Merge pull request #100 from refgenie/bugfix

v0.9.2
refgenie · Aug 19, 2020 · f22a06d · f22a06d
2 parents bf42570 + c35f578
commit f22a06d
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Showing 5 changed files with 23 additions and 9 deletions.
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -2,6 +2,11 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. 
 
+## [0.9.2] - 2020-08-19
+
+### Added
+- in `pull` the genome description is fetched from the server
+
 ## [0.9.1] - 2020-07-29
 
 ### Added

diff --git a/refgenconf/_version.py b/refgenconf/_version.py
@@ -1 +1 @@
-__version__ = "0.9.1"
+__version__ = "0.9.2"
diff --git a/refgenconf/const.py b/refgenconf/const.py
@@ -28,6 +28,8 @@
 API_ID_ARCHIVE = CUSTOM_PFX + "_archive"
 API_ID_DEFAULT_TAG = CUSTOM_PFX + "_default_tag"
 API_ID_ASSET_ATTRS = CUSTOM_PFX + "_asset_attrs"
+API_ID_GENOME_ATTRS = "download_genome_attributes_v2_genome__genome__get" # temporary, default operation ID assigned by FastAPI. Switch to custom once refgenieserver supports it
+# API_ID_GENOME_ATTRS = CUSTOM_PFX + "_genome_attrs"
 API_ID_DIGEST = CUSTOM_PFX + "_asset_digest"
 API_ID_RECIPE = CUSTOM_PFX + "_asset_recipe"
 API_ID_LOG = CUSTOM_PFX + "_asset_log"
@@ -38,14 +40,16 @@
 # for systematic links generation in the splash pages
 OPERATION_IDS = {
     "asset": {
-        API_ID_ARCHIVE: "archive", API_ID_ASSET_ATTRS: "attributes", API_ID_DIGEST: "asset digest",
-        API_ID_ARCHIVE_DIGEST: "archive digest", API_ID_RECIPE: "build recipe", API_ID_LOG: "build log"
+        API_ID_ARCHIVE: "archive", API_ID_ASSET_ATTRS: "attributes",
+        API_ID_DIGEST: "asset digest", API_ID_ARCHIVE_DIGEST: "archive digest",
+        API_ID_RECIPE: "build recipe", API_ID_LOG: "build log"
     }
 }
 
 API_IDS = [
-    "API_ID_ASSETS", "API_ID_ARCHIVE", "API_ID_DEFAULT_TAG", "API_ID_ASSET_ATTRS", "API_ID_DIGEST",
-    "API_ID_RECIPE", "API_ID_LOG", "API_ID_SPLASH", "API_ID_ARCHIVE_DIGEST"
+    "API_ID_ASSETS", "API_ID_ARCHIVE", "API_ID_DEFAULT_TAG", "API_ID_LOG",
+    "API_ID_DIGEST", "API_ID_RECIPE", "API_ID_ASSET_ATTRS", "API_ID_SPLASH",
+    "API_ID_ARCHIVE_DIGEST", "API_ID_GENOME_ATTRS"
 ]
 
 CFG_FOLDER_KEY = "genome_folder"

diff --git a/refgenconf/refgenconf.py b/refgenconf/refgenconf.py
@@ -715,19 +715,22 @@ def _raise_unpack_error():
                 _LOGGER.debug("Determined tag: {}".format(determined_tag))
                 unpack or _raise_unpack_error()
             gat = [genome, asset, determined_tag]
-            url_attrs = get_json_url(server_url, API_ID_ASSET_ATTRS).format(genome=genome, asset=asset)
+            url_asset_attrs = get_json_url(server_url, API_ID_ASSET_ATTRS).format(genome=genome, asset=asset)
+            url_genome_attrs = get_json_url(server_url, API_ID_GENOME_ATTRS).format(genome=genome)
             url_archive = get_json_url(server_url, API_ID_ARCHIVE).format(genome=genome, asset=asset)
 
             try:
-                archive_data = _download_json(url_attrs, params={"tag": determined_tag})
-                _LOGGER.debug("Determined server URL: {}".format(server_url))
+                archive_data = _download_json(url_asset_attrs, params={"tag": determined_tag})
             except DownloadJsonError:
                 no_asset_json.append(server_url)
                 if num_servers == len(self[CFG_SERVERS_KEY]):
                     _LOGGER.error("Asset '{}/{}:{}' not available on any of the following servers: {}".
                                   format(genome, asset, determined_tag, ", ".join(self[CFG_SERVERS_KEY])))
                     return _null_return()
                 continue
+            else:
+                _LOGGER.debug("Determined server URL: {}".format(server_url))
+                genome_archive_data = _download_json(url_genome_attrs)
 
             if sys.version_info[0] == 2:
                 archive_data = asciify_json_dict(archive_data)
@@ -826,19 +829,22 @@ def preserve():
                     shutil.move(os.path.join(tmpdir, asset), tag_dir)
                 if os.path.isfile(filepath):
                     os.remove(filepath)
+
             if self.file_path:
                 with self as rgc:
                     [rgc.chk_digest_update_child(gat[0], x, "{}/{}:{}".format(*gat), server_url)
                      for x in archive_data[CFG_ASSET_PARENTS_KEY] if CFG_ASSET_PARENTS_KEY in archive_data]
                     rgc.update_tags(*gat, data={attr: archive_data[attr]
                                                 for attr in ATTRS_COPY_PULL if attr in archive_data})
                     rgc.set_default_pointer(*gat)
+                    rgc.update_genomes(genome=genome, data=genome_archive_data)
             else:
                 [self.chk_digest_update_child(gat[0], x, "{}/{}:{}".format(*gat), server_url)
                  for x in archive_data[CFG_ASSET_PARENTS_KEY] if CFG_ASSET_PARENTS_KEY in archive_data]
                 self.update_tags(*gat, data={attr: archive_data[attr]
                                              for attr in ATTRS_COPY_PULL if attr in archive_data})
                 self.set_default_pointer(*gat)
+                self.update_genomes(genome=genome, data=genome_archive_data)
             self.run_plugins(POST_PULL_HOOK)
             return gat, archive_data, server_url
 

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -3,5 +3,4 @@ pyyaml
 requests
 tqdm>=4.38.0
 yacman>=0.6.9
-future
 pyfaidx