test_data/successfulGetContextResponse.json";
+        $jsonStringFromApi = file_get_contents($jsonFilePath); // returns string
+        $mockResponse = [
+            "result" => $jsonStringFromApi,
+            "httpcode" => 200
+        ];
+        $apiclient->method("call_persistence")->willReturn($mockResponse);
+        $persistence = new PostgresPersistence($apiclient);
+        $response = $persistence->getContext($vis_id);
+        $this->assertIsArray($response);
+    }
+
+    public function testWhenDBMissingReturnsAResponseObjectWeCanHandle(): void {
+        $apiclient = $this->createMock(APIClient::class);
+        $jsonFilePath = __DIR__ . "/test_data/unsuccessfulGetContextDBHostCannotBeResolved.json";
+        $jsonStringFromApi = file_get_contents($jsonFilePath); // returns string
+        $mockResponse = [
+            "result" => $jsonStringFromApi,
+            "httpcode" => 503
+        ];
+        $apiclient->method("call_persistence")->willReturn($mockResponse);
+        $persistence = new PostgresPersistence($apiclient);
+        $response = $persistence->getContext($vis_id);
+        var_dump($response);
+        $this->assertIsArray($response);
+    }
+
+    public function testWhenVisIDNotInDBReturnsAResponseObjectWeCanHandle(): void {
+        $apiclient = $this->createMock(APIClient::class);
+        $jsonFilePath = __DIR__ . "/test_data/unsuccessfulgetContextResponseVisIdNotInDB.json";
+        $jsonStringFromApi = file_get_contents($jsonFilePath); // returns string
+        $mockResponse = [
+            "result" => $jsonStringFromApi,
+            "httpcode" => 200
+        ];
+        $apiclient->method("call_persistence")->willReturn($mockResponse);
+        $persistence = new PostgresPersistence($apiclient);
+        $response = $persistence->getContext($vis_id);
+        $this->assertIsArray($response);
+    }
+}
\ No newline at end of file
diff --git a/server/classes/headstart/tests/test_data/successfulGetContextResponse.json b/server/classes/headstart/tests/test_data/successfulGetContextResponse.json
new file mode 100644
index 000000000..a51a87e37
--- /dev/null
+++ b/server/classes/headstart/tests/test_data/successfulGetContextResponse.json
@@ -0,0 +1,7 @@
+{
+    "rev_timestamp": "Thu, 12 Sep 2024 10:23:47 GMT",
+    "rev_vis": "d161dba364a1e8c0468b9c74407e3575",
+    "vis_params": "{\"id\": \"d161dba364a1e8c0468b9c74407e3575\", \"query\": \"\\\\\\\"climate change\\\\\\\" and impact\", \"service\": \"base\", \"timestamp\": \"Wed, 24 Aug 2022 14:24:13 GMT\", \"params\": \"{\\\"from\\\":\\\"1665-01-01\\\",\\\"to\\\":\\\"2022-08-24\\\",\\\"document_types\\\":[\\\"121\\\"],\\\"sorting\\\":\\\"most-relevant\\\",\\\"min_descsize\\\":\\\"300\\\"}\"}",
+    "vis_query": "\\\"climate change\\\" and impact",
+    "vis_title": "base"
+  }
\ No newline at end of file
diff --git a/server/classes/headstart/tests/test_data/unsuccessfulGetContextDBHostCannotBeResolved.json b/server/classes/headstart/tests/test_data/unsuccessfulGetContextDBHostCannotBeResolved.json
new file mode 100644
index 000000000..03c1e0ac2
--- /dev/null
+++ b/server/classes/headstart/tests/test_data/unsuccessfulGetContextDBHostCannotBeResolved.json
@@ -0,0 +1,6 @@
+{
+    "reason": [
+      "database connection error"
+    ],
+    "success": false
+  }
\ No newline at end of file
diff --git a/server/classes/headstart/tests/test_data/unsuccessfulgetContextResponseVisIdNotInDB.json b/server/classes/headstart/tests/test_data/unsuccessfulgetContextResponseVisIdNotInDB.json
new file mode 100644
index 000000000..8a19cdb2f
--- /dev/null
+++ b/server/classes/headstart/tests/test_data/unsuccessfulgetContextResponseVisIdNotInDB.json
@@ -0,0 +1,3 @@
+[
+    false
+]
\ No newline at end of file
diff --git a/server/services/getContext.php b/server/services/getContext.php
index 109e19a36..91f5e722b 100644
--- a/server/services/getContext.php
+++ b/server/services/getContext.php
@@ -18,11 +18,27 @@
 $revision_context =  isset($_GET["revision_context"]) ? library\CommUtils::getParameter($_GET, "revision_context") : false;
 
 $apiclient = new headstart\library\APIClient($ini_array);
-$postgresPersistence = new \headstart\persistence\PostgresPersistence($apiclient);
-$persistence = new \headstart\persistence\DispatchingPersistence($postgresPersistence);
+$persistence = new \headstart\persistence\PostgresPersistence($apiclient);
 
+// Remove the calls to this getContext on the persistence object. Replace instead with a getContextResultBuilder that returns a result object
+// This should contain the httpStatusCode to pass to the client, the result in string form (some json encoded string) and it should never throw.
 
+
+// [thing that formats the response for the user] - [thing that parses responses from the persistence api] - [thing that makes requests to persisent api and handles the network calls etc.]
+
+// Err... why is the only caller of this having to unpack the array to take the first result? Is someone wrapping this reponse in an array unecessarily?
 $data = $persistence->getContext($vis_id)[0];
+
+/*
+It it works
+{
+  "rev_timestamp": "Thu, 12 Sep 2024 10:23:47 GMT",
+  "rev_vis": "d161dba364a1e8c0468b9c74407e3575",
+  "vis_params": "{\"id\": \"d161dba364a1e8c0468b9c74407e3575\", \"query\": \"\\\\\\\"climate change\\\\\\\" and impact\", \"service\": \"base\", \"timestamp\": \"Wed, 24 Aug 2022 14:24:13 GMT\", \"params\": \"{\\\"from\\\":\\\"1665-01-01\\\",\\\"to\\\":\\\"2022-08-24\\\",\\\"document_types\\\":[\\\"121\\\"],\\\"sorting\\\":\\\"most-relevant\\\",\\\"min_descsize\\\":\\\"300\\\"}\"}",
+  "vis_query": "\\\"climate change\\\" and impact",
+  "vis_title": "base"
+}
+*/
 $return_data = array("id" => $data["rev_vis"],
                       "query" => $data["vis_query"],
                       "service" => $data["vis_title"],
@@ -32,4 +48,5 @@
   $return_data = array_merge($return_data, $data["additional_context"]);
 }
 $jsonData = json_encode($return_data);
+// To investigate: is anyone needing the callback version of this??
 library\CommUtils::echoOrCallback($jsonData, $_GET);

From 82facbb3c8ff1e7da2aa9554d7626716a7e87322 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Tue, 17 Dec 2024 01:04:32 +0100
Subject: [PATCH 08/20] add some more comments

---
 server/services/getContext.php | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/server/services/getContext.php b/server/services/getContext.php
index 109e19a36..4e70eb558 100644
--- a/server/services/getContext.php
+++ b/server/services/getContext.php
@@ -23,6 +23,10 @@
 
 
 $data = $persistence->getContext($vis_id)[0];
+// if e.g. the db host is missing, error handling should happen here
+// we should return a JSON with an error message instead
+error_log("Data in getContext.php: " . print_r($data, true));
+// is the database connection error maybe swallowed here? No, but it is not handled either
 $return_data = array("id" => $data["rev_vis"],
                       "query" => $data["vis_query"],
                       "service" => $data["vis_title"],
@@ -32,4 +36,5 @@
   $return_data = array_merge($return_data, $data["additional_context"]);
 }
 $jsonData = json_encode($return_data);
+// in case of db host missing error, it returns HTML from the warnings, and a JSON with null values
 library\CommUtils::echoOrCallback($jsonData, $_GET);

From 07dd70cd26d28cfc05f28a5de7ec8a0a880b265f Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Tue, 17 Dec 2024 19:44:11 +0100
Subject: [PATCH 09/20] php services cleanup

---
 server/services/GSheetUpdateAvailable.php |  44 -----
 server/services/addBookmark.php           |  26 ---
 server/services/autoViper.php             | 208 ----------------------
 server/services/createHeadstart.php       | 133 --------------
 server/services/createNewGSheet.php       |  45 -----
 server/services/getBookmarks.php          |  28 ---
 server/services/getGSheetsMap.php         |  63 -------
 server/services/markProjectChanged.php    |  18 --
 server/services/removeBookmark.php        |  24 ---
 server/services/searchDOAJ.php            |  23 ---
 server/services/searchPLOS.php            |  22 ---
 server/services/searchTRIPLE.php          |  36 ----
 server/services/staticFiles.php           |  29 ---
 server/services/updateGSheetsMap.php      |  44 -----
 server/services/updateViper.php           | 186 -------------------
 server/services/writeActionToLog.php      |  26 ---
 16 files changed, 955 deletions(-)
 delete mode 100644 server/services/GSheetUpdateAvailable.php
 delete mode 100644 server/services/addBookmark.php
 delete mode 100644 server/services/autoViper.php
 delete mode 100644 server/services/createHeadstart.php
 delete mode 100644 server/services/createNewGSheet.php
 delete mode 100644 server/services/getBookmarks.php
 delete mode 100644 server/services/getGSheetsMap.php
 delete mode 100644 server/services/markProjectChanged.php
 delete mode 100644 server/services/removeBookmark.php
 delete mode 100644 server/services/searchDOAJ.php
 delete mode 100644 server/services/searchPLOS.php
 delete mode 100644 server/services/searchTRIPLE.php
 delete mode 100644 server/services/staticFiles.php
 delete mode 100644 server/services/updateGSheetsMap.php
 delete mode 100644 server/services/updateViper.php
 delete mode 100644 server/services/writeActionToLog.php

