jlab · sjanssen2 · May 8, 2025 · Mar 11, 2025 · Mar 11, 2025 · Mar 11, 2025
diff --git a/Images/nginx/nginx_qiita.conf b/Images/nginx/nginx_qiita.conf
@@ -13,9 +13,9 @@ http {
     # ports to redirect for mainqiita
     upstream mainqiita {
         server qiita:21174;
-        server qiita-container-anna-qiita-worker-1:21175;
-        server qiita-container-anna-qiita-worker-2:21175;
-        server qiita-container-anna-qiita-worker-3:21175;
+        server tinqiita-qiita-worker-1:21175;
+        server tinqiita-qiita-worker-2:21175;
+        server tinqiita-qiita-worker-3:21175;
     }
 
     # define variables for the actions that shall be taken for websocket handshake

diff --git a/Images/plugin_collector/collect_configs.py b/Images/plugin_collector/collect_configs.py
@@ -23,7 +23,7 @@
     if container == "":
         continue
     print('  (%i/%i) %s' % (i+1, len(containers), container), end="", file=sys.stderr)
-    url = 'http://qiita-container-anna-%s-1:%s/%s' % (container, PORT, API_ENDPOINT)
+    url = 'http://%s%s-1:%s/%s' % ('tinqiita-', container, PORT, API_ENDPOINT)
     print(" '%s'" % url, end="", file=sys.stderr)
 
     req = requests.get(url)

diff --git a/Images/plugin_collector/stefan_cert.conf b/Images/plugin_collector/stefan_cert.conf
@@ -5,8 +5,8 @@ subjectAltName = @alt_names
 
 [alt_names]
 DNS.1 = localhost
-DNS.2 = qiita-container-anna-qiita-1
-DNS.3 = qiita-container-anna-qiita-worker-1
-DNS.4 = qiita-container-anna-qiita-worker-2
-DNS.5 = qiita-container-anna-qiita-worker-3
-DNS.6 = qiita-container-anna-nginx-1
+DNS.2 = tinqiita-qiita-1
+DNS.3 = tinqiita-qiita-worker-1
+DNS.4 = tinqiita-qiita-worker-2
+DNS.5 = tinqiita-qiita-worker-3
+DNS.6 = tinqiita-nginx-1
diff --git a/Images/plugin_collector/stefan_csr.conf b/Images/plugin_collector/stefan_csr.conf
@@ -19,8 +19,8 @@ subjectAltName = @alt_names
 [ alt_names ]
 DNS.1 = localhost
 IP.1 = 127.0.0.1
-DNS.2 = qiita-container-anna-qiita-1
-DNS.3 = qiita-container-anna-qiita-worker-1
-DNS.4 = qiita-container-anna-qiita-worker-2
-DNS.5 = qiita-container-anna-qiita-worker-3
-DNS.6 = qiita-container-anna-nginx-1
+DNS.2 = tinqiita-qiita-1
+DNS.3 = tinqiita-qiita-worker-1
+DNS.4 = tinqiita-qiita-worker-2
+DNS.5 = tinqiita-qiita-worker-3
+DNS.6 = tinqiita-nginx-1
diff --git a/Images/qiita/config_qiita_oidc.cfg b/Images/qiita/config_qiita_oidc.cfg
@@ -23,7 +23,7 @@ LOG_DIR = /logs/
 REQUIRE_APPROVAL = True
 
 # Base URL: DO NOT ADD TRAILING SLASH
-BASE_URL = https://qiita-container-anna-nginx-1:8383
+BASE_URL = https://tinqiita-nginx-1:8383
 
