User defined archive access url (local branch PR)

.github/workflows/live-preview.yaml

@@ -26,7 +26,7 @@ jobs:
     steps:
     - uses: actions/setup-python@v4
       with:
-        python-version: "3.7"
+        python-version: "3.8"
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
@@ -63,7 +63,7 @@ jobs:
       run: |
         cd deploy-preview
 
-        dir_list=`for tl in $TOOL_LIST ; do echo $tl | awk -F '/' '{print $2}'; done | uniq`
+        dir_list=`for tl in $TOOL_LIST ; do echo $tl | awk -F '/' '{for(i=2;i<=(NF-1);i++) printf("%s%s",$i,i==(NF-1)?" ":FS)}'; done | uniq`
 
         for dr in $dir_list; do
           tools_list=`for tl in $TOOL_LIST; do if [[ "$tl" == *"$dr"*  ]] ; then basename $tl ; fi ; done`

deploy-preview/deploy.yml

@@ -12,6 +12,12 @@
 
 
   tasks:
+    - name: Create tool dir
+      ansible.builtin.file:
+        path: "{{ dest_tools_dir }}/{{ tool_dir }}_pr{{ pr_num }}"
+        state: directory
+        mode: 0755
+
     - name: Sync tool dir
       ansible.posix.synchronize:
         src: "{{ src_tools_dir }}/{{ tool_dir }}/"
@@ -29,8 +35,8 @@
     - name: Make name unique
       replace:
         path: "{{ dest_tools_dir }}/{{ tool_dir }}_pr{{ pr_num }}/{{ item }}"
-        regexp: '<tool(.*)name="([a-z0-9_]+)"'
-        replace: '<tool\1name="\2_pr{{ pr_num }}"'
+        regexp: '<tool(.*)name="([^"]+)"'
+        replace: '<tool\1name="\2 (PR {{ pr_num }})"'
       loop: "{{ tools_list }}"
 
     - name: Clean previous references

environment.yml

@@ -4,4 +4,4 @@ channels:
   - defaults
 dependencies:
   - pip:
-      - planemo==0.75.7
+      - planemo==0.75.20

tools/archives/pyvo_integration/astronomical_archives.py

@@ -2,6 +2,7 @@
 import functools
 import json
 import os
+import re
 import signal
 import sys
 import urllib
@@ -17,6 +18,10 @@
 MAX_ALLOWED_ENTRIES = 100
 MAX_REGISTRIES_TO_SEARCH = 100
 
+ARCHIVES_TIMEOUT_BYPASS = [
+    "https://datalab.noirlab.edu/tap"
+]
+
 
 class TimeoutException(Exception):
     pass
@@ -217,28 +222,34 @@ def _set_archive_tables(self):
 
         self.tables = []
 
-        for table in self.archive_service.tables:
-            archive_table = {
-                'name': table.name,
-                'type': table.type,
-                'fields': None
-            }
-
-            fields = []
-
-            for table_field in table.columns:
-                field = {
-                    'name': table_field.name,
-                    'description': table_field.description,
-                    'unit': table_field.unit,
-                    'datatype': table_field.datatype.content
+        try:
+            for table in self.archive_service.tables:
+                archive_table = {
+                    'name': table.name,
+                    'type': table.type,
+                    'fields': None
                 }
 
-                fields.append(field)
+                fields = []
+
+                for table_field in table.columns:
+                    field = {
+                        'name': table_field.name,
+                        'description': table_field.description,
+                        'unit': table_field.unit,
+                        'datatype': table_field.datatype.content
+                    }
+
+                    fields.append(field)
 
-            archive_table['fields'] = fields
+                archive_table['fields'] = fields
 
-            self.tables.append(archive_table)
+                self.tables.append(archive_table)
+
+        # Exception is raised when a table schema is missing
+        # Missing table will be omitted so no action needed
+        except DALServiceError:
+            pass
 
     def _is_query_valid(self, query) -> bool:
         is_valid = True
@@ -507,6 +518,20 @@ def _set_archive(self):
             self._archives.append(
                 TapArchive(access_url=self._service_access_url))
 