diff --git a/server/services/GSheetUpdateAvailable.php b/server/services/GSheetUpdateAvailable.php
deleted file mode 100644
index 37bdfc2af..000000000
--- a/server/services/GSheetUpdateAvailable.php
+++ /dev/null
@@ -1,44 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/Toolkit.php';
-require dirname(__FILE__) . '/../classes/headstart/persistence/SQLitePersistence.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/APIClient.php';
-use headstart\library;
-
-$INI_DIR = dirname(__FILE__) . "/../preprocessing/conf/";
-$ini_array = library\Toolkit::loadIni($INI_DIR);
-$apiclient = new \headstart\library\APIClient($ini_array);
-$persistence = new headstart\persistence\SQLitePersistence($ini_array["connection"]["sqlite_db"]);
-
-$vis_id = library\CommUtils::getParameter($_GET, "vis_id");
-$gsheet_last_updated = library\CommUtils::getParameter($_GET, "gsheet_last_updated");
-$persistence_backend = $ini_array["general"]["persistence_backend"];
-
-if ($persistence_backend == "api") {
-  $payload = json_encode(array("vis_id" => $vis_id, "details" => false, "context" => true));
-  $res = $apiclient->call_persistence("getLastVersion", $payload);
-  if ($res["httpcode"] != 200) {
-    library\CommUtils::echoOrCallback($res, $_GET);
-  } else {
-    $data = json_decode($res["result"], true);
-    $rev_data = json_decode($data["rev_data"], true);
-    $timestamp_old = $rev_data["last_update"];
-    $update_available = ($timestamp_old != $gsheet_last_updated) ? true : false;
-    $return_data = array("update_available" => $update_available);
-    $jsonData = json_encode($return_data);
-    library\CommUtils::echoOrCallback($jsonData, $_GET);
-  }
-} else {
-  $data = $persistence->getLastVersion($vis_id, $details = false, $context = true)[0];
-  $rev_data = json_decode($data["rev_data"], true);
-  $timestamp_old = $rev_data["last_update"];
-  $update_available = ($timestamp_old != $gsheet_last_updated) ? true : false;
-  $return_data = array("update_available" => $update_available);
-  $jsonData = json_encode($return_data);
-  library\CommUtils::echoOrCallback($jsonData, $_GET);
-}
-
-?>
diff --git a/server/services/addBookmark.php b/server/services/addBookmark.php
deleted file mode 100644
index ef2e68d33..000000000
--- a/server/services/addBookmark.php
+++ /dev/null
@@ -1,26 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require dirname(__FILE__) . '/../classes/headstart/personalization/DBConnectionPersonalization.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/Toolkit.php';
-
-require 'helper.php';
-
-use headstart\library;
-
-$INI_DIR = dirname(__FILE__) . "/../preprocessing/conf/";
-
-$ini_array = library\Toolkit::loadIni($INI_DIR);
-
-$user_id = library\CommUtils::getParameter($_GET, "user_id");
-$conference_id = library\CommUtils::getParameter($_GET, "content_id");
-
-$connection = new headstart\personalization\DBConnectionPersonalization($ini_array);
-$connection->establishConnection();
-$bookmarking_data = $connection->addPersonalBookmark($user_id, $conference_id);
-
-$jsonData = json_encode($bookmarking_data);
-
-library\CommUtils::echoOrCallback($jsonData, $_GET);
diff --git a/server/services/autoViper.php b/server/services/autoViper.php
deleted file mode 100644
index c04c8ad82..000000000
--- a/server/services/autoViper.php
+++ /dev/null
@@ -1,208 +0,0 @@
-<?php
-
-require 'search.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/Toolkit.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-use headstart\library;
-use headstart\persistence;
-use headstart\search;
-
-// var_dump($argv);
-
-$INI_DIR = dirname(__FILE__) . "/../preprocessing/conf/";
-$ini_array = library\Toolkit::loadIni($INI_DIR);
-
-# define options
-# vis_changed, required: true/false
-# object_ids, optional: path to csv of series of unique object IDs as given by openaire
-# funder, optional: funder ID
-# project_id, optional: project_id
-# test: flag for testing purposes
-$shortopts = "";
-$longopts = array(
-  "object_ids::",
-  "funderproject::",
-  "test::"
-);
-
-# parse options and determine action
-
-$options = getopt($shortopts, $longopts);
-$action = parseOptions($options);
-
-if ($action == 'getByObjectIDs') {
-  $object_ids = array_map('str_getcsv', file($options['object_ids']));
-  $response = getCandidatesByObjectIDs($object_ids, NULL);
-} elseif ($action == 'getByFunderProject') {
-  $funderparamslist = array_map('str_getcsv', file($options['funderproject']));
-  $responses = array();
-  foreach($funderparamslist as $funderparams) {
-    $responses[] = getProjectsbyFunder($funderparams);
-  };
-} else {
-  echo "No valid action.\n";
-}
-
-# main logic
-# currently defaults to getCandidates if no specific action is identified
-$filtered_project_ids = array();
-foreach($responses as $response) {
-  $parsed_response = parseProjects($response);
-  $funder = $parsed_response[0];
-  $objid2projid = $parsed_response[3];
-  $resource_counts = getResourceCounts($parsed_response);
-  $filtered_projects = filterProjects($resource_counts);
-  foreach($filtered_projects as $fp) {
-    $proj_id = $objid2projid[$fp];
-    $filtered_project_ids[$proj_id] = $funder;
-  };
-}
-
-var_dump($filtered_project_ids);
-
-
-
-
-# define functions
-
-function parseOptions($options) {
-  if (array_key_exists('object_ids', $options) and
-      !array_key_exists('funderproject', $options)) {
-    $action = "getByObjectIDs";
-  } elseif (array_key_exists('funderproject', $options) and
-            !array_key_exists('object_ids', $options)) {
-    $action = "getByFunderProject";
-  } else {
-    echo "Invalid combination of options.\n";
-    $action = NULL;
-  }
-  return $action;
-}
-
-
-function parseProjects($response) {
-  $xml = simplexml_load_string($response);
-  $namespaces = $xml->getNamespaces(true);
-  $xml->registerXPathNamespace('oaf', 'http://namespace.openaire.eu/oaf');
-  $xml->registerXPathNamespace('dri', 'http://www.driver-repository.eu/namespace/dri');
-  $xml->registerXPathNamespace('xsi', 'http://www.w3.org/2001/XMLSchema-instance');
-  $projects = $xml->xpath("//result//oaf:project");
-  $project_ids = $xml->xpath("//code");
-  $funders = $xml->xpath("//fundingtree/funder/shortname");
-  $funderstr = array();
-  foreach($funders as $f) {
-    $funderstr[] = (string)$f;
-  }
-  $obj_ids = $xml->xpath("//header//dri:objIdentifier");
-  $obj_idstr = array();
-  foreach($obj_ids as $obj_id) {
-    $obj_idstr[] = (string)$obj_id;
-  }
-  $proj_idstr = array();
-  foreach($project_ids as $proj_id) {
-    $proj_idstr[] = (string)$proj_id;
-  }
-  $parsed_projects = array_combine($proj_idstr, $funderstr);
-  $projid2objid = array_combine($proj_idstr, $obj_idstr);
-  $objid2projid = array_combine($obj_idstr, $proj_idstr);
-  return array($funderstr[0], $parsed_projects, $projid2objid, $objid2projid);
-}
-
-function filterProjects($resource_counts) {
-  $filtered_projects = array();
-  foreach($resource_counts as $obj_id => $rc) {
-    if ($rc["publications"] + $rc["datasets"] > 0) {
-      $filtered_projects[] = $obj_id;
-    }
-  }
-  return $filtered_projects;
-}
-
-function getProjectsbyFunder($funderparams) {
-  $funder = $funderparams[0];
-  $startYear = $funderparams[1];
-  $endYear = $funderparams[2];
-  $participantCountries = $funderparams[3];
-  $participantAcronyms = $funderparams[4];
-
-  $url = 'http://api.openaire.eu/search/projects?format=xml'
-      . "&funder=" . $funder
-      . "&size=" . "1000"
-      . "&startYear=" . $startYear
-      . "&endYear=" . $endYear;
-  if ($participantCountries) {
-    $url = $url . "&participantCountries=" . $participantCountries;
-  }
-  if ($participantAcronyms) {
-    $url = $url . "&participantAcronyms=" . $participantAcronyms;
-  }
-  $ch = curl_init();
-
-  curl_setopt_array($ch, array(
-      CURLOPT_RETURNTRANSFER => 1,
-      CURLOPT_URL => $url
-  ));
-
-  $response = curl_exec($ch);
-  return $response;
-}
-
-
-# functions for getting resources
-
-function createAndAddMultiHandle($url, &$multi_array, &$mh, $id) {
-  $multi_array[$id] = curl_init();
-  curl_setopt($multi_array[$id], CURLOPT_URL, $url);
-  curl_setopt($multi_array[$id], CURLOPT_RETURNTRANSFER, 1);
-  curl_multi_add_handle($mh, $multi_array[$id]);
-}
-
-function getResourceCounts($parsed_response) {
-  $parsed_projects = $parsed_response[1];
-  $projid2objid = $parsed_response[2];
-  $multi_array = array();
-  $results = array();
-  $mh = curl_multi_init();
-  foreach ($parsed_projects as $project_id => $funder) {
-    $url_publications = "http://api.openaire.eu/search/publications?projectID="
-            . urlencode($project_id)
-            . "&funder=" . $funder . "&format=json&size=0";
-    $url_datasets = "http://api.openaire.eu/search/datasets?projectID="
-            . urlencode($project_id)
-            . "&funder=" . $funder . "&format=json&size=0";
-
-    $id = $projid2objid[$project_id];
-    createAndAddMultiHandle($url_publications, $multi_array, $mh, "p_" . $id);
-    createAndAddMultiHandle($url_datasets, $multi_array, $mh, "d_" . $id);
-  }
-  $index=null;
-  do {
-    curl_multi_exec($mh,$index);
-  } while($index > 0);
-
-  foreach($multi_array as $id => $ch) {
-    $results[$id] = curl_multi_getcontent($ch);
-    curl_multi_remove_handle($mh, $ch);
-  }
-
-  curl_multi_close($mh);
-
-  $return_array = array();
-
-  foreach($results as $id => $result) {
-      $prefix = substr($id, 0, 2);
-      $obj_id = substr($id, 2);
-
-      $result_array = json_decode($result, true);
-
-      if($prefix  == "p_") {
-          $return_array[$obj_id]["publications"] = $result_array["response"]["header"]["total"]["$"];
-      } else if($prefix  == "d_") {
-          $return_array[$obj_id]["datasets"] = $result_array["response"]["header"]["total"]["$"];
-      }
-  }
-  return $return_array;
-
-}
-
-?>
diff --git a/server/services/createHeadstart.php b/server/services/createHeadstart.php
deleted file mode 100644
index 8e74feb81..000000000
--- a/server/services/createHeadstart.php
+++ /dev/null
@@ -1,133 +0,0 @@
-<?php
-
-if (file_exists(dirname(__FILE__) . '/config_local.ini')) {
-    $ini_services = parse_ini_file(dirname(__FILE__) . "/config_local.ini", true);
-} else {
-    $ini_services = parse_ini_file(dirname(__FILE__) . "/config.ini", true);
-}
-
-$path = $ini_services["path_to_headstart_server"];
-
-require $path . 'classes/headstart/preprocessing/calculation/RCalculation.php';
-require $path . 'classes/headstart/preprocessing/naming/KeywordNaming.php';
-require_once $path . 'classes/headstart/library/CommUtils.php';
-require_once $path . 'classes/headstart/library/Toolkit.php';
-
-require $path . 'services/helper.php';
-
-use headstart\library;
-
-header('Content-type: application/json');
-
-$url = $_POST["url"];
-
-$ch = curl_init();
-curl_setopt($ch, CURLOPT_URL, $url);
-curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
-
-$output = curl_exec($ch);
-
-$input_json = substr($output, 2, strlen($output) - 4);
-
-$test = mb_detect_encoding($input_json);
-
-//$input_json = $test_json;
-
-$input_array = json_decode($input_json, true);
-
-$input_array = $input_array["data"];
-
-$cooc = calculateCooccurrences($input_array, "keywords");
-
-$cooc_json = json_encode($cooc);
-
-$INI_DIR = $path . "preprocessing/conf/";
-
-$ini_array = library\Toolkit::loadIni($INI_DIR);
-
-$settings = $ini_array["general"];
-
-$metadata_file = tmpfile();
-fwrite($metadata_file, json_encode($input_array, JSON_HEX_QUOT | JSON_HEX_TAG | JSON_HEX_AMP | JSON_HEX_APOS));
