Merge pull request #101 from pepkit/dev

release 0.11.1
pepkit · Nov 29, 2022 · 16794b6 · 16794b6
2 parents 7934ed6 + 83a9cd4
commit 16794b6
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Showing 7 changed files with 32 additions and 19 deletions.
diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.7", "3.10"]
+        python-version: ["3.8", "3.9", "3.10"]
         os: [ubuntu-latest]
 
     steps:

diff --git a/docs/changelog.md b/docs/changelog.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.11.1] -- 2022-11-28
+- Fixed requirements file
+- Fixed bug in expanding metadata list
+- Fixed bug in metadata links
+
 ## [0.11.0] -- 2022-10-26
 - Added initialization of peppy Project without saving any files (from within Python using an API)
 - Added Finder (searching GSE tool)

diff --git a/geofetch/_version.py b/geofetch/_version.py
@@ -1 +1 @@
-__version__ = "0.11.0"
+__version__ = "0.11.1"
diff --git a/geofetch/geofetch.py b/geofetch/geofetch.py
@@ -353,7 +353,8 @@ def fetch_all(self, input: str, name: str = None) -> Union[NoReturn, peppy.Proje
         acc_GSE_list = parse_accessions(
             input, self.metadata_expanded, self.just_metadata
         )
-
+        if len(acc_GSE_list) == 1:
+            self.disable_progressbar = True
         metadata_dict_combined = {}
         subannotation_dict_combined = {}
 
@@ -829,8 +830,18 @@ def _expand_metadata_list_item(self, metadata_list: list, dict_key: str):
         """
         try:
             element_is_list = any(
-                type(list_item.get(dict_key)) is list for list_item in metadata_list
+                isinstance(list_item.get(dict_key), list) for list_item in metadata_list
             )
+
+            # # checking if some items have two keys:
+            # # This code should deal with strings with few keys. e.g. "key1: key2: value"
+            # if not element_is_list:
+            #     if any(
+            #         (len(list_item.get(dict_key).split(": ")) > 0)
+            #         for list_item in metadata_list
+            #     ):
+            #         element_is_list = True
+
             if element_is_list:
                 for n_elem in range(len(metadata_list)):
                     try:
@@ -878,9 +889,10 @@ def _expand_metadata_list_item(self, metadata_list: list, dict_key: str):
                         else:
                             del metadata_list[n_elem][dict_key]
                     except KeyError as err:
-                        self._LOGGER.warning(
-                            f"expand_metadata_list: Key Error: {err}, continuing ..."
-                        )
+                        # self._LOGGER.warning(
+                        #     f"expand_metadata_list: Key Error: {err}, continuing ..."
+                        # )
+                        pass
 
                 return metadata_list
             else:
@@ -1472,7 +1484,6 @@ def _get_list_of_processed_files(
                         self.metadata_expanded, gse_numb + "_file_list.txt"
                     )
 
-                    # TODO: make new function of code below:
                     if not os.path.isfile(filelist_path) or self.refresh_metadata:
                         result = requests.get(tar_files_list_url)
                         if result.ok:
@@ -1702,8 +1713,8 @@ def _get_SRA_meta(self, file_gse_content: list, gsm_metadata, file_sra=None):
             # If I can't get an SRA accession, maybe raw data wasn't submitted to SRA
             # as part of this GEO submission. Can't proceed.
             self._LOGGER.warning(
-                "\033[91mUnable to get SRA accession (SRP#) from GEO GSE SOFT file. "
-                "No raw data detected! Continuing anyway...\033[0m"
+                "Unable to get SRA accession (SRP#) from GEO GSE SOFT file. "
+                "No raw data detected! Continuing anyway..."
             )
             # but wait; another possibility: there's no SRP linked to the GSE, but there
             # could still be an SRX linked to the (each) GSM.
@@ -1740,8 +1751,8 @@ def _get_SRA_meta(self, file_gse_content: list, gsm_metadata, file_sra=None):
 
                 except Exception as err:
                     self._LOGGER.warning(
-                        f"\033[91mError occurred, while downloading SRA Info Metadata of {acc_SRP}. "
-                        f"Error: {err}  \033[0m"
+                        f"Warning: error, while downloading SRA Info Metadata of {acc_SRP}. "
+                        f"Error: {err}. Probably no SRA metadata found"
                     )
                     return []
             else:

diff --git a/geofetch/utils.py b/geofetch/utils.py
@@ -130,7 +130,7 @@ def parse_SOFT_line(l: str) -> dict:
     :return dict[str, str]: A python Dict object representing the key-value.
     """
     elems = l[1:].split("=")
-    return {elems[0].rstrip(): elems[1].lstrip()}
+    return {elems[0].rstrip(): "=".join(elems[1:]).lstrip()}
 
 
 class AccessionException(Exception):
@@ -203,6 +203,7 @@ def fetch_metadata(
         _LOGGER.debug("Fetching: '%s'", full_url)
 
         result = requests.get(full_url)
+
         if result.ok:
             result.encoding = "UTF-8"
             result_text = result.text

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -1,10 +1,7 @@
 attmap>=0.1.8
 colorama>=0.3.9
-peppy>=0.19.1
-logmuse>=0.0.2
-ubiquerg>=0.4.4
-logmuse>=0.2.7
-ubiquerg>=0.6.0
+logmuse>=0.2.6
+ubiquerg>=0.6.2
 requests>=2.28.1
 xmltodict>=0.13.0
 pandas>=1.3.5

diff --git a/requirements/requirements-dev.txt b/requirements/requirements-dev.txt
@@ -1,2 +1 @@
-mock>=2.0.0
 pytest==3.10.1