 # Download path files
 UPLOAD_DATA_DIR = /qiita_data/uploads/

diff --git a/Images/qiita/drop_workflows.py b/Images/qiita/drop_workflows.py
@@ -0,0 +1,67 @@
+import qiita_db as qdb
+import sys
+
+
+def remove(self):
+    # store for later, after table entry is dropped
+    workflow_name = self.name
+
+    def _get_workflow_id(name):
+        with qdb.sql_connection.TRN:
+            sql = """SELECT default_workflow_id
+                     FROM qiita.default_workflow
+                     WHERE name = %s"""
+            qdb.sql_connection.TRN.add(sql, [name])
+            return qdb.sql_connection.TRN.execute_fetchlast()
+    def _get_node_ids(workflow_id):
+        with qdb.sql_connection.TRN:
+            sql = """SELECT default_workflow_node_id
+                     FROM qiita.default_workflow_node
+                     WHERE default_workflow_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [workflow_id])
+            return qdb.sql_connection.TRN.execute_fetchflatten()
+    def _get_edge_ids(node_ids):
+        if len(node_ids) > 0:
+            with qdb.sql_connection.TRN:
+                sql = """SELECT default_workflow_edge_id
+                         FROM qiita.default_workflow_edge
+                         WHERE parent_id in %s OR child_id in %s"""
+                qdb.sql_connection.TRN.add(sql, [tuple(node_ids), tuple(node_ids)])
+                return qdb.sql_connection.TRN.execute_fetchflatten()
+        else:
+            return []
+
+    workflow_id = _get_workflow_id(self.name)
+    node_ids = _get_node_ids(workflow_id)
+    edge_ids = _get_edge_ids(node_ids)
+    with qdb.sql_connection.TRN:
+        if len(edge_ids) > 0:
+            sql = """DELETE FROM qiita.default_workflow_edge_connections
+                     WHERE default_workflow_edge_id in %s"""
+            qdb.sql_connection.TRN.add(sql, [tuple(edge_ids)])
+
+            sql = """DELETE FROM qiita.default_workflow_edge
+                     WHERE default_workflow_edge_id in %s"""
+            qdb.sql_connection.TRN.add(sql, [tuple(edge_ids)])
+
+        if workflow_id is not None:
+            sql = """DELETE FROM qiita.default_workflow_node
+                     WHERE default_workflow_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [workflow_id])
+
+            sql = """DELETE FROM qiita.default_workflow_data_type
+                     WHERE default_workflow_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [workflow_id])
+
+            sql = """DELETE FROM qiita.default_workflow
+                     WHERE default_workflow_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [workflow_id])
+    print("removed workflow '%s': ID=%i with %i nodes and %i edges" % (workflow_name, workflow_id, len(node_ids), len(edge_ids)), file=sys.stderr)
+
+def remove_workflows():
+    for w in qdb.software.DefaultWorkflow.iter():
+        w.remove = remove
+        w.remove(w)
+
+
+remove_workflows()
diff --git a/Images/qiita/qiita.dockerfile b/Images/qiita/qiita.dockerfile
@@ -77,4 +77,7 @@ RUN rm -f /qiita/qiita_pet/nginx_example.conf /qiita/qiita_pet/supervisor_exampl
 
 COPY drop_workflows.py /drop_workflows.py
 
+# install aspera client for ENA submission
+RUN conda install hcc::aspera-cli
+
 # CMD ["conda", "run", "-n", "qiita"]
diff --git a/Images/qiita/start_plugin.py b/Images/qiita/start_plugin.py
@@ -8,7 +8,7 @@
 
 pluginname, qiita_server_url, job_id, output_dir = sys.argv[1:]
 
-req = requests.post('http://qiita-container-anna-%s-1:%s/run' % (pluginname, PORT),
+req = requests.post('http://%s%s-1:%s/run' % ('tinqiita-', pluginname, PORT),
                     json={'url': qiita_server_url,
                           'job_id': job_id,
                           'output_dir': output_dir})

diff --git a/Images/qp-deblur/start_qp-deblur.sh b/Images/qp-deblur/start_qp-deblur.sh
@@ -1,17 +1,5 @@
 #!/bin/bash
 
-#export QIITA_ROOTCA_CERT=/qiita/qiita_core/support_files/ci_server.crt
-export QIITA_CONFIG_FP=/qiita_configurations/qiita_server.cfg
-CONDA_DIR=/opt/conda
-ENV_NAME=qp-deblur
-
-# Commented out because I wanted to jump onto the container to crawl into the code (it crashes during the start_biom step)
-
-#configure_biom --env-script "source /opt/conda/bin/activate ; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT
-
-#start_biom https://localhost:8383 register ignored
-#start_biom http://qiita:8383 register ignored
-#source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd / && python trigger.py
 cd / && python trigger.py deblur start_deblur /qp-deblur
 
 tail -f /dev/null
diff --git a/Images/qp-qiime2/start_qp-qiime2.sh b/Images/qp-qiime2/start_qp-qiime2.sh
@@ -1,17 +1,5 @@
 #!/bin/bash
 
-#export QIITA_ROOTCA_CERT=/qiita/qiita_core/support_files/ci_server.crt
-export QIITA_CONFIG_FP=/qiita_configurations/qiita_server.cfg
-CONDA_DIR=/opt/conda
-ENV_NAME=qp-qiime2
-
-# Commented out because I wanted to jump onto the container to crawl into the code (it crashes during the start_biom step)
-
-#configure_biom --env-script "source /opt/conda/bin/activate ; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT
-
-#start_biom https://localhost:8383 register ignored
-#start_biom http://qiita:8383 register ignored
-#source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd / && python trigger.py
 cd / && python trigger.py qiime2 start_qiime2 /qp-qiime2
 
 tail -f /dev/null
diff --git a/Images/qp-target-gene/start_qp-target-gene.sh b/Images/qp-target-gene/start_qp-target-gene.sh
@@ -1,17 +1,5 @@
 #!/bin/bash
 