-$metadata_meta = stream_get_meta_data($metadata_file);
-$metadata_filename = $metadata_meta["uri"];
-
-$cooc_file = tmpfile();
-fwrite($cooc_file, $cooc_json);
-$cooc_meta = stream_get_meta_data($cooc_file);
-$cooc_filename = $cooc_meta["uri"];
-
-$calculation = new \headstart\preprocessing\calculation\RCalculation($ini_array);
-$output = $calculation->performCalculationAndReturnOutputAsJSON($metadata_filename, $cooc_filename);
-
-fclose($metadata_file);
-fclose($cooc_file);
-
-$output_json = end($output);
-
-$output_json = iconv(mb_detect_encoding($output_json), "UTF-8", $output_json);
-
-$output_json = html_entity_decode(preg_replace("/<U\+([0-9A-F]{4})>/", "&#x\\1;", $output_json), ENT_NOQUOTES, 'UTF-8');
-
-if (!library\Toolkit::isJSON($output_json)) {
-    echo "Sorry! Something went wrong - most likely we haven't found any documents matching your search term. Please <a href=\"http://" . $settings["host"] . $settings["vis_path"] . "\">go back and try again.</a>";
-//    echo $output_json;
-    return;
-}
-
-$result = json_decode($output_json, true);
-
-$naming = new \headstart\preprocessing\naming\KeywordNaming($ini_array);
-$naming->performNamingTfIdf($result, 3, "area_uri", "keywords", ",", null);
-
-echo json_encode($result);
-
-function calculateCooccurrences($array, $key) {
-    $working = array();
-    $output = array();
-
-    foreach ($array as $entry) {
-
-        $id = $entry["id"];
-        $keywords = explode(",", $entry[$key]);
-
-        array_walk($keywords, function(&$value, &$key) {
-            $value = trim($value);
-        });
-
-        $working[$id] = $keywords;
-    }
-
-
-    $row = 0;
-    $keys = array_keys($working);
-    foreach($working as $id => $keywords) {
-
-        for ($corow = $row; $corow < count($working); $corow++) {
-            $id2 = $keys[$corow];
-            $intersect = array_intersect($keywords, $working[$id2]);
-
-            if ($corow == $row) {
-                $output[] = array("id1" => $id, "id2" => $id2, "count" => count($intersect));
-            } else {
-                $output[] = array("id1" => $id, "id2" => $id2, "count" => count($intersect));
-                $output[] = array("id1" => $id2, "id2" => $id, "count" => count($intersect));
-            }
-
-            $corow++;
-        }
-
-        $row++;
-    }
-
-    return $output;
-
-}
-
-function entities_to_unicode($str) {
-    $str = html_entity_decode($str, ENT_QUOTES, 'UTF-8');
-    $str = preg_replace_callback("/(&#[0-9]+;)/", function($m) { return mb_convert_encoding($m[1], "UTF-8", "HTML-ENTITIES"); }, $str);
-    return $str;
-}
-
-?>
\ No newline at end of file
diff --git a/server/services/createNewGSheet.php b/server/services/createNewGSheet.php
deleted file mode 100644
index 9d7fc3f5b..000000000
--- a/server/services/createNewGSheet.php
+++ /dev/null
@@ -1,45 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/APIClient.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/Toolkit.php';
-use headstart\library;
-
-$INI_DIR = dirname(__FILE__) . "/../preprocessing/conf/";
-$ini_array = library\Toolkit::loadIni($INI_DIR);
-$apiclient = new \headstart\library\APIClient($ini_array);
-
-if(php_sapi_name() == 'cli') {
-    // Called from command-line, maybe cron
-    # parse options
-    $shortopts = "";
-    $longopts = array(
-      "sheet_name:",
-      "project_name:",
-      "main_curator_email:",
-      "knowledge_base_template_id:"
-    );
-    $options = getopt($shortopts, $longopts);
-    $sheet_name = $options["sheet_name"];
-    $project_name = $options["project_name"];
-    $main_curator_email = $options["main_curator_email"];
-    $knowledge_base_template_id = $options["knowledge_base_template_id"];
-} elseif(php_sapi_name() == 'apache2handler') {
-  echo "Call not accepted.";
-}
-
-$payload = json_encode(array("sheet_name" => $sheet_name,
-                             "project_name" => $project_name,
-                             "main_curator_email" => $main_curator_email,
-                             "knowledge_base_template_id" => $knowledge_base_template_id));
-$res = $apiclient->call_api("/gsheets" . "/createKnowledgebase", $payload);
-if ($res["httpcode"] != 200) {
-  echo json_encode($res);
-} else {
-  $result = json_decode($res["result"], true);
-  echo $result;
-}
-
-?>
diff --git a/server/services/getBookmarks.php b/server/services/getBookmarks.php
deleted file mode 100644
index 24fb550d0..000000000
--- a/server/services/getBookmarks.php
+++ /dev/null
@@ -1,28 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require dirname(__FILE__) . '/../classes/headstart/personalization/DBConnectionPersonalization.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/Toolkit.php';
-
-use headstart\library;
-
-$INI_DIR = dirname(__FILE__) . "/../preprocessing/conf/";
-
-$ini_array = library\Toolkit::loadIni($INI_DIR);
-
-$user_id = library\CommUtils::getParameter($_GET, "user");
-$conference_id = library\CommUtils::getParameter($_GET, "conference");
-
-$connection = new headstart\personalization\DBConnectionPersonalization($ini_array);
-$connection->establishConnection();
-$bookmarking_data = $connection->getPersonalBookmarks($user_id, $conference_id);
-$recommendation_data = $connection->getPersonalRecommendations($user_id, $conference_id);
-$bookmarking_data_all = $connection->getConferenceBookmarks($conference_id);
-
-$data = array("bookmarks" => $bookmarking_data, "recommendations" => $recommendation_data, "bookmarks_all" => $bookmarking_data_all);
-
-$jsonData = json_encode($data);
-
-library\CommUtils::echoOrCallback($jsonData, $_GET);
diff --git a/server/services/getGSheetsMap.php b/server/services/getGSheetsMap.php
deleted file mode 100644
index 896d9d356..000000000
--- a/server/services/getGSheetsMap.php
+++ /dev/null
@@ -1,63 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/Toolkit.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/APIClient.php';
-require 'search.php';
-
-use headstart\library;
-
-$INI_DIR = dirname(__FILE__) . "/../preprocessing/conf/";
-
-$ini_array = library\Toolkit::loadIni($INI_DIR);
-$apiclient = new \headstart\library\APIClient($ini_array);
-$persistence = new headstart\persistence\SQLitePersistence($ini_array["connection"]["sqlite_db"]);
-
-$vis_id = library\CommUtils::getParameter($_GET, "vis_id");
-$persistence_backend = $ini_array["general"]["persistence_backend"];
-
-if ($persistence_backend === "api") {
-  $payload = json_encode(array("vis_id" => $vis_id, "details" => false, "context" => true));
-  $res = $apiclient->call_persistence("getLastVersion", $payload);
-  if ($res["httpcode"] != 200) {
-    library\CommUtils::echoOrCallback($res, $_GET);
-  } else {
-    $data = json_decode($res["result"], true);
-    $rev_data = json_decode($data["rev_data"], true);
-    $context = array("id" => $data["rev_vis"],
-                                   "query" => $data["vis_query"],
-                                   "service" => $data["vis_title"],
-                                   "timestamp" => $data["rev_timestamp"],
-                                   "params" => $data["vis_params"],
-                                   "sheet_id" => $rev_data["sheet_id"],
-                                   "last_update" => $rev_data["last_update"]);
-    if (array_key_exists("additional_context", $rev_data)) {
-      $context = array_merge($context, $rev_data["additional_context"]);
-    }
-    $return_data = array("context" => $context,
-                         "data" => $rev_data["data"],
-                         "errors" => $rev_data["errors"]);
-    $jsonData = json_encode($return_data);
-    library\CommUtils::echoOrCallback($jsonData, $_GET);
-  }
-} else {
-  $data = $persistence->getLastVersion($vis_id, $details = false, $context = true)[0];
-  $rev_data = json_decode($data["rev_data"], true);
-  $context = array("id" => $data["rev_vis"],
-                                 "query" => $data["vis_query"],
-                                 "service" => $data["vis_title"],
-                                 "timestamp" => $data["rev_timestamp"],
-                                 "params" => $data["vis_params"],
-                                 "sheet_id" => $rev_data["sheet_id"],
-                                 "last_update" => $rev_data["last_update"]);
-  if (array_key_exists("additional_context", $rev_data)) {
-    $context = array_merge($context, $rev_data["additional_context"]);
-  }
-  $return_data = array("context" => $context,
-                       "data" => $rev_data["data"],
-                       "errors" => $rev_data["errors"]);
-  $jsonData = json_encode($return_data);
-  library\CommUtils::echoOrCallback($jsonData, $_GET);
-}
diff --git a/server/services/markProjectChanged.php b/server/services/markProjectChanged.php
deleted file mode 100644
index 391f0b13b..000000000
--- a/server/services/markProjectChanged.php
+++ /dev/null
@@ -1,18 +0,0 @@
-<?php
-header('Content-type: application/json');
-
-require dirname(__FILE__) . '/../classes/headstart/persistence/ViperUpdater.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/Toolkit.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-
-use headstart\library;
-use headstart\persistence;
-
-$INI_DIR = dirname(__FILE__) . "/../preprocessing/conf/";
-$ini_array = library\Toolkit::loadIni($INI_DIR);
-
-$vis_id = library\CommUtils::getParameter($_GET, "vis_id");
-
-$persistence = new headstart\persistence\ViperUpdater($ini_array["connection"]["sqlite_db"]);
-
-$persistence->markVisChanged($vis_id);
\ No newline at end of file
diff --git a/server/services/removeBookmark.php b/server/services/removeBookmark.php
deleted file mode 100644
index 5c3e988f8..000000000
--- a/server/services/removeBookmark.php
+++ /dev/null
@@ -1,24 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require dirname(__FILE__) . '/../classes/headstart/personalization/DBConnectionPersonalization.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/Toolkit.php';
-
-use headstart\library;
-
-$INI_DIR = dirname(__FILE__) . "/../preprocessing/conf/";
-
-$ini_array = library\Toolkit::loadIni($INI_DIR);
-
-$user_id = library\CommUtils::getParameter($_GET, "user_id");
-$conference_id = library\CommUtils::getParameter($_GET, "content_id");
-
-$connection = new headstart\personalization\DBConnectionPersonalization($ini_array);
-$connection->establishConnection();
-$bookmarking_data = $connection->removePersonalBookmark($user_id, $conference_id);
-
-$jsonData = json_encode($bookmarking_data);
-
-library\CommUtils::echoOrCallback($jsonData, $_GET);
diff --git a/server/services/searchDOAJ.php b/server/services/searchDOAJ.php
deleted file mode 100644
index b221cb9ea..000000000
--- a/server/services/searchDOAJ.php
+++ /dev/null
@@ -1,23 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-require 'search.php';
-
-use headstart\library;
-
-$dirty_query = library\CommUtils::getParameter($_POST, "q");
-$precomputed_id = (isset($_POST["unique_id"]))?($_POST["unique_id"]):(null);
-
-$post_params = $_POST;
-
-$result = search("doaj", $dirty_query
-                  , $post_params, array("from", "to", "today", "sorting")
-                  , true
-                  , true, null
-                  , $precomputed_id, false);
-
-echo $result
-
-?>
diff --git a/server/services/searchPLOS.php b/server/services/searchPLOS.php
deleted file mode 100644
index b5f9822fd..000000000