+        elif self._archive_type == 'custom':
+            self._service_access_url = \
+                self._json_parameters['archive_selection']['access_url']
+
+            if Utils.is_valid_url(self._service_access_url):
+                self._archives.append(
+                    TapArchive(access_url=self._service_access_url))
+            else:
+                error_message = "archive access url is not a valid url"
+                Logger.create_action_log(
+                    Logger.ACTION_ERROR,
+                    Logger.ACTION_TYPE_ARCHIVE_CONNECTION,
+                    error_message)
+
         else:
             keyword = \
                 self._json_parameters['archive_selection']['keyword']
@@ -752,6 +777,11 @@ def run(self):
 
             for archive in self._archives:
                 try:
+
+                    if archive.access_url in ARCHIVES_TIMEOUT_BYPASS:
+                        archive.get_resources = \
+                            timeout(40)(TapArchive.get_resources.__get__(archive))  # noqa: E501
+
                     _file_url, error_message = archive.get_resources(
                         self._adql_query,
                         self._number_of_files,
@@ -1250,9 +1280,9 @@ def write_urls_to_output(urls: [], output, access_url="access_url"):
         with open(output, "w") as file_output:
             for url in urls:
                 try:
-                    file_output.write(url[access_url] + ',')
+                    file_output.write(str(url[access_url]) + ',')
                 except Exception:
-                    error_message = "url field not found for url"
+                    error_message = f"url field {access_url} not found for url"
                     Logger.create_action_log(
                         Logger.ACTION_ERROR,
                         Logger.ACTION_TYPE_WRITE_URL,
@@ -1305,6 +1335,11 @@ def collect_resource_keys(urls_data: list) -> list:
                     resource_keys.append(key)
         return resource_keys
 
+    @staticmethod
+    def is_valid_url(url: str) -> bool:
+        regex_url = re.compile(r'^https?://(?:[A-Za-z0-9-]+\.)+[A-Za-z]{2,6}(?::\d+)?(?:/[^\s]*)?$')  # noqa: E501
+        return re.match(regex_url, url) is not None
+
 
 class Logger:
     _logs = []

tools/archives/pyvo_integration/astronomical_archives.xml

@@ -1,4 +1,4 @@
-<tool id="astronomical_archives" name="Astronomical Archives (IVOA)" version="0.9.1">
+<tool id="astronomical_archives" name="Astronomical Archives (IVOA)" version="0.10.0">
     <description>queries astronomical archives through Virtual Observatory protocols</description>
     <edam_operations>
         <edam_operation>operation_0224</edam_operation>
@@ -24,6 +24,7 @@
             <param name="archive_type" type="select" label="Archive Selection">
               <option value="archive">Query specific IVOA archive</option>
               <option value="registry">Query all matching IVOA archives</option>
+              <option value="custom">Query custom TAP archive</option>
             </param>
             <when value="registry">
               <param name="keyword" type="text" label="Keyword" />
@@ -47,6 +48,11 @@
                 <options from_data_table="astronomical_archives" />
               </param>
             </when>
+            <when value="custom">
+              <param name="access_url" type="text" label="TAP archive access url">
+                <validator type="regex" message="URL seems invalid">^https?://[A-Za-z0-9]([A-Za-z0-9-\.]{0,61}[A-Za-z0-9])?\.[A-Za-z]{2,6}(:\d+)?(/[^\s]*)?$</validator>
+              </param>
+            </when>
         </conditional>
         <section name="query_section" title="Query selection" expanded="true">
           <conditional name="query_selection">
@@ -255,6 +261,40 @@
             </assert_contents>
           </output>
         </test>
+        <test expect_num_outputs="2">
+          <param name="output_selection" value="c"/>
+          <param name="number_of_files" value="1"/>
+          <conditional name="archive_selection">
+              <param name="archive_type" value="custom"/>
+              <param name="access_url" value="https://datalab.noirlab.edu/tap"/>
+          </conditional>
+          <conditional name="query_selection">
+              <param name="query_type" value="raw_query" />
+              <param name="table" value="allwise.source" />
+              <param name="url_field" value="random_id" />
+          </conditional>
+          <output name="output_csv" count="1">
+            <assert_contents>
+                <has_text_matching expression=".*\S+.*" />
+            </assert_contents>
+          </output>
+        </test>
+        <test expect_num_outputs="2">
+          <param name="output_selection" value="c"/>
+          <param name="number_of_files" value="1"/>
+          <conditional name="archive_selection">
+              <param name="archive_type" value="custom"/>
+              <param name="access_url" value="http://voparis-tap-he.obspm.fr/tap"/>
+          </conditional>
+          <conditional name="query_selection">
+              <param name="query_type" value="obscore_query" />
+          </conditional>
+          <output name="output_csv" count="1">
+            <assert_contents>
+                <has_text_matching expression=".*\S+.*" />
+            </assert_contents>
+          </output>
+        </test>
     </tests>
     <help>
 