-#export QIITA_ROOTCA_CERT=/qiita/qiita_core/support_files/ci_server.crt
-export QIITA_CONFIG_FP=/qiita_configurations/qiita_server.cfg
-CONDA_DIR=/opt/conda
-ENV_NAME=qp-target-gene
-
-# Commented out because I wanted to jump onto the container to crawl into the code (it crashes during the start_biom step)
-
-#configure_biom --env-script "source /opt/conda/bin/activate ; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT
-
-#start_biom https://localhost:8383 register ignored
-#start_biom http://qiita:8383 register ignored
-#source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd / && python trigger.py
 cd / && python trigger.py qp-target-gene start_target_gene /qp-target-gene
 
 tail -f /dev/null
diff --git a/Images/qtp-biom/start_qtp-biom.sh b/Images/qtp-biom/start_qtp-biom.sh
@@ -1,17 +1,5 @@
 #!/bin/bash
 
-#export QIITA_ROOTCA_CERT=/qiita/qiita_core/support_files/ci_server.crt
-export QIITA_CONFIG_FP=/qiita_configurations/qiita_server.cfg
-CONDA_DIR=/opt/conda
-ENV_NAME=qtp-biom
-
-# Commented out because I wanted to jump onto the container to crawl into the code (it crashes during the start_biom step)
-
-#configure_biom --env-script "source /opt/conda/bin/activate ; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT
-
-#start_biom https://localhost:8383 register ignored
-#start_biom http://qiita:8383 register ignored
-#source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd / && python trigger.py
 cd / && python trigger.py qtp-biom start_biom /qtp-biom
 
 tail -f /dev/null
diff --git a/Images/qtp-diversity/start_qtp-diversity.sh b/Images/qtp-diversity/start_qtp-diversity.sh
@@ -1,17 +1,5 @@
 #!/bin/bash
 
-#export QIITA_ROOTCA_CERT=/qiita/qiita_core/support_files/ci_server.crt
-export QIITA_CONFIG_FP=/qiita_configurations/qiita_server.cfg
-CONDA_DIR=/opt/conda
-ENV_NAME=qtp-sequencing
-
-# Commented out because I wanted to jump onto the container to crawl into the code (it crashes during the start_biom step)
-
-#configure_biom --env-script "source /opt/conda/bin/activate ; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT
-
-#start_biom https://localhost:8383 register ignored
-#start_biom http://qiita:8383 register ignored
-#source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd / && python trigger.py
 cd / && python trigger.py qiime2 start_diversity_types /qtp-diversity
 
 tail -f /dev/null
diff --git a/Images/qtp-job-output-folder/start_qtp-job-output-folder.sh b/Images/qtp-job-output-folder/start_qtp-job-output-folder.sh
@@ -1,17 +1,5 @@
 #!/bin/bash
 
-#export QIITA_ROOTCA_CERT=/qiita/qiita_core/support_files/ci_server.crt
-export QIITA_CONFIG_FP=/qiita_configurations/qiita_server.cfg
-CONDA_DIR=/opt/conda
-ENV_NAME=qtp-sequencing
-
-# Commented out because I wanted to jump onto the container to crawl into the code (it crashes during the start_biom step)
-
-#configure_biom --env-script "source /opt/conda/bin/activate ; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT
-
-#start_biom https://localhost:8383 register ignored
-#start_biom http://qiita:8383 register ignored
-#source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd / && python trigger.py
 cd / && python trigger.py qtp-job-output-folder start_qtp_job_output_folder /qtp-job-output-folder
 
 tail -f /dev/null
diff --git a/Images/qtp-sequencing/start_qtp-sequencing.sh b/Images/qtp-sequencing/start_qtp-sequencing.sh
@@ -1,17 +1,5 @@
 #!/bin/bash
 
-#export QIITA_ROOTCA_CERT=/qiita/qiita_core/support_files/ci_server.crt
-export QIITA_CONFIG_FP=/qiita_configurations/qiita_server.cfg
-CONDA_DIR=/opt/conda
-ENV_NAME=qtp-sequencing
-
-# Commented out because I wanted to jump onto the container to crawl into the code (it crashes during the start_biom step)
-
-#configure_biom --env-script "source /opt/conda/bin/activate ; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT
-
-#start_biom https://localhost:8383 register ignored
-#start_biom http://qiita:8383 register ignored
-#source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd / && python trigger.py
 cd / && python trigger.py qtp-sequencing start_qtp_sequencing /qtp-sequencing
 
 tail -f /dev/null
diff --git a/Images/qtp-visualization/start_qtp-visualization.sh b/Images/qtp-visualization/start_qtp-visualization.sh
@@ -1,17 +1,5 @@
 #!/bin/bash
 