--- a/server/services/searchPLOS.php
+++ /dev/null
@@ -1,22 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-require 'search.php';
-
-use headstart\library;
-
-$dirty_query = library\CommUtils::getParameter($_POST, "q");
-$precomputed_id = (isset($_POST["unique_id"]))?($_POST["unique_id"]):(null);
-
-$post_params = $_POST;
-
-$result = search("plos", $dirty_query, $post_params
-                    , array("article_types", "journals", "from", "to", "sorting")
-                    , true, true, null
-                    , $precomputed_id, false);
-
-echo $result
-
-?>
diff --git a/server/services/searchTRIPLE.php b/server/services/searchTRIPLE.php
deleted file mode 100644
index 41a9bc58a..000000000
--- a/server/services/searchTRIPLE.php
+++ /dev/null
@@ -1,36 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-require 'search.php';
-
-use headstart\library;
-
-$dirty_query = library\CommUtils::getParameter($_POST, "q");
-$precomputed_id = (isset($_POST["unique_id"]))?($_POST["unique_id"]):(null);
-
-$post_params = $_POST;
-
-if (isset($post_params["service"]) && $post_params["service"] === "triple_km") {
-  $service_integration = $post_params["service"];
-  $post_params["vis_type"] = "overview";
-  $post_params["service"] = "triple";
-  $param_types = array("from", "to", "sorting", "language");
-}
-if (isset($post_params["service"]) && $post_params["service"] === "triple_sg") {
-  $service_integration = $post_params["service"];
-  $post_params["vis_type"] = "timeline";
-  $post_params["service"] = "triple";
-  $param_types = array("from", "to", "sorting", "language", "limit", "sg_method");
-}
-
-$result = search($service_integration, $dirty_query
-                , $post_params, $param_types
-                , true
-                , true, null
-                , $precomputed_id, true, false);
-
-echo $result
-
-?>
diff --git a/server/services/staticFiles.php b/server/services/staticFiles.php
deleted file mode 100644
index 26b6be545..000000000
--- a/server/services/staticFiles.php
+++ /dev/null
@@ -1,29 +0,0 @@
-<?php
-header('Content-type: application/json');
-
-$arr = array(
-    array(
-    	'title'=>'edu1',
-    	'file'=>"/data/educational-technology.csv"
-    	),
-    array(
-    	'title'=>'edu2',
-    	'file'=>"/data/edu2.csv"
-    	),
-    // array(
-    // 	'title'=>'edu3',
-    // 	'file'=>"/data/edu3.csv"
-    // 	),
-    // array(
-    // 	'title'=>'edu4',
-    // 	'file'=>"/data/edu4.csv"
-    // 	),
-    array(
-    	'title'=>'edu5',
-    	'file'=>"/data/edu5.csv")
-    );
-
-echo json_encode($arr);
-
-exit();
-?>
\ No newline at end of file
diff --git a/server/services/updateGSheetsMap.php b/server/services/updateGSheetsMap.php
deleted file mode 100644
index 333ffcaac..000000000
--- a/server/services/updateGSheetsMap.php
+++ /dev/null
@@ -1,44 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-require 'search.php';
-
-use headstart\library;
-
-
-if(php_sapi_name() == 'cli') {
-    // Called from command-line, maybe cron
-    # parse options
-    $shortopts = "";
-    $longopts = array(
-      "q:",
-      "sheet_id:",
-      "last_update:"
-    );
-    $options = getopt($shortopts, $longopts);
-    $dirty_query = $options["q"];
-    $sheet_id = $options["sheet_id"];
-    $last_update = $options["last_update"];
-} elseif(php_sapi_name() == 'apache2handler') {
-    // Called from the apache2 webserver upon web request
-    $dirty_query = library\CommUtils::getParameter($_GET, "q");
-    $sheet_id = library\CommUtils::getParameter($_GET, "sheet_id");
-    $last_update = isset($_GET["gsheet_last_updated"]) ? library\CommUtils::getParameter($_GET, "gsheet_last_updated") : null;
-}
-
-$params = array("q" => $dirty_query, "sheet_id" => $sheet_id, "sheet_range" => "Resources!A1:AG200");
-if(isset($last_update)) {
-    $params["last_update"] = $last_update;
-}
-
-$result = search("gsheets", $dirty_query
-                    , $params, array("sheet_id")
-                    , false
-                    , false, null
-                    , $sheet_id, false);
-
-echo $result;
-
-?>
diff --git a/server/services/updateViper.php b/server/services/updateViper.php
deleted file mode 100644
index 2a7768790..000000000
--- a/server/services/updateViper.php
+++ /dev/null
@@ -1,186 +0,0 @@
-<?php
-
-require 'search.php';
-require_once dirname(__FILE__) . '/../classes/headstart/persistence/ViperUpdater.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/Toolkit.php';
-use headstart\library;
-use headstart\persistence;
-use headstart\search;
-
-// var_dump($argv);
-
-$INI_DIR = dirname(__FILE__) . "/../preprocessing/conf/";
-$ini_array = library\Toolkit::loadIni($INI_DIR);
-
-# define options
-# vis_changed, required: true/false
-# object_ids, optional: path to csv of series of unique object IDs as given by openaire
-# funder, optional: funder ID
-# project_id, optional: project_id
-# test: flag for testing purposes
-$shortopts = "";
-$longopts = array(
-  "vis_changed:",
-  "object_ids::",
-  "funderproject::",
-  "test::"
-);
-
-# parse options and determine action
-
-$options = getopt($shortopts, $longopts);
-$action = parseOptions($options);
-if ($options['vis_changed'] == 'true') {
-  $vis_changed = true;
-} elseif ($options['vis_changed'] == 'false') {
-  $vis_changed = false;
-} else {
-  // echo "invalid argument for vis_changed\n";
-};
-
-
-
-# persistence is a SQLitePersistence class with added Viper functionalities
-if (array_key_exists('test', $options)) {
-  $persistence = new headstart\persistence\ViperUpdater('server/storage/headstart_test.sqlite');
-} else {
-  $persistence = new headstart\persistence\ViperUpdater($ini_array["connection"]["sqlite_db"]);
-}
-
-
-# main logic
-# currently defaults to getCandidates if no specific action is identified
-if ($action == 'getByObjectIDs') {
-  $object_ids = array_map('str_getcsv', file($options['object_ids']));
-  $updateCandidates = getCandidatesByObjectIDs($vis_changed, $persistence, $object_ids);
-} elseif ($action == 'getByFunderProject') {
-  $funderprojects = array_map('str_getcsv', file($options['funderproject']));
-  $updateCandidates = getCandidatesByFunderProject($vis_changed, $persistence, $funderprojects);
-} elseif ($action == 'getByFlag') {
-  $updateCandidates = getCandidates($vis_changed, $persistence);
-} else {
-  // echo "No valid action.\n";
-}
-
-runUpdates($updateCandidates, $persistence);
-
-
-
-
-# define functions
-
-function parseOptions($options) {
-  if (array_key_exists('vis_changed', $options) and
-      !array_key_exists('object_ids', $options) and
-      !array_key_exists('funderproject', $options)) {
-    $action = "getByFlag";
-  } elseif (array_key_exists('object_ids', $options) and
-      !array_key_exists('funderproject', $options)) {
-    $action = "getByObjectIDs";
-  } elseif (array_key_exists('funderproject', $options) and
-            !array_key_exists('object_ids', $options)) {
-    $action = "getByFunderProject";
-  } else {
-    // echo "Invalid combination of options.\n";
-    $action = NULL;
-  }
-  return $action;
-}
-
-function getCandidates($vis_changed, $persistence) {
-  # get candidates via DB query
-  $maps = $persistence->getUpdateMaps($vis_changed);
-  $updateCandidates = array();
-  foreach($maps as $map) {
-    $params = json_decode($map['vis_params'], true);
-    $vis_id = $map['vis_id'];
-    $updateCandidates[$vis_id]['vis_query'] = $map['vis_query'];
-    $updateCandidates[$vis_id]['vis_params'] = $params;
-    $updateCandidates[$vis_id]['vis_changed_timestamp'] = $map['vis_changed_timestamp'];
-  }
-  return $updateCandidates;
-}
-
-function getCandidatesByObjectIDs($vis_changed, $persistence, $object_ids) {
-  # get candidates via DB query
-  # object IDs needs to be a comma separated list of IDs
-  $obj_ids = array();
-  foreach($object_ids as $obj_id){
-    $obj_ids[] = $obj_id[0];
-  }
-  $maps = $persistence->getUpdateMaps($vis_changed);
-  $updateCandidates = array();
-  foreach($maps as $map) {
-    $params = json_decode($map['vis_params'], true);
-    $obj_id = $params['obj_id'];
-    if (in_array($obj_id, $obj_ids)) {
-      $vis_id = $map['vis_id'];
-      $updateCandidates[$vis_id]['vis_query'] = $map['vis_query'];
-      $updateCandidates[$vis_id]['vis_params'] = $params;
-      $updateCandidates[$vis_id]['vis_changed_timestamp'] = $map['vis_changed_timestamp'];
-    }
-  }
-  return $updateCandidates;
-}
-
-function getCandidatesByFunderProject($vis_changed, $persistence, $funderproject) {
-  # get candidates via DB query
-  $updateCandidates = array();
-  $maps = $persistence->getUpdateMaps($vis_changed);
-  foreach($funderproject as $fp){
-    foreach($maps as $map) {
-      $params = json_decode($map['vis_params'], true);
-      if ($params['funder'] == $fp[0] and $params['project_id'] == $fp[1]) {
-        $vis_id = $map['vis_id'];
-        $updateCandidates[$vis_id]['vis_query'] = $map['vis_query'];
-        $updateCandidates[$vis_id]['vis_params'] = $params;
-        $updateCandidates[$vis_id]['vis_changed_timestamp'] = $map['vis_changed_timestamp'];
-      }
-    }
-  }
-  return $updateCandidates;
-}
-
-function runUpdate($acronymtitle, $params) {
-  // echo "$acronymtitle";
-  // echo "\n";
-  $decoded_params = decodeParams($params);
-  $post_params = $decoded_params[0];
-  $param_types = $decoded_params[1];
-  $params_for_id = array("project_id", "funder");
-  $result = search("openaire", $acronymtitle,
-                                     $params, $param_types,
-                                     ";", null, false, false, $params_for_id);
-  echo $result;
-}
-
-function checkFlagAge($vis_id, $vis_changed_timestamp, $persistence) {
-  $timestamp = strtotime($vis_changed_timestamp);
-  $curtime = time();
-  if(($curtime-$timestamp) > 86400) {
-    $persistence->resetFlag($vis_id);
-  }
-}
-
-function runUpdates($updateCandidates, $persistence) {
-  foreach($updateCandidates as $vis_id => $map) {
-    $params = $map['vis_params'];
-    $acronymtitle = $map['vis_query'];
-    $vis_changed_timestamp = $map['vis_changed_timestamp'];
-    runUpdate($acronymtitle, $params);
-    checkFlagAge($vis_id, $vis_changed_timestamp, $persistence);
-    sleep(10);
-  }
-}
-
-function decodeParams($paramString) {
-  $post_params = array();
-  $param_types = array();
-  foreach($paramString as $x => $x_value) {
-    $post_params[] = $x_value;
-    $param_types[] = $x;
-  }
-  return array($post_params, $param_types);
-}
-
-?>
diff --git a/server/services/writeActionToLog.php b/server/services/writeActionToLog.php
deleted file mode 100644
index c8af689d5..000000000
--- a/server/services/writeActionToLog.php
+++ /dev/null
@@ -1,26 +0,0 @@
-<?php
-
-header('Content-type: application/json');
-
-require_once dirname(__FILE__) . '/../classes/headstart/evaluation/logger/FileLogger.php';
-require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
-
-use headstart\evaluation\logger;
-use headstart\library;
-
-$user_id = library\CommUtils::getParameter($_GET, "user");
-$serverData = array("addr"=>$_SERVER['REMOTE_ADDR'], "user_agent"=>$_SERVER['HTTP_USER_AGENT'], "user_id"=>$user_id);
-
-$logData = array_merge($serverData, $_GET);
-
-if($_POST != null)
-    $logData = array_merge($logData, $_POST);
-
-$logger = new logger\FileLogger(dirname(__FILE__) . '/../../log/', null);
-$logger->writeToLog($logData);
-
-$jsonData = json_encode($logData);
-
-library\CommUtils::echoOrCallback($jsonData, $_GET["jsoncallback"]);
-
-

