Merge branch 'test-util-db' of https://github.com/Gossty/qiita into test-util-db

Gossty · Gossty · commit b77ef2ebe8bf · 2024-06-05T12:15:33.000-07:00
diff --git a/INSTALL.md b/INSTALL.md
@@ -78,7 +78,7 @@ You can reboot the system with `sudo reboot` in case any packages were updated.
 Next, we need to add the Postgres repository to our system:
 ```bash
 sudo apt update
-sudo apt install curl gpg gnupg2 software-properties-common apt-transport-https lsb-release ca-certificates
+sudo apt install curl gpg gnupg2 software-properties-common apt-transport-https lsb-release ca-certificates git
 curl -fsSL https://www.postgresql.org/media/keys/ACCC4CF8.asc|sudo gpg --dearmor -o /etc/apt/trusted.gpg.d/postgresql.gpg
 echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" |sudo tee  /etc/apt/sources.list.d/pgdg.list
 ```
@@ -238,6 +238,9 @@ If you are using [NGINX](https://www.nginx.com/) via conda, you are going to nee
 mkdir -p ${CONDA_PREFIX}/var/run/nginx/
 ```
 
+Note that the shipped nginx version from conda, does **not** contain the mod_zip module: https://github.com/evanmiller/mod_zip
+This leads to unexpected behaviour when generating a download link for anonymous artefact sharing, i.e. Qiita returns a flat file listing artifact filepaths instead of generating a ZIP archive that contains those files. You need to compile nginx with the additional mod_zip module yourself. (I've invested multiple hours to realize that the configure routine does not properly link shared libraries to the nginx binary. Try adding `--with-ld-opt=" -Wl,-rpath,/home/foo/lib "` to the `./auto/configure` call.)
+
 ## Start Qiita
 
 Start postgres (instructions vary depending on operating system and install method).
diff --git a/qiita_core/configuration_manager.py b/qiita_core/configuration_manager.py
@@ -389,4 +389,4 @@ def _get_portal(self, config):
                 raise ValueError(msg % (name, val, 'larger than 180°'))
 
     def _iframe(self, config):
-        self.iframe_qiimp = config.get('iframe', 'QIIMP')
+        self.iframe_qiimp = config.get('iframe', 'QIIMP', fallback=None)
diff --git a/qiita_core/support_files/cert.conf b/qiita_core/support_files/cert.conf
@@ -0,0 +1,7 @@
+authorityKeyIdentifier=keyid,issuer
+basicConstraints=CA:FALSE
+keyUsage = digitalSignature, nonRepudiation, keyEncipherment, dataEncipherment
+subjectAltName = @alt_names
+
+[alt_names]
+DNS.1 = localhost
diff --git a/qiita_core/support_files/ci_rootca.crt b/qiita_core/support_files/ci_rootca.crt
@@ -1,20 +1,20 @@
 -----BEGIN CERTIFICATE-----
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 -----END CERTIFICATE-----
diff --git a/qiita_core/support_files/ci_rootca.key b/qiita_core/support_files/ci_rootca.key
@@ -0,0 +1,28 @@
+-----BEGIN PRIVATE KEY-----
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+-----END PRIVATE KEY-----
diff --git a/qiita_core/support_files/ci_rootca.srl b/qiita_core/support_files/ci_rootca.srl
@@ -1 +1 @@
-2FB946B7AAF21FDC0387BAA7B5ABF5D91E0D9F4B
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diff --git a/qiita_core/support_files/ci_server.crt b/qiita_core/support_files/ci_server.crt
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 -----BEGIN CERTIFICATE-----
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 -----END CERTIFICATE-----
diff --git a/qiita_core/support_files/ci_server.csr b/qiita_core/support_files/ci_server.csr
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 -----END CERTIFICATE REQUEST-----
diff --git a/qiita_core/support_files/ci_server.key b/qiita_core/support_files/ci_server.key
@@ -1,28 +1,28 @@
 -----BEGIN PRIVATE KEY-----
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 -----END PRIVATE KEY-----
diff --git a/qiita_core/support_files/config_test.cfg b/qiita_core/support_files/config_test.cfg
@@ -193,6 +193,6 @@ STATS_MAP_CENTER_LONGITUDE =
 
 # ----------------------------- iframes settings ---------------------------
 [iframe]