-#export QIITA_ROOTCA_CERT=/qiita/qiita_core/support_files/ci_server.crt
-export QIITA_CONFIG_FP=/qiita_configurations/qiita_server.cfg
-CONDA_DIR=/opt/conda
-ENV_NAME=qtp-sequencing
-
-# Commented out because I wanted to jump onto the container to crawl into the code (it crashes during the start_biom step)
-
-#configure_biom --env-script "source /opt/conda/bin/activate ; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT
-
-#start_biom https://localhost:8383 register ignored
-#start_biom http://qiita:8383 register ignored
-#source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd / && python trigger.py
 cd / && python trigger.py qtp-visualization start_visualization_types /qtp-visualization
 
 tail -f /dev/null
diff --git a/Makefile b/Makefile
@@ -2,6 +2,7 @@ PODMAN_FLAGS =
 PODMAN_BIN = docker buildx
 CERTNAME=stefan
 OPENSSL=/bin/openssl
+# docker compose prepends name of directory to containers
 
 TMPDIR := $(shell mktemp -d)
 ifeq ($(origin tmpdir), undefined)
@@ -12,13 +13,14 @@ Certificates/: Images/plugin_collector/stefan_csr.conf Images/plugin_collector/s
 	# === create own certificates ===
 	mkdir -p Certificates/
 	# Generate a new root CA private key and certificate
-	cd $@/ && $(OPENSSL) req -x509 -sha256 -days 356 -nodes -newkey rsa:2048 -subj "/CN=qiita-container-anna-qiita-1/C=DE/L=Giessen" -keyout $(CERTNAME)_rootca.key -out $(CERTNAME)_rootca.crt
+	cd $@/ && $(OPENSSL) req -x509 -sha256 -days 356 -nodes -newkey rsa:2048 -subj "/CN=tinqiita-nginx-1/C=DE/L=Giessen" -keyout $(CERTNAME)_rootca.key -out $(CERTNAME)_rootca.crt
 	# Generate a new server private key
 	cd $@/ && $(OPENSSL) genrsa -out $(CERTNAME)_server.key 2048
 	# Copy the following to a new file named csr.conf and modify to suit your needs
 	# Copy the following to a new file named cert.conf and modify to suit your needs
 	# Nils: alt_names is the important aspect. Make entries for all valid hostnames with which services shall be addressed
-	cp $^ $@/
+	for f in `echo "$^"`; do cat $$f > $@/`basename $$f`; done
+	#cp $^ $@/
 	# Generate a certificate signing request
 	cd $@/ && $(OPENSSL) req -new -key $(CERTNAME)_server.key -out $(CERTNAME)_server.csr -config $(CERTNAME)_csr.conf
 	# Generate a new signed server.crt to use with your server.key
@@ -88,13 +90,14 @@ plugin: Images/qtp-biom/trigger.py Certificates/
 	test -d src/qiita || git clone -b auth_oidc https://github.com/jlab/qiita.git src/qiita
 	# remove configuration and certificate files from upstream qiita repo
 	rm -rf src/qiita/qiita_core/support_files
-	cd Images/qiita && $(PODMAN_BIN) build . -f `basename $<` $(PODMAN_FLAGS) -t local-qiita
+	cd Images/qiita && $(PODMAN_BIN) build . -f `basename $<` $(PODMAN_FLAGS) -t local-qiita  --no-cache
 	touch .built_image_qiita
 
 .built_image_plugin_collector: Images/plugin_collector/plugin_collector.dockerfile Images/plugin_collector/fix_test_db.py Images/plugin_collector/collect_configs.py Images/plugin_collector/startup_plugin_collector.sh
 	tmpdir=$(TMPDIR) $(MAKE) plugin
-	cp -r Certificates/ Images/plugin_collector/
-	cd Images/plugin_collector && $(PODMAN_BIN) build . -f `basename $<` $(PODMAN_FLAGS) -t local-plugin_collector
+	cp $^ $(TMPDIR)
+	cp -r Certificates/ $(tmpdir)/
+	$(PODMAN_BIN) build $(TMPDIR)/ -f $(TMPDIR)/`basename $<` $(PODMAN_FLAGS) -t local-plugin_collector
 	touch .built_image_plugin_collector
 
 images: .built_image_qtp-biom .built_image_nginx .built_image_qiita .built_image_plugin_collector .built_image_qtp-sequencing .built_image_qp-target-gene .built_image_qtp-visualization .built_image_qtp-diversity .built_image_qp-deblur .built_image_qp-qiime2 .built_image_qp-qiime2 .built_image_qtp-job-output-folder
@@ -108,4 +111,10 @@ environments/qiita.env: environments/qiita.env.example
 
 config: environments/qiita_db.env environments/qiita.env
 
+make clean:
+	rm .built_image_*
+	rm -rf Certificates
+	rm -rf /var/lib/docker/volumes/tinqiita_server-certificates/_data/*
+	rm -rf /var/lib/docker/volumes/tinqiita_server-plugin-configs/_data/*
+
 all: config images