From 1963fece4b7a4a5702c24e01a03ebd695d9f61ea Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Tue, 17 Dec 2024 19:45:23 +0100
Subject: [PATCH 10/20] first draft of getContextResultBuilder

---
 .../classes/headstart/library/APIClient.php   |  5 +++
 .../classes/headstart/library/CommUtils.php   |  1 +
 .../library/getContextResultBuilder.php       | 37 +++++++++++++++++++
 server/services/getContext.php                | 27 ++++++++------
 server/services/search.php                    | 21 ++++++-----
 server/workers/persistence/src/persistence.py |  5 ++-
 6 files changed, 75 insertions(+), 21 deletions(-)
 create mode 100644 server/classes/headstart/library/getContextResultBuilder.php

diff --git a/server/classes/headstart/library/APIClient.php b/server/classes/headstart/library/APIClient.php
index e5d9d0612..f3528a27d 100644
--- a/server/classes/headstart/library/APIClient.php
+++ b/server/classes/headstart/library/APIClient.php
@@ -53,6 +53,9 @@ public function call_persistence($endpoint, $payload) {
             return $res;
         }
         catch (Exception $e) {
+            // what happens here is instead of bubbling the error up,
+            // it is caught and we fake a response that looks like an error
+            // because of the hardcoded reason we loose the original error information
             $res = array("status"=>"error",
                          "httpcode"=>500,
                          "reason"=>array("unexpected data processing error"));
@@ -71,6 +74,8 @@ public function handle_api_errors($res) {
         error_log(("Trying to handle API errors: " . print_r($res, true)));
         $res["status"] = "error";
         if ($res["httpcode"] == 503) {
+            // we had a 503 for the database connection error
+            // this implementation actively suppresses the reason by resetting to an empty array
             $res["reason"] = array();
         }
         if (!array_key_exists("reason", $res)) {
diff --git a/server/classes/headstart/library/CommUtils.php b/server/classes/headstart/library/CommUtils.php
index b59fdd945..2f69b5942 100644
--- a/server/classes/headstart/library/CommUtils.php
+++ b/server/classes/headstart/library/CommUtils.php
@@ -53,6 +53,7 @@ public static function call_api($route, $payload) {
         curl_close($ch);
         $httpcode = curl_getinfo($ch, CURLINFO_HTTP_CODE);
         if ($result === false) 
+            // in this case, the curl call result is false and $result is a string with the CURL error
             $result = curl_error($ch);
         return array("result" => $result, "httpcode" => $httpcode);
     }
diff --git a/server/classes/headstart/library/getContextResultBuilder.php b/server/classes/headstart/library/getContextResultBuilder.php
new file mode 100644
index 000000000..b32f2ee8e
--- /dev/null
+++ b/server/classes/headstart/library/getContextResultBuilder.php
@@ -0,0 +1,37 @@
+<?php
+
+namespace headstart\library;
+
+/**
+ * Description of getContextResultBuilder:
+ * This class is responsible for building the context result for the services endpoints.
+ * It is a thin layer on top of the Persistence class and is used to build the context result
+ * from the database response.
+ *
+ * @author pkraker
+ */
+
+
+class getContextResultBuilder {
+
+    private $persistence;
+
+    public function __construct($persistence) {
+        $this->persistence = $persistence;
+    }
+
+    public function getContext($vis_id) {
+        $data = $this->persistence->getContext($vis_id);
+        $return_data = array("id" => $data["rev_vis"],
+                      "query" => $data["vis_query"],
+                      "service" => $data["vis_title"],
+                      "timestamp" => $data["rev_timestamp"],
+                      "params" => $data["vis_params"]);
+        if (array_key_exists("additional_context", $data)) {
+        $return_data = array_merge($return_data, $data["additional_context"]);
+        }
+        $result = json_encode($return_data);
+        return $result;
+    }
+
+}
\ No newline at end of file
diff --git a/server/services/getContext.php b/server/services/getContext.php
index 91f5e722b..ab14720e0 100644
--- a/server/services/getContext.php
+++ b/server/services/getContext.php
@@ -7,6 +7,7 @@
 require_once dirname(__FILE__) . '/../classes/headstart/library/CommUtils.php';
 require_once dirname(__FILE__) . '/../classes/headstart/library/Toolkit.php';
 require_once dirname(__FILE__) . '/../classes/headstart/library/APIClient.php';
+require_once dirname(__FILE__) . '/../classes/headstart/library/getContextResultBuilder.php';
 
 use headstart\library;
 
@@ -23,11 +24,13 @@
 // Remove the calls to this getContext on the persistence object. Replace instead with a getContextResultBuilder that returns a result object
 // This should contain the httpStatusCode to pass to the client, the result in string form (some json encoded string) and it should never throw.
 
+$getContextResultBuilder = new \headstart\library\getContextResultBuilder($persistence);
 
 // [thing that formats the response for the user] - [thing that parses responses from the persistence api] - [thing that makes requests to persisent api and handles the network calls etc.]
 