-# The real world QIIMP will always need to be accessed with https because Qiita
-# runs on https too
-QIIMP = https://localhost:8898/
+# On May 2024, we removed QIIMP from the code base but we will leave this
+# section in case we need to add access to another iframe in the future; note
+# that the qiita-terms are also accessed via iframe but this is internal
diff --git a/qiita_core/support_files/csr.conf b/qiita_core/support_files/csr.conf
@@ -0,0 +1,21 @@
+[ req ]
+default_bits = 2048
+prompt = no
+default_md = sha256
+req_extensions = req_ext
+distinguished_name = dn
+
+[ dn ]
+C = US
+ST = California
+L = San Diego
+O = UCSD
+OU = Knight Lab
+CN = localhost
+
+[ req_ext ]
+subjectAltName = @alt_names
+
+[ alt_names ]
+DNS.1 = localhost
+IP.1 = 127.0.0.1
diff --git a/qiita_core/tests/test_configuration_manager.py b/qiita_core/tests/test_configuration_manager.py
@@ -109,7 +109,7 @@ def test_init(self):
         self.assertEqual(obs.portal_dir, "/portal")
 
         # iframe section
-        self.assertEqual(obs.iframe_qiimp, "https://localhost:8898/")
+        self.assertIsNone(obs.iframe_qiimp)
 
     def test_init_error(self):
         with open(self.conf_fp, 'w') as f:
@@ -471,7 +471,6 @@ def test_get_portal_latlong(self):
 
 # ----------------------------- iframes settings ---------------------------
 [iframe]
-QIIMP = https://localhost:8898/
 """
 
 if __name__ == '__main__':
diff --git a/qiita_pet/handlers/admin_processing_job.py b/qiita_pet/handlers/admin_processing_job.py
@@ -82,7 +82,8 @@ def get(self):
                 msg = job.log.msg
             elif job.status == 'running':
                 msg = job.step
-            msg = msg.replace('\n', '</br>')
+            if msg is not None:
+                msg = msg.replace('\n', '</br>')
             outputs = []
             if job.status == 'success':
                 outputs = [[k, v.id] for k, v in job.outputs.items()]
diff --git a/qiita_pet/support_files/doc/source/index.rst b/qiita_pet/support_files/doc/source/index.rst
@@ -27,7 +27,6 @@ Looking for information about getting started? Please see the document here:
 
    gettingstartedguide/index.rst
    qiita-philosophy/index.rst
-   qiimp.rst
 
 Looking for information about how to process your data? Please see the document here:
 
diff --git a/qiita_pet/support_files/doc/source/qiimp.rst b/qiita_pet/support_files/doc/source/qiimp.rst
diff --git a/qiita_pet/templates/iframe.html b/qiita_pet/templates/iframe.html
@@ -3,8 +3,6 @@
 
 {% if iframe == 'qiita-terms' %}
   <iframe style="margin: 0; padding: 0; width: 100%; height: 800px;" src="{% raw qiita_config.portal_dir %}/static/qiita_data_terms_of_use.html"></iframe>
-{% elif iframe == 'qiimp' %}
-  <iframe style="margin: 0; padding: 0; width: 100%; height: 800px;" src="{{qiita_config.iframe_qiimp}}"></iframe>
 {% else %}
   <b>No content</b>
 {% end %}
diff --git a/qiita_pet/templates/sitebase.html b/qiita_pet/templates/sitebase.html
@@ -464,11 +464,6 @@
                 <a href="/redbiom/">redbiom</a>
               </li>
             </ul>
-            <ul class="nav navbar-nav">
-              <li>
-                <a href="{% raw qiita_config.portal_dir %}/iframe/?iframe=qiimp">Qiimp</a>
-              </li>
-            </ul>
             <ul class="nav navbar-nav">
               <!-- downloads -->
               <li class="dropdown">
diff --git a/qiita_pet/templates/user_profile.html b/qiita_pet/templates/user_profile.html
@@ -19,7 +19,7 @@ <h3>User Information</h3>
         {% raw form_item(class_='form-control') %}
       </div>
       {% end %}
-      <div style="color:red;">{{msg}}</div>
+      <div style="color:{% if msg.startswith('ERROR:') %}red{% else %}darkgreen{% end %};">{{msg}}</div>
       <button type="submit" class="btn btn-success">Save Edits</button>
     </form>
   </div>

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-2FB946B7AAF21FDC0387BAA7B5ABF5D91E0D9F4B`
	`1`	`+2FB946B7AAF21FDC0387BAA7B5ABF5D91E0D9F4C`