@@ -460,7 +500,7 @@ The Table Access Protocol (TAP) lets you execute queries against our database ta
 
 -----
 
-The MAST Archive at STScI TAP end point for the TESS Input Catalog.

The TIC is used to help identify two-minute cadence target selection for the TESS mission, and to calculate physical and observational properties of planet candidates. It is for use by both the TESS science team and the public, and it is periodically updated – the current version is TIC-8. TIC-8 uses the GAIA DR2 catalog as a base and merges a large number of other photometric catalogs, including 2MASS, UCAC4, APASS, SDSS, WISE, etc. There are roughly 1.5 billion stellar and extended sources in TIC-8, containing compiled magnitudes including B, V, u, g, r, i, z, J, H, K, W1-W4, and G.
+The MAST Archive at STScI TAP end point for the TESS Input Catalog.The TIC is used to help identify two-minute cadence target selection for the TESS mission, and to calculate physical and observational properties of planet candidates. It is for use by both the TESS science team and the public, and it is periodically updated – the current version is TIC-8. TIC-8 uses the GAIA DR2 catalog as a base and merges a large number of other photometric catalogs, including 2MASS, UCAC4, APASS, SDSS, WISE, etc. There are roughly 1.5 billion stellar and extended sources in TIC-8, containing compiled magnitudes including B, V, u, g, r, i, z, J, H, K, W1-W4, and G.
 The TIC can be directly accessed through the Mikulski Archive for Space Telescopes (MAST), using either queries or bulk download.
 
 The Table Access Protocol (TAP) lets you execute queries against our database tables, and inspect various metadata.  Upload is not currently supported.
@@ -543,7 +583,7 @@ Tables exposed through this endpoint include: epn_core from the gem_mars schema,
 
 -----
 
-**ArVO Byu TAP** http://arvo-registry.sci.am/tap ArVO Byurakan TAP service
+**ArVO Byu TAP** arvo-registry.sci.am/tap ArVO Byurakan TAP service
 
 -----
 
@@ -612,7 +652,7 @@ Illumination by the Sun of each face of the comet 67P/Churyumov-Gerasimenko base
                 CSHP_DV_130_01_LORES_OBJ.OBJ. The service provides the cosine between the normal of each face (in the same order as the faces defined in the shape model) and the Sun direction; both
                 numerical values and images of the illumination are available. Each map is defined for a given position of the Sun
                 in the frame of 67P (67P/C-G_CK). Longitude 0 is at the center of each map. The code is developed by A. Beth,
-                Imperial College London, UK and the service is provided by CDPP (http://cdpp.eu). Acknowlegment: The illumination models
+                Imperial College London, UK and the service is provided by CDPP (cdpp.eu). Acknowlegment: The illumination models
                 have been developed at the Department of Physics at Imperial College London (UK) under the financial support of STFC
                 grant of UK ST/N000692/1 and ESA contract 4000119035/16/ES/JD (Rosetta RPC-PIU). We would also like to warmly
                 thank Bernhard Geiger (ESA) for his support in validating the 2D-illumination maps.