 // Err... why is the only caller of this having to unpack the array to take the first result? Is someone wrapping this reponse in an array unecessarily?
-$data = $persistence->getContext($vis_id)[0];
+// $data = $persistence->getContext($vis_id)[0];
+$result = $getContextResultBuilder->getContext($vis_id);
 
 /*
 It it works
@@ -39,14 +42,16 @@
   "vis_title": "base"
 }
 */
-$return_data = array("id" => $data["rev_vis"],
-                      "query" => $data["vis_query"],
-                      "service" => $data["vis_title"],
-                      "timestamp" => $data["rev_timestamp"],
-                      "params" => $data["vis_params"]);
-if (array_key_exists("additional_context", $data)) {
-  $return_data = array_merge($return_data, $data["additional_context"]);
-}
-$jsonData = json_encode($return_data);
+// $return_data = array("id" => $data["rev_vis"],
+//                       "query" => $data["vis_query"],
+//                       "service" => $data["vis_title"],
+//                       "timestamp" => $data["rev_timestamp"],
+//                       "params" => $data["vis_params"]);
+// if (array_key_exists("additional_context", $data)) {
+//   $return_data = array_merge($return_data, $data["additional_context"]);
+// }
+// $jsonData = json_encode($return_data);
 // To investigate: is anyone needing the callback version of this??
-library\CommUtils::echoOrCallback($jsonData, $_GET);
+// meaning, can this be simplified to just echo $result;
+// library\CommUtils::echoOrCallback($result, $_GET);
+echo $result;
diff --git a/server/services/search.php b/server/services/search.php
index 4fc9df002..ef8313ba4 100644
--- a/server/services/search.php
+++ b/server/services/search.php
@@ -73,8 +73,8 @@ function search($service, $dirty_query
         ? (cleanQuery($dirty_query, $transform_query_tolowercase, $add_slashes))
         : ($dirty_query);
 
-    $postgresPersistence = new \headstart\persistence\PostgresPersistence($apiclient);
-    $persistence = new \headstart\persistence\DispatchingPersistence($postgresPersistence);
+    $persistence = new \headstart\persistence\PostgresPersistence($apiclient);
+    // $persistence = new \headstart\persistence\DispatchingPersistence($postgresPersistence);
 
     // todo: move back into own function once error handling is refactored
     if ($service == "openaire") {
@@ -113,8 +113,17 @@ function search($service, $dirty_query
 
     if($retrieve_cached_map) {
       $last_version = $persistence->getLastVersion($unique_id, false, false);
+      error_log("search.php: last_version call returned " . print_r($last_version, true));
+      // check if last_version call has httpcode, this is not always the case for return values
+      // then check if success-status of last_version call is false      
+      if (isset($last_version["result"]["httpcode"]) && $last_version["result"]["httpcode"] != 200) {
+        error_log("search.php: last_version call failed with http code " . $last_version["result"]["httpcode"]);
+        error_log("search.php: last_version call failed with result " . $last_version["result"]);
+        echo json_encode($last_version["result"]);
+        return;
+      }
+
       if ($last_version != null && $last_version != "null" && $last_version != false) {
-          error_log("search.php: last_version call returned " . print_r($last_version, true));
           // for example, non-existant vis_id is handled here, which looks like [False]
           echo json_encode(array("query" => $query, "id" => $unique_id, "status" => "success"));
           return;
@@ -122,12 +131,6 @@ function search($service, $dirty_query
       //todo: log output of $last_version
       // log to docker logs
      
-      // check if success-status of last_version call is false
-      if ($last_version["httpcode"] != 200) {
-        error_log("search.php: last_version call failed with http code " . $last_version["httpcode"]);
-        error_log("search.php: last_version call failed with result " . $last_version["result"]);
-        return $last_version["result"];
-      }
     }
 
     $payload = json_encode($post_params);
diff --git a/server/workers/persistence/src/persistence.py b/server/workers/persistence/src/persistence.py
index 7017ddb69..076d66877 100644
--- a/server/workers/persistence/src/persistence.py
+++ b/server/workers/persistence/src/persistence.py
@@ -292,6 +292,7 @@ def post(self, database):
 
 
 @persistence_ns.route('/getContext/<database>')
+# this should be a GET request instead
 class getContext(Resource):
 
     @persistence_ns.produces(["application/json"])
@@ -315,10 +316,12 @@ def post(self, database):
             result = {'success': False, 'reason': ["database connection error"]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),
-                                 500,
+                                 503,
                                  headers)
         except Exception as e:
             persistence_ns.logger.error("getContext: %s" % str(e), exc_info=True)
+            # do we want to changes result reason to be more generic, but not open ended?
+            # at least we could map it to a specific error code/message on the fail page
             result = {'success': False, 'reason': [str(e)]}
             headers = {'ContentType': 'application/json'}
             return make_response(jsonify(result),

From f135059e1092aa21f9d45483fac7ec63f233511c Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Tue, 17 Dec 2024 20:58:36 +0100
Subject: [PATCH 11/20] first working draft of convoluted error handling logic
 in search.php

---
 .../classes/headstart/library/APIClient.php   |  2 +-
 .../library/getContextResultBuilder.php       |  3 ++-
 server/services/search.php                    | 20 ++++++++++++-------
 3 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/server/classes/headstart/library/APIClient.php b/server/classes/headstart/library/APIClient.php
index f3528a27d..a78701c38 100644
--- a/server/classes/headstart/library/APIClient.php
+++ b/server/classes/headstart/library/APIClient.php
@@ -76,7 +76,7 @@ public function handle_api_errors($res) {
         if ($res["httpcode"] == 503) {
             // we had a 503 for the database connection error
             // this implementation actively suppresses the reason by resetting to an empty array
-            $res["reason"] = array();
+            // $res["reason"] = array();
         }
         if (!array_key_exists("reason", $res)) {
             $res["reason"] = array();
diff --git a/server/classes/headstart/library/getContextResultBuilder.php b/server/classes/headstart/library/getContextResultBuilder.php
index b32f2ee8e..c1c1d88e9 100644
--- a/server/classes/headstart/library/getContextResultBuilder.php
+++ b/server/classes/headstart/library/getContextResultBuilder.php
@@ -21,7 +21,8 @@ public function __construct($persistence) {
     }
 
     public function getContext($vis_id) {
-        $data = $this->persistence->getContext($vis_id);
+        // TODO: remove the [0] unpacking from array
+        $data = $this->persistence->getContext($vis_id)[0];
         $return_data = array("id" => $data["rev_vis"],
                       "query" => $data["vis_query"],
                       "service" => $data["vis_title"],
diff --git a/server/services/search.php b/server/services/search.php
index ef8313ba4..ad9e2fbbf 100644
--- a/server/services/search.php
+++ b/server/services/search.php
@@ -115,14 +115,20 @@ function search($service, $dirty_query
       $last_version = $persistence->getLastVersion($unique_id, false, false);
       error_log("search.php: last_version call returned " . print_r($last_version, true));
       // check if last_version call has httpcode, this is not always the case for return values
-      // then check if success-status of last_version call is false      
-      if (isset($last_version["result"]["httpcode"]) && $last_version["result"]["httpcode"] != 200) {
-        error_log("search.php: last_version call failed with http code " . $last_version["result"]["httpcode"]);
-        error_log("search.php: last_version call failed with result " . $last_version["result"]);
-        echo json_encode($last_version["result"]);
-        return;
+      // then check if success-status of last_version call is false
+      if (is_array($last_version) && is_array(($last_version[0]))) {
+        $last_version = $last_version[0];
+        if (array_key_exists("httpcode", $last_version) && $last_version["httpcode"] != 200) {
+          $result = json_decode($last_version["result"], true);
+          $httpcode = $last_version["httpcode"];
+          error_log("search.php: last_version call failed with http code " . $httpcode);
+          error_log("search.php: last_version call failed with result " . print_r($result, true));
+          echo json_encode($result);
+          return;
+        }
       }
-
+      // TODO: This and the previous if are not mutually exclusive, so the second if should be an else if
+      // and also it should be refactored to a function that returns the result or throws an exception
       if ($last_version != null && $last_version != "null" && $last_version != false) {
           // for example, non-existant vis_id is handled here, which looks like [False]
           echo json_encode(array("query" => $query, "id" => $unique_id, "status" => "success"));

From f7b427cd374c60bf5235014e0b6ce3dfcb8fba76 Mon Sep 17 00:00:00 2001
From: Thomas Arrow <tom@openknowledgemaps.org>
Date: Mon, 16 Dec 2024 17:23:23 +0000
Subject: [PATCH 12/20] run phpunit82 --migrate-configuration

---
 server/classes/headstart/phpunit.xml     | 32 +++++++++---------------
 server/classes/headstart/phpunit.xml.bak | 22 ++++++++++++++++
 2 files changed, 34 insertions(+), 20 deletions(-)
 create mode 100644 server/classes/headstart/phpunit.xml.bak

diff --git a/server/classes/headstart/phpunit.xml b/server/classes/headstart/phpunit.xml
index ed664e150..d33ec4e22 100644
--- a/server/classes/headstart/phpunit.xml
+++ b/server/classes/headstart/phpunit.xml
@@ -1,22 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<phpunit xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:noNamespaceSchemaLocation="https://schema.phpunit.de/9.0/phpunit.xsd"
-         bootstrap="vendor/autoload.php"
-         executionOrder="depends,defects"
-         forceCoversAnnotation="true"
-         beStrictAboutCoversAnnotation="true"
-         beStrictAboutOutputDuringTests="true"
-         beStrictAboutTodoAnnotatedTests="true"
-         verbose="true">
-    <testsuites>
-        <testsuite name="default">
-            <directory suffix="Test.php">tests</directory>
-        </testsuite>
-    </testsuites>
-
-    <filter>
-        <whitelist processUncoveredFilesFromWhitelist="true">
-            <directory suffix=".php">src</directory>
-        </whitelist>
-    </filter>
+<phpunit xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://schema.phpunit.de/10.3/phpunit.xsd" bootstrap="vendor/autoload.php" executionOrder="depends,defects" beStrictAboutOutputDuringTests="true" cacheDirectory=".phpunit.cache" requireCoverageMetadata="true" beStrictAboutCoverageMetadata="true">
+  <coverage/>
+  <testsuites>
+    <testsuite name="default">
+      <directory suffix="Test.php">tests</directory>
+    </testsuite>
+  </testsuites>
+  <source>
+    <include>
+      <directory suffix=".php">src</directory>
+    </include>
+  </source>
 </phpunit>
diff --git a/server/classes/headstart/phpunit.xml.bak b/server/classes/headstart/phpunit.xml.bak
new file mode 100644
index 000000000..ed664e150
--- /dev/null
+++ b/server/classes/headstart/phpunit.xml.bak
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<phpunit xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:noNamespaceSchemaLocation="https://schema.phpunit.de/9.0/phpunit.xsd"
+         bootstrap="vendor/autoload.php"
+         executionOrder="depends,defects"
+         forceCoversAnnotation="true"
+         beStrictAboutCoversAnnotation="true"
+         beStrictAboutOutputDuringTests="true"
+         beStrictAboutTodoAnnotatedTests="true"
+         verbose="true">
+    <testsuites>
+        <testsuite name="default">
+            <directory suffix="Test.php">tests</directory>
+        </testsuite>
+    </testsuites>
+
+    <filter>
+        <whitelist processUncoveredFilesFromWhitelist="true">
+            <directory suffix=".php">src</directory>
+        </whitelist>
+    </filter>
+</phpunit>

From e9d4c73613620768cde885fc85d40b7f108a1248 Mon Sep 17 00:00:00 2001
From: Thomas Arrow <tom@openknowledgemaps.org>
Date: Mon, 16 Dec 2024 17:35:08 +0000
Subject: [PATCH 13/20] refactor common testSetup

---
 .../tests/PostgresPersistenceTest.php         | 42 +++++++++----------
 1 file changed, 19 insertions(+), 23 deletions(-)

diff --git a/server/classes/headstart/tests/PostgresPersistenceTest.php b/server/classes/headstart/tests/PostgresPersistenceTest.php
index 5b345ca6a..485c1b8e0 100644
--- a/server/classes/headstart/tests/PostgresPersistenceTest.php
+++ b/server/classes/headstart/tests/PostgresPersistenceTest.php
@@ -16,45 +16,41 @@
 class PostgresPersistenceTest extends TestCase
 {
     public function testThatInSuccesfulConditionsReturnsAResponseObjectWeCanHandle(): void {
-        $apiclient = $this->createMock(APIClient::class);
-        $jsonFilePath = __DIR__ . "/test_data/successfulGetContextResponse.json";
-        $jsonStringFromApi = file_get_contents($jsonFilePath); // returns string
-        $mockResponse = [
-            "result" => $jsonStringFromApi,
-            "httpcode" => 200
-        ];
-        $apiclient->method("call_persistence")->willReturn($mockResponse);
+        $apiclient = $this->getMockedApiclient("successfulGetContextResponse.json", 200);
         $persistence = new PostgresPersistence($apiclient);
+        $vis_id = "asdfasdf";
         $response = $persistence->getContext($vis_id);
+
         $this->assertIsArray($response);
     }
 
     public function testWhenDBMissingReturnsAResponseObjectWeCanHandle(): void {
-        $apiclient = $this->createMock(APIClient::class);
-        $jsonFilePath = __DIR__ . "/test_data/unsuccessfulGetContextDBHostCannotBeResolved.json";
-        $jsonStringFromApi = file_get_contents($jsonFilePath); // returns string
-        $mockResponse = [
-            "result" => $jsonStringFromApi,
-            "httpcode" => 503
-        ];
-        $apiclient->method("call_persistence")->willReturn($mockResponse);
+        $apiclient = $this->getMockedApiclient("unsuccessfulGetContextDBHostCannotBeResolved.json", 503);
         $persistence = new PostgresPersistence($apiclient);
+        $vis_id = "asdfasdf";
         $response = $persistence->getContext($vis_id);
-        var_dump($response);
+
         $this->assertIsArray($response);
     }
 
     public function testWhenVisIDNotInDBReturnsAResponseObjectWeCanHandle(): void {
+        $apiclient = $this->getMockedApiclient("unsuccessfulgetContextResponseVisIdNotInDB.json", 200);
+        $persistence = new PostgresPersistence($apiclient);
+        $vis_id = "asdfasdf";
+        $response = $persistence->getContext($vis_id);
+
+        $this->assertIsArray($response);
+    }
+
+    private function getMockedApiclient(string $jsonFileName, int $statusCode): Apiclient {
         $apiclient = $this->createMock(APIClient::class);
-        $jsonFilePath = __DIR__ . "/test_data/unsuccessfulgetContextResponseVisIdNotInDB.json";
-        $jsonStringFromApi = file_get_contents($jsonFilePath); // returns string
+        $jsonFilePath = __DIR__ . "/test_data/" . $jsonFileName;
+        $jsonStringFromApi = file_get_contents($jsonFilePath);
         $mockResponse = [
             "result" => $jsonStringFromApi,
-            "httpcode" => 200
+            "httpcode" => $statusCode
         ];
         $apiclient->method("call_persistence")->willReturn($mockResponse);
-        $persistence = new PostgresPersistence($apiclient);
-        $response = $persistence->getContext($vis_id);
-        $this->assertIsArray($response);
+        return $apiclient;
     }
 }
\ No newline at end of file

From 86f14a3d30c328e590c9ba65e00e7e16de7abe56 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Fri, 10 Jan 2025 22:28:43 +0100
Subject: [PATCH 14/20] PHP test updates; getContext refactoring

---
 server/classes/headstart/composer.lock        | 12 +++----
 .../library/getContextResultBuilder.php       | 35 +++++++++----------
 .../persistence/DispatchingPersistence.php    |  1 +
 .../persistence/PostgresPersistence.php       | 10 ++++++
 server/classes/headstart/phpunit.xml          |  9 +++--
 .../tests/PostgresPersistenceTest.php         | 19 ++++++++++
 server/services/getContext.php                | 10 +++---
 7 files changed, 66 insertions(+), 30 deletions(-)

diff --git a/server/classes/headstart/composer.lock b/server/classes/headstart/composer.lock
index 407da8237..4569d5fb4 100644
--- a/server/classes/headstart/composer.lock
+++ b/server/classes/headstart/composer.lock
@@ -69,16 +69,16 @@
         },
         {
             "name": "nikic/php-parser",
-            "version": "v5.3.1",
+            "version": "v5.4.0",
             "source": {
                 "type": "git",
                 "url": "https://github.com/nikic/PHP-Parser.git",
-                "reference": "8eea230464783aa9671db8eea6f8c6ac5285794b"
+                "reference": "447a020a1f875a434d62f2a401f53b82a396e494"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/nikic/PHP-Parser/zipball/8eea230464783aa9671db8eea6f8c6ac5285794b",
-                "reference": "8eea230464783aa9671db8eea6f8c6ac5285794b",
+                "url": "https://api.github.com/repos/nikic/PHP-Parser/zipball/447a020a1f875a434d62f2a401f53b82a396e494",
+                "reference": "447a020a1f875a434d62f2a401f53b82a396e494",
                 "shasum": ""
             },
             "require": {
@@ -121,9 +121,9 @@
             ],
             "support": {
                 "issues": "https://github.com/nikic/PHP-Parser/issues",
-                "source": "https://github.com/nikic/PHP-Parser/tree/v5.3.1"
+                "source": "https://github.com/nikic/PHP-Parser/tree/v5.4.0"
             },
-            "time": "2024-10-08T18:51:32+00:00"
+            "time": "2024-12-30T11:07:19+00:00"
         },
         {
             "name": "phar-io/manifest",
diff --git a/server/classes/headstart/library/getContextResultBuilder.php b/server/classes/headstart/library/getContextResultBuilder.php
index c1c1d88e9..acbce6982 100644
--- a/server/classes/headstart/library/getContextResultBuilder.php
+++ b/server/classes/headstart/library/getContextResultBuilder.php
@@ -1,6 +1,7 @@
 <?php
 
 namespace headstart\library;
+use headstart\persistence\VisualizationContext;
 
 /**
  * Description of getContextResultBuilder:
@@ -8,31 +9,29 @@
  * It is a thin layer on top of the Persistence class and is used to build the context result
  * from the database response.
  *
- * @author pkraker
+ * @author ckittel
  */
 
 
 class getContextResultBuilder {
 
-    private $persistence;
-
-    public function __construct($persistence) {
-        $this->persistence = $persistence;
-    }
-
-    public function getContext($vis_id) {
-        // TODO: remove the [0] unpacking from array
-        $data = $this->persistence->getContext($vis_id)[0];
-        $return_data = array("id" => $data["rev_vis"],
-                      "query" => $data["vis_query"],
-                      "service" => $data["vis_title"],
-                      "timestamp" => $data["rev_timestamp"],
-                      "params" => $data["vis_params"]);
-        if (array_key_exists("additional_context", $data)) {
-        $return_data = array_merge($return_data, $data["additional_context"]);
+    public function getContext(VisualizationContext $visualizationContext): string {
+        // if data result is not success, return error reason array
+        $httpcode = $visualizationContext->httpcode;
+        $data = $visualizationContext->data;
+        if ($httpcode === 200) {
+            $return_data = array("id" => $data["rev_vis"],
+                        "query" => $data["vis_query"],
+                        "service" => $data["vis_title"],
+                        "timestamp" => $data["rev_timestamp"],
+                        "params" => $data["vis_params"]);
+            if (array_key_exists("additional_context", $data)) {
+               $return_data = array_merge($return_data, $data["additional_context"]);
+            }
+        } else {
+                $return_data = $data;
         }
         $result = json_encode($return_data);
         return $result;
     }
-
 }
\ No newline at end of file
diff --git a/server/classes/headstart/persistence/DispatchingPersistence.php b/server/classes/headstart/persistence/DispatchingPersistence.php
index 5b5b47927..29af73e75 100644
--- a/server/classes/headstart/persistence/DispatchingPersistence.php
+++ b/server/classes/headstart/persistence/DispatchingPersistence.php
@@ -4,6 +4,7 @@
 
 /**
  * This class implements the PersistenceInterface and provides methods to interact with the database.
+ * Deprecated, this should now be removed.
  */
 class DispatchingPersistence implements Persistence
 {
diff --git a/server/classes/headstart/persistence/PostgresPersistence.php b/server/classes/headstart/persistence/PostgresPersistence.php
index 7bd67438c..c6d84258b 100644
--- a/server/classes/headstart/persistence/PostgresPersistence.php
+++ b/server/classes/headstart/persistence/PostgresPersistence.php
@@ -4,6 +4,7 @@
 use headstart\library\APIClient;
 
 require_once 'Persistence.php';
+require_once 'VisualizationContext.php';
 
 /**
  * This class implements the PersistenceInterface and provides methods to interact with the database.
@@ -98,6 +99,15 @@ public function getContext($vis_id): array|bool
         return array($data);
     }
 
+    public function getVisualizationContext($vis_id): VisualizationContext
+    {
+        $payload = json_encode(array("vis_id" => $vis_id));
+        $res = $this->api_client->call_persistence("getContext", $payload);
+        $data = json_decode($res["result"], true);
+        $httpcode = $res["httpcode"];
+        return new VisualizationContext($data, $httpcode);
+    }
+
     public function createID($string_array, $payload): string
     {
         $res = $this->api_client->call_persistence("createID", $payload);
diff --git a/server/classes/headstart/phpunit.xml b/server/classes/headstart/phpunit.xml
index d33ec4e22..71abfb957 100644
--- a/server/classes/headstart/phpunit.xml
+++ b/server/classes/headstart/phpunit.xml
@@ -1,5 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<phpunit xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://schema.phpunit.de/10.3/phpunit.xsd" bootstrap="vendor/autoload.php" executionOrder="depends,defects" beStrictAboutOutputDuringTests="true" cacheDirectory=".phpunit.cache" requireCoverageMetadata="true" beStrictAboutCoverageMetadata="true">
+<phpunit xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://schema.phpunit.de/10.3/phpunit.xsd" bootstrap="vendor/autoload.php" executionOrder="depends,defects" beStrictAboutOutputDuringTests="true" cacheDirectory=".phpunit.cache" requireCoverageMetadata="true" beStrictAboutCoverageMetadata="true"
+         displayDetailsOnTestsThatTriggerDeprecations="true"
+         displayDetailsOnTestsThatTriggerErrors="true"
+         displayDetailsOnTestsThatTriggerNotices="true"
+         displayDetailsOnTestsThatTriggerWarnings="true"
+>
   <coverage/>
   <testsuites>
     <testsuite name="default">
@@ -10,5 +15,5 @@
     <include>
       <directory suffix=".php">src</directory>
     </include>
-  </source>
+  </source>  
 </phpunit>
diff --git a/server/classes/headstart/tests/PostgresPersistenceTest.php b/server/classes/headstart/tests/PostgresPersistenceTest.php
index 485c1b8e0..7834bcc66 100644
--- a/server/classes/headstart/tests/PostgresPersistenceTest.php
+++ b/server/classes/headstart/tests/PostgresPersistenceTest.php
@@ -9,6 +9,7 @@
 use headstart\persistence\PostgresPersistence;
 use headstart\library\APIClient;
 use PHPUnit\Framework\TestCase;
+use headstart\persistence\VisualizationContext;
 
 /**
  * @covers \headstart\persistence\PostgresPersistence
@@ -42,6 +43,24 @@ public function testWhenVisIDNotInDBReturnsAResponseObjectWeCanHandle(): void {
         $this->assertIsArray($response);
     }
 
+    public function testThatInSuccesfulConditionsReturnsAVisualizationContextWeCanHandle(): void {
+        $apiclient = $this->getMockedApiclient("successfulGetContextResponse.json", 200);
+        $persistence = new PostgresPersistence($apiclient);
+        $vis_id = "asdfasdf";
+        $response = $persistence->getVisualizationContext($vis_id);
+
+        $this->assertInstanceOf(VisualizationContext::class, $response);
+    }
+
+    public function testWhenDBMissingReturnsAVisualizationContextWeCanHandle(): void {
+        $apiclient = $this->getMockedApiclient("unsuccessfulGetContextDBHostCannotBeResolved.json", 503);
+        $persistence = new PostgresPersistence($apiclient);
+        $vis_id = "asdfasdf";
+        $response = $persistence->getVisualizationContext($vis_id);
+
+        $this->assertInstanceOf(VisualizationContext::class, $response);
+    }
+
     private function getMockedApiclient(string $jsonFileName, int $statusCode): Apiclient {
         $apiclient = $this->createMock(APIClient::class);
         $jsonFilePath = __DIR__ . "/test_data/" . $jsonFileName;
diff --git a/server/services/getContext.php b/server/services/getContext.php
index ab14720e0..34e49ea07 100644
--- a/server/services/getContext.php
+++ b/server/services/getContext.php
@@ -24,16 +24,18 @@
 // Remove the calls to this getContext on the persistence object. Replace instead with a getContextResultBuilder that returns a result object
 // This should contain the httpStatusCode to pass to the client, the result in string form (some json encoded string) and it should never throw.
 
-$getContextResultBuilder = new \headstart\library\getContextResultBuilder($persistence);
+$getContextResultBuilder = new \headstart\library\getContextResultBuilder();
 
 // [thing that formats the response for the user] - [thing that parses responses from the persistence api] - [thing that makes requests to persisent api and handles the network calls etc.]
 
 // Err... why is the only caller of this having to unpack the array to take the first result? Is someone wrapping this reponse in an array unecessarily?
 // $data = $persistence->getContext($vis_id)[0];
-$result = $getContextResultBuilder->getContext($vis_id);
+// $result = $getContextResultBuilder->getContext($vis_id);
+$visualizationContext = $persistence->getVisualizationContext($vis_id);
+http_response_code($visualizationContext->httpcode);
 
 /*
-It it works
+If it works
 {
   "rev_timestamp": "Thu, 12 Sep 2024 10:23:47 GMT",
   "rev_vis": "d161dba364a1e8c0468b9c74407e3575",
@@ -54,4 +56,4 @@
 // To investigate: is anyone needing the callback version of this??
 // meaning, can this be simplified to just echo $result;
 // library\CommUtils::echoOrCallback($result, $_GET);
-echo $result;
+echo $getContextResultBuilder->getContext($visualizationContext);
\ No newline at end of file

From 3b5e9d0aea0ae43dda5818042cb29bf3980418d1 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Fri, 17 Jan 2025 22:29:56 +0100
Subject: [PATCH 15/20] requirements updates

---
 server/workers/persistence/Dockerfile       | 1 -
 server/workers/persistence/requirements.txt | 3 ++-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/server/workers/persistence/Dockerfile b/server/workers/persistence/Dockerfile
index f682ba27b..4401c95e7 100644
--- a/server/workers/persistence/Dockerfile
+++ b/server/workers/persistence/Dockerfile
@@ -8,5 +8,4 @@ WORKDIR /persistence
 COPY workers/persistence/requirements.txt .
 RUN pip install --upgrade pip
 RUN pip install --no-cache-dir -r requirements.txt
-RUN pip install git+https://github.com/python-restx/flask-restx
 COPY workers/persistence/src/ ./
\ No newline at end of file
diff --git a/server/workers/persistence/requirements.txt b/server/workers/persistence/requirements.txt
index 6eab26c89..e8f5c630e 100644
--- a/server/workers/persistence/requirements.txt
+++ b/server/workers/persistence/requirements.txt
@@ -17,4 +17,5 @@ SQLAlchemy==2.0.23
 SQLAlchemy-Utils==0.41.1
 typing_extensions==4.7.1
 Werkzeug==3.0.1
-zipp==3.15.0
\ No newline at end of file
+zipp==3.15.0
+flask-restx==1.3.0
\ No newline at end of file

From 65a550da923d06881201ad88e8729e9399545569 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Tue, 21 Jan 2025 23:45:03 +0100
Subject: [PATCH 16/20] add missing file

---
 .../persistence/VisualizationContext.php      | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 server/classes/headstart/persistence/VisualizationContext.php

diff --git a/server/classes/headstart/persistence/VisualizationContext.php b/server/classes/headstart/persistence/VisualizationContext.php
new file mode 100644
index 000000000..28dc4c91c
--- /dev/null
+++ b/server/classes/headstart/persistence/VisualizationContext.php
@@ -0,0 +1,19 @@
+<?php
+
+namespace headstart\persistence;
+
+class VisualizationContext
+{
+    public array $data;
+    public int $httpcode;
+
+    public function __construct(array $data, int $httpcode)
+    //do we want more validation than just array?
+    //e.g. checking that all things we rely on in getContext are there,
+    //if not then throw something which can be caught by the calling function
+    {
+        $this->data = $data;
+        $this->httpcode = $httpcode;
+    }
+
+}
\ No newline at end of file

From 13ef35fa9e80b4e4a625a5d013f904f019156497 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Tue, 28 Jan 2025 22:03:30 +0100
Subject: [PATCH 17/20] bugfix for metadata processing

---
 server/workers/base/src/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/server/workers/base/src/base.py b/server/workers/base/src/base.py
index d08b8f31d..ed0c9bf1b 100644
--- a/server/workers/base/src/base.py
+++ b/server/workers/base/src/base.py
@@ -234,7 +234,7 @@ def mark_duplicate_links(df):
 def identify_relations(df):
     for udoi in df.unversioned_doi.unique():
         if udoi:
-            tmp = df[df.identifier.str.contains(udoi)]
+            tmp = df[df.identifier.str.contains(udoi, regex=False)]
             if len(tmp) > 1:
                 relations = tmp.id
                 r = pd.Series([relations.values.tolist()]*len(tmp), index=relations.index)

From a9e9907e1cc54cd14af9c6e85c546f796a8ecf12 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Tue, 28 Jan 2025 22:05:11 +0100
Subject: [PATCH 18/20] bugfix for parameter processing

---
 server/workers/api/src/apis/pubmed.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/server/workers/api/src/apis/pubmed.py b/server/workers/api/src/apis/pubmed.py
index 2f85a77d7..498f75b9b 100644
--- a/server/workers/api/src/apis/pubmed.py
+++ b/server/workers/api/src/apis/pubmed.py
@@ -53,6 +53,7 @@ def post(self):
         if "optradio" in params:
             del params["optradio"]
         errors = search_param_schema.validate(params, partial=True)
+        params = sanitize_params(params)
         params["limit"] = 100
         params["list_size"] = 100
         pubmed_ns.logger.debug(errors)
@@ -91,4 +92,11 @@ def post(self):
 class ServiceVersion(Resource):
     def get(self):
         result = {"service_version": os.getenv("SERVICE_VERSION")}
-        return make_response(result, 200, {"Content-Type": "application/json"})
\ No newline at end of file
+        return make_response(result, 200, {"Content-Type": "application/json"})
+    
+def sanitize_params(params):
+    article_types = params.get("article_types")
+    if article_types:
+        [at.replace("\&#39;", "'") for at in article_types]
+    return params
+            
\ No newline at end of file

From 9713bd80507877075f3c9954afe26a28040d3435 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Tue, 28 Jan 2025 22:06:09 +0100
Subject: [PATCH 19/20] bugfix for parameter processing

---
 server/workers/api/src/apis/pubmed.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/server/workers/api/src/apis/pubmed.py b/server/workers/api/src/apis/pubmed.py
index 498f75b9b..dd2c76bd5 100644
--- a/server/workers/api/src/apis/pubmed.py
+++ b/server/workers/api/src/apis/pubmed.py
@@ -98,5 +98,6 @@ def sanitize_params(params):
     article_types = params.get("article_types")
     if article_types:
         [at.replace("\&#39;", "'") for at in article_types]
+        params["article_types"] = article_types
     return params
             
\ No newline at end of file

From 240cf7c4239d257d3bb1355ef725c61bd0b3c297 Mon Sep 17 00:00:00 2001
From: chreman <web@christopherkittel.eu>
Date: Wed, 29 Jan 2025 00:22:27 +0100
Subject: [PATCH 20/20] pubmed query bugfix

---
 server/workers/api/src/apis/pubmed.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/server/workers/api/src/apis/pubmed.py b/server/workers/api/src/apis/pubmed.py
index dd2c76bd5..ba56ed14f 100644
--- a/server/workers/api/src/apis/pubmed.py
+++ b/server/workers/api/src/apis/pubmed.py
@@ -97,7 +97,7 @@ def get(self):
 def sanitize_params(params):
     article_types = params.get("article_types")
     if article_types:
-        [at.replace("\&#39;", "'") for at in article_types]
+        article_types = [at.replace("&#39;", "'") for at in article_types]
         params["article_types"] = article_types
     return params
             
\ No newline at end of file